diff --git a/R/functions/correlated_fitness_surface.R b/R/functions/correlated_fitness_surface.R deleted file mode 100644 index 3ea1ee7..0000000 --- a/R/functions/correlated_fitness_surface.R +++ /dev/null @@ -1,324 +0,0 @@ -# ====================================================== -# correlated_fitness_surface.R -# Important Concept Explanation: -# This function calculates the Correlated Fitness Surface. -# Definition: Individual fitness ~ Individual phenotype -# Formula: w ~ z₁ + z₂ + z₁² + z₂² + z₁×z₂ -# -# IMPORTANT NOTES: Traits MUST be standardized BEFORE calling this function -# Use prepare_selection_data() with standardize = TRUE and optional group -# DO NOT use scale_traits = TRUE (double standardization) -# ====================================================== - -#' @noRd -`%||%` <- function(a, b) if (!is.null(a)) a else b - -#' Calculate the Correlated Fitness Surface -#' -#' Fits a model for individual fitness based on multiple individual phenotypes (w ~ z1 + z2 + interactions). -#' Traits MUST be standardized BEFORE calling this function. -#' -#' @param data A data frame containing fitness and trait measurements. -#' @param fitness_col A string specifying the name of the fitness column. -#' @param trait_cols A character vector of exactly length 2 specifying the trait column names. -#' @param grid_n Integer specifying the resolution of the prediction grid. Default is 60. -#' @param method A string specifying the modeling method: \code{"auto"}, \code{"gam"}, or \code{"tps"}. -#' @param scale_traits Deprecated. Logical. Set to \code{FALSE} to avoid double standardization. -#' @param group Optional string specifying a grouping variable. -#' @param k Integer specifying the basis dimension for the GAM smooth term. -#' -#' @return A list containing the fitted model, grid predictions, and metadata. -#' @export -#' -#' @examples -#' \dontrun{ -#' surf <- correlated_fitness_surface(my_data, "fitness", c("trait1", "trait2")) -#' } -correlated_fitness_surface <- function( - data, - fitness_col, - trait_cols, - grid_n = 60, - method = "auto", - scale_traits = FALSE, - group = NULL, - k = 30 -) { - stopifnot(length(trait_cols) == 2L) - need <- c(fitness_col, trait_cols) - - # Input validation - if (!all(need %in% names(data))) { - stop("Missing columns: ", paste(setdiff(need, names(data)), collapse = ", ")) - } - - if (!is.null(group) && !group %in% names(data)) { - stop("Group column '", group, "' not found in data") - } - - # DOUBLE STANDARDIZATION WARNING - if (scale_traits) { - warning( - "scale_traits = TRUE is deprecated. ", - "Traits should be standardized using prepare_selection_data() ", - "before calling this function. Setting scale_traits = FALSE." - ) - scale_traits <- FALSE - } - - message("IMPORTANT: Traits should already be standardized (mean = 0, SD = 1).") - message(" Do NOT apply scale() again within this function.") - - # Check if traits appear standardized - for (t in trait_cols) { - z_mean <- mean(data[[t]], na.rm = TRUE) - z_sd <- sd(data[[t]], na.rm = TRUE) - if (abs(z_mean) > 0.1 || abs(z_sd - 1) > 0.1) { - warning( - "Trait '", t, "' does not appear standardized ", - "(mean = ", round(z_mean, 3), ", SD = ", round(z_sd, 3), "). ", - "Consider using prepare_selection_data() first." - ) - } - } - - y <- as.numeric(data[[fitness_col]]) - x1 <- as.numeric(data[[trait_cols[1]]]) - x2 <- as.numeric(data[[trait_cols[2]]]) - - if (any(!is.numeric(y)) || any(!is.numeric(x1)) || any(!is.numeric(x2))) { - stop("Non-numeric values detected in fitness or trait columns") - } - - # Remove incomplete cases - keep <- stats::complete.cases(y, x1, x2) - y <- y[keep] - x1 <- x1[keep] - x2 <- x2[keep] - - if (!is.null(group)) { - grp <- data[[group]][keep] - } else { - grp <- NULL - } - - if (length(y) < 10) stop("Too few complete cases: ", length(y), " (<10)") - - # Detect binary fitness - uniq_y <- unique(y) - is_binary <- length(uniq_y) == 2 && all(sort(uniq_y) == c(0, 1)) - - if (method == "auto") { - method <- if (is_binary) "gam" else "tps" - } - - if (!method %in% c("gam", "tps")) stop("method must be 'auto' | 'gam' | 'tps'") - - # Check trait variation - if (length(unique(x1)) < 3 || length(unique(x2)) < 3) { - stop( - "Too few unique trait values: ", - trait_cols[1], " has ", length(unique(x1)), - " unique values; ", trait_cols[2], " has ", length(unique(x2)), " unique values." - ) - } - - cat("Data type:", ifelse(is_binary, "binary", "continuous"), "\n") - cat("Selected method:", method, "\n") - cat("Data points:", length(y), "\n") - if (!is.null(group)) { - cat("Grouping variable:", group, "\n") - cat("Number of groups:", length(unique(grp)), "\n") - } - - x1s <- x1 - x2s <- x2 - - # For prediction grid (in original units, not standardized) - # But since traits are standardized, original = standardized - g1 <- seq(min(x1, na.rm = TRUE), max(x1, na.rm = TRUE), length.out = grid_n) - g2 <- seq(min(x2, na.rm = TRUE), max(x2, na.rm = TRUE), length.out = grid_n) - - grid <- expand.grid(g1, g2, KEEP.OUT.ATTRS = FALSE) - names(grid) <- trait_cols - - # Grid is already in standardized units - grid_scaled <- grid - - if (method == "gam") { - if (!requireNamespace("mgcv", quietly = TRUE)) { - stop("mgcv package required. Please install.packages('mgcv')") - } - - fam <- if (is_binary) stats::binomial("logit") else stats::gaussian() - - # Prepare data frame - df_fit <- data.frame( - .y = as.numeric(y), - trait1 = as.numeric(x1s), - trait2 = as.numeric(x2s) - ) - names(df_fit)[2:3] <- trait_cols - - if (!is.null(group)) { - df_fit[[group]] <- grp - } - - df_fit <- df_fit[complete.cases(df_fit), ] - - cat("GAM fitting with", nrow(df_fit), "observations\n") - - # Build formulas - k_adj <- min(k, nrow(df_fit) - 1) - - if (!is.null(group)) { - fml <- as.formula(paste( - ".y ~ ", group, " + s(", trait_cols[1], ", ", trait_cols[2], - ", bs = 'tp', k = ", k_adj, ")" - )) - fml_alt1 <- as.formula(paste( - ".y ~ ", group, " + s(", trait_cols[1], - ", k = min(floor(", k_adj, "/2), nrow(df_fit) - 1)) + s(", - trait_cols[2], - ", k = min(floor(", k_adj, "/2), nrow(df_fit) - 1))" - )) - fml_alt2 <- as.formula(paste(".y ~ ", group, " + ", trait_cols[1], " + ", trait_cols[2])) - } else { - fml <- as.formula(paste( - ".y ~ s(", trait_cols[1], ", ", trait_cols[2], - ", bs = 'tp', k = ", k_adj, ")" - )) - fml_alt1 <- as.formula(paste( - ".y ~ s(", trait_cols[1], - ", k = min(floor(", k_adj, "/2), nrow(df_fit) - 1)) + s(", - trait_cols[2], - ", k = min(floor(", k_adj, "/2), nrow(df_fit) - 1))" - )) - fml_alt2 <- as.formula(paste(".y ~ ", trait_cols[1], " + ", trait_cols[2])) - } - - try_formulas <- list( - main = fml, - alt1 = fml_alt1, - alt2 = fml_alt2 - ) - - fit <- NULL - formula_used <- NULL - - for (form_name in names(try_formulas)) { - if (is.null(fit)) { - tryCatch( - { - cat(" Trying formula:", form_name, "\n") - fit <- mgcv::gam(try_formulas[[form_name]], - data = df_fit, - family = fam, - method = "REML" - ) - formula_used <- form_name - cat("Success with formula:", form_name, "\n") - break - }, - error = function(e) { - cat("Failed with formula", form_name, ":", e$message, "\n") - } - ) - } - } - - if (is.null(fit)) { - stop("All GAM formula attempts failed") - } - - # Predict on grid - newdat <- grid_scaled[, trait_cols, drop = FALSE] - names(newdat) <- trait_cols - - if (!is.null(group)) { - group_levels <- unique(grp) - if (is.factor(df_fit[[group]])) { - ref_group <- names(sort(table(df_fit[[group]]), decreasing = TRUE))[1] - } else { - ref_group <- group_levels[which.min(abs(group_levels - median(group_levels)))] - } - newdat[[group]] <- ref_group - cat("Predictions use group = '", ref_group, "' as reference\n") - } - - .fit <- tryCatch( - { - as.numeric(stats::predict(fit, newdata = newdat, type = "response")) - }, - error = function(e) { - cat("Prediction failed, using mean:", e$message, "\n") - rep(mean(y, na.rm = TRUE), nrow(newdat)) - } - ) - - grid$.fit <- .fit - - if (anyNA(grid$.fit)) { - warning("NA predictions detected, using mean imputation") - grid$.fit[is.na(grid$.fit)] <- mean(grid$.fit, na.rm = TRUE) - } - - cat("Success Predictions range:", round(range(grid$.fit), 4), "\n") - - return(list( - model = fit, - grid = grid, - method = "gam", - formula_used = formula_used, - data_type = ifelse(is_binary, "binary", "continuous"), - trait_cols = trait_cols, - fitness_col = fitness_col, - group_used = group, - surface_type = "correlated_fitness", - note = "Correlated fitness surface (individual fitness)" - )) - } - - if (!requireNamespace("fields", quietly = TRUE)) { - stop("For continuous fitness with tps method, install fields: install.packages('fields')") - } - - if (is_binary) { - warning("Binary data detected but method='tps' chosen. Using Tps on binary outcomes (not ideal).") - } - - Xs <- cbind(as.numeric(x1s), as.numeric(x2s)) - - tps_model <- tryCatch( - fields::Tps(Xs, as.numeric(y)), - error = function(e) { - warning("Tps failed, retrying with m=2: ", e$message) - fields::Tps(Xs, as.numeric(y), m = 2) - } - ) - - grid_scaled_mat <- cbind( - as.numeric(grid_scaled[[trait_cols[1]]]), - as.numeric(grid_scaled[[trait_cols[2]]]) - ) - - .fit <- as.numeric(stats::predict(tps_model, grid_scaled_mat)) - grid$.fit <- .fit - - if (anyNA(grid$.fit)) { - warning("NA predictions, using mean imputation") - grid$.fit[is.na(grid$.fit)] <- mean(grid$.fit, na.rm = TRUE) - } - - return(list( - model = tps_model, - grid = grid, - method = "tps", - data_type = ifelse(is_binary, "binary", "continuous"), - trait_cols = trait_cols, - fitness_col = fitness_col, - group_used = group, - surface_type = "correlated_fitness", - note = "Correlated fitness surface (individual fitness)" - )) -} diff --git a/R/functions/univariate_spline.R b/R/functions/univariate_spline.R deleted file mode 100644 index fb8b4f2..0000000 --- a/R/functions/univariate_spline.R +++ /dev/null @@ -1,226 +0,0 @@ -# ====================================================== -# univariate_spline.R -# Estimate univariate correlated fitness function -# -# Important Concept Explanation: -# This function calculates a UNIVARIATE CORRELATED FITNESS FUNCTION -# Definition: Individual fitness ~ Individual phenotype (single trait) -# Formula: w ~ f(z) -# -# This is a special case of correlated fitness surface (1D instead of 2D) -# Adaptive landscape would require: Mean fitness ~ Population mean phenotype -# -# IMPORTANT NOTES -# - Traits should be standardized BEFORE calling this function -# - Use prepare_selection_data() with standardize = TRUE and optional group -# - The GAM smooth term estimates the shape of the fitness function -# - DO NOT use scale() within this function (double standardization) -# ====================================================== - - -#' Estimate univariate correlated fitness function -#' -#' This function calculates a univariate correlated fitness function using a GAM smooth term. -#' The formula is \code{w ~ f(z)}. Traits should be standardized BEFORE calling this function. -#' -#' @param data A data frame containing fitness and trait measurements. -#' @param fitness_col A string specifying the name of the fitness column. -#' @param trait_col A string specifying the name of the trait column (must be numeric and standardized). -#' @param fitness_type A string indicating the fitness type: either \code{"binary"} or \code{"continuous"}. -#' @param group Optional string specifying a grouping variable. If provided, group fixed effects are included. -#' @param k Integer specifying the basis dimension for the GAM smooth term. Default is 10. -#' -#' @return A list of class \code{"univariate_fitness"} containing the fitted GAM model, a prediction grid, and metadata. -#' @export -#' -#' @examples -#' \dontrun{ -#' result <- univariate_spline(data = my_data, fitness_col = "survival", trait_col = "size") -#' } -univariate_spline <- function(data, - fitness_col, - trait_col, - fitness_type = c("binary", "continuous"), - group = NULL, - k = 10) { - fitness_type <- match.arg(fitness_type) - - # Input validation - if (length(trait_col) != 1L) { - stop("`trait_col` must be a single column name.") - } - if (!trait_col %in% names(data)) { - stop("`trait_col` not found in `data`.") - } - if (!is.numeric(data[[trait_col]])) { - stop("`trait_col` must be numeric (standardize upstream if needed).") - } - - # Check if group column exists - if (!is.null(group) && !group %in% names(data)) { - stop("Group column '", group, "' not found in data") - } - - # CHECK FOR DOUBLE STANDARDIZATION - # Warn users not to use scale() within this function - message("IMPORTANT: Traits should already be standardized (mean = 0, SD = 1).") - message(" Do NOT apply scale() again within this function.") - - # Check if trait appears to be standardized - z_mean <- mean(data[[trait_col]], na.rm = TRUE) - z_sd <- sd(data[[trait_col]], na.rm = TRUE) - - if (abs(z_mean) > 0.1 || abs(z_sd - 1) > 0.1) { - warning( - "Trait '", trait_col, "' does not appear standardized ", - "(mean = ", round(z_mean, 3), ", SD = ", round(z_sd, 3), "). ", - "Consider using prepare_selection_data() first." - ) - } else { - message("Trait appears standardized (mean ≈ 0, SD ≈ 1)") - } - - if (fitness_type == "continuous") { - # For continuous fitness, use relative fitness if available - if ("relative_fitness" %in% names(data)) { - y <- data[["relative_fitness"]] - fit_note <- "Using relative_fitness column" - } else { - # Compute relative fitness on the fly (warning: not group-specific) - if (!is.null(group)) { - warning( - "Group specified but no relative_fitness column found. ", - "Consider using prepare_selection_data() first." - ) - } - y <- data[[fitness_col]] / mean(data[[fitness_col]], na.rm = TRUE) - fit_note <- "Computed relative fitness on the fly (pooled)" - } - fam <- stats::gaussian() - family_name <- "gaussian" - } else { - # Binary fitness - use original 0/1 values - y <- data[[fitness_col]] - fam <- stats::binomial("logit") - family_name <- "binomial(logit)" - - # Check if really binary - unique_vals <- unique(y[!is.na(y)]) - if (!all(unique_vals %in% c(0, 1))) { - warning( - "fitness_type = 'binary' but values are not all 0/1. ", - "Proceeding but results may be unreliable." - ) - } - fit_note <- "Using original binary fitness" - } - - df <- data - df[[".y"]] <- y - - # Adjust k based on unique values (avoid GAM errors) - n_unique <- length(unique(df[[trait_col]][complete.cases(df[[trait_col]])])) - n_obs <- sum(complete.cases(df[[trait_col]], y)) - - # k should not exceed n_unique - 1 - k_adj <- min(k, max(3, n_unique - 1)) - if (k_adj < k) { - warning( - "Reducing k from ", k, " to ", k_adj, - " (only ", n_unique, " unique values)" - ) - k <- k_adj - } - - # Check if sample size is sufficient - if (n_obs < k * 2) { - warning( - "Sample size (", n_obs, ") may be insufficient for k = ", k, - ". Consider reducing k." - ) - } - - # Create formula with smooth term - if (!is.null(group)) { - fml <- stats::as.formula(paste0(".y ~ ", group, " + s(", trait_col, ", k = ", k, ")")) - cat("Including group fixed effect: '", group, "'\n") - } else { - fml <- stats::as.formula(paste0(".y ~ s(", trait_col, ", k = ", k, ")")) - } - - # Fit GAM - fit <- tryCatch( - { - mgcv::gam(fml, - data = df, - family = fam, - method = "REML", - na.action = stats::na.omit - ) - }, - error = function(e) { - stop( - "GAM fitting failed: ", e$message, - "\nTry reducing k (currently k = ", k, ")" - ) - } - ) - - # Check convergence - if (!is.null(fit$converged) && !fit$converged) { - warning("GAM algorithm did not fully converge") - } - - # Create prediction grid across observed trait range - rng <- range(df[[trait_col]], na.rm = TRUE) - grid <- data.frame(seq(rng[1], rng[2], length.out = 200)) - names(grid) <- trait_col - - # If group was specified, predictions need a reference group - if (!is.null(group)) { - group_levels <- unique(df[[group]]) - # Use the median group (or first) as reference - # For factor groups, use the most common level - if (is.factor(df[[group]])) { - ref_group <- names(sort(table(df[[group]]), decreasing = TRUE))[1] - } else { - ref_group <- group_levels[which.min(abs(group_levels - median(group_levels)))] - } - grid[[group]] <- ref_group - cat("Predictions use group = '", ref_group, "' as reference\n") - } - - # Predict on link scale, then transform to response scale - pr <- stats::predict(fit, newdata = grid, se.fit = TRUE, type = "link") - linkinv <- fit$family$linkinv - - grid$fit <- linkinv(pr$fit) - grid$lwr <- linkinv(pr$fit - 1.96 * pr$se.fit) - grid$upr <- linkinv(pr$fit + 1.96 * pr$se.fit) - - # Ensure confidence bounds stay within [0,1] for binary fitness - if (fitness_type == "binary") { - grid$lwr <- pmax(grid$lwr, 0) - grid$upr <- pmin(grid$upr, 1) - } - - result <- list( - model = fit, - grid = grid, - trait = trait_col, - fitness_type = fitness_type, - family = family_name, - k = k, - n_obs = n_obs, - fit_note = fit_note, - group_used = group, - trait_mean = z_mean, - trait_sd = z_sd, - surface_type = "correlated_fitness_univariate", - note = "Univariate correlated fitness function (individual fitness)" - ) - - class(result) <- "univariate_fitness" - - return(result) -} diff --git a/R/results/bumpus_sparrows_results/figures/adaptive_landscape_2d_HL_KL.png b/R/results/bumpus_sparrows_results/figures/adaptive_landscape_2d_HL_KL.png deleted file mode 100644 index 941af1d..0000000 Binary files a/R/results/bumpus_sparrows_results/figures/adaptive_landscape_2d_HL_KL.png and /dev/null differ diff --git a/R/results/bumpus_sparrows_results/figures/adaptive_landscape_2d_HL_WT.png b/R/results/bumpus_sparrows_results/figures/adaptive_landscape_2d_HL_WT.png deleted file mode 100644 index 6d1b8b9..0000000 Binary files a/R/results/bumpus_sparrows_results/figures/adaptive_landscape_2d_HL_WT.png and /dev/null differ diff --git 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a/R/results/bumpus_sparrows_results/models/spline_TL.rds and /dev/null differ diff --git a/R/results/bumpus_sparrows_results/models/spline_WT.rds b/R/results/bumpus_sparrows_results/models/spline_WT.rds deleted file mode 100644 index aeec0ff..0000000 Binary files a/R/results/bumpus_sparrows_results/models/spline_WT.rds and /dev/null differ diff --git a/R/results/bumpus_sparrows_results/tables/adaptive_landscape_summary_all.csv b/R/results/bumpus_sparrows_results/tables/adaptive_landscape_summary_all.csv deleted file mode 100644 index 1f23fec..0000000 --- a/R/results/bumpus_sparrows_results/tables/adaptive_landscape_summary_all.csv +++ /dev/null @@ -1,13 +0,0 @@ -"Trait1","Trait2","Optimal_Trait1","Optimal_Trait2","Optimal_Fitness" -"TL","HL",-2.961,3.102,0.997 -"TL","WT",-0.073,-3.122,0.684 -"TL","KL",-2.961,3.169,0.995 -"HL","WT",3.102,-3.122,0.998 -"HL","KL",3.102,3.169,0.799 -"WT","KL",-3.122,3.169,0.994 -"TL","HL",-2.861,3.102,0.997 -"TL","WT",-0.162,-3.122,0.685 -"TL","KL",-2.961,3.169,0.995 -"HL","WT",3.102,-3.122,0.998 -"HL","KL",3.102,3.054,0.801 -"WT","KL",-3.122,3.054,0.993 diff --git a/R/results/bumpus_sparrows_results/tables/comparison_correlation_HL_KL.csv b/R/results/bumpus_sparrows_results/tables/comparison_correlation_HL_KL.csv deleted file mode 100644 index 1502f28..0000000 --- a/R/results/bumpus_sparrows_results/tables/comparison_correlation_HL_KL.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","correlation","n_points" -"HL","KL",0.99959326623067,3600 diff --git a/R/results/bumpus_sparrows_results/tables/comparison_correlation_HL_WT.csv b/R/results/bumpus_sparrows_results/tables/comparison_correlation_HL_WT.csv deleted file mode 100644 index 5f7115b..0000000 --- a/R/results/bumpus_sparrows_results/tables/comparison_correlation_HL_WT.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","correlation","n_points" -"HL","WT",0.995803928306483,3600 diff --git a/R/results/bumpus_sparrows_results/tables/comparison_correlation_TL_HL.csv b/R/results/bumpus_sparrows_results/tables/comparison_correlation_TL_HL.csv deleted file mode 100644 index 388d44c..0000000 --- a/R/results/bumpus_sparrows_results/tables/comparison_correlation_TL_HL.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","correlation","n_points" -"TL","HL",0.99906540815391,3600 diff --git a/R/results/bumpus_sparrows_results/tables/comparison_correlation_TL_KL.csv b/R/results/bumpus_sparrows_results/tables/comparison_correlation_TL_KL.csv deleted file mode 100644 index dcb90e0..0000000 --- a/R/results/bumpus_sparrows_results/tables/comparison_correlation_TL_KL.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","correlation","n_points" -"TL","KL",0.996617616423912,3600 diff --git a/R/results/bumpus_sparrows_results/tables/comparison_correlation_TL_WT.csv b/R/results/bumpus_sparrows_results/tables/comparison_correlation_TL_WT.csv deleted file mode 100644 index 8488243..0000000 --- a/R/results/bumpus_sparrows_results/tables/comparison_correlation_TL_WT.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","correlation","n_points" -"TL","WT",0.971782435477459,3600 diff --git a/R/results/bumpus_sparrows_results/tables/comparison_correlation_WT_KL.csv b/R/results/bumpus_sparrows_results/tables/comparison_correlation_WT_KL.csv deleted file mode 100644 index 7bf6466..0000000 --- a/R/results/bumpus_sparrows_results/tables/comparison_correlation_WT_KL.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","correlation","n_points" -"WT","KL",0.997908367732552,3600 diff --git a/R/results/bumpus_sparrows_results/tables/comparison_summary.csv b/R/results/bumpus_sparrows_results/tables/comparison_summary.csv deleted file mode 100644 index 2fba877..0000000 --- a/R/results/bumpus_sparrows_results/tables/comparison_summary.csv +++ /dev/null @@ -1,7 +0,0 @@ -"Trait_Pair","Correlation" -"TL_HL",0.9991 -"TL_WT",0.9718 -"TL_KL",0.9966 -"HL_WT",0.9958 -"HL_KL",0.9996 -"WT_KL",0.9979 diff --git a/R/results/bumpus_sparrows_results/tables/correlated_fitness_surfaces_summary.csv b/R/results/bumpus_sparrows_results/tables/correlated_fitness_surfaces_summary.csv deleted file mode 100644 index 7e36b01..0000000 --- a/R/results/bumpus_sparrows_results/tables/correlated_fitness_surfaces_summary.csv +++ /dev/null @@ -1,7 +0,0 @@ -"pair","method","data_type","grid_points" -"TL_HL","gam","binary",3600 -"TL_WT","gam","binary",3600 -"TL_KL","gam","binary",3600 -"HL_WT","gam","binary",3600 -"HL_KL","gam","binary",3600 -"WT_KL","gam","binary",3600 diff --git a/R/results/bumpus_sparrows_results/tables/disruptive_HL.csv b/R/results/bumpus_sparrows_results/tables/disruptive_HL.csv deleted file mode 100644 index e447a85..0000000 --- a/R/results/bumpus_sparrows_results/tables/disruptive_HL.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"HL","Linear",0.0691378467669277,0.0449395647427481,0.116031606277718,0.00201956447926765 -"HL²","Quadratic",-0.0760360007350176,0.062066030897844,0.202910800498447,0.00385219219141212 diff --git a/R/results/bumpus_sparrows_results/tables/disruptive_KL.csv b/R/results/bumpus_sparrows_results/tables/disruptive_KL.csv deleted file mode 100644 index 34fe1ea..0000000 --- a/R/results/bumpus_sparrows_results/tables/disruptive_KL.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"KL","Linear",0.0677836295266952,0.0430437423996892,0.117736017754752,0.0018527637597708 -"KL²","Quadratic",-0.0280787801328603,0.0691254790749753,0.684505567627735,0.00477833185734485 diff --git a/R/results/bumpus_sparrows_results/tables/disruptive_TL.csv b/R/results/bumpus_sparrows_results/tables/disruptive_TL.csv deleted file mode 100644 index 4a0dbea..0000000 --- a/R/results/bumpus_sparrows_results/tables/disruptive_TL.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"TL","Linear",-0.132371564338776,0.0413180907875325,0.0024278232997004,0.00170718462632678 -"TL²","Quadratic",-0.171830973467527,0.0727013103015189,0.0196945423364785,0.00528548051955774 diff --git a/R/results/bumpus_sparrows_results/tables/disruptive_WT.csv b/R/results/bumpus_sparrows_results/tables/disruptive_WT.csv deleted file mode 100644 index cbd25b9..0000000 --- a/R/results/bumpus_sparrows_results/tables/disruptive_WT.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"WT","Linear",-0.0943493742640029,0.0456710882310841,0.0358091107407509,0.00208584830021147 -"WT²","Quadratic",-0.0413471658675293,0.052177650341478,0.321540693542714,0.00272250719515754 diff --git a/R/results/bumpus_sparrows_results/tables/disruptive_selection_summary.csv b/R/results/bumpus_sparrows_results/tables/disruptive_selection_summary.csv deleted file mode 100644 index ca6e6f8..0000000 --- a/R/results/bumpus_sparrows_results/tables/disruptive_selection_summary.csv +++ /dev/null @@ -1,5 +0,0 @@ -"trait","linear","quadratic","p_linear","p_quadratic" -"TL",-0.132371564338776,-0.171830973467527,0.0024278232997004,0.0196945423364785 -"HL",0.0691378467669277,-0.0760360007350176,0.116031606277718,0.202910800498447 -"WT",-0.0943493742640029,-0.0413471658675293,0.0358091107407509,0.321540693542714 -"KL",0.0677836295266952,-0.0280787801328603,0.117736017754752,0.684505567627735 diff --git a/R/results/bumpus_sparrows_results/tables/selection_TL_HL.csv b/R/results/bumpus_sparrows_results/tables/selection_TL_HL.csv deleted file mode 100644 index 298ad5f..0000000 --- a/R/results/bumpus_sparrows_results/tables/selection_TL_HL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value" -"TL","Linear",-0.22895082477631,0.0455925211362093,1.80688149520216e-05 -"HL","Linear",0.203578619267936,0.0455925211362093,8.66828718262618e-05 -"TL²","Quadratic",-0.215041119103549,0.162620898181262,0.170645536799718 -"HL²","Quadratic",-0.0561808048723459,0.148155270477674,0.59714766906793 -"TL × HL","Correlational",-0.0146881017632016,0.107914555160481,0.723439898989453 diff --git a/R/results/bumpus_sparrows_results/tables/selection_TL_HL_WT.csv b/R/results/bumpus_sparrows_results/tables/selection_TL_HL_WT.csv deleted file mode 100644 index 6dd9285..0000000 --- a/R/results/bumpus_sparrows_results/tables/selection_TL_HL_WT.csv +++ /dev/null @@ -1,10 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value" -"TL","Linear",-0.166943956939029,0.0488148235190487,0.00158281113461758 -"HL","Linear",0.255871221238866,0.0475462280474279,8.41603336064868e-06 -"WT","Linear",-0.151853081141983,0.0503858803989128,0.00570476374837237 -"TL²","Quadratic",-0.13859643449833,0.208845622352169,0.393588285551038 -"HL²","Quadratic",0.00562531196731185,0.168099930484475,0.716545812021283 -"WT²","Quadratic",-0.0097818996272233,0.172845055038332,0.722228359034652 -"TL × HL","Correlational",-0.0317071702026084,0.119072190538501,0.75702620049041 -"TL × WT","Correlational",-0.0333720279103151,0.160908585409515,0.544937919356763 -"HL × WT","Correlational",0.021935634316356,0.155985630125617,0.56769782197074 diff --git a/R/results/bumpus_sparrows_results/tables/selection_TL_HL_WT_KL.csv b/R/results/bumpus_sparrows_results/tables/selection_TL_HL_WT_KL.csv deleted file mode 100644 index bf2d919..0000000 --- a/R/results/bumpus_sparrows_results/tables/selection_TL_HL_WT_KL.csv +++ /dev/null @@ -1,15 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value" -"TL","Linear",-0.198443518901218,0.0483495283164539,0.000217028959691374 -"HL","Linear",0.208058528257272,0.0485417307627409,0.000151632311771967 -"WT","Linear",-0.182597539284166,0.0497899727959841,0.000858619342464965 -"KL","Linear",0.147380624293337,0.0473064544367199,0.00318127133161743 -"TL²","Quadratic",-0.0780878008851174,0.209707275913856,0.890740131756136 -"HL²","Quadratic",-0.00110749316445996,0.176840500171238,0.617159381022388 -"WT²","Quadratic",-0.113984867696742,0.18240603305353,0.441234125899648 -"KL²","Quadratic",0.0273172810294443,0.172542973557174,0.430391383259057 -"TL × HL","Correlational",0.0214596847187308,0.123951884001563,0.453620834279192 -"TL × WT","Correlational",0.0307297490627403,0.160569469538851,0.91313728438774 -"TL × KL","Correlational",-0.224548768138053,0.134788113746966,0.0885168914226775 -"HL × WT","Correlational",0.0274025032596178,0.160131527784201,0.544702612937317 -"HL × KL","Correlational",0.000732224429643223,0.131201365225286,0.86690347113047 -"WT × KL","Correlational",0.12742587530868,0.14101762790143,0.502965882378961 diff --git a/R/results/bumpus_sparrows_results/tables/selection_differentials.csv b/R/results/bumpus_sparrows_results/tables/selection_differentials.csv deleted file mode 100644 index 83bf75a..0000000 --- a/R/results/bumpus_sparrows_results/tables/selection_differentials.csv +++ /dev/null @@ -1,5 +0,0 @@ -"trait","differential" -"TL",-0.234716055158291 -"HL",0.162894123623553 -"WT",-0.202418707542421 -"KL",0.128475456583716 diff --git a/R/results/extended_tests/tables/bootstrap_ci.csv b/R/results/extended_tests/tables/bootstrap_ci.csv deleted file mode 100644 index fd3db35..0000000 --- a/R/results/extended_tests/tables/bootstrap_ci.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","est","lwr","upr" -"size","Linear",0.0910165365808788,-0.470607067745545,0.494785313002583 -"speed","Linear",-0.144639784052061,-0.425999225091872,0.181200243447631 -"size²","Quadratic",0.402591069131511,-0.164480962378244,1.21279766762013 -"speed²","Quadratic",0.0218970734483146,-0.323895558167426,0.604550913959529 -"size × speed","Correlational",-0.121725317575994,-0.400589904485058,0.148398351925861 diff --git a/R/results/extended_tests/tables/selection_binary.csv b/R/results/extended_tests/tables/selection_binary.csv deleted file mode 100644 index a2aa2f8..0000000 --- a/R/results/extended_tests/tables/selection_binary.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"size","Linear",0.105036692185697,0.229833011910793,0.64766164551854,0.0528232133639866 -"speed","Linear",0.31389539156892,0.232082567392143,0.176210295823653,0.0538623180873288 -"size²","Quadratic",0.432724154554936,0.3338038142697,0.194857426435059,0.111424986421 -"speed²","Quadratic",0.171981112711459,0.425321637062577,0.685951371316174,0.18089849495359 -"size × speed","Correlational",-0.379609055590874,0.2968068107668,0.200905189547171,0.0880942829175589 diff --git a/R/results/extended_tests/tables/selection_continuous.csv b/R/results/extended_tests/tables/selection_continuous.csv deleted file mode 100644 index 5615de6..0000000 --- a/R/results/extended_tests/tables/selection_continuous.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"size","Linear",0.0195027146393764,0.0477041189642697,0.683801736949462,0.0022756829661572 -"speed","Linear",-0.0320661103772255,0.0477041189642697,0.503476401863023,0.00227568296615719 -"size²","Quadratic",0.0837596260850392,0.0796747981055651,0.296556117916126,0.00634807345316255 -"speed²","Quadratic",0.0122552368949205,0.067247096766026,0.855891235202132,0.00452217202345927 -"size × speed","Correlational",-0.0374428040336,0.0525616841787993,0.478482396704399,0.00276273064371184 diff --git a/R/results/medium_grouped_finch_results/models/cfs_2003.rds b/R/results/medium_grouped_finch_results/models/cfs_2003.rds deleted file mode 100644 index ebeada7..0000000 Binary files a/R/results/medium_grouped_finch_results/models/cfs_2003.rds and /dev/null differ diff --git a/R/results/medium_grouped_finch_results/models/cfs_2004.rds b/R/results/medium_grouped_finch_results/models/cfs_2004.rds deleted file mode 100644 index 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a/R/results/medium_grouped_finch_results/models/spline_2008.rds b/R/results/medium_grouped_finch_results/models/spline_2008.rds deleted file mode 100644 index f829b48..0000000 Binary files a/R/results/medium_grouped_finch_results/models/spline_2008.rds and /dev/null differ diff --git a/R/results/medium_grouped_finch_results/models/spline_2009.rds b/R/results/medium_grouped_finch_results/models/spline_2009.rds deleted file mode 100644 index 62582f4..0000000 Binary files a/R/results/medium_grouped_finch_results/models/spline_2009.rds and /dev/null differ diff --git a/R/results/medium_grouped_finch_results/models/spline_2010.rds b/R/results/medium_grouped_finch_results/models/spline_2010.rds deleted file mode 100644 index fa8cad2..0000000 Binary files a/R/results/medium_grouped_finch_results/models/spline_2010.rds and /dev/null differ diff --git a/R/results/medium_grouped_finch_results/models/spline_2011.rds b/R/results/medium_grouped_finch_results/models/spline_2011.rds deleted file mode 100644 index 2e86290..0000000 Binary files a/R/results/medium_grouped_finch_results/models/spline_2011.rds and /dev/null differ diff --git a/R/results/medium_grouped_finch_results/tables/combined_selection_results.csv b/R/results/medium_grouped_finch_results/tables/combined_selection_results.csv deleted file mode 100644 index 33b83a4..0000000 --- a/R/results/medium_grouped_finch_results/tables/combined_selection_results.csv +++ /dev/null @@ -1,46 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Year" -"Beak_PC1","Linear",0.157034120813058,0.5354071119957,0.769293974428903,0.286660775575576,2003 -"PC.body1","Linear",0.729178470539137,0.563914857462183,0.195988637055055,0.317999966466594,2003 -"Beak_PC1²","Quadratic",-0.941413463848283,1.38597005452214,0.496982531856332,1.9209129920321,2003 -"PC.body1²","Quadratic",-0.912287581526172,1.75350457737264,0.602878679102832,3.07477830286681,2003 -"Beak_PC1 × PC.body1","Correlational",0.550433277132843,1.39726438950502,0.693628009406304,1.95234777417885,2003 -"Beak_PC1","Linear",-0.384979108506153,0.38053697940942,0.311694277249877,0.144808392698045,2004 -"PC.body1","Linear",0.266300907311267,0.378599674844514,0.48181655123231,0.143337713792372,2004 -"Beak_PC1²","Quadratic",-0.212312556007557,1.0535177018795,0.840286301280265,1.10989954817347,2004 -"PC.body1²","Quadratic",-1.42271681850908,1.25124670829522,0.255521811189631,1.56561832501961,2004 -"Beak_PC1 × PC.body1","Correlational",0.724681724814364,1.03317319099764,0.483044938565499,1.06744684259625,2004 -"Beak_PC1","Linear",-0.313422114842596,0.334421955506562,0.348652832250871,0.111838044324833,2005 -"PC.body1","Linear",0.246422678346832,0.331379472392259,0.457102245463944,0.109812354722972,2005 -"Beak_PC1²","Quadratic",-0.456166505850973,1.04405751370474,0.662171522414209,1.09005609192333,2005 -"PC.body1²","Quadratic",0.29933364107309,0.957641782584079,0.754604557318401,0.917077783750812,2005 -"Beak_PC1 × PC.body1","Correlational",-0.0573478033628712,0.927128441241396,0.950678068598861,0.859567146558702,2005 -"Beak_PC1","Linear",-0.391369642165724,0.266366615175114,0.141754312730473,0.0709511736798471,2006 -"PC.body1","Linear",0.490260564935097,0.268931870274224,0.0683046493660777,0.072324350849192,2006 -"Beak_PC1²","Quadratic",-1.22330174727523,0.783769314111778,0.118572573045541,0.614294337743246,2006 -"PC.body1²","Quadratic",-0.927171553515021,0.705310383280175,0.188658423397669,0.497462736762827,2006 -"Beak_PC1 × PC.body1","Correlational",1.14584849944074,0.69419011180202,0.0988148923336032,0.481899911323702,2006 -"Beak_PC1","Linear",-0.765409211782432,0.568482074198161,0.178170745985092,0.323171868684643,2007 -"PC.body1","Linear",0.787751517236819,0.56689150211593,0.164650865688176,0.321365975171255,2007 -"Beak_PC1²","Quadratic",-2.96832275347639,2.69788366827047,0.271227045745994,7.27857628752051,2007 -"PC.body1²","Quadratic",-5.64855577658353,3.49542752278408,0.106097721420698,12.2180135670365,2007 -"Beak_PC1 × PC.body1","Correlational",3.68032212299857,2.89338542249423,0.203380994989291,8.37167920310211,2007 -"Beak_PC1","Linear",0.0169475967438167,0.326684285860255,0.958626222760257,0.106722622628025,2008 -"PC.body1","Linear",-0.472493915941149,0.327766613097613,0.149427678793456,0.10743095266148,2008 -"Beak_PC1²","Quadratic",-0.829997303937714,0.819499204130572,0.311150739633348,0.671578945570641,2008 -"PC.body1²","Quadratic",0.181425957525393,0.761185719176359,0.811612352930676,0.579403699078031,2008 -"Beak_PC1 × PC.body1","Correlational",0.394516757586104,0.655459983437501,0.547245382600809,0.429627789887889,2008 -"Beak_PC1","Linear",1.14336994883516,0.374319955396192,0.00225416649936562,0.140115429007807,2009 -"PC.body1","Linear",-0.779715940573539,0.372489883768767,0.036326486253675,0.13874871351007,2009 -"Beak_PC1²","Quadratic",-1.28060499578713,1.28860200421342,0.320323146786786,1.66049512526283,2009 -"PC.body1²","Quadratic",-2.00938131253789,1.31546207029516,0.1266342716809,1.73044045838522,2009 -"Beak_PC1 × PC.body1","Correlational",1.9453355637236,1.24205137641691,0.11729526485083,1.54269162165914,2009 -"Beak_PC1","Linear",-0.632783589442991,0.472579896245778,0.180571287123798,0.22333175833567,2010 -"PC.body1","Linear",0.125924929373963,0.470296249788173,0.788886671967752,0.22117856256482,2010 -"Beak_PC1²","Quadratic",-0.411712667078607,1.50599209728215,0.784558804189573,2.26801219707628,2010 -"PC.body1²","Quadratic",-1.04431855579443,1.52158862708174,0.492502286712417,2.31523195006448,2010 -"Beak_PC1 × PC.body1","Correlational",0.526808766765032,1.3500770839251,0.696383903127642,1.82270813253971,2010 -"Beak_PC1","Linear",-1.47572827455361e-07,43691.9740543333,0.999999999997305,1908988596.76454,2011 -"PC.body1","Linear",4.60354079146197e-08,43691.9744793498,0.999999999999159,1908988633.90416,2011 -"Beak_PC1²","Quadratic",-3.73923980613574e-06,108825.262499253,0.999999999972585,11842937758.0312,2011 -"PC.body1²","Quadratic",-1.0141357864923e-06,115654.148114801,0.999999999993004,13375881976.1603,2011 -"Beak_PC1 × PC.body1","Correlational",2.06392762728927e-06,101438.433716069,0.999999999983766,10289755834.7694,2011 diff --git a/R/results/medium_grouped_finch_results/tables/comparison_correlation_2009.csv b/R/results/medium_grouped_finch_results/tables/comparison_correlation_2009.csv deleted file mode 100644 index 638ed05..0000000 --- a/R/results/medium_grouped_finch_results/tables/comparison_correlation_2009.csv +++ /dev/null @@ -1,2 +0,0 @@ -"Year","trait1","trait2","correlation","n_points" -2009,"Beak_PC1","PC.body1",0.982679408086704,2500 diff --git a/R/results/medium_grouped_finch_results/tables/disruptive_2003.csv b/R/results/medium_grouped_finch_results/tables/disruptive_2003.csv deleted file mode 100644 index 9123a9f..0000000 --- a/R/results/medium_grouped_finch_results/tables/disruptive_2003.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",0.931471324419863,0.443635447627208,0.0357611973356478,0.196812410391393 -"Beak_PC1²","Quadratic",-0.606077449894362,0.73948973979816,0.412450605749448,0.546845075266751 diff --git a/R/results/medium_grouped_finch_results/tables/disruptive_2004.csv b/R/results/medium_grouped_finch_results/tables/disruptive_2004.csv deleted file mode 100644 index 2efa5a1..0000000 --- a/R/results/medium_grouped_finch_results/tables/disruptive_2004.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",-0.186556062616738,0.230154435690401,0.41761319576889,0.0529710642679667 -"Beak_PC1²","Quadratic",0.110405893051567,0.449977840593368,0.806178850527553,0.202480057025071 diff --git a/R/results/medium_grouped_finch_results/tables/disruptive_2005.csv b/R/results/medium_grouped_finch_results/tables/disruptive_2005.csv deleted file mode 100644 index 3cf98b5..0000000 --- a/R/results/medium_grouped_finch_results/tables/disruptive_2005.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",0.04493658821583,0.220798974911511,0.838730098679639,0.0487521873219742 -"Beak_PC1²","Quadratic",-0.371119188307051,0.353265372591698,0.293470191662365,0.124796423472351 diff --git a/R/results/medium_grouped_finch_results/tables/disruptive_2006.csv b/R/results/medium_grouped_finch_results/tables/disruptive_2006.csv deleted file mode 100644 index d5cce9b..0000000 --- a/R/results/medium_grouped_finch_results/tables/disruptive_2006.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",-0.039645846609433,0.208477442407277,0.849177078610708,0.0434628439926793 -"Beak_PC1²","Quadratic",0.0485395656494751,0.2772200800545,0.861005792726034,0.0768509727854233 diff --git a/R/results/medium_grouped_finch_results/tables/disruptive_2007.csv b/R/results/medium_grouped_finch_results/tables/disruptive_2007.csv deleted file mode 100644 index fa3d15d..0000000 --- a/R/results/medium_grouped_finch_results/tables/disruptive_2007.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",0.0940884569097048,0.413100987049408,0.819831740561458,0.170652425501195 -"Beak_PC1²","Quadratic",-0.377385718923095,0.636997105336175,0.553552673068217,0.405765312206666 diff --git a/R/results/medium_grouped_finch_results/tables/disruptive_2008.csv b/R/results/medium_grouped_finch_results/tables/disruptive_2008.csv deleted file mode 100644 index 3dbeb1a..0000000 --- a/R/results/medium_grouped_finch_results/tables/disruptive_2008.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",-0.327149138252539,0.237569864036858,0.168492161071607,0.0564394402984913 -"Beak_PC1²","Quadratic",-0.0571332155754746,0.335406936668395,0.864742760180668,0.112497813165277 diff --git a/R/results/medium_grouped_finch_results/tables/disruptive_2009.csv b/R/results/medium_grouped_finch_results/tables/disruptive_2009.csv deleted file mode 100644 index 5bf2860..0000000 --- a/R/results/medium_grouped_finch_results/tables/disruptive_2009.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",0.0989750793191558,0.2271988646788,0.663103802326313,0.0516193241113358 -"Beak_PC1²","Quadratic",0.551184504321127,0.25683788726285,0.0318697487820652,0.0659657003336442 diff --git a/R/results/medium_grouped_finch_results/tables/disruptive_2010.csv b/R/results/medium_grouped_finch_results/tables/disruptive_2010.csv deleted file mode 100644 index b763b7d..0000000 --- a/R/results/medium_grouped_finch_results/tables/disruptive_2010.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",-0.525131626978204,0.287713030715053,0.0679720055643439,0.0827787880432411 -"Beak_PC1²","Quadratic",-0.203101746509598,0.554740404967238,0.714275279417836,0.307736916903215 diff --git a/R/results/medium_grouped_finch_results/tables/disruptive_2011.csv b/R/results/medium_grouped_finch_results/tables/disruptive_2011.csv deleted file mode 100644 index c13e2ed..0000000 --- a/R/results/medium_grouped_finch_results/tables/disruptive_2011.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",2.17016843710123e-06,32314.6914920181,0.999999999946416,1044239286.22431 -"Beak_PC1²","Quadratic",-2.47875077813045e-06,39777.9384618187,0.99999999995028,1582284388.27224 diff --git a/R/results/medium_grouped_finch_results/tables/multi_year_summary.csv b/R/results/medium_grouped_finch_results/tables/multi_year_summary.csv deleted file mode 100644 index bc8ca00..0000000 --- a/R/results/medium_grouped_finch_results/tables/multi_year_summary.csv +++ /dev/null @@ -1,10 +0,0 @@ -"Year","N","Survival_Rate","Gamma","SE","P_Value","Significant" -2003,49,0.408,-0.6061,0.7395,0.4125,FALSE -2004,110,0.345,0.1104,0.45,0.8062,FALSE -2005,185,0.276,-0.3711,0.3533,0.2935,FALSE -2006,233,0.172,0.0485,0.2772,0.861,FALSE -2007,61,0.328,-0.3774,0.637,0.5536,FALSE -2008,127,0.291,-0.0571,0.3354,0.8647,FALSE -2009,196,0.173,0.5512,0.2568,0.0319,TRUE -2010,175,0.12,-0.2031,0.5547,0.7143,FALSE -2011,211,1,0,39777.9385,1,FALSE diff --git a/R/results/medium_grouped_finch_results/tables/selection_2003.csv b/R/results/medium_grouped_finch_results/tables/selection_2003.csv deleted file mode 100644 index fe7b3dd..0000000 --- a/R/results/medium_grouped_finch_results/tables/selection_2003.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",0.157034120813058,0.5354071119957,0.769293974428903,0.286660775575576 -"PC.body1","Linear",0.729178470539137,0.563914857462183,0.195988637055055,0.317999966466594 -"Beak_PC1²","Quadratic",-0.941413463848283,1.38597005452214,0.496982531856332,1.9209129920321 -"PC.body1²","Quadratic",-0.912287581526172,1.75350457737264,0.602878679102832,3.07477830286681 -"Beak_PC1 × PC.body1","Correlational",0.550433277132843,1.39726438950502,0.693628009406304,1.95234777417885 diff --git a/R/results/medium_grouped_finch_results/tables/selection_2004.csv b/R/results/medium_grouped_finch_results/tables/selection_2004.csv deleted file mode 100644 index 6605539..0000000 --- a/R/results/medium_grouped_finch_results/tables/selection_2004.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",-0.384979108506153,0.38053697940942,0.311694277249877,0.144808392698045 -"PC.body1","Linear",0.266300907311267,0.378599674844514,0.48181655123231,0.143337713792372 -"Beak_PC1²","Quadratic",-0.212312556007557,1.0535177018795,0.840286301280265,1.10989954817347 -"PC.body1²","Quadratic",-1.42271681850908,1.25124670829522,0.255521811189631,1.56561832501961 -"Beak_PC1 × PC.body1","Correlational",0.724681724814364,1.03317319099764,0.483044938565499,1.06744684259625 diff --git a/R/results/medium_grouped_finch_results/tables/selection_2005.csv b/R/results/medium_grouped_finch_results/tables/selection_2005.csv deleted file mode 100644 index 5199fdf..0000000 --- a/R/results/medium_grouped_finch_results/tables/selection_2005.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",-0.313422114842596,0.334421955506562,0.348652832250871,0.111838044324833 -"PC.body1","Linear",0.246422678346832,0.331379472392259,0.457102245463944,0.109812354722972 -"Beak_PC1²","Quadratic",-0.456166505850973,1.04405751370474,0.662171522414209,1.09005609192333 -"PC.body1²","Quadratic",0.29933364107309,0.957641782584079,0.754604557318401,0.917077783750812 -"Beak_PC1 × PC.body1","Correlational",-0.0573478033628712,0.927128441241396,0.950678068598861,0.859567146558702 diff --git a/R/results/medium_grouped_finch_results/tables/selection_2006.csv b/R/results/medium_grouped_finch_results/tables/selection_2006.csv deleted file mode 100644 index f32402e..0000000 --- a/R/results/medium_grouped_finch_results/tables/selection_2006.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",-0.391369642165724,0.266366615175114,0.141754312730473,0.0709511736798471 -"PC.body1","Linear",0.490260564935097,0.268931870274224,0.0683046493660777,0.072324350849192 -"Beak_PC1²","Quadratic",-1.22330174727523,0.783769314111778,0.118572573045541,0.614294337743246 -"PC.body1²","Quadratic",-0.927171553515021,0.705310383280175,0.188658423397669,0.497462736762827 -"Beak_PC1 × PC.body1","Correlational",1.14584849944074,0.69419011180202,0.0988148923336032,0.481899911323702 diff --git a/R/results/medium_grouped_finch_results/tables/selection_2007.csv b/R/results/medium_grouped_finch_results/tables/selection_2007.csv deleted file mode 100644 index d3db94f..0000000 --- a/R/results/medium_grouped_finch_results/tables/selection_2007.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",-0.765409211782432,0.568482074198161,0.178170745985092,0.323171868684643 -"PC.body1","Linear",0.787751517236819,0.56689150211593,0.164650865688176,0.321365975171255 -"Beak_PC1²","Quadratic",-2.96832275347639,2.69788366827047,0.271227045745994,7.27857628752051 -"PC.body1²","Quadratic",-5.64855577658353,3.49542752278408,0.106097721420698,12.2180135670365 -"Beak_PC1 × PC.body1","Correlational",3.68032212299857,2.89338542249423,0.203380994989291,8.37167920310211 diff --git a/R/results/medium_grouped_finch_results/tables/selection_2008.csv b/R/results/medium_grouped_finch_results/tables/selection_2008.csv deleted file mode 100644 index 60ba983..0000000 --- a/R/results/medium_grouped_finch_results/tables/selection_2008.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",0.0169475967438167,0.326684285860255,0.958626222760257,0.106722622628025 -"PC.body1","Linear",-0.472493915941149,0.327766613097613,0.149427678793456,0.10743095266148 -"Beak_PC1²","Quadratic",-0.829997303937714,0.819499204130572,0.311150739633348,0.671578945570641 -"PC.body1²","Quadratic",0.181425957525393,0.761185719176359,0.811612352930676,0.579403699078031 -"Beak_PC1 × PC.body1","Correlational",0.394516757586104,0.655459983437501,0.547245382600809,0.429627789887889 diff --git a/R/results/medium_grouped_finch_results/tables/selection_2009.csv b/R/results/medium_grouped_finch_results/tables/selection_2009.csv deleted file mode 100644 index 7208f8e..0000000 --- a/R/results/medium_grouped_finch_results/tables/selection_2009.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",1.14336994883516,0.374319955396192,0.00225416649936562,0.140115429007807 -"PC.body1","Linear",-0.779715940573539,0.372489883768767,0.036326486253675,0.13874871351007 -"Beak_PC1²","Quadratic",-1.28060499578713,1.28860200421342,0.320323146786786,1.66049512526283 -"PC.body1²","Quadratic",-2.00938131253789,1.31546207029516,0.1266342716809,1.73044045838522 -"Beak_PC1 × PC.body1","Correlational",1.9453355637236,1.24205137641691,0.11729526485083,1.54269162165914 diff --git a/R/results/medium_grouped_finch_results/tables/selection_2010.csv b/R/results/medium_grouped_finch_results/tables/selection_2010.csv deleted file mode 100644 index b195885..0000000 --- a/R/results/medium_grouped_finch_results/tables/selection_2010.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",-0.632783589442991,0.472579896245778,0.180571287123798,0.22333175833567 -"PC.body1","Linear",0.125924929373963,0.470296249788173,0.788886671967752,0.22117856256482 -"Beak_PC1²","Quadratic",-0.411712667078607,1.50599209728215,0.784558804189573,2.26801219707628 -"PC.body1²","Quadratic",-1.04431855579443,1.52158862708174,0.492502286712417,2.31523195006448 -"Beak_PC1 × PC.body1","Correlational",0.526808766765032,1.3500770839251,0.696383903127642,1.82270813253971 diff --git a/R/results/medium_grouped_finch_results/tables/selection_2011.csv b/R/results/medium_grouped_finch_results/tables/selection_2011.csv deleted file mode 100644 index 8898154..0000000 --- a/R/results/medium_grouped_finch_results/tables/selection_2011.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"Beak_PC1","Linear",-1.47572827455361e-07,43691.9740543333,0.999999999997305,1908988596.76454 -"PC.body1","Linear",4.60354079146197e-08,43691.9744793498,0.999999999999159,1908988633.90416 -"Beak_PC1²","Quadratic",-3.73923980613574e-06,108825.262499253,0.999999999972585,11842937758.0312 -"PC.body1²","Quadratic",-1.0141357864923e-06,115654.148114801,0.999999999993004,13375881976.1603 -"Beak_PC1 × PC.body1","Correlational",2.06392762728927e-06,101438.433716069,0.999999999983766,10289755834.7694 diff --git a/R/results/plant_results/models/adaptive_landscape_FDsnow_height.rds b/R/results/plant_results/models/adaptive_landscape_FDsnow_height.rds deleted file mode 100644 index c09803d..0000000 Binary files a/R/results/plant_results/models/adaptive_landscape_FDsnow_height.rds and /dev/null differ diff --git a/R/results/plant_results/models/adaptive_landscape_SLA_FDsnow.rds b/R/results/plant_results/models/adaptive_landscape_SLA_FDsnow.rds deleted file mode 100644 index 374376b..0000000 Binary files a/R/results/plant_results/models/adaptive_landscape_SLA_FDsnow.rds and /dev/null differ diff --git a/R/results/plant_results/models/adaptive_landscape_SLA_deltaC13.rds b/R/results/plant_results/models/adaptive_landscape_SLA_deltaC13.rds deleted file mode 100644 index c70c503..0000000 Binary files a/R/results/plant_results/models/adaptive_landscape_SLA_deltaC13.rds and /dev/null differ diff --git a/R/results/plant_results/models/adaptive_landscape_SLA_height.rds b/R/results/plant_results/models/adaptive_landscape_SLA_height.rds deleted file mode 100644 index 82697fb..0000000 Binary files a/R/results/plant_results/models/adaptive_landscape_SLA_height.rds and /dev/null differ diff --git a/R/results/plant_results/models/adaptive_landscape_deltaC13_FDsnow.rds b/R/results/plant_results/models/adaptive_landscape_deltaC13_FDsnow.rds deleted file mode 100644 index 20c9be9..0000000 Binary files a/R/results/plant_results/models/adaptive_landscape_deltaC13_FDsnow.rds and /dev/null differ diff --git a/R/results/plant_results/models/adaptive_landscape_deltaC13_height.rds b/R/results/plant_results/models/adaptive_landscape_deltaC13_height.rds deleted file mode 100644 index a9b211e..0000000 Binary files a/R/results/plant_results/models/adaptive_landscape_deltaC13_height.rds and /dev/null differ diff --git a/R/results/plant_results/models/cfs_FDsnow_height.rds b/R/results/plant_results/models/cfs_FDsnow_height.rds deleted file mode 100644 index d3fa7f7..0000000 Binary files a/R/results/plant_results/models/cfs_FDsnow_height.rds and /dev/null differ diff --git a/R/results/plant_results/models/cfs_SLA_FDsnow.rds b/R/results/plant_results/models/cfs_SLA_FDsnow.rds deleted file mode 100644 index 2a32022..0000000 Binary files a/R/results/plant_results/models/cfs_SLA_FDsnow.rds and /dev/null differ diff --git a/R/results/plant_results/models/cfs_SLA_deltaC13.rds b/R/results/plant_results/models/cfs_SLA_deltaC13.rds deleted file mode 100644 index 4b3340a..0000000 Binary files a/R/results/plant_results/models/cfs_SLA_deltaC13.rds and /dev/null differ diff --git a/R/results/plant_results/models/cfs_SLA_height.rds b/R/results/plant_results/models/cfs_SLA_height.rds deleted file mode 100644 index a5a676c..0000000 Binary files a/R/results/plant_results/models/cfs_SLA_height.rds and /dev/null differ diff --git a/R/results/plant_results/models/cfs_deltaC13_FDsnow.rds b/R/results/plant_results/models/cfs_deltaC13_FDsnow.rds deleted file mode 100644 index 0b72270..0000000 Binary files a/R/results/plant_results/models/cfs_deltaC13_FDsnow.rds and /dev/null differ diff --git a/R/results/plant_results/models/cfs_deltaC13_height.rds b/R/results/plant_results/models/cfs_deltaC13_height.rds deleted file mode 100644 index c8b6b7b..0000000 Binary files a/R/results/plant_results/models/cfs_deltaC13_height.rds and /dev/null differ diff --git a/R/results/plant_results/tables/disruptive_selection.csv b/R/results/plant_results/tables/disruptive_selection.csv deleted file mode 100644 index 5c09675..0000000 --- a/R/results/plant_results/tables/disruptive_selection.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Trait","Beta","Gamma","P_Linear","P_Quadratic" -"SLA",0.0476259163621036,-0.100056733921985,0.476890961132518,0.281356584173955 -"deltaC13",-0.011073134823742,-0.046034146815972,0.854663354111405,0.623298218388449 -"FDsnow",-0.13130019385937,-0.0528847820612453,0.0256334813871458,0.558628105292545 -"height",-0.0674159642230305,-0.0859613170953237,0.260467489253676,0.365031981418163 diff --git a/R/results/plant_results/tables/selection_2011.csv b/R/results/plant_results/tables/selection_2011.csv deleted file mode 100644 index 7a47e5d..0000000 --- a/R/results/plant_results/tables/selection_2011.csv +++ /dev/null @@ -1,15 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"SLA","Linear",0.05902363747125,0.112219281952377,0.601147223307564,0.0125931672419071 -"deltaC13","Linear",0.0619766637823494,0.0981704126927149,0.530598646442826,0.00963742992825795 -"FDsnow","Linear",-0.151391717295305,0.109808151959988,0.17389187515583,0.0120578302368677 -"height","Linear",-0.229310795220014,0.101796269544657,0.0285282249805593,0.0103624804932084 -"SLA²","Quadratic",-0.131260212085616,0.252937963851596,0.606524769371412,0.0639776135573911 -"deltaC13²","Quadratic",-0.194998524287815,0.194963430906559,0.322951212780519,0.0380107393908568 -"FDsnow²","Quadratic",-0.42853553103927,0.32001068512974,0.187731370596782,0.102406838597206 -"height²","Quadratic",-0.109088585895452,0.218708607581467,0.620533233504075,0.0478334550302241 -"SLA × deltaC13","Correlational",-0.0485983830956867,0.163311425316665,0.767489968321122,0.0266706216389607 -"SLA × FDsnow","Correlational",-0.167104494504259,0.142387390531177,0.247171500799718,0.020274168982278 -"SLA × height","Correlational",0.0368524741432567,0.138569599386369,0.791579547360351,0.0192015338740988 -"deltaC13 × FDsnow","Correlational",0.0935750828984882,0.134362552440843,0.489991633963578,0.0180532954984183 -"deltaC13 × height","Correlational",0.038291732145487,0.139291428618141,0.784738033709312,0.0194021020864828 -"FDsnow × height","Correlational",-0.23827697952905,0.195654911850164,0.230081390689747,0.0382808445310955 diff --git a/R/results/plant_results/tables/selection_2012.csv b/R/results/plant_results/tables/selection_2012.csv deleted file mode 100644 index 4e18514..0000000 --- a/R/results/plant_results/tables/selection_2012.csv +++ /dev/null @@ -1,15 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"SLA","Linear",-0.0881785642181782,0.0603313773748249,0.15130103402027,0.00363987509594353 -"deltaC13","Linear",-0.00169688535787948,0.0540490322586798,0.975103014797394,0.00292129788809981 -"FDsnow","Linear",-0.106502460492457,0.0573952174660967,0.0705374143343047,0.00329421098798054 -"height","Linear",0.0654817961081827,0.0579382886415924,0.264805559810151,0.00335684529071648 -"SLA²","Quadratic",-0.00317423929158592,0.11258411524276,0.977682224811052,0.012675183004995 -"deltaC13²","Quadratic",0.0201296835562432,0.0907878517319454,0.825939038029146,0.00824243402210171 -"FDsnow²","Quadratic",0.251077124182269,0.0977262454408589,0.0150588662797741,0.009550419047967 -"height²","Quadratic",-0.0989185212331775,0.118333270303028,0.40939207499307,0.0140027628606095 -"SLA × deltaC13","Correlational",0.122424844057274,0.103526113258666,0.245699761817661,0.0107176561264462 -"SLA × FDsnow","Correlational",0.0355388378991694,0.0930870285133141,0.705147541757324,0.00866519487743854 -"SLA × height","Correlational",-0.14113327647184,0.0777646259301612,0.0789264781367424,0.0060473370460579 -"deltaC13 × FDsnow","Correlational",0.0793891302406412,0.0612827928913953,0.204430859971732,0.00375558070456966 -"deltaC13 × height","Correlational",-0.0323633094850103,0.0712542892109461,0.65275466218369,0.00507717373095714 -"FDsnow × height","Correlational",-0.183031935219124,0.0776811059289721,0.0247524277862347,0.00603435421834819 diff --git a/R/results/plant_results/tables/selection_combined.csv b/R/results/plant_results/tables/selection_combined.csv deleted file mode 100644 index fc33336..0000000 --- a/R/results/plant_results/tables/selection_combined.csv +++ /dev/null @@ -1,15 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"SLA","Linear",-0.0563405874312375,0.0643563580786868,0.3834497505348,0.00414174082515216 -"deltaC13","Linear",0.0322281425559652,0.0599075935176079,0.591809097219966,0.00358891976107093 -"FDsnow","Linear",-0.146576837715669,0.0653200994479195,0.027060929603723,0.0042667153918861 -"height","Linear",-0.069465602210005,0.0598032130108675,0.248203176301178,0.0035764242864232 -"SLA²","Quadratic",-0.083149511171098,0.123450546277277,0.502345995999226,0.0152400373761581 -"deltaC13²","Quadratic",-0.0589894980330239,0.107811774945739,0.585643258658725,0.0116233788169507 -"FDsnow²","Quadratic",-0.0754412311979613,0.143617738360195,0.600686535484921,0.0206260547716974 -"height²","Quadratic",-0.126569959607138,0.117146143813477,0.282863228775715,0.0137232190103679 -"SLA × deltaC13","Correlational",-0.0432665654977066,0.0910577105240945,0.635840221994145,0.00829150664588979 -"SLA × FDsnow","Correlational",-0.0630038721066949,0.0812111353598148,0.439921779290363,0.00659524850643017 -"SLA × height","Correlational",-0.0476232459288535,0.0706808117577035,0.502197975598992,0.00499577715072791 -"deltaC13 × FDsnow","Correlational",0.041443187691231,0.0753107548636706,0.583495073145639,0.00567170979813589 -"deltaC13 × height","Correlational",0.0321362404282255,0.0738055961018494,0.664313634402176,0.00544726601594933 -"FDsnow × height","Correlational",-0.162381938400619,0.0933553506866509,0.0854224209490992,0.00871522150182757 diff --git a/R/results/plant_results/tables/selection_differentials.csv b/R/results/plant_results/tables/selection_differentials.csv deleted file mode 100644 index 7678bc2..0000000 --- a/R/results/plant_results/tables/selection_differentials.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Trait","S_2011","S_2012" -"SLA",0.0848995152711299,-0.0745157059262795 -"deltaC13",-0.00642394246179183,-0.00223859161690406 -"FDsnow",-0.185299201303204,-0.0518274863169748 -"height",-0.203245825381072,0.073810218635867 diff --git a/R/results/plant_results/tables/selection_differentials_combined.csv b/R/results/plant_results/tables/selection_differentials_combined.csv deleted file mode 100644 index aa0a4d3..0000000 --- a/R/results/plant_results/tables/selection_differentials_combined.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Trait","S_Combined" -"SLA",0.0129189643790086 -"deltaC13",-0.0045546497070298 -"FDsnow",-0.125591407211315 -"height",-0.0784194107252992 diff --git a/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Crescent_Pond_2d.png b/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Crescent_Pond_2d.png deleted file mode 100644 index da91ac2..0000000 Binary files a/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Crescent_Pond_2d.png and /dev/null differ diff --git a/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Crescent_Pond_3d.png b/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Crescent_Pond_3d.png deleted file mode 100644 index 4e99b4e..0000000 Binary files a/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Crescent_Pond_3d.png and /dev/null differ diff --git a/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Little_Lake_2d.png b/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Little_Lake_2d.png deleted file mode 100644 index 8e5f0d1..0000000 Binary files a/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Little_Lake_2d.png and /dev/null differ diff --git a/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Little_Lake_3d.png b/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Little_Lake_3d.png deleted file mode 100644 index b4a047d..0000000 Binary files a/R/results/pupfish_results/figures/adaptive_landscape_binary_body_SL_Little_Lake_3d.png and /dev/null differ diff --git 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index 2ef4d67..0000000 Binary files a/R/results/pupfish_results/models/spline_continuous_mouth.rds and /dev/null differ diff --git a/R/results/pupfish_results/models/spline_continuous_mouth_Crescent Pond.rds b/R/results/pupfish_results/models/spline_continuous_mouth_Crescent Pond.rds deleted file mode 100644 index 7735d4b..0000000 Binary files a/R/results/pupfish_results/models/spline_continuous_mouth_Crescent Pond.rds and /dev/null differ diff --git a/R/results/pupfish_results/models/spline_continuous_mouth_Little Lake.rds b/R/results/pupfish_results/models/spline_continuous_mouth_Little Lake.rds deleted file mode 100644 index 94b7f7d..0000000 Binary files a/R/results/pupfish_results/models/spline_continuous_mouth_Little Lake.rds and /dev/null differ diff --git a/R/results/pupfish_results/models/spline_continuous_nasal.rds b/R/results/pupfish_results/models/spline_continuous_nasal.rds deleted file mode 100644 index 6cd3e0b..0000000 Binary files a/R/results/pupfish_results/models/spline_continuous_nasal.rds and /dev/null differ diff --git a/R/results/pupfish_results/models/spline_continuous_nasal_Crescent Pond.rds b/R/results/pupfish_results/models/spline_continuous_nasal_Crescent Pond.rds deleted file mode 100644 index 6a052a1..0000000 Binary files a/R/results/pupfish_results/models/spline_continuous_nasal_Crescent Pond.rds and /dev/null differ diff --git a/R/results/pupfish_results/models/spline_continuous_nasal_Little Lake.rds b/R/results/pupfish_results/models/spline_continuous_nasal_Little Lake.rds deleted file mode 100644 index 3fd6323..0000000 Binary files a/R/results/pupfish_results/models/spline_continuous_nasal_Little Lake.rds and /dev/null differ diff --git a/R/results/pupfish_results/tables/adaptive_landscape_summary.csv b/R/results/pupfish_results/tables/adaptive_landscape_summary.csv deleted file mode 100644 index f428b4e..0000000 --- a/R/results/pupfish_results/tables/adaptive_landscape_summary.csv +++ /dev/null @@ -1,91 +0,0 @@ -"Trait1","Trait2","Fitness","Site","Site_Type","Optimum_Trait1","Optimum_Trait2","Max_Fitness" -"jaw","eye","Binary","Overall","overall",3.5107,1.4675,0.3638 -"jaw","body","Binary","Overall","overall",2.5786,-2.2785,0.2717 -"jaw","nasal","Binary","Overall","overall",3.5107,-6.1005,0.957 -"jaw","mouth","Binary","Overall","overall",3.5107,-5.0389,0.4672 -"jaw","SL","Binary","Overall","overall",3.2444,-3.2489,0.372 -"eye","body","Binary","Overall","overall",1.2763,-5.2508,0.2929 -"eye","nasal","Binary","Overall","overall",-1.0175,-6.1005,0.7629 -"eye","mouth","Binary","Overall","overall",6.0552,-5.0389,0.3243 -"eye","SL","Binary","Overall","overall",-5.2229,5.5871,0.8187 -"body","nasal","Binary","Overall","overall",-5.2508,-6.1005,0.9623 -"body","mouth","Binary","Overall","overall",-5.2508,-5.0389,0.526 -"body","SL","Binary","Overall","overall",3.6662,-6.8255,0.5515 -"nasal","mouth","Binary","Overall","overall",-6.1005,-5.0389,0.8565 -"nasal","SL","Binary","Overall","overall",-6.1005,-6.6151,0.9607 -"mouth","SL","Binary","Overall","overall",-5.0389,-6.8255,0.8677 -"jaw","eye","Continuous","Overall","overall",-4.3462,6.0552,0.0916 -"jaw","body","Continuous","Overall","overall",-4.3462,-5.2508,0.155 -"jaw","nasal","Continuous","Overall","overall",-4.3462,4.4052,0.0603 -"jaw","mouth","Continuous","Overall","overall",-4.3462,4.3742,0.1534 -"jaw","SL","Continuous","Overall","overall",-4.3462,-6.6151,0.1435 -"eye","body","Continuous","Overall","overall",6.0552,-0.6272,0.0018 -"eye","nasal","Continuous","Overall","overall",6.0552,4.4052,0.0874 -"eye","mouth","Continuous","Overall","overall",6.0552,4.3742,0.2153 -"eye","SL","Continuous","Overall","overall",6.0552,1.8002,0.0168 -"body","nasal","Continuous","Overall","overall",4.1616,4.4052,-0.0758 -"body","mouth","Continuous","Overall","overall",4.1616,4.3742,-0.0144 -"body","SL","Continuous","Overall","overall",-5.2508,5.5871,-0.1092 -"nasal","mouth","Continuous","Overall","overall",4.4052,4.3742,0.0778 -"nasal","SL","Continuous","Overall","overall",4.4052,5.5871,-0.0348 -"mouth","SL","Continuous","Overall","overall",4.3742,-0.3036,-0.0124 -"jaw","eye","Binary","Crescent Pond","pond",3.3446,4.0397,0.7827 -"jaw","body","Binary","Crescent Pond","pond",3.2164,-2.942,0.528 -"jaw","nasal","Binary","Crescent Pond","pond",3.3446,-6.0106,0.9769 -"jaw","mouth","Binary","Crescent Pond","pond",3.3446,-4.9385,0.7437 -"jaw","SL","Binary","Crescent Pond","pond",3.3446,-4.8391,0.7157 -"eye","body","Binary","Crescent Pond","pond",-3.1446,3.9556,0.4089 -"eye","nasal","Binary","Crescent Pond","pond",-0.7498,-6.0106,0.8969 -"eye","mouth","Binary","Crescent Pond","pond",1.3456,-4.9385,0.4869 -"eye","SL","Binary","Crescent Pond","pond",-4.0426,3.6865,0.7121 -"body","nasal","Binary","Crescent Pond","pond",-5.0879,-6.0106,0.9798 -"body","mouth","Binary","Crescent Pond","pond",-5.0879,-4.7817,0.8329 -"body","SL","Binary","Crescent Pond","pond",3.9556,-4.8391,0.91 -"nasal","mouth","Binary","Crescent Pond","pond",-6.0106,-4.9385,0.9531 -"nasal","SL","Binary","Crescent Pond","pond",-6.0106,-4.6946,0.9958 -"mouth","SL","Binary","Crescent Pond","pond",-4.9385,-4.8391,0.9297 -"jaw","eye","Binary","Little Lake","lake",3.5315,6.0902,0.4075 -"jaw","body","Binary","Little Lake","lake",3.5315,4.4984,0.34 -"jaw","nasal","Binary","Little Lake","lake",3.5315,4.1378,0.2888 -"jaw","mouth","Binary","Little Lake","lake",3.5315,-5.0459,0.332 -"jaw","SL","Binary","Little Lake","lake",-0.0439,5.605,0.2567 -"eye","body","Binary","Little Lake","lake",6.0902,3.7338,0.2748 -"eye","nasal","Binary","Little Lake","lake",6.0902,4.1378,0.3238 -"eye","mouth","Binary","Little Lake","lake",6.0902,-5.0459,0.4059 -"eye","SL","Binary","Little Lake","lake",-5.2551,-6.8271,0.4019 -"body","nasal","Binary","Little Lake","lake",4.1926,4.1378,0.186 -"body","mouth","Binary","Little Lake","lake",4.3455,-5.0459,0.2422 -"body","SL","Binary","Little Lake","lake",4.4984,-6.8271,0.3026 -"nasal","mouth","Binary","Little Lake","lake",4.1378,-5.0459,0.4662 -"nasal","SL","Binary","Little Lake","lake",0.7973,-3.4557,0.2373 -"mouth","SL","Binary","Little Lake","lake",-5.0459,-6.8271,0.5162 -"jaw","eye","Continuous","Crescent Pond","pond",-4.2172,4.6383,0.1092 -"jaw","body","Continuous","Crescent Pond","pond",-4.2172,-5.0879,0.301 -"jaw","nasal","Continuous","Crescent Pond","pond",-4.2172,3.6007,0.1888 -"jaw","mouth","Continuous","Crescent Pond","pond",-4.2172,4.3129,0.2948 -"jaw","SL","Continuous","Crescent Pond","pond",-4.2172,-4.8391,0.3109 -"eye","body","Continuous","Crescent Pond","pond",4.788,3.4958,0.0935 -"eye","nasal","Continuous","Crescent Pond","pond",4.788,3.7664,0.1853 -"eye","mouth","Continuous","Crescent Pond","pond",4.788,4.3129,0.142 -"eye","SL","Continuous","Crescent Pond","pond",4.788,3.542,0.0811 -"body","nasal","Continuous","Crescent Pond","pond",3.9556,3.7664,0.0486 -"body","mouth","Continuous","Crescent Pond","pond",3.9556,4.3129,0.0943 -"body","SL","Continuous","Crescent Pond","pond",3.9556,3.6865,-0.0789 -"nasal","mouth","Continuous","Crescent Pond","pond",-6.0106,4.3129,0.2227 -"nasal","SL","Continuous","Crescent Pond","pond",3.7664,3.6865,0.0405 -"mouth","SL","Continuous","Crescent Pond","pond",4.3129,3.6865,0.4354 -"jaw","eye","Continuous","Little Lake","lake",-4.2813,6.0902,-0.0013 -"jaw","body","Continuous","Little Lake","lake",-4.2813,-4.5233,0.1254 -"jaw","nasal","Continuous","Little Lake","lake",-4.2813,3.9926,-0.0501 -"jaw","mouth","Continuous","Little Lake","lake",-4.2813,4.3166,0.0063 -"jaw","SL","Continuous","Little Lake","lake",-4.2813,-6.8271,0.0352 -"eye","body","Continuous","Little Lake","lake",6.0902,-4.5233,0.0025 -"eye","nasal","Continuous","Little Lake","lake",6.0902,4.1378,-0.0332 -"eye","mouth","Continuous","Little Lake","lake",6.0902,4.3166,0.0397 -"eye","SL","Continuous","Little Lake","lake",6.0902,-6.8271,0.0048 -"body","nasal","Continuous","Little Lake","lake",-4.5233,4.1378,-0.0766 -"body","mouth","Continuous","Little Lake","lake",-4.5233,4.3166,0.0225 -"body","SL","Continuous","Little Lake","lake",-4.5233,2.2336,-0.1025 -"nasal","mouth","Continuous","Little Lake","lake",-4.4314,4.3166,-0.023 -"nasal","SL","Continuous","Little Lake","lake",4.1378,5.605,-0.1157 -"mouth","SL","Continuous","Little Lake","lake",4.3166,4.9729,-0.0619 diff --git a/R/results/pupfish_results/tables/comparison_binary_body_SL_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_body_SL_Crescent_Pond_correlation.csv deleted file mode 100644 index 9619d07..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_body_SL_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"body","SL","binary","site","Crescent Pond","pond",0.85065165144424,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_body_SL_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_body_SL_Little_Lake_correlation.csv deleted file mode 100644 index bb7d26d..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_body_SL_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"body","SL","binary","site","Little Lake","lake",0.955139720085588,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_body_SL_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_body_SL_overall_correlation.csv deleted file mode 100644 index cbd4d7b..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_body_SL_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"body","SL","binary","overall","Overall",0.99748407194691,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_body_mouth_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_body_mouth_Crescent_Pond_correlation.csv deleted file mode 100644 index fdc1551..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_body_mouth_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"body","mouth","binary","site","Crescent Pond","pond",0.995412949260678,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_body_mouth_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_body_mouth_Little_Lake_correlation.csv deleted file mode 100644 index d54dcd3..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_body_mouth_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"body","mouth","binary","site","Little Lake","lake",0.999490940536273,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_body_mouth_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_body_mouth_overall_correlation.csv deleted file mode 100644 index ace459d..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_body_mouth_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"body","mouth","binary","overall","Overall",0.999332900283822,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_body_nasal_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_body_nasal_Crescent_Pond_correlation.csv deleted file mode 100644 index 106e85f..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_body_nasal_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"body","nasal","binary","site","Crescent Pond","pond",0.985836490943478,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_body_nasal_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_body_nasal_Little_Lake_correlation.csv deleted file mode 100644 index 4aa397f..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_body_nasal_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"body","nasal","binary","site","Little Lake","lake",0.999721083006148,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_body_nasal_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_body_nasal_overall_correlation.csv deleted file mode 100644 index 1bc4fad..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_body_nasal_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"body","nasal","binary","overall","Overall",0.96893547472572,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_SL_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_SL_Crescent_Pond_correlation.csv deleted file mode 100644 index 4f59410..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_SL_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"eye","SL","binary","site","Crescent Pond","pond",0.369806565543883,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_SL_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_SL_Little_Lake_correlation.csv deleted file mode 100644 index 8ddb28c..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_SL_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"eye","SL","binary","site","Little Lake","lake",0.937551690591591,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_SL_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_SL_overall_correlation.csv deleted file mode 100644 index 7099db3..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_SL_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"eye","SL","binary","overall","Overall",0.213305322154226,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_body_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_body_Crescent_Pond_correlation.csv deleted file mode 100644 index 6293022..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_body_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"eye","body","binary","site","Crescent Pond","pond",0.83681218792774,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_body_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_body_Little_Lake_correlation.csv deleted file mode 100644 index 5b41e47..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_body_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"eye","body","binary","site","Little Lake","lake",0.999330010600787,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_body_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_body_overall_correlation.csv deleted file mode 100644 index 67795d3..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_body_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"eye","body","binary","overall","Overall",0.982653629208924,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_mouth_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_mouth_Crescent_Pond_correlation.csv deleted file mode 100644 index 7e2d0c9..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_mouth_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"eye","mouth","binary","site","Crescent Pond","pond",0.96620000334916,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_mouth_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_mouth_Little_Lake_correlation.csv deleted file mode 100644 index 3b1e660..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_mouth_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"eye","mouth","binary","site","Little Lake","lake",0.998683887926048,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_mouth_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_mouth_overall_correlation.csv deleted file mode 100644 index 014ced4..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_mouth_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"eye","mouth","binary","overall","Overall",0.999261807155887,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_nasal_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_nasal_Crescent_Pond_correlation.csv deleted file mode 100644 index 8599bc5..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_nasal_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"eye","nasal","binary","site","Crescent Pond","pond",0.986946326152538,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_nasal_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_nasal_Little_Lake_correlation.csv deleted file mode 100644 index 4dec171..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_nasal_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"eye","nasal","binary","site","Little Lake","lake",0.999054373917768,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_eye_nasal_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_eye_nasal_overall_correlation.csv deleted file mode 100644 index 66a8318..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_eye_nasal_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"eye","nasal","binary","overall","Overall",0.987607992814082,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_SL_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_SL_Crescent_Pond_correlation.csv deleted file mode 100644 index df238a3..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_SL_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","SL","binary","site","Crescent Pond","pond",0.939449640746555,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_SL_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_SL_Little_Lake_correlation.csv deleted file mode 100644 index 13a2a91..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_SL_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","SL","binary","site","Little Lake","lake",0.721989076951852,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_SL_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_SL_overall_correlation.csv deleted file mode 100644 index 8586a81..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_SL_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"jaw","SL","binary","overall","Overall",0.843442245393546,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_body_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_body_Crescent_Pond_correlation.csv deleted file mode 100644 index 4a52c2a..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_body_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","body","binary","site","Crescent Pond","pond",0.920923886601619,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_body_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_body_Little_Lake_correlation.csv deleted file mode 100644 index 10ad551..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_body_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","body","binary","site","Little Lake","lake",0.99865580473683,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_body_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_body_overall_correlation.csv deleted file mode 100644 index ae63918..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_body_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"jaw","body","binary","overall","Overall",0.881832744313269,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_eye_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_eye_Crescent_Pond_correlation.csv deleted file mode 100644 index bdb09b4..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_eye_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","eye","binary","site","Crescent Pond","pond",0.9928846568638,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_eye_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_eye_Little_Lake_correlation.csv deleted file mode 100644 index 3a42916..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_eye_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","eye","binary","site","Little Lake","lake",0.998448324924181,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_eye_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_eye_overall_correlation.csv deleted file mode 100644 index de386f2..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_eye_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"jaw","eye","binary","overall","Overall",0.980038048562054,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_mouth_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_mouth_Crescent_Pond_correlation.csv deleted file mode 100644 index 7c79769..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_mouth_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","mouth","binary","site","Crescent Pond","pond",0.997586810657535,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_mouth_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_mouth_Little_Lake_correlation.csv deleted file mode 100644 index beb8092..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_mouth_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","mouth","binary","site","Little Lake","lake",0.998780289390251,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_mouth_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_mouth_overall_correlation.csv deleted file mode 100644 index 1845488..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_mouth_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"jaw","mouth","binary","overall","Overall",0.998591120664776,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_nasal_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_nasal_Crescent_Pond_correlation.csv deleted file mode 100644 index 49c5863..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_nasal_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","nasal","binary","site","Crescent Pond","pond",0.987482319396728,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_nasal_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_nasal_Little_Lake_correlation.csv deleted file mode 100644 index 182f822..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_nasal_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","nasal","binary","site","Little Lake","lake",0.998943535813675,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_jaw_nasal_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_jaw_nasal_overall_correlation.csv deleted file mode 100644 index 04033fa..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_jaw_nasal_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"jaw","nasal","binary","overall","Overall",0.963739022321552,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_mouth_SL_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_mouth_SL_Crescent_Pond_correlation.csv deleted file mode 100644 index 956fbdf..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_mouth_SL_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"mouth","SL","binary","site","Crescent Pond","pond",0.993201895656785,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_mouth_SL_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_mouth_SL_Little_Lake_correlation.csv deleted file mode 100644 index bd44129..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_mouth_SL_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"mouth","SL","binary","site","Little Lake","lake",0.993300064523256,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_mouth_SL_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_mouth_SL_overall_correlation.csv deleted file mode 100644 index 0d6189e..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_mouth_SL_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"mouth","SL","binary","overall","Overall",0.99614143399323,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_nasal_SL_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_nasal_SL_Crescent_Pond_correlation.csv deleted file mode 100644 index ce2fae0..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_nasal_SL_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"nasal","SL","binary","site","Crescent Pond","pond",0.993167825509168,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_nasal_SL_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_nasal_SL_Little_Lake_correlation.csv deleted file mode 100644 index 0a92fb8..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_nasal_SL_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"nasal","SL","binary","site","Little Lake","lake",0.970037511254223,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_nasal_SL_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_nasal_SL_overall_correlation.csv deleted file mode 100644 index 38d1cfe..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_nasal_SL_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"nasal","SL","binary","overall","Overall",0.967096617042514,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_nasal_mouth_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_nasal_mouth_Crescent_Pond_correlation.csv deleted file mode 100644 index 951b676..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_nasal_mouth_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"nasal","mouth","binary","site","Crescent Pond","pond",0.983313492214665,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_nasal_mouth_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_nasal_mouth_Little_Lake_correlation.csv deleted file mode 100644 index 4b9b904..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_nasal_mouth_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"nasal","mouth","binary","site","Little Lake","lake",0.998427630957439,3600 diff --git a/R/results/pupfish_results/tables/comparison_binary_nasal_mouth_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_binary_nasal_mouth_overall_correlation.csv deleted file mode 100644 index 5580529..0000000 --- a/R/results/pupfish_results/tables/comparison_binary_nasal_mouth_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"nasal","mouth","binary","overall","Overall",0.983024288278013,3600 diff --git a/R/results/pupfish_results/tables/comparison_continuous_jaw_body_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_continuous_jaw_body_Crescent_Pond_correlation.csv deleted file mode 100644 index 79663c0..0000000 --- a/R/results/pupfish_results/tables/comparison_continuous_jaw_body_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","body","continuous","site","Crescent Pond","pond",0.999889587969105,3600 diff --git a/R/results/pupfish_results/tables/comparison_continuous_jaw_body_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_continuous_jaw_body_Little_Lake_correlation.csv deleted file mode 100644 index 7128220..0000000 --- a/R/results/pupfish_results/tables/comparison_continuous_jaw_body_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","body","continuous","site","Little Lake","lake",0.999914908452964,3600 diff --git a/R/results/pupfish_results/tables/comparison_continuous_jaw_body_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_continuous_jaw_body_overall_correlation.csv deleted file mode 100644 index 22c6e49..0000000 --- a/R/results/pupfish_results/tables/comparison_continuous_jaw_body_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"jaw","body","continuous","overall","Overall",0.980187363237471,3600 diff --git a/R/results/pupfish_results/tables/comparison_continuous_jaw_eye_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_continuous_jaw_eye_Crescent_Pond_correlation.csv deleted file mode 100644 index b74f1dd..0000000 --- a/R/results/pupfish_results/tables/comparison_continuous_jaw_eye_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","eye","continuous","site","Crescent Pond","pond",0.988155244833054,3600 diff --git a/R/results/pupfish_results/tables/comparison_continuous_jaw_eye_Little_Lake_correlation.csv b/R/results/pupfish_results/tables/comparison_continuous_jaw_eye_Little_Lake_correlation.csv deleted file mode 100644 index 90e7986..0000000 --- a/R/results/pupfish_results/tables/comparison_continuous_jaw_eye_Little_Lake_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","eye","continuous","site","Little Lake","lake",0.999867665279911,3600 diff --git a/R/results/pupfish_results/tables/comparison_continuous_jaw_eye_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_continuous_jaw_eye_overall_correlation.csv deleted file mode 100644 index 5ca839d..0000000 --- a/R/results/pupfish_results/tables/comparison_continuous_jaw_eye_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"jaw","eye","continuous","overall","Overall",0.991416184932145,3600 diff --git a/R/results/pupfish_results/tables/comparison_continuous_jaw_nasal_Crescent_Pond_correlation.csv b/R/results/pupfish_results/tables/comparison_continuous_jaw_nasal_Crescent_Pond_correlation.csv deleted file mode 100644 index 4e068c6..0000000 --- a/R/results/pupfish_results/tables/comparison_continuous_jaw_nasal_Crescent_Pond_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","site_type","correlation","n_points" -"jaw","nasal","continuous","site","Crescent Pond","pond",0.99984198524331,3600 diff --git a/R/results/pupfish_results/tables/comparison_continuous_jaw_nasal_overall_correlation.csv b/R/results/pupfish_results/tables/comparison_continuous_jaw_nasal_overall_correlation.csv deleted file mode 100644 index 0c61cc8..0000000 --- a/R/results/pupfish_results/tables/comparison_continuous_jaw_nasal_overall_correlation.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","fitness","comparison_type","site","correlation","n_points" -"jaw","nasal","continuous","overall","Overall",0.999842462786073,3600 diff --git a/R/results/pupfish_results/tables/disruptive_binary_SL.csv b/R/results/pupfish_results/tables/disruptive_binary_SL.csv deleted file mode 100644 index 0cac7a1..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_SL.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"SL","Linear",-0.0423674013046771,0.0086416300910552,1.16872714149573e-05,7.46777706306307e-05 -"SL²","Quadratic",0.0290755172511569,0.0107455321462261,0.0959925971941464,0.000115466461105579 diff --git a/R/results/pupfish_results/tables/disruptive_binary_SL_group.csv b/R/results/pupfish_results/tables/disruptive_binary_SL_group.csv deleted file mode 100644 index 77ddba1..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_SL_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"SL","Linear",-0.0617054973331821,0.013249250611213,5.61624786818762e-05,0.000175542641758729,"Crescent Pond" -"SL²","Quadratic",0.0435425040566177,0.0185129666431996,0.194567559300714,0.00034272993393222,"Crescent Pond" -"SL","Linear",-0.0234183566563103,0.0113740889683448,0.0604074366252379,0.000129369899859822,"Little Lake" -"SL²","Quadratic",0.0189512574709231,0.0129383268344886,0.276484365558835,0.000167400301276048,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_binary_body.csv b/R/results/pupfish_results/tables/disruptive_binary_body.csv deleted file mode 100644 index 5a38f9c..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_body.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"body","Linear",-0.0241469071432867,0.00854574826687727,0.00786212912568211,7.30298134408359e-05 -"body²","Quadratic",0.0177230291465243,0.0119255917214915,0.229581488784786,0.000142219737907708 diff --git a/R/results/pupfish_results/tables/disruptive_binary_body_group.csv b/R/results/pupfish_results/tables/disruptive_binary_body_group.csv deleted file mode 100644 index 9651749..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_body_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"body","Linear",-0.0502156167285567,0.0130140930014131,0.000478442741014737,0.000169366616649428,"Crescent Pond" -"body²","Quadratic",0.0252933822026663,0.018215543867598,0.45893878212582,0.000331806038392388,"Crescent Pond" -"body","Linear",0.000644015186418565,0.0112767536675377,0.954419804826341,0.000127165173278325,"Little Lake" -"body²","Quadratic",0.00503915729215002,0.0156038470559796,0.746438311218204,0.000243480042946405,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_binary_eye.csv b/R/results/pupfish_results/tables/disruptive_binary_eye.csv deleted file mode 100644 index fc3b930..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_eye.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"eye","Linear",0.0113031748780985,0.00855899344056498,0.175086865508152,7.32563687156344e-05 -"eye²","Quadratic",-0.0140559141650256,0.0110448287548439,0.193848687707229,0.000121988242223827 diff --git a/R/results/pupfish_results/tables/disruptive_binary_eye_group.csv b/R/results/pupfish_results/tables/disruptive_binary_eye_group.csv deleted file mode 100644 index df68c41..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_eye_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"eye","Linear",0.0088820577591637,0.0129539910893565,0.473063602141322,0.000167805885143128,"Crescent Pond" -"eye²","Quadratic",-0.0469817827029989,0.0181383991065186,0.0108748287058619,0.000329001522147356,"Crescent Pond" -"eye","Linear",0.0151406915582481,0.0112979721411413,0.199615940889765,0.000127644174502004,"Little Lake" -"eye²","Quadratic",0.00858909316922807,0.0136306768389126,0.61042964232915,0.000185795351086869,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_binary_jaw.csv b/R/results/pupfish_results/tables/disruptive_binary_jaw.csv deleted file mode 100644 index 562946b..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_jaw.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.0387337729026381,0.00890004883400853,1.49290517378608e-05,7.92108692477366e-05 -"jaw²","Quadratic",0.00851067252300987,0.0131697770385805,0.916732926378334,0.000173443027245922 diff --git a/R/results/pupfish_results/tables/disruptive_binary_jaw_group.csv b/R/results/pupfish_results/tables/disruptive_binary_jaw_group.csv deleted file mode 100644 index b889706..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_jaw_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.0626142024044959,0.0133194622577704,6.37258724369025e-06,0.00017740807483617,"Crescent Pond" -"jaw²","Quadratic",0.0276317062784559,0.021033479109769,0.518229615042563,0.00044240724346109,"Crescent Pond" -"jaw","Linear",0.016625044328096,0.011850246571361,0.144451674586646,0.000140428343802054,"Little Lake" -"jaw²","Quadratic",-0.00717745094614307,0.0165264651772437,0.566584807287573,0.000273124051254648,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_binary_mouth.csv b/R/results/pupfish_results/tables/disruptive_binary_mouth.csv deleted file mode 100644 index ce9db6e..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_mouth.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"mouth","Linear",-0.0121129583541284,0.00863378289194249,0.170481956182479,7.45422070251988e-05 -"mouth²","Quadratic",0.00523405558999719,0.0114599952512688,0.701656939224536,0.000131331491159104 diff --git a/R/results/pupfish_results/tables/disruptive_binary_mouth_group.csv b/R/results/pupfish_results/tables/disruptive_binary_mouth_group.csv deleted file mode 100644 index 16d42e7..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_mouth_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"mouth","Linear",-0.00687173995107481,0.0129916062628452,0.624709465641745,0.000168781833288798,"Crescent Pond" -"mouth²","Quadratic",0.0245058391261297,0.017335145756022,0.169271422884621,0.000300507278382529,"Crescent Pond" -"mouth","Linear",-0.016153235896095,0.0114733316025389,0.152953464822668,0.000131637338061818,"Little Lake" -"mouth²","Quadratic",-0.0111192159327666,0.0151293659722108,0.420348940284801,0.00022889771472109,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_binary_nasal.csv b/R/results/pupfish_results/tables/disruptive_binary_nasal.csv deleted file mode 100644 index b77aac6..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_nasal.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"nasal","Linear",-0.012102951164629,0.00877048464720661,0.21734005137158,7.69214009468868e-05 -"nasal²","Quadratic",0.0280742479863929,0.0109784998815918,0.0214609456692061,0.000120527459650112 diff --git a/R/results/pupfish_results/tables/disruptive_binary_nasal_group.csv b/R/results/pupfish_results/tables/disruptive_binary_nasal_group.csv deleted file mode 100644 index 1043533..0000000 --- a/R/results/pupfish_results/tables/disruptive_binary_nasal_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"nasal","Linear",-0.0288170299306194,0.0134308787227537,0.0732356446561339,0.000180388503265319,"Crescent Pond" -"nasal²","Quadratic",0.0574260367524172,0.0148152241567129,0.00275989029954688,0.00021949086681365,"Crescent Pond" -"nasal","Linear",0.0053076187428154,0.0114029126211306,0.606724479231334,0.000130026416245139,"Little Lake" -"nasal²","Quadratic",-0.0230172611824015,0.0165558853320761,0.158050521064775,0.000274097339128852,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_continuous_SL.csv b/R/results/pupfish_results/tables/disruptive_continuous_SL.csv deleted file mode 100644 index 15e9fd2..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_SL.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"SL","Linear",0.00479104959569507,0.0121456024116813,0.69328083854681,0.000147515657942637 -"SL²","Quadratic",-0.0301829206398442,0.0151025859444149,0.0458047597636893,0.000228088102208437 diff --git a/R/results/pupfish_results/tables/disruptive_continuous_SL_group.csv b/R/results/pupfish_results/tables/disruptive_continuous_SL_group.csv deleted file mode 100644 index f417ee9..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_SL_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"SL","Linear",0.0115056405070842,0.0156960502040719,0.46373473583863,0.000246365992008745,"Crescent Pond" -"SL²","Quadratic",-0.0208092237056277,0.0219318407044128,0.342973389169412,0.00048100563668374,"Crescent Pond" -"SL","Linear",-0.000457419495420601,0.0183543398035395,0.980122624934808,0.000336881789623794,"Little Lake" -"SL²","Quadratic",-0.0352449178461371,0.0208785466572639,0.0917149220408403,0.000435913710519546,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_continuous_body.csv b/R/results/pupfish_results/tables/disruptive_continuous_body.csv deleted file mode 100644 index a9b4c6b..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_body.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"body","Linear",-0.00205982462625423,0.0119338291155088,0.86298159887502,0.000142416277358166 -"body²","Quadratic",-0.018348338673801,0.0166536585517293,0.270708317749203,0.000277344343157587 diff --git a/R/results/pupfish_results/tables/disruptive_continuous_body_group.csv b/R/results/pupfish_results/tables/disruptive_continuous_body_group.csv deleted file mode 100644 index 1befe40..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_body_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"body","Linear",0.0137815001361187,0.0152729922886646,0.367118320901039,0.000233264293449609,"Crescent Pond" -"body²","Quadratic",-0.0164887282947349,0.0213772762338066,0.440722029500333,0.000456987939176475,"Crescent Pond" -"body","Linear",-0.0180026443741385,0.0181407009115178,0.321254956476763,0.000329085029561143,"Little Lake" -"body²","Quadratic",-0.0195220076534475,0.0251016144235242,0.436924207644738,0.000630091046667279,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_continuous_eye.csv b/R/results/pupfish_results/tables/disruptive_continuous_eye.csv deleted file mode 100644 index c0c1921..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_eye.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"eye","Linear",0.0244559618750738,0.0119152573839803,0.040261452190246,0.000141973358526497 -"eye²","Quadratic",0.00576993475045167,0.0153758708065168,0.707510554352581,0.000236417403058696 diff --git a/R/results/pupfish_results/tables/disruptive_continuous_eye_group.csv b/R/results/pupfish_results/tables/disruptive_continuous_eye_group.csv deleted file mode 100644 index bced28d..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_eye_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"eye","Linear",0.0273086576694784,0.0150335150678034,0.0696275354854509,0.000226006575293872,"Crescent Pond" -"eye²","Quadratic",0.0435686402323717,0.0210501840238046,0.0387640255042029,0.000443110247436038,"Crescent Pond" -"eye","Linear",0.0201151330999511,0.0181919353734663,0.269123172542391,0.000330946512632375,"Little Lake" -"eye²","Quadratic",-0.0208504231786506,0.0219480442200006,0.342353948044445,0.0004817166450831,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_continuous_jaw.csv b/R/results/pupfish_results/tables/disruptive_continuous_jaw.csv deleted file mode 100644 index bd68698..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_jaw.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",-0.0348905270937624,0.012431417823441,0.00505821032199496,0.000154540149100966 -"jaw²","Quadratic",-0.00202760679543762,0.0183952924373355,0.912243431321971,0.000338386783855091 diff --git a/R/results/pupfish_results/tables/disruptive_continuous_jaw_group.csv b/R/results/pupfish_results/tables/disruptive_continuous_jaw_group.csv deleted file mode 100644 index 1db2d7a..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_jaw_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",-0.0522073617813825,0.0155663749500577,0.000830635806450342,0.000242312029085784,"Crescent Pond" -"jaw²","Quadratic",-0.0145664798418474,0.0245816997706391,0.553616875201954,0.000604259963613837,"Crescent Pond" -"jaw","Linear",-0.0181722099700154,0.0190930813627456,0.341451053236671,0.000364545755924422,"Little Lake" -"jaw²","Quadratic",0.00639550897535734,0.0266273906089242,0.810237323894308,0.000709017930640225,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_continuous_mouth.csv b/R/results/pupfish_results/tables/disruptive_continuous_mouth.csv deleted file mode 100644 index 0d03e6f..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_mouth.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"mouth","Linear",0.0153124381207326,0.0120215055397533,0.202909662251097,0.000144516595442319 -"mouth²","Quadratic",-0.017156237899163,0.0159566667500112,0.282434878474172,0.000254615213770914 diff --git a/R/results/pupfish_results/tables/disruptive_continuous_mouth_group.csv b/R/results/pupfish_results/tables/disruptive_continuous_mouth_group.csv deleted file mode 100644 index bdf8179..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_mouth_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"mouth","Linear",0.00273249872777463,0.0150560024768775,0.856025142251952,0.00022668321058374,"Crescent Pond" -"mouth²","Quadratic",-0.0521313524652416,0.0200897404184832,0.0096170524883032,0.000403597670082037,"Crescent Pond" -"mouth","Linear",0.0288301050524786,0.0184678062816251,0.118826174722435,0.000341059868855632,"Little Lake" -"mouth²","Quadratic",0.0139521606829818,0.0243526649118004,0.566830754017789,0.000593052288306434,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_continuous_nasal.csv b/R/results/pupfish_results/tables/disruptive_continuous_nasal.csv deleted file mode 100644 index f2b4bcc..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_nasal.csv +++ /dev/null @@ -1,3 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"nasal","Linear",0.0191562235636786,0.0122411365143871,0.117774961268347,0.000149845423163861 -"nasal²","Quadratic",-0.00289921280664484,0.0153229064503923,0.849950606970111,0.000234791462087472 diff --git a/R/results/pupfish_results/tables/disruptive_continuous_nasal_group.csv b/R/results/pupfish_results/tables/disruptive_continuous_nasal_group.csv deleted file mode 100644 index 47089d0..0000000 --- a/R/results/pupfish_results/tables/disruptive_continuous_nasal_group.csv +++ /dev/null @@ -1,5 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"nasal","Linear",0.0263952507527099,0.0157978100286722,0.0951097838997096,0.000249570801702016,"Crescent Pond" -"nasal²","Quadratic",-0.0192900826546456,0.0174261194365069,0.268609030641982,0.000303669638615405,"Crescent Pond" -"nasal","Linear",0.0107004638060126,0.0183701483082449,0.560370721469023,0.000337462348866913,"Little Lake" -"nasal²","Quadratic",0.0248029271936748,0.0266716126861262,0.352634920375583,0.000711374923278726,"Little Lake" diff --git a/R/results/pupfish_results/tables/disruptive_selection_summary.csv b/R/results/pupfish_results/tables/disruptive_selection_summary.csv deleted file mode 100644 index 443fca8..0000000 --- a/R/results/pupfish_results/tables/disruptive_selection_summary.csv +++ /dev/null @@ -1,13 +0,0 @@ -"Trait","Fitness","Analysis","Beta","P_Beta","Gamma","P_Gamma","Selection" -"jaw","Binary","Overall",0.0387,1.49290517378608e-05,0.0085,0.916732926378334,"None" -"jaw","Continuous","Overall",-0.0349,0.00505821032199496,-0.002,0.912243431321971,"None" -"eye","Binary","Overall",0.0113,0.175086865508152,-0.0141,0.193848687707229,"None" -"eye","Continuous","Overall",0.0245,0.040261452190246,0.0058,0.707510554352581,"None" -"body","Binary","Overall",-0.0241,0.00786212912568211,0.0177,0.229581488784786,"None" -"body","Continuous","Overall",-0.0021,0.86298159887502,-0.0183,0.270708317749203,"None" -"nasal","Binary","Overall",-0.0121,0.21734005137158,0.0281,0.0214609456692061,"Disruptive" -"nasal","Continuous","Overall",0.0192,0.117774961268347,-0.0029,0.849950606970111,"None" -"mouth","Binary","Overall",-0.0121,0.170481956182479,0.0052,0.701656939224536,"None" -"mouth","Continuous","Overall",0.0153,0.202909662251097,-0.0172,0.282434878474172,"None" -"SL","Binary","Overall",-0.0424,1.16872714149573e-05,0.0291,0.0959925971941464,"None" -"SL","Continuous","Overall",0.0048,0.69328083854681,-0.0302,0.0458047597636893,"Stabilizing" diff --git a/R/results/pupfish_results/tables/fitness_surfaces_comparison_summary.csv b/R/results/pupfish_results/tables/fitness_surfaces_comparison_summary.csv deleted file mode 100644 index 309e6be..0000000 --- a/R/results/pupfish_results/tables/fitness_surfaces_comparison_summary.csv +++ /dev/null @@ -1,51 +0,0 @@ -"Comparison","Correlation","Site" -"binary_jaw_eye_overall",0.98,"Overall" -"binary_jaw_eye_Crescent_Pond",0.9929,"Crescent Pond" -"binary_jaw_eye_Little_Lake",0.9984,"Little Lake" -"binary_jaw_body_overall",0.8818,"Overall" -"binary_jaw_body_Crescent_Pond",0.9209,"Crescent Pond" -"binary_jaw_body_Little_Lake",0.9987,"Little Lake" -"binary_jaw_nasal_overall",0.9637,"Overall" -"binary_jaw_nasal_Crescent_Pond",0.9875,"Crescent Pond" -"binary_jaw_nasal_Little_Lake",0.9989,"Little Lake" -"binary_jaw_mouth_overall",0.9986,"Overall" -"binary_jaw_mouth_Crescent_Pond",0.9976,"Crescent Pond" -"binary_jaw_mouth_Little_Lake",0.9988,"Little Lake" -"binary_jaw_SL_overall",0.8434,"Overall" -"binary_jaw_SL_Crescent_Pond",0.9394,"Crescent Pond" -"binary_jaw_SL_Little_Lake",0.722,"Little Lake" -"binary_eye_body_overall",0.9827,"Overall" -"binary_eye_body_Crescent_Pond",0.8368,"Crescent Pond" -"binary_eye_body_Little_Lake",0.9993,"Little Lake" -"binary_eye_nasal_overall",0.9876,"Overall" -"binary_eye_nasal_Crescent_Pond",0.9869,"Crescent Pond" -"binary_eye_nasal_Little_Lake",0.9991,"Little Lake" -"binary_eye_mouth_overall",0.9993,"Overall" -"binary_eye_mouth_Crescent_Pond",0.9662,"Crescent Pond" -"binary_eye_mouth_Little_Lake",0.9987,"Little Lake" -"binary_eye_SL_overall",0.2133,"Overall" -"binary_eye_SL_Crescent_Pond",0.3698,"Crescent Pond" -"binary_eye_SL_Little_Lake",0.9376,"Little Lake" -"binary_body_nasal_overall",0.9689,"Overall" -"binary_body_nasal_Crescent_Pond",0.9858,"Crescent Pond" -"binary_body_nasal_Little_Lake",0.9997,"Little Lake" -"binary_body_mouth_overall",0.9993,"Overall" -"binary_body_mouth_Crescent_Pond",0.9954,"Crescent Pond" -"binary_body_mouth_Little_Lake",0.9995,"Little Lake" -"binary_body_SL_overall",0.9975,"Overall" -"binary_body_SL_Crescent_Pond",0.8507,"Crescent Pond" -"binary_body_SL_Little_Lake",0.9551,"Little Lake" -"binary_nasal_mouth_overall",0.983,"Overall" -"binary_nasal_mouth_Crescent_Pond",0.9833,"Crescent Pond" -"binary_nasal_mouth_Little_Lake",0.9984,"Little Lake" -"binary_nasal_SL_overall",0.9671,"Overall" -"binary_nasal_SL_Crescent_Pond",0.9932,"Crescent Pond" -"binary_nasal_SL_Little_Lake",0.97,"Little Lake" -"binary_mouth_SL_overall",0.9961,"Overall" -"binary_mouth_SL_Crescent_Pond",0.9932,"Crescent Pond" -"binary_mouth_SL_Little_Lake",0.9933,"Little Lake" -"continuous_jaw_eye_Crescent_Pond",0.9882,"Crescent Pond" -"continuous_jaw_eye_Little_Lake",0.9999,"Little Lake" -"continuous_jaw_body_Crescent_Pond",0.9999,"Crescent Pond" -"continuous_jaw_body_Little_Lake",0.9999,"Little Lake" -"continuous_jaw_nasal_Crescent_Pond",0.9998,"Crescent Pond" diff --git a/R/results/pupfish_results/tables/selection_binary_body_SL.csv b/R/results/pupfish_results/tables/selection_binary_body_SL.csv deleted file mode 100644 index 1eaeed8..0000000 --- a/R/results/pupfish_results/tables/selection_binary_body_SL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"body","Linear",0.00193688633252302,0.0102435435252159,0.847499539472611,0.000104930183952993 -"SL","Linear",-0.0486246247268912,0.0102435435252159,3.52675512501627e-06,0.000104930183952993 -"body²","Quadratic",-0.00267026583744995,0.0164088129780523,0.856865950820973,0.000269249143348698 -"SL²","Quadratic",0.0202310488942889,0.0151097159601167,0.565436652817956,0.000228303516395407 -"body × SL","Correlational",0.00955425514777994,0.0129295546065952,0.466293643935927,0.000167173382324927 diff --git a/R/results/pupfish_results/tables/selection_binary_body_SL_group.csv b/R/results/pupfish_results/tables/selection_binary_body_SL_group.csv deleted file mode 100644 index 9dda2b9..0000000 --- a/R/results/pupfish_results/tables/selection_binary_body_SL_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"body","Linear",-0.00986447843400718,0.0173249381639714,0.578540223580401,0.000300153482385433,"Crescent Pond" -"SL","Linear",-0.064512949466934,0.0173249381639714,0.000345906887244886,0.000300153482385433,"Crescent Pond" -"body²","Quadratic",0.0138559360389904,0.0323810132954943,0.692949805550536,0.00104853002204298,"Crescent Pond" -"SL²","Quadratic",0.0552091699170465,0.0343938215775109,0.259698745405798,0.00118293496270565,"Crescent Pond" -"body × SL","Correlational",-0.0130746222067621,0.0285600328673973,0.612221324242852,0.000815675477386812,"Crescent Pond" -"body","Linear",0.0155495265354477,0.0126006164496442,0.217484728000389,0.000158775534911044,"Little Lake" -"SL","Linear",-0.0330897356544592,0.0126006164496442,0.00900935168960987,0.000158775534911044,"Little Lake" -"body²","Quadratic",-0.00514637342139462,0.0188957704839712,0.724659650177448,0.000357050142182917,"Little Lake" -"SL²","Quadratic",0.0150904246899322,0.0165662597237821,0.66091789087027,0.000274440961235804,"Little Lake" -"body × SL","Correlational",0.00593226883068148,0.0146625898391972,0.58559125499745,0.000214991540792529,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_body_mouth.csv b/R/results/pupfish_results/tables/selection_binary_body_mouth.csv deleted file mode 100644 index 613519d..0000000 --- a/R/results/pupfish_results/tables/selection_binary_body_mouth.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"body","Linear",-0.025691457020824,0.00849088368058361,0.00256094121710118,7.20951056772011e-05 -"mouth","Linear",-0.012989020816934,0.00849088368058361,0.12479507096385,7.2095105677201e-05 -"body²","Quadratic",0.0173886205112638,0.01194593469826,0.250857021255268,0.000142705355815092 -"mouth²","Quadratic",0.00176756952314867,0.0114771588741849,0.995265650816929,0.000131725175823281 -"body × mouth","Correlational",0.0148398052922758,0.00827877336338366,0.12545882089929,6.85380884022708e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_body_mouth_group.csv b/R/results/pupfish_results/tables/selection_binary_body_mouth_group.csv deleted file mode 100644 index 1664d5d..0000000 --- a/R/results/pupfish_results/tables/selection_binary_body_mouth_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"body","Linear",-0.0548467727705779,0.0127688206641336,2.51840522723315e-05,0.000163042781152804,"Crescent Pond" -"mouth","Linear",-0.013233796750047,0.0127688206641335,0.290999100645226,0.000163042781152804,"Crescent Pond" -"body²","Quadratic",0.0264271088568315,0.0182157958723854,0.437934326710474,0.000331815219264412,"Crescent Pond" -"mouth²","Quadratic",0.0114088438960401,0.0173854218327965,0.61964841276346,0.000302252892304277,"Crescent Pond" -"body × mouth","Correlational",0.0272287240075935,0.0124247841171679,0.0630120863571219,0.000154375260358227,"Crescent Pond" -"body","Linear",0.00130637655767321,0.0112795605514176,0.909154128396856,0.000127228486233095,"Little Lake" -"mouth","Linear",-0.0146085719086065,0.0112795605514176,0.195381914540515,0.000127228486233096,"Little Lake" -"body²","Quadratic",0.00506449287925207,0.0157245012490522,0.754538499183818,0.000247259939531444,"Little Lake" -"mouth²","Quadratic",-0.0115566503044721,0.0151687831990304,0.400366918138668,0.000230091983739186,"Little Lake" -"body × mouth","Correlational",0.00508774202075153,0.0110940667219355,0.637516671218499,0.000123078316430758,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_body_nasal.csv b/R/results/pupfish_results/tables/selection_binary_body_nasal.csv deleted file mode 100644 index bc8c2ca..0000000 --- a/R/results/pupfish_results/tables/selection_binary_body_nasal.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"body","Linear",-0.0270385696267641,0.00850692076495009,0.00161501911282015,7.2367700901139e-05 -"nasal","Linear",-0.0197079849123346,0.00850692076495009,0.0214728903147696,7.2367700901139e-05 -"body²","Quadratic",0.0192628435306875,0.0119814722209008,0.206651687982411,0.000143555676580219 -"nasal²","Quadratic",0.0235947875434494,0.0110107727848664,0.0757848532832348,0.000121237117319956 -"body × nasal","Correlational",0.0154626231776237,0.00818257091826975,0.15770450642762,6.69544668325138e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_body_nasal_group.csv b/R/results/pupfish_results/tables/selection_binary_body_nasal_group.csv deleted file mode 100644 index b823050..0000000 --- a/R/results/pupfish_results/tables/selection_binary_body_nasal_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"body","Linear",-0.0579292718070422,0.0126736709108935,1.15674359957453e-05,0.000160621934357628,"Crescent Pond" -"nasal","Linear",-0.050589538491094,0.0126736709108935,0.000140599859810277,0.000160621934357628,"Crescent Pond" -"body²","Quadratic",0.0211381209718277,0.0181150993684864,0.547138966032539,0.000328156825130138,"Crescent Pond" -"nasal²","Quadratic",0.047529969279842,0.0149771265612704,0.0131677294655261,0.000224314320032313,"Crescent Pond" -"body × nasal","Correlational",0.0123218515235814,0.0118379834754745,0.625576741377311,0.000140137852765607,"Crescent Pond" -"body","Linear",0.00111912797864516,0.0112997766454718,0.920608781144017,0.000127684952237551,"Little Lake" -"nasal","Linear",0.00788055224195536,0.0112997766454718,0.485092905866736,0.000127684952237551,"Little Lake" -"body²","Quadratic",0.00670230545810437,0.0157609341507101,0.689885315867408,0.000248407045303022,"Little Lake" -"nasal²","Quadratic",-0.0223452531666544,0.0166057946310333,0.162248614181349,0.000275752415328054,"Little Lake" -"body × nasal","Correlational",0.00965121191637354,0.0113464832109067,0.379264708692007,0.000128742681255387,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_eye_SL.csv b/R/results/pupfish_results/tables/selection_binary_eye_SL.csv deleted file mode 100644 index 6e7eeaf..0000000 --- a/R/results/pupfish_results/tables/selection_binary_eye_SL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"eye","Linear",0.0109539660829504,0.00844248976311919,0.240831281963812,7.12756334003724e-05 -"SL","Linear",-0.0477163427141762,0.00844248976311919,3.5796106886509e-08,7.12756334003722e-05 -"eye²","Quadratic",-0.0209440583721675,0.0113874339283006,0.0618564115501188,0.000129673651471411 -"SL²","Quadratic",0.0303021971259512,0.0111292699841347,0.0556835010885576,0.000123860650379762 -"eye × SL","Correlational",0.000893222365844005,0.00791757832479399,0.85894495973359,6.26880465292476e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_eye_SL_group.csv b/R/results/pupfish_results/tables/selection_binary_eye_SL_group.csv deleted file mode 100644 index 0171859..0000000 --- a/R/results/pupfish_results/tables/selection_binary_eye_SL_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"eye","Linear",0.0185715755249924,0.0128770009197581,0.176325569546661,0.000165817152687451,"Crescent Pond" -"SL","Linear",-0.0748272431446487,0.0128770009197581,2.3646126097546e-08,0.000165817152687451,"Crescent Pond" -"eye²","Quadratic",-0.0297756716178485,0.0179931791074997,0.0372945021040424,0.000323754494394562,"Crescent Pond" -"SL²","Quadratic",0.0519823924112476,0.018973578711179,0.114107147400084,0.000359996689109305,"Crescent Pond" -"eye × SL","Correlational",-0.0531796494985735,0.0149409729004536,0.000973311690738257,0.000223232671212088,"Crescent Pond" -"eye","Linear",0.0121665495004086,0.0113591487353117,0.311834941550161,0.000129030259990933,"Little Lake" -"SL","Linear",-0.024270838796785,0.0113591487353117,0.0366115792361509,0.000129030259990934,"Little Lake" -"eye²","Quadratic",0.0179717646211551,0.0158663793108818,0.326930268361283,0.000251741992436776,"Little Lake" -"SL²","Quadratic",0.0322782951848235,0.0147135384844673,0.0540960638240434,0.0002164882147339,"Little Lake" -"eye × SL","Correlational",0.0283134726133375,0.0109999258409242,0.0107556175207171,0.000120998368505832,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_eye_body.csv b/R/results/pupfish_results/tables/selection_binary_eye_body.csv deleted file mode 100644 index f76cbcb..0000000 --- a/R/results/pupfish_results/tables/selection_binary_eye_body.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"eye","Linear",0.0120511652424027,0.00851371193528629,0.15816563955735,7.24832909170362e-05 -"body","Linear",-0.0264563487052518,0.00851371193528628,0.00198633620408464,7.2483290917036e-05 -"eye²","Quadratic",-0.0186848579138557,0.0110963294390793,0.0557740030024713,0.000123128527020578 -"body²","Quadratic",0.017087118998265,0.0119025585119022,0.313439211013845,0.000141670899129257 -"eye × body","Correlational",-0.0247982705898486,0.00881819310833541,0.00798720792030218,7.77605296958941e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_eye_body_group.csv b/R/results/pupfish_results/tables/selection_binary_eye_body_group.csv deleted file mode 100644 index ba98fbb..0000000 --- a/R/results/pupfish_results/tables/selection_binary_eye_body_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"eye","Linear",0.0138824099787371,0.0129323063991386,0.275844280065149,0.000167244548801202,"Crescent Pond" -"body","Linear",-0.0563413458916361,0.0129323063991386,1.9614239359894e-05,0.000167244548801202,"Crescent Pond" -"eye²","Quadratic",-0.0384977191061259,0.0179288050366063,0.0110477794331058,0.000321442050040638,"Crescent Pond" -"body²","Quadratic",0.0365972640513194,0.0184652764550788,0.315638060613789,0.000340966434562487,"Crescent Pond" -"eye × body","Correlational",-0.0593897022422858,0.014731482588473,8.3020991397888e-05,0.000217016579254483,"Crescent Pond" -"eye","Linear",0.0157380697638066,0.0112670228218958,0.162542070574072,0.00012694580326912,"Little Lake" -"body","Linear",0.000959422577439395,0.0112670228218958,0.925919953650519,0.00012694580326912,"Little Lake" -"eye²","Quadratic",0.00698024380198608,0.0142151812243335,0.736269990774644,0.000202071377240645,"Little Lake" -"body²","Quadratic",0.0029832106791655,0.0158902236281603,0.871889770772641,0.000252499206952943,"Little Lake" -"eye × body","Correlational",-0.0049222031047102,0.011560432005374,0.706640317242462,0.000133643588150875,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_eye_mouth.csv b/R/results/pupfish_results/tables/selection_binary_eye_mouth.csv deleted file mode 100644 index 6e78fd2..0000000 --- a/R/results/pupfish_results/tables/selection_binary_eye_mouth.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"eye","Linear",0.00998082439871983,0.00850892963681442,0.241024141511983,7.24018835642588e-05 -"mouth","Linear",-0.0126539345361246,0.00850892963681441,0.137272293987753,7.24018835642586e-05 -"eye²","Quadratic",-0.0145385737454571,0.0110615922571236,0.177902380031239,0.000122358823262857 -"mouth²","Quadratic",0.00499638997859843,0.0114697519935762,0.715161708291579,0.000131555210794144 -"eye × mouth","Correlational",0.00123433700685566,0.00882966163546589,0.829847469234607,7.79629245968182e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_eye_mouth_group.csv b/R/results/pupfish_results/tables/selection_binary_eye_mouth_group.csv deleted file mode 100644 index 998bcc1..0000000 --- a/R/results/pupfish_results/tables/selection_binary_eye_mouth_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"eye","Linear",0.00361894044952076,0.0128933336983023,0.778820987095499,0.000166238053855777,"Crescent Pond" -"mouth","Linear",-0.00929767529609951,0.0128933336983023,0.470444610623329,0.000166238053855777,"Crescent Pond" -"eye²","Quadratic",-0.0461051246665624,0.0181817721033024,0.0114361226988875,0.000330576836816424,"Crescent Pond" -"mouth²","Quadratic",0.0232110593270861,0.0173807527895919,0.197311923716642,0.000302090567532908,"Crescent Pond" -"eye × mouth","Correlational",-0.00610690839975883,0.013507036512188,0.58690744476567,0.000182440035341581,"Crescent Pond" -"eye","Linear",0.0161844396292952,0.0112587050288797,0.15075627762191,0.000126758438927321,"Little Lake" -"mouth","Linear",-0.0150482561220172,0.0112587050288797,0.181464868286531,0.000126758438927321,"Little Lake" -"eye²","Quadratic",0.00760085980857681,0.0136478119680705,0.711106919418438,0.000186262771515809,"Little Lake" -"mouth²","Quadratic",-0.00963945612679649,0.0151619158655118,0.44965470734825,0.000229883692712859,"Little Lake" -"eye × mouth","Correlational",0.00755865330424147,0.0116273757109717,0.446221246884471,0.000135195865924095,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_eye_nasal.csv b/R/results/pupfish_results/tables/selection_binary_eye_nasal.csv deleted file mode 100644 index 23aa26c..0000000 --- a/R/results/pupfish_results/tables/selection_binary_eye_nasal.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"eye","Linear",0.00889552270258136,0.00852673246164277,0.296712146197167,7.27051664724326e-05 -"nasal","Linear",-0.0170656479323061,0.00852673246164277,0.0457774727915905,7.27051664724325e-05 -"eye²","Quadratic",-0.0119347191917373,0.0110878335600119,0.226411282790859,0.000122940053054526 -"nasal²","Quadratic",0.0288834481270288,0.0109881261083444,0.0202014962616848,0.000120738915372881 -"eye × nasal","Correlational",0.0143150176010954,0.0087194287645448,0.0908980329893726,7.60284379799712e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_eye_nasal_group.csv b/R/results/pupfish_results/tables/selection_binary_eye_nasal_group.csv deleted file mode 100644 index 1650e3f..0000000 --- a/R/results/pupfish_results/tables/selection_binary_eye_nasal_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"eye","Linear",-0.00193266637830761,0.0128945259040084,0.889079931913508,0.000166268798289144,"Crescent Pond" -"nasal","Linear",-0.0462869218790449,0.0128945259040084,0.000416569567971439,0.000166268798289144,"Crescent Pond" -"eye²","Quadratic",-0.0395826446748347,0.0183528425566699,0.0188878979340509,0.000336826829909915,"Crescent Pond" -"nasal²","Quadratic",0.0612274313291885,0.0149254621651718,0.00192398638971629,0.000222769420843976,"Crescent Pond" -"eye × nasal","Correlational",0.0285133147429925,0.0133687719513036,0.0408695285667814,0.000178724063485962,"Crescent Pond" -"eye","Linear",0.0158567605225348,0.0112623282117472,0.159238807318156,0.000126840036749117,"Little Lake" -"nasal","Linear",0.00808195312818565,0.0112623282117472,0.472392507315703,0.000126840036749117,"Little Lake" -"eye²","Quadratic",0.00831791747843452,0.0136370071286532,0.638058077901338,0.000185967963426938,"Little Lake" -"nasal²","Quadratic",-0.0230034790859793,0.016608380980921,0.155774184404708,0.000275838318807418,"Little Lake" -"eye × nasal","Correlational",0.00692724628948376,0.0115788116457984,0.601501957778033,0.000134068879128877,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_jaw_SL.csv b/R/results/pupfish_results/tables/selection_binary_jaw_SL.csv deleted file mode 100644 index 8a6548c..0000000 --- a/R/results/pupfish_results/tables/selection_binary_jaw_SL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.014766091754244,0.0102480167867174,0.131541583870294,0.000105021848060842 -"SL","Linear",-0.0391536787528223,0.0102480167867174,0.00025766719002865,0.000105021848060842 -"jaw²","Quadratic",-0.0407622248062538,0.0181914021205096,0.0143167199936487,0.00033092711111008 -"SL²","Quadratic",0.00315174407599064,0.0156454322928571,0.512189590696025,0.000244779551630377 -"jaw × SL","Correlational",-0.0373666074488995,0.0144327928976762,0.0101733348236625,0.000208305510827212 diff --git a/R/results/pupfish_results/tables/selection_binary_jaw_SL_group.csv b/R/results/pupfish_results/tables/selection_binary_jaw_SL_group.csv deleted file mode 100644 index b1b7feb..0000000 --- a/R/results/pupfish_results/tables/selection_binary_jaw_SL_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.016610013861275,0.0172598944838523,0.270362443139306,0.000297903957593716,"Crescent Pond" -"SL","Linear",-0.0599480062885014,0.0172598944838523,0.00132333113117372,0.000297903957593716,"Crescent Pond" -"jaw²","Quadratic",-0.0271511869550819,0.0345356433383446,0.336055217098482,0.00119271066079335,"Crescent Pond" -"SL²","Quadratic",0.0306986091907303,0.0351759625762319,0.722978369831773,0.00123734834316447,"Crescent Pond" -"jaw × SL","Correlational",-0.0192135696762641,0.0302614235318122,0.500209916199863,0.000915753754171715,"Crescent Pond" -"jaw","Linear",0.00796025858616023,0.0126496813555116,0.522634234727428,0.000160014438395978,"Little Lake" -"SL","Linear",-0.0223991652556964,0.0126496813555116,0.0815096429421875,0.000160014438395978,"Little Lake" -"jaw²","Quadratic",-0.0428269375917368,0.0213044864878779,0.0360680166724341,0.000453881144512172,"Little Lake" -"SL²","Quadratic",-0.00221095921547796,0.0172312181607297,0.489711119865328,0.000296914879302661,"Little Lake" -"jaw × SL","Correlational",-0.0354216059046544,0.0167685523074246,0.0316494606463603,0.000281184346486835,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_jaw_body.csv b/R/results/pupfish_results/tables/selection_binary_jaw_body.csv deleted file mode 100644 index de3c34f..0000000 --- a/R/results/pupfish_results/tables/selection_binary_jaw_body.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.0331794996481173,0.0103184642075282,0.00121950004709184,0.00010647070360204 -"body","Linear",-0.00664500995854027,0.0103184642075282,0.585161774283123,0.00010647070360204 -"jaw²","Quadratic",-0.00565308784670844,0.0179735284648057,0.481949268280993,0.000323047725475181 -"body²","Quadratic",0.00861696959925098,0.0172382151221781,0.718716984484252,0.000297156060598491 -"jaw × body","Correlational",-0.00956194751240066,0.014255502839351,0.486149040478089,0.000203219361202743 diff --git a/R/results/pupfish_results/tables/selection_binary_jaw_body_group.csv b/R/results/pupfish_results/tables/selection_binary_jaw_body_group.csv deleted file mode 100644 index 818950f..0000000 --- a/R/results/pupfish_results/tables/selection_binary_jaw_body_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.0385808895112125,0.0171860005746972,0.0209156970931695,0.000295358615753491,"Crescent Pond" -"body","Linear",-0.0279833006582241,0.0171860005746972,0.155259458806856,0.000295358615753491,"Crescent Pond" -"jaw²","Quadratic",0.0129969602651264,0.0331407124999241,0.880061955021006,0.00109830682500263,"Crescent Pond" -"body²","Quadratic",0.0261648637654588,0.0331312091098849,0.507418064695006,0.00109767701708292,"Crescent Pond" -"jaw × body","Correlational",0.00376347157661571,0.0286698207243785,0.812524129120042,0.000821958620368004,"Crescent Pond" -"jaw","Linear",0.0236766295458869,0.0127337487416561,0.0636493113416195,0.000162148357015627,"Little Lake" -"body","Linear",0.0116420340837928,0.012733748741656,0.354096658983793,0.000162148357015627,"Little Lake" -"jaw²","Quadratic",-0.0119908848602238,0.0208883428998102,0.446303187570252,0.000436322869100052,"Little Lake" -"body²","Quadratic",0.000547616548687881,0.0197959232278549,0.968265371945941,0.000391878576443125,"Little Lake" -"jaw × body","Correlational",-0.0068710210392333,0.0160808073611716,0.572824380138783,0.000258592365387112,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_jaw_eye.csv b/R/results/pupfish_results/tables/selection_binary_jaw_eye.csv deleted file mode 100644 index d82e310..0000000 --- a/R/results/pupfish_results/tables/selection_binary_jaw_eye.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.0437990445107047,0.0088538807590727,1.13930383821057e-06,7.83912044958778e-05 -"eye","Linear",0.023086497928363,0.00885388075907272,0.00965184621780231,7.8391204495878e-05 -"jaw²","Quadratic",0.0161023166735199,0.0136361673229301,0.637471067809269,0.000185945059258945 -"eye²","Quadratic",-0.00917588015774827,0.0112943372132788,0.240553983861041,0.000127562053087254 -"jaw × eye","Correlational",0.0181546770761755,0.00899641313561506,0.0864045553827983,8.09354493066672e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_jaw_eye_group.csv b/R/results/pupfish_results/tables/selection_binary_jaw_eye_group.csv deleted file mode 100644 index 6013a62..0000000 --- a/R/results/pupfish_results/tables/selection_binary_jaw_eye_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.081013066652368,0.0147665967671691,1.1115715569363e-07,0.000218052380084168,"Crescent Pond" -"eye","Linear",0.0458608599944701,0.0147665967671691,0.00227609711839053,0.000218052380084168,"Crescent Pond" -"jaw²","Quadratic",0.0761245325274763,0.0257443685071784,0.0503079799767873,0.000662772509833397,"Crescent Pond" -"eye²","Quadratic",0.00468542675224352,0.022491980631182,0.682441956546961,0.000505889192713465,"Crescent Pond" -"jaw × eye","Correlational",0.0643169666434832,0.0197313833326618,0.00454620017882634,0.000389327488220444,"Crescent Pond" -"jaw","Linear",0.0196966215456539,0.0112861444047448,0.0832591716506994,0.000127377055524751,"Little Lake" -"eye","Linear",0.0173755861832075,0.0112861444047448,0.125655843392255,0.000127377055524751,"Little Lake" -"jaw²","Quadratic",-0.00621715189494463,0.0165447159990539,0.58307776434768,0.000273727627489351,"Little Lake" -"eye²","Quadratic",0.00651145979376842,0.0136826441445181,0.766846533399925,0.000187214750785515,"Little Lake" -"jaw × eye","Correlational",0.00700290508676183,0.0115659466016557,0.672020948062256,0.000133771120792351,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_jaw_mouth.csv b/R/results/pupfish_results/tables/selection_binary_jaw_mouth.csv deleted file mode 100644 index 257897f..0000000 --- a/R/results/pupfish_results/tables/selection_binary_jaw_mouth.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.0374734110793642,0.00847242114418976,1.20905407007805e-05,7.17819200445137e-05 -"mouth","Linear",-0.0141065724840007,0.00847242114418976,0.0955953653294871,7.17819200445137e-05 -"jaw²","Quadratic",0.00845146750376642,0.0131855339198184,0.949647857962197,0.000173858304750682 -"mouth²","Quadratic",0.00489872462961492,0.0115280945955435,0.750459306094082,0.000132896965003799 -"jaw × mouth","Correlational",0.00224044820127175,0.00820594864988469,0.540352679917389,6.73375932445443e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_jaw_mouth_group.csv b/R/results/pupfish_results/tables/selection_binary_jaw_mouth_group.csv deleted file mode 100644 index 5b7067b..0000000 --- a/R/results/pupfish_results/tables/selection_binary_jaw_mouth_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.059433700604988,0.012811932378391,6.1415438185926e-06,0.000164145611268464,"Crescent Pond" -"mouth","Linear",-0.0167003123388301,0.012811932378391,0.197739987973619,0.000164145611268464,"Crescent Pond" -"jaw²","Quadratic",0.0307847820002146,0.0213069454221182,0.44624138546382,0.000453985923221126,"Crescent Pond" -"mouth²","Quadratic",0.015483498312072,0.017283211341623,0.444215728231371,0.000298709394279207,"Crescent Pond" -"jaw × mouth","Correlational",-0.0150482666353673,0.012854946411143,0.364991164908321,0.000165249647233359,"Crescent Pond" -"jaw","Linear",0.0175946761038375,0.0112631490552321,0.117133998375254,0.000126858526640376,"Little Lake" -"mouth","Linear",-0.0137268798937196,0.0112631490552321,0.22068457222545,0.000126858526640376,"Little Lake" -"jaw²","Quadratic",-0.00330070073445469,0.0167137685167907,0.618518892090537,0.000279350058032863,"Little Lake" -"mouth²","Quadratic",-0.00643754786962459,0.0153654086884676,0.500166935623981,0.000236095784163637,"Little Lake" -"jaw × mouth","Correlational",0.0136870870441567,0.0108504438518205,0.118630408298151,0.000117732131781509,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_jaw_nasal.csv b/R/results/pupfish_results/tables/selection_binary_jaw_nasal.csv deleted file mode 100644 index bc5376a..0000000 --- a/R/results/pupfish_results/tables/selection_binary_jaw_nasal.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.036469414534232,0.0084685255706684,1.95507381417895e-05,7.17159253410646e-05 -"nasal","Linear",-0.0166072468200506,0.0084685255706684,0.0497799494586856,7.17159253410646e-05 -"jaw²","Quadratic",0.00702964938283158,0.0132391279691419,0.981501714751162,0.000175274509383316 -"nasal²","Quadratic",0.0254373112682563,0.0110597528955913,0.0411726131948343,0.000122318134111541 -"jaw × nasal","Correlational",-0.00633366537428777,0.00849432697481239,0.658917867014734,7.21535907550254e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_jaw_nasal_group.csv b/R/results/pupfish_results/tables/selection_binary_jaw_nasal_group.csv deleted file mode 100644 index bd43978..0000000 --- a/R/results/pupfish_results/tables/selection_binary_jaw_nasal_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.0596350080212642,0.0126379798484752,5.38438119356445e-06,0.000159718534650465,"Crescent Pond" -"nasal","Linear",-0.048748580361638,0.0126379798484752,0.000199609610619302,0.000159718534650465,"Crescent Pond" -"jaw²","Quadratic",0.0263387162215989,0.020739425875425,0.541221555367018,0.000430123785642249,"Crescent Pond" -"nasal²","Quadratic",0.0464005651437471,0.0148258287578944,0.0144704840489306,0.000219805198358409,"Crescent Pond" -"jaw × nasal","Correlational",-0.0300766541299467,0.0123123161656142,0.0722773368080078,0.000151593129362045,"Crescent Pond" -"jaw","Linear",0.0192283356150096,0.0113144913417436,0.0905717144980045,0.00012801771432239,"Little Lake" -"nasal","Linear",0.0097658966597475,0.0113144913417436,0.39158739677165,0.00012801771432239,"Little Lake" -"jaw²","Quadratic",-0.00197894510713588,0.0172030571398524,0.719445040702284,0.000295945174957028,"Little Lake" -"nasal²","Quadratic",-0.0192018594195803,0.0167560980030154,0.202346872748313,0.000280766820286656,"Little Lake" -"jaw × nasal","Correlational",0.0146382323788356,0.0119736739470667,0.19513032639972,0.000143368867790665,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_mouth_SL.csv b/R/results/pupfish_results/tables/selection_binary_mouth_SL.csv deleted file mode 100644 index b381e27..0000000 --- a/R/results/pupfish_results/tables/selection_binary_mouth_SL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"mouth","Linear",-0.0131926304705864,0.00843984952981694,0.121558212241253,7.12310600859512e-05 -"SL","Linear",-0.0476438324168111,0.00843984952981694,3.09758958190233e-08,7.12310600859513e-05 -"mouth²","Quadratic",-0.00355950872428846,0.011434001506015,0.59167251986579,0.000130736390439553 -"SL²","Quadratic",0.0310901505526256,0.010744051176864,0.0684562910370905,0.000115434635691073 -"mouth × SL","Correlational",0.0240621320221873,0.00839847865864797,0.018367870882103,7.05344437797653e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_mouth_SL_group.csv b/R/results/pupfish_results/tables/selection_binary_mouth_SL_group.csv deleted file mode 100644 index f103b0b..0000000 --- a/R/results/pupfish_results/tables/selection_binary_mouth_SL_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"mouth","Linear",-0.0164096900296969,0.0126963609590678,0.198070666032481,0.000161197581602941,"Crescent Pond" -"SL","Linear",-0.0728080586286397,0.0126963609590678,3.43679556457997e-08,0.000161197581602941,"Crescent Pond" -"mouth²","Quadratic",0.0103062505238172,0.0170457054936415,0.688151268814546,0.000290556075775962,"Crescent Pond" -"SL²","Quadratic",0.0531164192828374,0.0186317783627577,0.0956536362452645,0.000347143164958924,"Crescent Pond" -"mouth × SL","Correlational",0.0404089306086284,0.0123836548427519,0.00798286894885338,0.000153354907264413,"Crescent Pond" -"mouth","Linear",-0.0127809501058698,0.0112639920088281,0.260491979658345,0.000126877515974942,"Little Lake" -"SL","Linear",-0.0251541582191899,0.0112639920088281,0.0264833983228718,0.000126877515974943,"Little Lake" -"mouth²","Quadratic",-0.0161218077179584,0.0153436348428945,0.244185322911384,0.000235427130192087,"Little Lake" -"SL²","Quadratic",0.0185325218722613,0.0129361763635046,0.265044655372977,0.000167344658907695,"Little Lake" -"mouth × SL","Correlational",0.0150716868469469,0.0115365614752174,0.237534932949746,0.000133092250671471,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_nasal_SL.csv b/R/results/pupfish_results/tables/selection_binary_nasal_SL.csv deleted file mode 100644 index be116e2..0000000 --- a/R/results/pupfish_results/tables/selection_binary_nasal_SL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"nasal","Linear",-0.0230424218411509,0.00847669318317126,0.00769146405881526,7.18543273216221e-05 -"SL","Linear",-0.0499856800752722,0.00847669318317126,8.40133273321425e-09,7.18543273216221e-05 -"nasal²","Quadratic",0.0185931436005978,0.0109465414839121,0.196348082019648,0.00011982677045901 -"SL²","Quadratic",0.0344535742179069,0.0108937597986396,0.0493236951710343,0.000118674002550455 -"nasal × SL","Correlational",0.0245407734070355,0.00831837992621946,0.0382344901742288,6.91954445969309e-05 diff --git a/R/results/pupfish_results/tables/selection_binary_nasal_SL_group.csv b/R/results/pupfish_results/tables/selection_binary_nasal_SL_group.csv deleted file mode 100644 index f058d15..0000000 --- a/R/results/pupfish_results/tables/selection_binary_nasal_SL_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"nasal","Linear",-0.053038617432708,0.0125799219268181,6.92977605973324e-05,0.000158254435684838,"Crescent Pond" -"SL","Linear",-0.0761349207176611,0.0125799219268181,1.04911901199466e-08,0.000158254435684838,"Crescent Pond" -"nasal²","Quadratic",0.0351289708799053,0.0149075967076931,0.0466592357920118,0.000222236439599221,"Crescent Pond" -"SL²","Quadratic",0.048964993016971,0.0184265971567859,0.0792815326456793,0.00033953948277847,"Crescent Pond" -"nasal × SL","Correlational",0.0386538549032089,0.0118190009415358,0.0159418866301619,0.000139688783256024,"Crescent Pond" -"nasal","Linear",0.00473665659378262,0.0113250450102666,0.675721882650388,0.000128256644484564,"Little Lake" -"SL","Linear",-0.0254793076063475,0.0113250450102666,0.0251450397566239,0.000128256644484564,"Little Lake" -"nasal²","Quadratic",-0.0247488525801434,0.0165722157153603,0.129290326616901,0.000274638333716434,"Little Lake" -"SL²","Quadratic",0.018582931363183,0.0132773029362145,0.288209773188215,0.000176286773260011,"Little Lake" -"nasal × SL","Correlational",-0.000355487137748903,0.0117799312228051,0.998861167735202,0.000138766779614017,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_binary_nasal_mouth.csv b/R/results/pupfish_results/tables/selection_binary_nasal_mouth.csv deleted file mode 100644 index 0907464..0000000 --- a/R/results/pupfish_results/tables/selection_binary_nasal_mouth.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"nasal","Linear",-0.0150126251484421,0.00958452515793596,0.118600573033017,9.18631225031074e-05 -"mouth","Linear",-0.00585648901955639,0.00958452515793596,0.539591632917845,9.18631225031073e-05 -"nasal²","Quadratic",0.0262717370114442,0.0147974528895689,0.121586515068092,0.000218964612019012 -"mouth²","Quadratic",-0.00588391070325582,0.0147206253218745,0.709371898280817,0.000216696809867012 -"nasal × mouth","Correlational",0.00362994610415225,0.0116398299985168,0.803560721572865,0.000135485642394371 diff --git a/R/results/pupfish_results/tables/selection_binary_nasal_mouth_group.csv b/R/results/pupfish_results/tables/selection_binary_nasal_mouth_group.csv deleted file mode 100644 index 9bd9ca7..0000000 --- a/R/results/pupfish_results/tables/selection_binary_nasal_mouth_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"nasal","Linear",-0.0515943829815887,0.0141755197858036,0.000359504346940071,0.00020094536119771,"Crescent Pond" -"mouth","Linear",0.0128391368200212,0.0141755197858036,0.369589328159901,0.00020094536119771,"Crescent Pond" -"nasal²","Quadratic",0.0379697346635837,0.0209625045359194,0.276803989869338,0.000439426596418442,"Crescent Pond" -"mouth²","Quadratic",-0.0107932847038485,0.0209819210539313,0.579671405067996,0.000440241011113406,"Crescent Pond" -"nasal × mouth","Correlational",0.0220643369912687,0.016980388544829,0.209295777872151,0.00028833359513336,"Crescent Pond" -"nasal","Linear",0.0195279396564982,0.0128857987872605,0.130118307169798,0.000166043810385764,"Little Lake" -"mouth","Linear",-0.0240596543591129,0.0128857987872605,0.0611320494954801,0.000166043810385764,"Little Lake" -"nasal²","Quadratic",-0.00114870246215013,0.0211015613566582,0.780112360168129,0.000445275891688813,"Little Lake" -"mouth²","Quadratic",0.0116879616240776,0.0204745370915941,0.721811192590958,0.000419206669115062,"Little Lake" -"nasal × mouth","Correlational",-0.0229657972332331,0.0160143495171759,0.183619421814033,0.000256459390458272,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_coefficients_summary_all.csv b/R/results/pupfish_results/tables/selection_coefficients_summary_all.csv deleted file mode 100644 index 1a86f56..0000000 --- a/R/results/pupfish_results/tables/selection_coefficients_summary_all.csv +++ /dev/null @@ -1,271 +0,0 @@ -"Trait1","Trait2","Term","Fitness","Analysis","Type","Coefficient","P_Value" -"jaw","eye","jaw","Binary","Overall","Linear",0.0438,1.13930383821057e-06 -"jaw","eye","eye","Binary","Overall","Linear",0.0231,0.00965184621780231 -"jaw","eye","jaw²","Binary","Overall","Quadratic",0.0161,0.637471067809269 -"jaw","eye","eye²","Binary","Overall","Quadratic",-0.0092,0.240553983861041 -"jaw","eye","jaw × eye","Binary","Overall","Correlational",0.0182,0.0864045553827983 -"jaw","eye","jaw","Continuous","Overall","Linear",0.1771,0.0165801781887572 -"jaw","eye","eye","Continuous","Overall","Linear",-0.0963,0.192168311651963 -"jaw","eye","jaw²","Continuous","Overall","Quadratic",0.0833,0.463811955924066 -"jaw","eye","eye²","Continuous","Overall","Quadratic",0.0139,0.882810857114886 -"jaw","eye","jaw × eye","Continuous","Overall","Correlational",0.1679,0.0253391311742754 -"jaw","eye","jaw","Binary","Group: ","Linear",0.081,1.1115715569363e-07 -"jaw","eye","eye","Binary","Group: ","Linear",0.0459,0.00227609711839053 -"jaw","eye","jaw","Binary","Group: ","Linear",0.0197,0.0832591716506994 -"jaw","eye","eye","Binary","Group: ","Linear",0.0174,0.125655843392255 -"jaw","eye","jaw","Continuous","Group: ","Linear",0.2967,0.00941340284151178 -"jaw","eye","eye","Continuous","Group: ","Linear",-0.0556,0.625594783042654 -"jaw","eye","jaw","Continuous","Group: ","Linear",0.0997,0.318724904975654 -"jaw","eye","eye","Continuous","Group: ","Linear",-0.0944,0.3450114715515 -"jaw","body","jaw","Binary","Overall","Linear",0.0332,0.00121950004709184 -"jaw","body","body","Binary","Overall","Linear",-0.0066,0.585161774283123 -"jaw","body","jaw²","Binary","Overall","Quadratic",-0.0057,0.481949268280993 -"jaw","body","body²","Binary","Overall","Quadratic",0.0086,0.718716984484252 -"jaw","body","jaw × body","Binary","Overall","Correlational",-0.0096,0.486149040478089 -"jaw","body","jaw","Continuous","Overall","Linear",0.3078,0.000345360989217721 -"jaw","body","body","Continuous","Overall","Linear",0.1791,0.0370937863816712 -"jaw","body","jaw²","Continuous","Overall","Quadratic",0.1351,0.366507475941174 -"jaw","body","body²","Continuous","Overall","Quadratic",0.2175,0.129503234470466 -"jaw","body","jaw × body","Continuous","Overall","Correlational",0.142,0.231230940579018 -"jaw","body","jaw","Binary","Group: ","Linear",0.0386,0.0209156970931695 -"jaw","body","body","Binary","Group: ","Linear",-0.028,0.155259458806856 -"jaw","body","jaw","Binary","Group: ","Linear",0.0237,0.0636493113416195 -"jaw","body","body","Binary","Group: ","Linear",0.0116,0.354096658983793 -"jaw","body","jaw","Continuous","Group: ","Linear",0.4635,0.000468734562780552 -"jaw","body","body","Continuous","Group: ","Linear",0.2053,0.120256899082602 -"jaw","body","jaw","Continuous","Group: ","Linear",0.1961,0.0818807555962431 -"jaw","body","body","Continuous","Group: ","Linear",0.189,0.0935581878388418 -"jaw","nasal","jaw","Binary","Overall","Linear",0.0365,1.95507381417895e-05 -"jaw","nasal","nasal","Binary","Overall","Linear",-0.0166,0.0497799494586856 -"jaw","nasal","jaw²","Binary","Overall","Quadratic",0.007,0.981501714751162 -"jaw","nasal","nasal²","Binary","Overall","Quadratic",0.0254,0.0411726131948343 -"jaw","nasal","jaw × nasal","Binary","Overall","Correlational",-0.0063,0.658917867014734 -"jaw","nasal","jaw","Continuous","Overall","Linear",0.2022,0.0042095231098737 -"jaw","nasal","nasal","Continuous","Overall","Linear",-0.1116,0.11399563894641 -"jaw","nasal","jaw²","Continuous","Overall","Quadratic",0.0265,0.810458372521133 -"jaw","nasal","nasal²","Continuous","Overall","Quadratic",0.021,0.82036153315409 -"jaw","nasal","jaw × nasal","Continuous","Overall","Correlational",0.0575,0.416977205338964 -"jaw","nasal","jaw","Binary","Group: ","Linear",0.0596,5.38438119356445e-06 -"jaw","nasal","nasal","Binary","Group: ","Linear",-0.0487,0.000199609610619302 -"jaw","nasal","jaw","Binary","Group: ","Linear",0.0192,0.0905717144980045 -"jaw","nasal","nasal","Binary","Group: ","Linear",0.0098,0.39158739677165 -"jaw","nasal","jaw","Continuous","Group: ","Linear",0.3356,0.000608709370681565 -"jaw","nasal","nasal","Continuous","Group: ","Linear",-0.2269,0.020266734251864 -"jaw","nasal","jaw","Continuous","Group: ","Linear",0.1043,0.298117985000041 -"jaw","nasal","nasal","Continuous","Group: ","Linear",-0.0334,0.739139761840289 -"jaw","mouth","jaw","Binary","Overall","Linear",0.0375,1.20905407007805e-05 -"jaw","mouth","mouth","Binary","Overall","Linear",-0.0141,0.0955953653294871 -"jaw","mouth","jaw²","Binary","Overall","Quadratic",0.0085,0.949647857962197 -"jaw","mouth","mouth²","Binary","Overall","Quadratic",0.0049,0.750459306094082 -"jaw","mouth","jaw × mouth","Binary","Overall","Correlational",0.0022,0.540352679917389 -"jaw","mouth","jaw","Continuous","Overall","Linear",0.2095,0.00302421065937975 -"jaw","mouth","mouth","Continuous","Overall","Linear",-0.1117,0.113591700837273 -"jaw","mouth","jaw²","Continuous","Overall","Quadratic",0.008,0.941723937288164 -"jaw","mouth","mouth²","Continuous","Overall","Quadratic",0.1044,0.27681762554321 -"jaw","mouth","jaw × mouth","Continuous","Overall","Correlational",0.0249,0.715253909230157 -"jaw","mouth","jaw","Binary","Group: ","Linear",0.0594,6.1415438185926e-06 -"jaw","mouth","mouth","Binary","Group: ","Linear",-0.0167,0.197739987973619 -"jaw","mouth","jaw","Binary","Group: ","Linear",0.0176,0.117133998375254 -"jaw","mouth","mouth","Binary","Group: ","Linear",-0.0137,0.22068457222545 -"jaw","mouth","jaw","Continuous","Group: ","Linear",0.3369,0.000649254363486232 -"jaw","mouth","mouth","Continuous","Group: ","Linear",-0.0957,0.331388668530345 -"jaw","mouth","jaw","Continuous","Group: ","Linear",0.1011,0.31069455284802 -"jaw","mouth","mouth","Continuous","Group: ","Linear",-0.1426,0.152804246172593 -"jaw","SL","jaw","Binary","Overall","Linear",0.0148,0.131541583870294 -"jaw","SL","SL","Binary","Overall","Linear",-0.0392,0.00025766719002865 -"jaw","SL","jaw²","Binary","Overall","Quadratic",-0.0408,0.0143167199936487 -"jaw","SL","SL²","Binary","Overall","Quadratic",0.0032,0.512189590696025 -"jaw","SL","jaw × SL","Binary","Overall","Correlational",-0.0374,0.0101733348236625 -"jaw","SL","jaw","Continuous","Overall","Linear",0.2524,0.00325010100790486 -"jaw","SL","SL","Continuous","Overall","Linear",0.0826,0.334741481745242 -"jaw","SL","jaw²","Continuous","Overall","Quadratic",-0.1753,0.250249139874247 -"jaw","SL","SL²","Continuous","Overall","Quadratic",0.0634,0.628799366396729 -"jaw","SL","jaw × SL","Continuous","Overall","Correlational",-0.1732,0.15203243024376 -"jaw","SL","jaw","Binary","Group: ","Linear",0.0166,0.270362443139306 -"jaw","SL","SL","Binary","Group: ","Linear",-0.0599,0.00132333113117372 -"jaw","SL","jaw","Binary","Group: ","Linear",0.008,0.522634234727428 -"jaw","SL","SL","Binary","Group: ","Linear",-0.0224,0.0815096429421875 -"jaw","SL","jaw","Continuous","Group: ","Linear",0.4721,0.000416317218343471 -"jaw","SL","SL","Continuous","Group: ","Linear",0.2157,0.105910977349794 -"jaw","SL","jaw","Continuous","Group: ","Linear",0.1222,0.276027467751411 -"jaw","SL","SL","Continuous","Group: ","Linear",0.0317,0.77764971299486 -"eye","body","eye","Binary","Overall","Linear",0.0121,0.15816563955735 -"eye","body","body","Binary","Overall","Linear",-0.0265,0.00198633620408464 -"eye","body","eye²","Binary","Overall","Quadratic",-0.0187,0.0557740030024713 -"eye","body","body²","Binary","Overall","Quadratic",0.0171,0.313439211013845 -"eye","body","eye × body","Binary","Overall","Correlational",-0.0248,0.00798720792030218 -"eye","body","eye","Continuous","Overall","Linear",-0.1497,0.0346601131215863 -"eye","body","body","Continuous","Overall","Linear",0.0143,0.840505232738581 -"eye","body","eye²","Continuous","Overall","Quadratic",-0.0572,0.536091529451545 -"eye","body","body²","Continuous","Overall","Quadratic",0.1076,0.278021244335881 -"eye","body","eye × body","Continuous","Overall","Correlational",-0.1613,0.028242019440645 -"eye","body","eye","Binary","Group: ","Linear",0.0139,0.275844280065149 -"eye","body","body","Binary","Group: ","Linear",-0.0563,1.9614239359894e-05 -"eye","body","eye","Binary","Group: ","Linear",0.0157,0.162542070574072 -"eye","body","body","Binary","Group: ","Linear",0.001,0.925919953650519 -"eye","body","eye","Continuous","Group: ","Linear",-0.1957,0.0496539289714967 -"eye","body","body","Continuous","Group: ","Linear",-0.0729,0.464281138804449 -"eye","body","eye","Continuous","Group: ","Linear",-0.1005,0.313454726615115 -"eye","body","body","Continuous","Group: ","Linear",0.0947,0.341870492921776 -"eye","nasal","eye","Binary","Overall","Linear",0.0089,0.296712146197167 -"eye","nasal","nasal","Binary","Overall","Linear",-0.0171,0.0457774727915905 -"eye","nasal","eye²","Binary","Overall","Quadratic",-0.0119,0.226411282790859 -"eye","nasal","nasal²","Binary","Overall","Quadratic",0.0289,0.0202014962616848 -"eye","nasal","eye × nasal","Binary","Overall","Correlational",0.0143,0.0908980329893726 -"eye","nasal","eye","Continuous","Overall","Linear",-0.1581,0.0256218627418881 -"eye","nasal","nasal","Continuous","Overall","Linear",-0.1292,0.0681301357893733 -"eye","nasal","eye²","Continuous","Overall","Quadratic",-0.0263,0.775982931664029 -"eye","nasal","nasal²","Continuous","Overall","Quadratic",0.0189,0.836380586919684 -"eye","nasal","eye × nasal","Continuous","Overall","Correlational",0.0786,0.2789463042668 -"eye","nasal","eye","Binary","Group: ","Linear",-0.0019,0.889079931913508 -"eye","nasal","nasal","Binary","Group: ","Linear",-0.0463,0.000416569567971439 -"eye","nasal","eye","Binary","Group: ","Linear",0.0159,0.159238807318156 -"eye","nasal","nasal","Binary","Group: ","Linear",0.0081,0.472392507315703 -"eye","nasal","eye","Continuous","Group: ","Linear",-0.2404,0.0150075544967796 -"eye","nasal","nasal","Continuous","Group: ","Linear",-0.2433,0.0138294647013776 -"eye","nasal","eye","Continuous","Group: ","Linear",-0.1037,0.298534997151577 -"eye","nasal","nasal","Continuous","Group: ","Linear",-0.0458,0.645619067281995 -"eye","mouth","eye","Binary","Overall","Linear",0.01,0.241024141511983 -"eye","mouth","mouth","Binary","Overall","Linear",-0.0127,0.137272293987753 -"eye","mouth","eye²","Binary","Overall","Quadratic",-0.0145,0.177902380031239 -"eye","mouth","mouth²","Binary","Overall","Quadratic",0.005,0.715161708291579 -"eye","mouth","eye × mouth","Binary","Overall","Correlational",0.0012,0.829847469234607 -"eye","mouth","eye","Continuous","Overall","Linear",-0.15,0.0337817331661864 -"eye","mouth","mouth","Continuous","Overall","Linear",-0.1061,0.133114556327772 -"eye","mouth","eye²","Continuous","Overall","Quadratic",-0.0377,0.681262228285711 -"eye","mouth","mouth²","Continuous","Overall","Quadratic",0.0958,0.314344906334386 -"eye","mouth","eye × mouth","Continuous","Overall","Correlational",0.0526,0.473087032893104 -"eye","mouth","eye","Binary","Group: ","Linear",0.0036,0.778820987095499 -"eye","mouth","mouth","Binary","Group: ","Linear",-0.0093,0.470444610623329 -"eye","mouth","eye","Binary","Group: ","Linear",0.0162,0.15075627762191 -"eye","mouth","mouth","Binary","Group: ","Linear",-0.015,0.181464868286531 -"eye","mouth","eye","Continuous","Group: ","Linear",-0.2123,0.0309828484324542 -"eye","mouth","mouth","Continuous","Group: ","Linear",-0.0676,0.491707328700928 -"eye","mouth","eye","Continuous","Group: ","Linear",-0.0983,0.323676896650816 -"eye","mouth","mouth","Continuous","Group: ","Linear",-0.1442,0.147995352432396 -"eye","SL","eye","Binary","Overall","Linear",0.011,0.240831281963812 -"eye","SL","SL","Binary","Overall","Linear",-0.0477,3.5796106886509e-08 -"eye","SL","eye²","Binary","Overall","Quadratic",-0.0209,0.0618564115501188 -"eye","SL","SL²","Binary","Overall","Quadratic",0.0303,0.0556835010885576 -"eye","SL","eye × SL","Binary","Overall","Correlational",9e-04,0.85894495973359 -"eye","SL","eye","Continuous","Overall","Linear",-0.1477,0.0366837869955305 -"eye","SL","SL","Continuous","Overall","Linear",-0.058,0.41186945822777 -"eye","SL","eye²","Continuous","Overall","Quadratic",-0.0523,0.583251304842555 -"eye","SL","SL²","Continuous","Overall","Quadratic",0.22,0.0183803313071098 -"eye","SL","eye × SL","Continuous","Overall","Correlational",0.0271,0.68325547609008 -"eye","SL","eye","Binary","Group: ","Linear",0.0186,0.176325569546661 -"eye","SL","SL","Binary","Group: ","Linear",-0.0748,2.3646126097546e-08 -"eye","SL","eye","Binary","Group: ","Linear",0.0122,0.311834941550161 -"eye","SL","SL","Binary","Group: ","Linear",-0.0243,0.0366115792361509 -"eye","SL","eye","Continuous","Group: ","Linear",-0.1952,0.0511724629292849 -"eye","SL","SL","Continuous","Group: ","Linear",-0.0681,0.495804149002297 -"eye","SL","eye","Continuous","Group: ","Linear",-0.1087,0.2806389580061 -"eye","SL","SL","Continuous","Group: ","Linear",-0.0403,0.689489232716917 -"body","nasal","body","Binary","Overall","Linear",-0.027,0.00161501911282015 -"body","nasal","nasal","Binary","Overall","Linear",-0.0197,0.0214728903147696 -"body","nasal","body²","Binary","Overall","Quadratic",0.0193,0.206651687982411 -"body","nasal","nasal²","Binary","Overall","Quadratic",0.0236,0.0757848532832348 -"body","nasal","body × nasal","Binary","Overall","Correlational",0.0155,0.15770450642762 -"body","nasal","body","Continuous","Overall","Linear",-0.0053,0.94035317131404 -"body","nasal","nasal","Continuous","Overall","Linear",-0.1181,0.095861105617492 -"body","nasal","body²","Continuous","Overall","Quadratic",0.1119,0.263765459811899 -"body","nasal","nasal²","Continuous","Overall","Quadratic",0.0111,0.904245849527981 -"body","nasal","body × nasal","Continuous","Overall","Correlational",0.0171,0.802943582003218 -"body","nasal","body","Binary","Group: ","Linear",-0.0579,1.15674359957453e-05 -"body","nasal","nasal","Binary","Group: ","Linear",-0.0506,0.000140599859810277 -"body","nasal","body","Binary","Group: ","Linear",0.0011,0.920608781144017 -"body","nasal","nasal","Binary","Group: ","Linear",0.0079,0.485092905866736 -"body","nasal","body","Continuous","Group: ","Linear",-0.1241,0.207428227901726 -"body","nasal","nasal","Continuous","Group: ","Linear",-0.2214,0.0246111406208546 -"body","nasal","body","Continuous","Group: ","Linear",0.0946,0.343704661661349 -"body","nasal","nasal","Continuous","Group: ","Linear",-0.0374,0.708316906490616 -"body","mouth","body","Binary","Overall","Linear",-0.0257,0.00256094121710118 -"body","mouth","mouth","Binary","Overall","Linear",-0.013,0.12479507096385 -"body","mouth","body²","Binary","Overall","Quadratic",0.0174,0.250857021255268 -"body","mouth","mouth²","Binary","Overall","Quadratic",0.0018,0.995265650816929 -"body","mouth","body × mouth","Binary","Overall","Correlational",0.0148,0.12545882089929 -"body","mouth","body","Continuous","Overall","Linear",0.0025,0.971251085530779 -"body","mouth","mouth","Continuous","Overall","Linear",-0.1042,0.140477202058872 -"body","mouth","body²","Continuous","Overall","Quadratic",0.1061,0.286458981772469 -"body","mouth","mouth²","Continuous","Overall","Quadratic",0.0885,0.354394490362797 -"body","mouth","body × mouth","Continuous","Overall","Correlational",0.089,0.196764428412936 -"body","mouth","body","Binary","Group: ","Linear",-0.0548,2.51840522723315e-05 -"body","mouth","mouth","Binary","Group: ","Linear",-0.0132,0.290999100645226 -"body","mouth","body","Binary","Group: ","Linear",0.0013,0.909154128396856 -"body","mouth","mouth","Binary","Group: ","Linear",-0.0146,0.195381914540515 -"body","mouth","body","Continuous","Group: ","Linear",-0.1109,0.260682034314516 -"body","mouth","mouth","Continuous","Group: ","Linear",-0.0624,0.526284780180389 -"body","mouth","body","Continuous","Group: ","Linear",0.105,0.29247738487165 -"body","mouth","mouth","Continuous","Group: ","Linear",-0.1526,0.126121758587196 -"body","SL","body","Binary","Overall","Linear",0.0019,0.847499539472611 -"body","SL","SL","Binary","Overall","Linear",-0.0486,3.52675512501627e-06 -"body","SL","body²","Binary","Overall","Quadratic",-0.0027,0.856865950820973 -"body","SL","SL²","Binary","Overall","Quadratic",0.0202,0.565436652817956 -"body","SL","body × SL","Binary","Overall","Correlational",0.0096,0.466293643935927 -"body","SL","body","Continuous","Overall","Linear",0.0554,0.51826989397266 -"body","SL","SL","Continuous","Overall","Linear",-0.0919,0.284169338743914 -"body","SL","body²","Continuous","Overall","Quadratic",0.0277,0.840329195409329 -"body","SL","SL²","Continuous","Overall","Quadratic",0.1482,0.241967284896641 -"body","SL","body × SL","Continuous","Overall","Correlational",0.0245,0.820791183289012 -"body","SL","body","Binary","Group: ","Linear",-0.0099,0.578540223580401 -"body","SL","SL","Binary","Group: ","Linear",-0.0645,0.000345906887244886 -"body","SL","body","Binary","Group: ","Linear",0.0155,0.217484728000389 -"body","SL","SL","Binary","Group: ","Linear",-0.0331,0.00900935168960987 -"body","SL","body","Continuous","Group: ","Linear",-0.0646,0.631553779587758 -"body","SL","SL","Continuous","Group: ","Linear",-0.0615,0.647710461118245 -"body","SL","body","Continuous","Group: ","Linear",0.1362,0.223134328248968 -"body","SL","SL","Continuous","Group: ","Linear",-0.086,0.441491383138662 -"nasal","mouth","nasal","Binary","Overall","Linear",-0.015,0.118600573033017 -"nasal","mouth","mouth","Binary","Overall","Linear",-0.0059,0.539591632917845 -"nasal","mouth","nasal²","Binary","Overall","Quadratic",0.0263,0.121586515068092 -"nasal","mouth","mouth²","Binary","Overall","Quadratic",-0.0059,0.709371898280817 -"nasal","mouth","nasal × mouth","Binary","Overall","Correlational",0.0036,0.803560721572865 -"nasal","mouth","nasal","Continuous","Overall","Linear",-0.0884,0.267002621035042 -"nasal","mouth","mouth","Continuous","Overall","Linear",-0.0635,0.425156312889078 -"nasal","mouth","nasal²","Continuous","Overall","Quadratic",0.0683,0.578969707170761 -"nasal","mouth","mouth²","Continuous","Overall","Quadratic",0.1709,0.162835529390787 -"nasal","mouth","nasal × mouth","Continuous","Overall","Correlational",-0.0918,0.343218573480284 -"nasal","mouth","nasal","Binary","Group: ","Linear",-0.0516,0.000359504346940071 -"nasal","mouth","mouth","Binary","Group: ","Linear",0.0128,0.369589328159901 -"nasal","mouth","nasal","Binary","Group: ","Linear",0.0195,0.130118307169798 -"nasal","mouth","mouth","Binary","Group: ","Linear",-0.0241,0.0611320494954801 -"nasal","mouth","nasal","Continuous","Group: ","Linear",-0.2312,0.0339353133138514 -"nasal","mouth","mouth","Continuous","Group: ","Linear",0.0452,0.677782316228389 -"nasal","mouth","nasal","Continuous","Group: ","Linear",0.0364,0.749641814129489 -"nasal","mouth","mouth","Continuous","Group: ","Linear",-0.165,0.148280411519355 -"nasal","SL","nasal","Binary","Overall","Linear",-0.023,0.00769146405881526 -"nasal","SL","SL","Binary","Overall","Linear",-0.05,8.40133273321425e-09 -"nasal","SL","nasal²","Binary","Overall","Quadratic",0.0186,0.196348082019648 -"nasal","SL","SL²","Binary","Overall","Quadratic",0.0345,0.0493236951710343 -"nasal","SL","nasal × SL","Binary","Overall","Correlational",0.0245,0.0382344901742288 -"nasal","SL","nasal","Continuous","Overall","Linear",-0.1256,0.0773887977467498 -"nasal","SL","SL","Continuous","Overall","Linear",-0.0739,0.298446567084017 -"nasal","SL","nasal²","Continuous","Overall","Quadratic",-0.0014,0.988165806535125 -"nasal","SL","SL²","Continuous","Overall","Quadratic",0.1913,0.0370747378919488 -"nasal","SL","nasal × SL","Continuous","Overall","Correlational",0.0531,0.448103309720054 -"nasal","SL","nasal","Binary","Group: ","Linear",-0.053,6.92977605973324e-05 -"nasal","SL","SL","Binary","Group: ","Linear",-0.0761,1.04911901199466e-08 -"nasal","SL","nasal","Binary","Group: ","Linear",0.0047,0.675721882650388 -"nasal","SL","SL","Binary","Group: ","Linear",-0.0255,0.0251450397566239 -"nasal","SL","nasal","Continuous","Group: ","Linear",-0.2232,0.0235918507641798 -"nasal","SL","SL","Continuous","Group: ","Linear",-0.1262,0.200123328908918 -"nasal","SL","nasal","Continuous","Group: ","Linear",-0.0476,0.635365033272835 -"nasal","SL","SL","Continuous","Group: ","Linear",-0.0301,0.764482629217862 -"mouth","SL","mouth","Binary","Overall","Linear",-0.0132,0.121558212241253 -"mouth","SL","SL","Binary","Overall","Linear",-0.0476,3.09758958190233e-08 -"mouth","SL","mouth²","Binary","Overall","Quadratic",-0.0036,0.59167251986579 -"mouth","SL","SL²","Binary","Overall","Quadratic",0.0311,0.0684562910370905 -"mouth","SL","mouth × SL","Binary","Overall","Correlational",0.0241,0.018367870882103 -"mouth","SL","mouth","Continuous","Overall","Linear",-0.1048,0.138285300630177 -"mouth","SL","SL","Continuous","Overall","Linear",-0.0614,0.384829173981041 -"mouth","SL","mouth²","Continuous","Overall","Quadratic",0.0685,0.474718952210891 -"mouth","SL","SL²","Continuous","Overall","Quadratic",0.1958,0.0298371203046045 -"mouth","SL","mouth × SL","Continuous","Overall","Correlational",0.1859,0.00832856400570597 -"mouth","SL","mouth","Binary","Group: ","Linear",-0.0164,0.198070666032481 -"mouth","SL","SL","Binary","Group: ","Linear",-0.0728,3.43679556457997e-08 -"mouth","SL","mouth","Binary","Group: ","Linear",-0.0128,0.260491979658345 -"mouth","SL","SL","Binary","Group: ","Linear",-0.0252,0.0264833983228718 -"mouth","SL","mouth","Continuous","Group: ","Linear",-0.0655,0.507047104966808 -"mouth","SL","SL","Continuous","Group: ","Linear",-0.1119,0.257422315774937 -"mouth","SL","mouth","Continuous","Group: ","Linear",-0.1463,0.143211539909428 -"mouth","SL","SL","Continuous","Group: ","Linear",-0.0141,0.887559232449272 diff --git a/R/results/pupfish_results/tables/selection_continuous_body_SL.csv b/R/results/pupfish_results/tables/selection_continuous_body_SL.csv deleted file mode 100644 index 30a79cd..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_body_SL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"body","Linear",0.0554121623901786,0.0857590788644786,0.51826989397266,0.00735461960768387 -"SL","Linear",-0.0918744756104042,0.0857590788644787,0.284169338743914,0.00735461960768387 -"body²","Quadratic",0.027709117750409,0.137513813667901,0.840329195409329,0.0189100489494902 -"SL²","Quadratic",0.148211117437308,0.126626750386732,0.241967284896641,0.0160343339135038 -"body × SL","Correlational",0.0245490694852454,0.108355940515529,0.820791183289012,0.0117410098450049 diff --git a/R/results/pupfish_results/tables/selection_continuous_body_SL_group.csv b/R/results/pupfish_results/tables/selection_continuous_body_SL_group.csv deleted file mode 100644 index 04632fd..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_body_SL_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"body","Linear",-0.0645829887843224,0.134630088155872,0.631553779587758,0.0181252606368578,"Crescent Pond" -"SL","Linear",-0.0615394850326396,0.134630088155872,0.647710461118245,0.0181252606368578,"Crescent Pond" -"body²","Quadratic",-0.0601887116319557,0.252245108423926,0.811461630844101,0.063627594723798,"Crescent Pond" -"SL²","Quadratic",-0.0159157779839573,0.267924699383622,0.952643784797569,0.071783644539804,"Crescent Pond" -"body × SL","Correlational",0.13197555128402,0.222480023138433,0.553197494084138,0.0494973606956779,"Crescent Pond" -"body","Linear",0.136201768062896,0.111730874598472,0.223134328248968,0.0124837883385394,"Little Lake" -"SL","Linear",-0.0860320172554611,0.111730874598472,0.441491383138662,0.0124837883385394,"Little Lake" -"body²","Quadratic",0.0337843239175147,0.167483102775092,0.84017976747791,0.0280505897151721,"Little Lake" -"SL²","Quadratic",0.159480377431038,0.146835429773592,0.277698140921763,0.0215606434367954,"Little Lake" -"body × SL","Correlational",0.035414331246787,0.129962207313559,0.785297956871591,0.0168901753298124,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_body_mouth.csv b/R/results/pupfish_results/tables/selection_continuous_body_mouth.csv deleted file mode 100644 index 7e7fc14..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_body_mouth.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"body","Linear",0.00254775498421842,0.0706844496001426,0.971251085530779,0.0049962914152751 -"mouth","Linear",-0.104234433420397,0.0706844496001426,0.140477202058872,0.0049962914152751 -"body²","Quadratic",0.10607896288394,0.0994899308965982,0.286458981772469,0.00989824634980989 -"mouth²","Quadratic",0.0885440431473214,0.095585801540356,0.354394490362797,0.00913664545611233 -"body × mouth","Correlational",0.089032392310613,0.068948526058125,0.196764428412936,0.00475389924558794 diff --git a/R/results/pupfish_results/tables/selection_continuous_body_mouth_group.csv b/R/results/pupfish_results/tables/selection_continuous_body_mouth_group.csv deleted file mode 100644 index 032b505..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_body_mouth_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"body","Linear",-0.110871544928121,0.0985089219492349,0.260682034314516,0.00970400770360044,"Crescent Pond" -"mouth","Linear",-0.0624484852126932,0.0985089219492348,0.526284780180389,0.00970400770360043,"Crescent Pond" -"body²","Quadratic",0.104697256324898,0.140432248951195,0.456145666465093,0.0197212165454905,"Crescent Pond" -"mouth²","Quadratic",0.300154978841327,0.134030591034786,0.0253739675546442,0.017964199333134,"Crescent Pond" -"body × mouth","Correlational",0.146427326364991,0.095787216135426,0.126702458884305,0.00917519077497481,"Crescent Pond" -"body","Linear",0.10496893296453,0.0996595934223985,0.29247738487165,0.00993203456111776,"Little Lake" -"mouth","Linear",-0.152568224582945,0.0996595934223986,0.126121758587196,0.00993203456111779,"Little Lake" -"body²","Quadratic",0.111463153901572,0.138917327138459,0.422535863294293,0.0192980237792937,"Little Lake" -"mouth²","Quadratic",-0.084548427388801,0.134007863561274,0.528241012322216,0.0179581074962569,"Little Lake" -"body × mouth","Correlational",0.0223884907648442,0.0980099827458697,0.819359706633152,0.00960595671784568,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_body_nasal.csv b/R/results/pupfish_results/tables/selection_continuous_body_nasal.csv deleted file mode 100644 index 7ea1f7b..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_body_nasal.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"body","Linear",-0.0053031835941747,0.0708639924424862,0.94035317131404,0.00502170542488874 -"nasal","Linear",-0.118066708887809,0.0708639924424862,0.095861105617492,0.00502170542488874 -"body²","Quadratic",0.111863962359118,0.100068532971855,0.263765459811899,0.0100137112911392 -"nasal²","Quadratic",0.0110644148635088,0.0919613098585615,0.904245849527981,0.00845688251090236 -"body × nasal","Correlational",0.0170560422183626,0.0683403385354469,0.802943582003218,0.00467040187113949 diff --git a/R/results/pupfish_results/tables/selection_continuous_body_nasal_group.csv b/R/results/pupfish_results/tables/selection_continuous_body_nasal_group.csv deleted file mode 100644 index 65c97e1..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_body_nasal_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"body","Linear",-0.124051921344915,0.098330029200701,0.207428227901726,0.00966879464261071,"Crescent Pond" -"nasal","Linear",-0.221368708798688,0.0983300292007009,0.0246111406208546,0.00966879464261069,"Crescent Pond" -"body²","Quadratic",0.081328995043746,0.141538732500681,0.565703704064376,0.0200332127978992,"Crescent Pond" -"nasal²","Quadratic",0.11693778464312,0.117020804957451,0.317926795364391,0.0136938687928898,"Crescent Pond" -"body × nasal","Correlational",-0.0373818990943485,0.0924937336748738,0.686195529522412,0.00855509076911849,"Crescent Pond" -"body","Linear",0.0946294158730839,0.0998902586711323,0.343704661661349,0.00997806377738571,"Little Lake" -"nasal","Linear",-0.0373816748075895,0.0998902586711324,0.708316906490616,0.00997806377738573,"Little Lake" -"body²","Quadratic",0.118784805725462,0.139408596213461,0.394390497047761,0.0194347566982078,"Little Lake" -"nasal²","Quadratic",-0.13140934626086,0.146881555140377,0.371190421588684,0.0215741912404555,"Little Lake" -"body × nasal","Correlational",0.0376593828243596,0.100361899952538,0.707567357306083,0.0100725109620832,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_eye_SL.csv b/R/results/pupfish_results/tables/selection_continuous_eye_SL.csv deleted file mode 100644 index 65a6fcf..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_eye_SL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"eye","Linear",-0.147685776265562,0.0706369590834473,0.0366837869955305,0.0049895799885566 -"SL","Linear",-0.0579782962617404,0.0706369590834472,0.41186945822777,0.00498957998855659 -"eye²","Quadratic",-0.0523461809522118,0.0953937965184566,0.583251304842555,0.0090999764142047 -"SL²","Quadratic",0.220020578247746,0.0932311285360805,0.0183803313071098,0.00869204332811117 -"eye × SL","Correlational",0.0270670739801953,0.0663264314322179,0.68325547609008,0.0043991955065327 diff --git a/R/results/pupfish_results/tables/selection_continuous_eye_SL_group.csv b/R/results/pupfish_results/tables/selection_continuous_eye_SL_group.csv deleted file mode 100644 index 70d255a..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_eye_SL_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"eye","Linear",-0.195194998377412,0.0999632378053819,0.0511724629292849,0.00999264891253533,"Crescent Pond" -"SL","Linear",-0.0681136432540388,0.0999632378053818,0.495804149002297,0.00999264891253532,"Crescent Pond" -"eye²","Quadratic",-0.24836742338171,0.140974959518614,0.0784506407249939,0.019873939211275,"Crescent Pond" -"SL²","Quadratic",0.169137386217083,0.148656303299778,0.255522139666913,0.0220986965107557,"Crescent Pond" -"eye × SL","Correlational",-0.11808720751264,0.117061195090991,0.313362878468018,0.013703323396131,"Crescent Pond" -"eye","Linear",-0.108725745893293,0.100719814648017,0.2806389580061,0.010144481062731,"Little Lake" -"SL","Linear",-0.0402544620245297,0.100719814648017,0.689489232716917,0.010144481062731,"Little Lake" -"eye²","Quadratic",0.202894861012742,0.140620794575819,0.149386266893516,0.0197742078671348,"Little Lake" -"SL²","Quadratic",0.325970162229908,0.130403378878549,0.0125943794878637,0.0170050412229425,"Little Lake" -"eye × SL","Correlational",0.228782187343377,0.0974903146910767,0.0191406282026216,0.00950436145856516,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_eye_body.csv b/R/results/pupfish_results/tables/selection_continuous_eye_body.csv deleted file mode 100644 index c56ee61..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_eye_body.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"eye","Linear",-0.149712951166828,0.0708245316382895,0.0346601131215863,0.00501611428178308 -"body","Linear",0.0142552348821648,0.0708245316382895,0.840505232738581,0.00501611428178306 -"eye²","Quadratic",-0.057213176973965,0.0924509185759948,0.536091529451545,0.00854717234554522 -"body²","Quadratic",0.107606647300221,0.0991681505015944,0.278021244335881,0.00983432207390688 -"eye × body","Correlational",-0.161313071317687,0.0734702459513278,0.028242019440645,0.0053978770401486 diff --git a/R/results/pupfish_results/tables/selection_continuous_eye_body_group.csv b/R/results/pupfish_results/tables/selection_continuous_eye_body_group.csv deleted file mode 100644 index 0a06bb2..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_eye_body_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"eye","Linear",-0.195737898889197,0.099580954919888,0.0496539289714967,0.00991636658275677,"Crescent Pond" -"body","Linear",-0.0729063755687882,0.099580954919888,0.464281138804449,0.00991636658275677,"Crescent Pond" -"eye²","Quadratic",-0.252003614879189,0.139100617919296,0.0703765718417076,0.0193489819055299,"Crescent Pond" -"body²","Quadratic",0.151622898564958,0.143262830942038,0.290182194339322,0.020524238729527,"Crescent Pond" -"eye × body","Correlational",-0.282068020665278,0.114294194551174,0.0137783053219195,0.0130631629081016,"Crescent Pond" -"eye","Linear",-0.100480024178915,0.0996308226316504,0.313454726615115,0.00992630081825937,"Little Lake" -"body","Linear",0.0947431737600543,0.0996308226316503,0.341870492921776,0.00992630081825935,"Little Lake" -"eye²","Quadratic",0.107142996671325,0.125626708062215,0.393943711445937,0.0157820697785491,"Little Lake" -"body²","Quadratic",0.0961345245190529,0.140429900489841,0.493777418278517,0.0197205569515865,"Little Lake" -"eye × body","Correlational",-0.0408932434947925,0.102165353623925,0.689049547192611,0.0104377594811016,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_eye_mouth.csv b/R/results/pupfish_results/tables/selection_continuous_eye_mouth.csv deleted file mode 100644 index 42d3905..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_eye_mouth.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"eye","Linear",-0.149975008176053,0.0706018033515842,0.0337817331661864,0.00498461463649576 -"mouth","Linear",-0.106085513409544,0.0706018033515841,0.133114556327772,0.00498461463649575 -"eye²","Quadratic",-0.037707053889027,0.0917880094977984,0.681262228285711,0.00842503868756793 -"mouth²","Quadratic",0.095785831964768,0.0951748790275442,0.314344906334386,0.00905825759790767 -"eye × mouth","Correlational",0.0525777202467182,0.0732676677298928,0.473087032893104,0.00536815113457798 diff --git a/R/results/pupfish_results/tables/selection_continuous_eye_mouth_group.csv b/R/results/pupfish_results/tables/selection_continuous_eye_mouth_group.csv deleted file mode 100644 index e200888..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_eye_mouth_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"eye","Linear",-0.212334549571416,0.0982699013759601,0.0309828484324542,0.00965697351644093,"Crescent Pond" -"mouth","Linear",-0.0675979712221403,0.0982699013759601,0.491707328700928,0.00965697351644092,"Crescent Pond" -"eye²","Quadratic",-0.273839464628082,0.138424997656098,0.0482097389265805,0.0191614799760906,"Crescent Pond" -"mouth²","Quadratic",0.331750744675656,0.132326521886361,0.0123519510690662,0.0175103083945417,"Crescent Pond" -"eye × mouth","Correlational",-0.0102873646987145,0.102834392979816,0.920336651410827,0.0105749123795273,"Crescent Pond" -"eye","Linear",-0.0983358634631488,0.0995874287304447,0.323676896650816,0.0099176559611414,"Little Lake" -"mouth","Linear",-0.144182951017594,0.0995874287304447,0.147995352432396,0.0099176559611414,"Little Lake" -"eye²","Quadratic",0.105492536033754,0.120693246334473,0.382305313642581,0.0145668597107537,"Little Lake" -"mouth²","Quadratic",-0.075265938119092,0.1340830933735,0.574697186683503,0.0179782759286067,"Little Lake" -"eye × mouth","Correlational",0.0709184548106128,0.10282569280636,0.490550941590172,0.0105731231011078,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_eye_nasal.csv b/R/results/pupfish_results/tables/selection_continuous_eye_nasal.csv deleted file mode 100644 index ceb12af..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_eye_nasal.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"eye","Linear",-0.158062974520825,0.070763184256274,0.0256218627418881,0.00500742824608739 -"nasal","Linear",-0.129157361135432,0.070763184256274,0.0681301357893733,0.00500742824608738 -"eye²","Quadratic",-0.0262553540016377,0.0922537908465763,0.775982931664029,0.00851076192556384 -"nasal²","Quadratic",0.0188840595837532,0.0914241977306454,0.836380586919684,0.00835838393069215 -"eye × nasal","Correlational",0.0785699240186497,0.0725480187984598,0.2789463042668,0.00526321503158168 diff --git a/R/results/pupfish_results/tables/selection_continuous_eye_nasal_group.csv b/R/results/pupfish_results/tables/selection_continuous_eye_nasal_group.csv deleted file mode 100644 index afd3d0b..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_eye_nasal_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"eye","Linear",-0.240401479611828,0.0986490939384887,0.0150075544967796,0.00973164373488477,"Crescent Pond" -"nasal","Linear",-0.243323822109753,0.0986490939384887,0.0138294647013776,0.00973164373488476,"Crescent Pond" -"eye²","Quadratic",-0.248419780623508,0.141861391568693,0.0802670740116997,0.0201246544178061,"Crescent Pond" -"nasal²","Quadratic",0.144194162414809,0.115368876838518,0.211683207285664,0.013309977742981,"Crescent Pond" -"eye × nasal","Correlational",0.166138016143703,0.103336177309885,0.108247746438524,0.0106783655410199,"Crescent Pond" -"eye","Linear",-0.10365070826052,0.0996509235772524,0.298534997151577,0.00993030656979939,"Little Lake" -"nasal","Linear",-0.0458394584131149,0.0996509235772523,0.645619067281995,0.00993030656979938,"Little Lake" -"eye²","Quadratic",0.112835404782215,0.120710698976627,0.350145905032684,0.0145710728474258,"Little Lake" -"nasal²","Quadratic",-0.137234420457616,0.147012409553172,0.350800735134714,0.0216126485626295,"Little Lake" -"eye × nasal","Correlational",-0.00230129294344781,0.102492169571893,0.982090953104042,0.0105046448235536,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_jaw_SL.csv b/R/results/pupfish_results/tables/selection_continuous_jaw_SL.csv deleted file mode 100644 index 8c7acba..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_jaw_SL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.252409187270599,0.0856536431611035,0.00325010100790486,0.00733654658676966 -"SL","Linear",0.082643560279297,0.0856536431611036,0.334741481745242,0.00733654658676966 -"jaw²","Quadratic",-0.175255496669835,0.152382359423569,0.250249139874247,0.0232203834634938 -"SL²","Quadratic",0.0633651487868469,0.13105575211816,0.628799366396729,0.0171756101632566 -"jaw × SL","Correlational",-0.173244018771886,0.120897939600822,0.15203243024376,0.0146163117997239 diff --git a/R/results/pupfish_results/tables/selection_continuous_jaw_SL_group.csv b/R/results/pupfish_results/tables/selection_continuous_jaw_SL_group.csv deleted file mode 100644 index e59f450..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_jaw_SL_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.472094114549841,0.133249968953998,0.000416317218343471,0.0177555542262415,"Crescent Pond" -"SL","Linear",0.215664214194628,0.133249968953998,0.105910977349794,0.0177555542262415,"Crescent Pond" -"jaw²","Quadratic",0.185122182530711,0.267278132804903,0.488729543230642,0.0714376002756753,"Crescent Pond" -"SL²","Quadratic",0.237391822683531,0.272233689260733,0.383436509894957,0.0741111815685092,"Crescent Pond" -"jaw × SL","Correlational",0.081521280339489,0.234199105496924,0.727858761754929,0.0548492210155593,"Crescent Pond" -"jaw","Linear",0.122197593702357,0.112118074707155,0.276027467751411,0.0125704626760391,"Little Lake" -"SL","Linear",0.0316690701937688,0.112118074707155,0.77764971299486,0.0125704626760391,"Little Lake" -"jaw²","Quadratic",-0.305240848259622,0.188883310427363,0.106414286628602,0.0356769049579994,"Little Lake" -"SL²","Quadratic",0.0160481035525547,0.152770146830181,0.916359998184461,0.0233387177625151,"Little Lake" -"jaw × SL","Correlational",-0.286482738602349,0.148668200601921,0.0542730999722982,0.022102233870213,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_jaw_body.csv b/R/results/pupfish_results/tables/selection_continuous_jaw_body.csv deleted file mode 100644 index 9427d67..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_jaw_body.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.307752348269503,0.0858371553115353,0.000345360989217721,0.00736801723197662 -"body","Linear",0.17907585711369,0.0858371553115353,0.0370937863816712,0.00736801723197662 -"jaw²","Quadratic",0.135051840681421,0.149516809977103,0.366507475941174,0.0223552764657292 -"body²","Quadratic",0.217499931671543,0.14339994174288,0.129503234470466,0.0205635432918614 -"jaw × body","Correlational",0.142018818727007,0.118587583586211,0.231230940579018,0.0140630149808166 diff --git a/R/results/pupfish_results/tables/selection_continuous_jaw_body_group.csv b/R/results/pupfish_results/tables/selection_continuous_jaw_body_group.csv deleted file mode 100644 index c0a16c0..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_jaw_body_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.463460975181736,0.131999579209538,0.000468734562780552,0.0174238889114952,"Crescent Pond" -"body","Linear",0.205284332474969,0.131999579209538,0.120256899082602,0.0174238889114952,"Crescent Pond" -"jaw²","Quadratic",0.225032781191504,0.2546411058744,0.377084263493233,0.0648420928009376,"Crescent Pond" -"body²","Quadratic",0.160567944534848,0.254568085303429,0.528368909867757,0.064804910055054,"Crescent Pond" -"jaw × body","Correlational",0.0983135909350875,0.22028840974657,0.655493299885365,0.0485269834686726,"Crescent Pond" -"jaw","Linear",0.196063138023678,0.112571018795941,0.0818807555962431,0.0126722342727562,"Little Lake" -"body","Linear",0.188958207750646,0.112571018795941,0.0935581878388418,0.0126722342727561,"Little Lake" -"jaw²","Quadratic",0.0546081986611354,0.184583572722172,0.767411676388142,0.0340710953188813,"Little Lake" -"body²","Quadratic",0.190364095978543,0.174930211183219,0.276765253234673,0.0306005787846054,"Little Lake" -"jaw × body","Correlational",0.11413177923108,0.14210092630225,0.422071499796103,0.0201926732559575,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_jaw_eye.csv b/R/results/pupfish_results/tables/selection_continuous_jaw_eye.csv deleted file mode 100644 index f0cafb9..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_jaw_eye.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.177053780232182,0.0738321632928003,0.0165801781887572,0.00545118833649473 -"eye","Linear",-0.0963262083262564,0.0738321632928004,0.192168311651963,0.00545118833649474 -"jaw²","Quadratic",0.0833432111108388,0.113742511500015,0.463811955924066,0.0129373589223311 -"eye²","Quadratic",0.0138889283686893,0.0942087501527061,0.882810857114886,0.00887528860533501 -"jaw × eye","Correlational",0.167942168726791,0.0750412194499758,0.0253391311742754,0.00563118461653942 diff --git a/R/results/pupfish_results/tables/selection_continuous_jaw_eye_group.csv b/R/results/pupfish_results/tables/selection_continuous_jaw_eye_group.csv deleted file mode 100644 index b6e6c68..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_jaw_eye_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.296666728036158,0.114000461738101,0.00941340284151178,0.0129961052765003,"Crescent Pond" -"eye","Linear",-0.055644364220004,0.114000461738102,0.625594783042654,0.0129961052765003,"Crescent Pond" -"jaw²","Quadratic",0.288989107633192,0.199960130782765,0.148745855953742,0.0399840539026605,"Crescent Pond" -"eye²","Quadratic",-0.116646612816774,0.174698376746764,0.504497136910466,0.0305195228379543,"Crescent Pond" -"jaw × eye","Correlational",0.21203662090821,0.153256429289528,0.16684738768886,0.023487533118576,"Crescent Pond" -"jaw","Linear",0.0997109651950113,0.0999514161135996,0.318724904975654,0.00999028558311394,"Little Lake" -"eye","Linear",-0.0944311201232813,0.0999514161135997,0.3450114715515,0.00999028558311395,"Little Lake" -"jaw²","Quadratic",-0.036644764081387,0.146418359230572,0.802428329078111,0.0214383359197727,"Little Lake" -"eye²","Quadratic",0.102097532840424,0.121089434577825,0.399348556699309,0.0146626511663773,"Little Lake" -"jaw × eye","Correlational",0.1163241986183,0.102356965478263,0.256047277809876,0.0104769483819183,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_jaw_mouth.csv b/R/results/pupfish_results/tables/selection_continuous_jaw_mouth.csv deleted file mode 100644 index ea81ad2..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_jaw_mouth.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.209504067267014,0.0705598138567703,0.00302421065937975,0.00497868733150208 -"mouth","Linear",-0.111696057589958,0.0705598138567703,0.113591700837273,0.00497868733150208 -"jaw²","Quadratic",0.00802740519586632,0.109794263040979,0.941723937288164,0.0120547801967116 -"mouth²","Quadratic",0.104422637550581,0.0959929767032002,0.27681762554321,0.00921465157634114 -"jaw × mouth","Correlational",0.0249311647513309,0.0683298901694085,0.715253909230157,0.00466897389056342 diff --git a/R/results/pupfish_results/tables/selection_continuous_jaw_mouth_group.csv b/R/results/pupfish_results/tables/selection_continuous_jaw_mouth_group.csv deleted file mode 100644 index 2a70888..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_jaw_mouth_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.336867234809827,0.0984327800285304,0.000649254363486232,0.00968901218414505,"Crescent Pond" -"mouth","Linear",-0.0956620661331911,0.0984327800285303,0.331388668530345,0.00968901218414504,"Crescent Pond" -"jaw²","Quadratic",0.117339004969398,0.163370479523677,0.472799452850401,0.0266899135797962,"Crescent Pond" -"mouth²","Quadratic",0.288620190349292,0.132518597511351,0.0296721195259795,0.0175611786863755,"Crescent Pond" -"jaw × mouth","Correlational",-0.138381447223262,0.098564985164862,0.160680720286724,0.00971505630054947,"Crescent Pond" -"jaw","Linear",0.101067615261318,0.0996431362028337,0.31069455284802,0.00992875459233648,"Little Lake" -"mouth","Linear",-0.14257126304861,0.0996431362028338,0.152804246172593,0.00992875459233648,"Little Lake" -"jaw²","Quadratic",0.00397852737009795,0.147829514691904,0.978534722719171,0.0218535654140439,"Little Lake" -"mouth²","Quadratic",-0.035071713579115,0.135903575975522,0.796413032382919,0.0184697819629344,"Little Lake" -"jaw × mouth","Correlational",0.145648177461728,0.0959697298185614,0.129430239501743,0.00921018904144768,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_jaw_nasal.csv b/R/results/pupfish_results/tables/selection_continuous_jaw_nasal.csv deleted file mode 100644 index bfcc710..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_jaw_nasal.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"jaw","Linear",0.202158486576387,0.0705477745305155,0.0042095231098737,0.00497698849120845 -"nasal","Linear",-0.111552151671067,0.0705477745305155,0.11399563894641,0.00497698849120845 -"jaw²","Quadratic",0.0264996970524475,0.110475773220532,0.810458372521133,0.0122048964686744 -"nasal²","Quadratic",0.020960102475555,0.0922896701063961,0.82036153315409,0.00851738320834742 -"jaw × nasal","Correlational",0.0575461906380626,0.0708821111721033,0.416977205338964,0.00502427368421441 diff --git a/R/results/pupfish_results/tables/selection_continuous_jaw_nasal_group.csv b/R/results/pupfish_results/tables/selection_continuous_jaw_nasal_group.csv deleted file mode 100644 index dcdbd7c..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_jaw_nasal_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"jaw","Linear",0.33563599802143,0.0975676732673298,0.000608709370681565,0.00951945086680041,"Crescent Pond" -"nasal","Linear",-0.226898557495646,0.0975676732673297,0.020266734251864,0.00951945086680041,"Crescent Pond" -"jaw²","Quadratic",0.0979574816841787,0.161695688980698,0.544793556392192,0.0261454958349427,"Crescent Pond" -"nasal²","Quadratic",0.0750445939393243,0.115590113733969,0.516357845276907,0.0133610743930318,"Crescent Pond" -"jaw × nasal","Correlational",-0.110924275290415,0.0959934212887838,0.248180724090734,0.00921473693072593,"Crescent Pond" -"jaw","Linear",0.104269192294848,0.100159011711137,0.298117985000041,0.0100318276269517,"Little Lake" -"nasal","Linear",-0.0333617748202439,0.100159011711137,0.739139761840289,0.0100318276269517,"Little Lake" -"jaw²","Quadratic",0.0593404394151823,0.152128683982401,0.696572613609778,0.0231431364902174,"Little Lake" -"nasal²","Quadratic",-0.0825456363989651,0.148176171081458,0.577603273223467,0.0219561776763615,"Little Lake" -"jaw × nasal","Correlational",0.229523369959506,0.105884625342659,0.0304268861132736,0.0112115538839552,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_mouth_SL.csv b/R/results/pupfish_results/tables/selection_continuous_mouth_SL.csv deleted file mode 100644 index 065abcc..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_mouth_SL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"mouth","Linear",-0.10479313322569,0.0706704072557303,0.138285300630177,0.00499430646169078 -"SL","Linear",-0.0614293805721551,0.0706704072557304,0.384829173981041,0.00499430646169079 -"mouth²","Quadratic",0.0685173323586366,0.0958328040044337,0.474718952210891,0.00918392632335221 -"SL²","Quadratic",0.195761425508628,0.0900500625353571,0.0298371203046045,0.00810901376262173 -"mouth × SL","Correlational",0.185922037515305,0.0703909089749753,0.00832856400570597,0.00495488006632325 diff --git a/R/results/pupfish_results/tables/selection_continuous_mouth_SL_group.csv b/R/results/pupfish_results/tables/selection_continuous_mouth_SL_group.csv deleted file mode 100644 index e2b8612..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_mouth_SL_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"mouth","Linear",-0.0655248592421448,0.0987249228129579,0.507047104966808,0.0097466103844245,"Crescent Pond" -"SL","Linear",-0.111878252051315,0.0987249228129579,0.257422315774937,0.0097466103844245,"Crescent Pond" -"mouth²","Quadratic",0.31077388229518,0.132528205502449,0.0192487801962034,0.0175637252536993,"Crescent Pond" -"SL²","Quadratic",0.203949123012459,0.1448597215678,0.159509151990821,0.0209843389327005,"Crescent Pond" -"mouth × SL","Correlational",0.30549192974614,0.0962813510114804,0.00156120853780563,0.00927009855259589,"Crescent Pond" -"mouth","Linear",-0.146267374293081,0.0998328632919056,0.143211539909428,0.00996660059306031,"Little Lake" -"SL","Linear",-0.0141194111365087,0.0998328632919057,0.887559232449272,0.00996660059306032,"Little Lake" -"mouth²","Quadratic",-0.0964793349942975,0.13603005790149,0.478340239019132,0.0185041766526826,"Little Lake" -"SL²","Quadratic",0.190395123360699,0.114686567933172,0.0972116144448286,0.0131530088642901,"Little Lake" -"mouth × SL","Correlational",0.0938419881359062,0.102278185157975,0.359100490681597,0.0104608271592089,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_nasal_SL.csv b/R/results/pupfish_results/tables/selection_continuous_nasal_SL.csv deleted file mode 100644 index c7479e4..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_nasal_SL.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"nasal","Linear",-0.125556255687065,0.0710553986333907,0.0773887977467498,0.00504886967495006 -"SL","Linear",-0.0739019526148279,0.0710553986333907,0.298446567084017,0.00504886967495006 -"nasal²","Quadratic",-0.00136678788417628,0.0921357500645917,0.988165806535125,0.0084889964399649 -"SL²","Quadratic",0.191308831547975,0.091691492837831,0.0370747378919488,0.00840732985883002 -"nasal × SL","Correlational",0.0531231620663139,0.0700148238556316,0.448103309720054,0.00490207555953511 diff --git a/R/results/pupfish_results/tables/selection_continuous_nasal_SL_group.csv b/R/results/pupfish_results/tables/selection_continuous_nasal_SL_group.csv deleted file mode 100644 index defaf5e..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_nasal_SL_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"nasal","Linear",-0.223224461329607,0.0984401114367389,0.0235918507641798,0.00969045553967757,"Crescent Pond" -"SL","Linear",-0.126215254896718,0.0984401114367389,0.200123328908918,0.00969045553967757,"Crescent Pond" -"nasal²","Quadratic",0.0800318035939225,0.118139470514021,0.498306892666132,0.0139569344933333,"Crescent Pond" -"SL²","Quadratic",0.14813498467237,0.146026785816822,0.310651183056001,0.021323822175992,"Crescent Pond" -"nasal × SL","Correlational",0.0964195201495037,0.0936630189705362,0.303558603620016,0.00877276112267502,"Crescent Pond" -"nasal","Linear",-0.0476311014918674,0.100415765984415,0.635365033272835,0.0100833260582368,"Little Lake" -"SL","Linear",-0.0300929692775344,0.100415765984415,0.764482629217862,0.0100833260582369,"Little Lake" -"nasal²","Quadratic",-0.136108785981635,0.146992474968228,0.354699089100692,0.0216067876972852,"Little Lake" -"SL²","Quadratic",0.189291044986387,0.117767210674681,0.108307929586863,0.0138691159100948,"Little Lake" -"nasal × SL","Correlational",-0.0101503126965145,0.104485801725999,0.922631075130573,0.0109172827623248,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_continuous_nasal_mouth.csv b/R/results/pupfish_results/tables/selection_continuous_nasal_mouth.csv deleted file mode 100644 index 9673d75..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_nasal_mouth.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"nasal","Linear",-0.0884033576714374,0.0796193948008897,0.267002621035042,0.00633924802845994 -"mouth","Linear",-0.0635110200099856,0.0796193948008896,0.425156312889078,0.00633924802845993 -"nasal²","Quadratic",0.0683093434474701,0.12308258201622,0.578969707170761,0.0151493219957796 -"mouth²","Quadratic",0.170949754159968,0.122443543968765,0.162835529390787,0.014992421459631 -"nasal × mouth","Correlational",-0.0917899844278663,0.0968180362619854,0.343218573480284,0.00937373214562711 diff --git a/R/results/pupfish_results/tables/selection_continuous_nasal_mouth_group.csv b/R/results/pupfish_results/tables/selection_continuous_nasal_mouth_group.csv deleted file mode 100644 index decfd43..0000000 --- a/R/results/pupfish_results/tables/selection_continuous_nasal_mouth_group.csv +++ /dev/null @@ -1,11 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"nasal","Linear",-0.231209048709561,0.108849157710507,0.0339353133138514,0.0118481391342868,"Crescent Pond" -"mouth","Linear",0.0452407903415363,0.108849157710507,0.677782316228389,0.0118481391342868,"Crescent Pond" -"nasal²","Quadratic",0.240037987122259,0.161652671505609,0.137926107915911,0.0261315862049004,"Crescent Pond" -"mouth²","Quadratic",0.451737193859887,0.161802402278599,0.00535261158396796,0.0261800173831255,"Crescent Pond" -"nasal × mouth","Correlational",-0.216005551317501,0.13094452367423,0.0993800693821319,0.017146468280271,"Crescent Pond" -"nasal","Linear",0.0364032581044512,0.114044460924474,0.749641814129489,0.013006139067554,"Little Lake" -"mouth","Linear",-0.16499773460107,0.114044460924474,0.148280411519355,0.013006139067554,"Little Lake" -"nasal²","Quadratic",-0.0950180553920083,0.187047030043828,0.611576078185437,0.0349865914482167,"Little Lake" -"mouth²","Quadratic",-0.0411377968148332,0.181489004049289,0.820729615170484,0.0329382585908029,"Little Lake" -"nasal × mouth","Correlational",-0.0126779826725153,0.141953311636174,0.928853299234702,0.0201507426844768,"Little Lake" diff --git a/R/results/pupfish_results/tables/selection_differentials_all.csv b/R/results/pupfish_results/tables/selection_differentials_all.csv deleted file mode 100644 index b1858de..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_all.csv +++ /dev/null @@ -1,49 +0,0 @@ -"Trait","Fitness","Analysis","S" -"jaw","Binary","Overall",0.0369525962244975 -"jaw","Binary","Weighted Mean",0.0369311791342258 -"jaw","Binary","Crescent Pond",0.0573499397655478 -"jaw","Binary","Little Lake",0.018212233108389 -"jaw","Continuous","Overall",0.205427009165109 -"jaw","Continuous","Weighted Mean",0.211530049556723 -"jaw","Continuous","Crescent Pond",0.324935130499448 -"jaw","Continuous","Little Lake",0.107565679360514 -"eye","Binary","Overall",0.010129787540103 -"eye","Binary","Weighted Mean",0.0101838833416811 -"eye","Binary","Crescent Pond",0.00416904283889292 -"eye","Binary","Little Lake",0.0156980022815445 -"eye","Continuous","Overall",-0.148600879298229 -"eye","Continuous","Weighted Mean",-0.153114493252233 -"eye","Continuous","Crescent Pond",-0.20806753603963 -"eye","Continuous","Little Lake",-0.102736164201505 -"body","Binary","Overall",-0.0255698971808109 -"body","Binary","Weighted Mean",-0.0254785378035767 -"body","Binary","Crescent Pond",-0.0538886608747751 -"body","Binary","Little Lake",0.000566508218529139 -"body","Continuous","Overall",0.00341133717896455 -"body","Continuous","Weighted Mean",-0.000261326125237785 -"body","Continuous","Crescent Pond",-0.106516200608373 -"body","Continuous","Little Lake",0.0971480757647487 -"nasal","Binary","Overall",-0.0177023481126581 -"nasal","Binary","Weighted Mean",-0.0179253490444364 -"nasal","Binary","Crescent Pond",-0.0459803501158854 -"nasal","Binary","Little Lake",0.00779413806320237 -"nasal","Continuous","Overall",-0.117612101319647 -"nasal","Continuous","Weighted Mean",-0.124033124790444 -"nasal","Continuous","Crescent Pond",-0.211371699318266 -"nasal","Continuous","Little Lake",-0.0439652846272198 -"mouth","Binary","Overall",-0.0127688657840682 -"mouth","Binary","Weighted Mean",-0.0121243439941684 -"mouth","Binary","Crescent Pond",-0.0095029477696486 -"mouth","Binary","Little Lake",-0.0145275150448073 -"mouth","Continuous","Overall",-0.104199685182385 -"mouth","Continuous","Weighted Mean",-0.10298874308062 -"mouth","Continuous","Crescent Pond",-0.0548666373774037 -"mouth","Continuous","Little Lake",-0.147104794763321 -"SL","Binary","Overall",-0.0475029039525889 -"SL","Binary","Weighted Mean",-0.0476176674693167 -"SL","Binary","Crescent Pond",-0.071173920033334 -"SL","Binary","Little Lake",-0.0260224184589328 -"SL","Continuous","Overall",-0.0604799263725375 -"SL","Continuous","Weighted Mean",-0.0631817314108729 -"SL","Continuous","Crescent Pond",-0.105553543280484 -"SL","Continuous","Little Lake",-0.0243372748973133 diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_SL_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_binary_SL_grouped.csv deleted file mode 100644 index d10505b..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_SL_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",-0.071173920033334,892 -"Little Lake",-0.0260224184589328,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_SL_overall.csv b/R/results/pupfish_results/tables/selection_differentials_binary_SL_overall.csv deleted file mode 100644 index 73c6e40..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_SL_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"SL",-0.0475029039525889,"binary","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_SL_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_binary_SL_weighted.csv deleted file mode 100644 index 0d161f5..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_SL_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"SL",-0.0476176674693167,"binary","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_body_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_binary_body_grouped.csv deleted file mode 100644 index a9cf36c..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_body_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",-0.0538886608747751,892 -"Little Lake",0.000566508218529139,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_body_overall.csv b/R/results/pupfish_results/tables/selection_differentials_binary_body_overall.csv deleted file mode 100644 index f48b84a..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_body_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"body",-0.0255698971808109,"binary","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_body_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_binary_body_weighted.csv deleted file mode 100644 index a199921..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_body_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"body",-0.0254785378035767,"binary","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_eye_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_binary_eye_grouped.csv deleted file mode 100644 index a892068..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_eye_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",0.00416904283889292,892 -"Little Lake",0.0156980022815445,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_eye_overall.csv b/R/results/pupfish_results/tables/selection_differentials_binary_eye_overall.csv deleted file mode 100644 index c5ca532..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_eye_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"eye",0.010129787540103,"binary","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_eye_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_binary_eye_weighted.csv deleted file mode 100644 index 51dc327..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_eye_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"eye",0.0101838833416811,"binary","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_jaw_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_binary_jaw_grouped.csv deleted file mode 100644 index d4d1d7b..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_jaw_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",0.0573499397655478,892 -"Little Lake",0.018212233108389,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_jaw_overall.csv b/R/results/pupfish_results/tables/selection_differentials_binary_jaw_overall.csv deleted file mode 100644 index d49bec9..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_jaw_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"jaw",0.0369525962244975,"binary","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_jaw_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_binary_jaw_weighted.csv deleted file mode 100644 index 1433cd4..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_jaw_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"jaw",0.0369311791342258,"binary","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_mouth_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_binary_mouth_grouped.csv deleted file mode 100644 index 7f1a8d6..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_mouth_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",-0.0095029477696486,892 -"Little Lake",-0.0145275150448073,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_mouth_overall.csv b/R/results/pupfish_results/tables/selection_differentials_binary_mouth_overall.csv deleted file mode 100644 index 42b4a5f..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_mouth_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"mouth",-0.0127688657840682,"binary","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_mouth_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_binary_mouth_weighted.csv deleted file mode 100644 index 9d4bc60..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_mouth_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"mouth",-0.0121243439941684,"binary","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_nasal_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_binary_nasal_grouped.csv deleted file mode 100644 index d02899f..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_nasal_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",-0.0459803501158854,892 -"Little Lake",0.00779413806320237,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_nasal_overall.csv b/R/results/pupfish_results/tables/selection_differentials_binary_nasal_overall.csv deleted file mode 100644 index 716ab38..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_nasal_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"nasal",-0.0177023481126581,"binary","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_binary_nasal_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_binary_nasal_weighted.csv deleted file mode 100644 index d1b1d25..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_binary_nasal_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"nasal",-0.0179253490444364,"binary","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_SL_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_SL_grouped.csv deleted file mode 100644 index 31e1ff0..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_SL_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",-0.105553543280484,892 -"Little Lake",-0.0243372748973133,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_SL_overall.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_SL_overall.csv deleted file mode 100644 index 6518316..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_SL_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"SL",-0.0604799263725375,"continuous","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_SL_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_SL_weighted.csv deleted file mode 100644 index 072b72a..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_SL_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"SL",-0.0631817314108729,"continuous","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_body_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_body_grouped.csv deleted file mode 100644 index f4da8ab..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_body_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",-0.106516200608373,892 -"Little Lake",0.0971480757647487,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_body_overall.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_body_overall.csv deleted file mode 100644 index bdfc2ae..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_body_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"body",0.00341133717896455,"continuous","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_body_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_body_weighted.csv deleted file mode 100644 index 4eb800f..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_body_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"body",-0.000261326125237785,"continuous","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_eye_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_eye_grouped.csv deleted file mode 100644 index ffe2bd9..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_eye_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",-0.20806753603963,892 -"Little Lake",-0.102736164201505,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_eye_overall.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_eye_overall.csv deleted file mode 100644 index 79fcd3d..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_eye_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"eye",-0.148600879298229,"continuous","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_eye_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_eye_weighted.csv deleted file mode 100644 index 87f173b..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_eye_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"eye",-0.153114493252233,"continuous","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_jaw_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_jaw_grouped.csv deleted file mode 100644 index a8f7611..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_jaw_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",0.324935130499448,892 -"Little Lake",0.107565679360514,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_jaw_overall.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_jaw_overall.csv deleted file mode 100644 index 185923f..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_jaw_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"jaw",0.205427009165109,"continuous","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_jaw_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_jaw_weighted.csv deleted file mode 100644 index 158b4ea..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_jaw_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"jaw",0.211530049556723,"continuous","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_mouth_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_mouth_grouped.csv deleted file mode 100644 index 4c55018..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_mouth_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",-0.0548666373774037,892 -"Little Lake",-0.147104794763321,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_mouth_overall.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_mouth_overall.csv deleted file mode 100644 index a721cd8..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_mouth_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"mouth",-0.104199685182385,"continuous","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_mouth_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_mouth_weighted.csv deleted file mode 100644 index ea44c83..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_mouth_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"mouth",-0.10298874308062,"continuous","weighted_mean" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_nasal_grouped.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_nasal_grouped.csv deleted file mode 100644 index 3998639..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_nasal_grouped.csv +++ /dev/null @@ -1,3 +0,0 @@ -"lake","S","n" -"Crescent Pond",-0.211371699318266,892 -"Little Lake",-0.0439652846272198,973 diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_nasal_overall.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_nasal_overall.csv deleted file mode 100644 index f17273f..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_nasal_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"nasal",-0.117612101319647,"continuous","overall" diff --git a/R/results/pupfish_results/tables/selection_differentials_continuous_nasal_weighted.csv b/R/results/pupfish_results/tables/selection_differentials_continuous_nasal_weighted.csv deleted file mode 100644 index c07951a..0000000 --- a/R/results/pupfish_results/tables/selection_differentials_continuous_nasal_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","fitness","method" -"nasal",-0.124033124790444,"continuous","weighted_mean" diff --git a/R/results/test_results/models/adaptive_landscape.rds b/R/results/test_results/models/adaptive_landscape.rds deleted file mode 100644 index c0eeedc..0000000 Binary files a/R/results/test_results/models/adaptive_landscape.rds and /dev/null differ diff --git a/R/results/test_results/tables/comparison_summary.csv b/R/results/test_results/tables/comparison_summary.csv deleted file mode 100644 index aac3a8f..0000000 --- a/R/results/test_results/tables/comparison_summary.csv +++ /dev/null @@ -1,4 +0,0 @@ -"Trait_Pair","Correlation","Distance" -"size_speed",0.9475,3.5216 -"size_color",0.963,1.2227 -"speed_color",0.9997,1.1995 diff --git a/R/results/test_results/tables/correlation_size_color.csv b/R/results/test_results/tables/correlation_size_color.csv deleted file mode 100644 index 82c66be..0000000 --- a/R/results/test_results/tables/correlation_size_color.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","correlation","distance","n_points" -"size","color",0.962998048077273,1.22265283697254,900 diff --git a/R/results/test_results/tables/correlation_size_speed.csv b/R/results/test_results/tables/correlation_size_speed.csv deleted file mode 100644 index 76aa647..0000000 --- a/R/results/test_results/tables/correlation_size_speed.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","correlation","distance","n_points" -"size","speed",0.947485285755361,3.52161323772398,900 diff --git a/R/results/test_results/tables/correlation_speed_color.csv b/R/results/test_results/tables/correlation_speed_color.csv deleted file mode 100644 index 9c0867c..0000000 --- a/R/results/test_results/tables/correlation_speed_color.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait1","trait2","correlation","distance","n_points" -"speed","color",0.999658980915382,1.19952761785085,900 diff --git a/R/results/test_results/tables/selection_binary.csv b/R/results/test_results/tables/selection_binary.csv deleted file mode 100644 index 0b46fb7..0000000 --- a/R/results/test_results/tables/selection_binary.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"size","Linear",0.00010439988853477,0.0555946007325279,0.997020874116327,0.00309075963060919 -"speed","Linear",0.0716959058765344,0.0555946007325279,0.197964700337217,0.00309075963060919 -"size²","Quadratic",0.113547449512619,0.0950674922817738,0.22358594391641,0.00903782808874513 -"speed²","Quadratic",-0.0704934889218843,0.092105809052434,0.469269243977355,0.00848348006120343 -"size × speed","Correlational",0.0626423196537158,0.0593083648513006,0.27423939418419,0.00351748214133498 diff --git a/R/results/test_results/tables/selection_binary_group.csv b/R/results/test_results/tables/selection_binary_group.csv deleted file mode 100644 index f447059..0000000 --- a/R/results/test_results/tables/selection_binary_group.csv +++ /dev/null @@ -1,16 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"size","Linear",0.0800910121150535,0.104395785982612,0.433785736171667,0.0108984801309273,2004 -"speed","Linear",0.1750344263524,0.104395785982612,0.109741675649285,0.0108984801309273,2004 -"size²","Quadratic",-0.264949636592544,0.215800949403595,0.189443730331677,0.046570049763493,2004 -"speed²","Quadratic",-0.128335740949447,0.270876150361869,0.61008661816194,0.0733738888348661,2004 -"size × speed","Correlational",-0.16529418883362,0.159140052347402,0.257003729480983,0.0253255562611339,2004 -"size","Linear",-0.13381240664992,0.11037170821956,0.22351232397871,0.0121819139753038,2003 -"speed","Linear",0.106721158798858,0.11037170821956,0.330087679086548,0.0121819139753038,2003 -"size²","Quadratic",0.427052663590162,0.290790754038054,0.115578854718423,0.0845592626340202,2003 -"speed²","Quadratic",0.0742639417441631,0.206419322888663,0.722426276756694,0.042608936861814,2003 -"size × speed","Correlational",-0.143716676604982,0.177495623591024,0.320406141644256,0.0315046963939665,2003 -"size","Linear",0.0510705368375278,0.0989610050673284,0.588346360771173,0.0097932805239358,2005 -"speed","Linear",0.0133482421559063,0.0989610050673284,0.885515558794263,0.0097932805239358,2005 -"size²","Quadratic",0.238195140668483,0.17221407409978,0.157332570219578,0.0296576873180444,2005 -"speed²","Quadratic",-0.00577965798751361,0.18720288917829,0.99855260315146,0.0350449217166993,2005 -"size × speed","Correlational",0.138044775972059,0.113832811768461,0.146861215532188,0.012957909035114,2005 diff --git a/R/results/test_results/tables/selection_continuous.csv b/R/results/test_results/tables/selection_continuous.csv deleted file mode 100644 index f07d1c8..0000000 --- a/R/results/test_results/tables/selection_continuous.csv +++ /dev/null @@ -1,6 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance" -"size","Linear",0.0341935980163312,0.0500616139794757,0.496637721969856,0.00250616519423004 -"speed","Linear",0.0259228270543217,0.0500616139794757,0.606069552890419,0.00250616519423004 -"size²","Quadratic",-0.203595419256164,0.0968811639881885,0.0390019970526359,0.00938595993570627 -"speed²","Quadratic",-0.0446916796295971,0.0785191852633628,0.570956513818376,0.00616526245442229 -"size × speed","Correlational",0.044711906291512,0.0594164041368235,0.454126858018177,0.00353030908055034 diff --git a/R/results/test_results/tables/selection_continuous_group.csv b/R/results/test_results/tables/selection_continuous_group.csv deleted file mode 100644 index aecaa0b..0000000 --- a/R/results/test_results/tables/selection_continuous_group.csv +++ /dev/null @@ -1,16 +0,0 @@ -"Term","Type","Beta_Coefficient","Standard_Error","P_Value","Variance","Group" -"size","Linear",0.173159193681669,0.104198843591229,0.116014090915012,0.0108573990057495,2005 -"speed","Linear",-0.100948373551552,0.104198843591229,0.347060315373789,0.0108573990057494,2005 -"size²","Quadratic",-0.162259972538419,0.195384563372272,0.42126638274472,0.0381751276041735,2005 -"speed²","Quadratic",-0.189013494720181,0.226836355703466,0.419744941932467,0.0514547322688292,2005 -"size × speed","Correlational",-0.0114790060956196,0.148546986075653,0.939581261741149,0.0220662070721601,2005 -"size","Linear",-0.102738458741499,0.0559226186331646,0.0752071121073522,0.00312733927479037,2003 -"speed","Linear",-0.0177865601539121,0.0559226186331646,0.75244604743019,0.00312733927479037,2003 -"size²","Quadratic",-0.0232291878120458,0.13580065381493,0.865330154522802,0.0184418175765625,2003 -"speed²","Quadratic",-0.0825355311787007,0.117083734281198,0.48629272930282,0.0137086008332302,2003 -"size × speed","Correlational",-0.0386975112786701,0.0593900815946144,0.519631630736984,0.00352718179181495,2003 -"size","Linear",0.177356853519097,0.101031208554476,0.093095953923841,0.010207305101978,2004 -"speed","Linear",0.152537342148404,0.101031208554476,0.145323152590988,0.010207305101978,2004 -"size²","Quadratic",-0.266783776713986,0.227019496757321,0.254448826697332,0.0515378519079471,2004 -"speed²","Quadratic",-0.138459822644869,0.201320078588947,0.499914912615447,0.0405297740430599,2004 -"size × speed","Correlational",0.12623707233059,0.131244750423575,0.348209838973798,0.0172251845137465,2004 diff --git a/R/results/test_results/tables/selection_differentials_grouped.csv b/R/results/test_results/tables/selection_differentials_grouped.csv deleted file mode 100644 index 4319711..0000000 --- a/R/results/test_results/tables/selection_differentials_grouped.csv +++ /dev/null @@ -1,4 +0,0 @@ -"year","S","n" -2003,5.00092647250763,36 -2004,5.43766339903827,25 -2005,5.26622055486301,19 diff --git a/R/results/test_results/tables/selection_differentials_overall.csv b/R/results/test_results/tables/selection_differentials_overall.csv deleted file mode 100644 index 514056c..0000000 --- a/R/results/test_results/tables/selection_differentials_overall.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","method","note" -"size",5.19730054280313,"overall","All data pooled (no grouping)" diff --git a/R/results/test_results/tables/selection_differentials_weighted.csv b/R/results/test_results/tables/selection_differentials_weighted.csv deleted file mode 100644 index b1069d1..0000000 --- a/R/results/test_results/tables/selection_differentials_weighted.csv +++ /dev/null @@ -1,2 +0,0 @@ -"trait","selection_differential","method","note" -"size",5.20041410660786,"weighted_mean","Weighted by group sample size" diff --git a/vignettes/Evolutionary Selection Analysis.Rmd b/vignettes/Evolutionary Selection Analysis.Rmd deleted file mode 100644 index 42f248f..0000000 --- a/vignettes/Evolutionary Selection Analysis.Rmd +++ /dev/null @@ -1,1259 +0,0 @@ -# Evolutionary Selection Analysis Framework - -## 1. Overview - -This project implements a comprehensive quantitative genetic framework for analyzing natural selection on phenotypic traits. The framework follows the Lande & Arnold (1983) approach while extending it with modern nonparametric methods for visualizing adaptive landscapes. - -**Key capabilities:** - -| Analysis Type | Description | -|---------------|-------------| -| Selection differentials ($\mathbf{S}$) | Total selection acting on traits | -| Linear selection gradients ($\boldsymbol{\beta}$) | Direct directional selection | -| Nonlinear selection gradients ($\boldsymbol{\gamma}$) | Stabilizing/disruptive and correlational selection | -| Univariate correlated fitness functions | Flexible spline-based fitness functions at the individual level | -| Bivariate correlated fitness surfaces | Thin-plate spline (TPS) or GAM surfaces of individual fitness as a function of two traits | -| Adaptive landscapes | Mean fitness as a function of population mean phenotype (requires simulation) | -| Binary fitness handling | Logistic regression for survival/reproduction data | - ---- - -## 2. Mathematical Framework - -### 2.1 Relative Fitness - -Individual fitness is converted to relative fitness to enable comparisons across populations and generations: - -$$w_i = \frac{W_i}{\bar{W}}$$ - -where: -- $W_i$ = absolute fitness of individual $i$ (e.g., offspring count, survival status) -- $\bar{W} = \frac{1}{n}\sum_{i=1}^n W_i$ = mean population fitness -- $w_i$ = relative fitness of individual $i$ - -**Why relative fitness?** Selection operates on relative, not absolute, differences in fitness. This standardization ensures that selection gradients are comparable across studies. -**File:** `prepare_selection_data.R` - -### 2.2 Trait Standardization - -Traits are standardized to mean 0 and variance 1 before analysis: - -$$z_i = \frac{x_i - \bar{x}}{s_x}$$ - -where: -- $x_i$ = original trait value -- $\bar{x}$ = sample mean -- $s_x$ = sample standard deviation -- $z_i$ = standardized trait value - -**Purpose:** Standardization puts all traits on the same scale, allowing direct comparison of selection gradients. A $\beta = 0.5$ means that a one-standard-deviation increase in the trait increases relative fitness by 0.5 units. -**File:** `prepare_selection_data.R` - -### 2.3 Selection Differential - -The selection differential ($S$) measures the total selection acting on a trait, including both direct and indirect effects through correlated traits: - -$$S = \text{Cov}(z, w) = \mathbb{E}[(z - \bar{z})(w - \bar{w})]$$ - -For multiple traits, the vector of selection differentials is: - -$$\mathbf{S} = \text{Cov}(\mathbf{z}, w) = \begin{bmatrix} \text{Cov}(z_1, w) \\ \text{Cov}(z_2, w) \\ \vdots \\ \text{Cov}(z_m, w) \end{bmatrix}$$ - -**Interpretation:** $S$ represents the shift in trait mean after one generation of selection. A positive $S$ indicates the trait mean increases. -**File:** `selection_differential.R` - -### 2.4 Linear Selection Gradients - -Linear selection gradients ($\boldsymbol{\beta}$) measure the direct directional selection on each trait, controlling for correlations with other traits: - -$$w = \alpha + \boldsymbol{\beta}^T \mathbf{z} + \varepsilon$$ - -In matrix form: - -$$\boldsymbol{\beta} = \mathbf{P}^{-1} \mathbf{S}$$ - -where $\mathbf{P}$ is the phenotypic variance-covariance matrix. - -For a model with two traits: - -$$w = \alpha + \beta_1 z_1 + \beta_2 z_2 + \varepsilon$$ - -**Interpretation:** $\beta_i$ is the partial regression coefficient—the change in relative fitness for a one-standard-deviation increase in trait $i$, holding all other traits constant. -**File:** `analyze_linear_selection.R` - -### 2.5 Nonlinear Selection Gradients - -Quadratic selection gradients ($\boldsymbol{\gamma}$) measure nonlinear selection, including stabilizing/disruptive selection (diagonal elements) and correlational selection (off-diagonal elements): - -$$w = \alpha + \boldsymbol{\beta}^T \mathbf{z} + \frac{1}{2} \mathbf{z}^T \boldsymbol{\gamma} \mathbf{z} + \varepsilon$$ - -For two traits, this expands to: - -$$w = \alpha + \beta_1 z_1 + \beta_2 z_2 + \frac{1}{2}\gamma_{11} z_1^2 + \frac{1}{2}\gamma_{22} z_2^2 + \gamma_{12} z_1 z_2 + \varepsilon$$ - -**Important:** The $\frac{1}{2}$ factor in the quadratic terms follows Lande & Arnold's convention, making $\gamma_{ii}$ the second derivative of the fitness surface. In practice, most implementations (including this one) report $2 \times$ the quadratic coefficient from regression, which equals $\gamma_{ii}$. - -**Interpretation:** - -| $\gamma$ value | Type | Interpretation | -|----------------|------|----------------| -| $\gamma_{ii} < 0$ | Stabilizing selection | Intermediate trait values have highest fitness | -| $\gamma_{ii} > 0$ | Disruptive selection | Extreme trait values have highest fitness | -| $\gamma_{ij} > 0$ | Positive correlational | Selection favors positive correlation between traits | -| $\gamma_{ij} < 0$ | Negative correlational | Selection favors negative correlation between traits | -**File:** `analyze_nonlinear_selection.R`, `analyze_disruptive_selection.R` - -### 2.6 Nonparametric Adaptive Landscapes - -Traditional quadratic models impose a fixed shape on the fitness function. Nonparametric methods allow the data to reveal unexpected patterns. - -**Univariate spline model:** - -$$w = \alpha + s(z) + \varepsilon$$ - -where $s(z)$ is a smooth function estimated from the data using penalized regression splines. - -**Multivariate thin-plate spline:** - -$$w = \alpha + f(z_1, z_2) + \varepsilon$$ - -where $f(z_1, z_2)$ is a two-dimensional smooth surface. This creates a visual "adaptive landscape" showing how fitness varies across trait combinations. - -**GAM formulation:** -$$ -w \sim \text{family}(\eta), \quad -\eta = \alpha + s(z_1, z_2) -$$ - -**File:** `correlated_fitness_surface.R` - -### 2.7 Adaptive Landscapes (Population Level) - -Following Sewall Wright's original concept, the adaptive landscape describes mean fitness as a function of population mean phenotype: - -$$ -\bar{W} = g(\bar{z}_1, \bar{z}_2) -$$ - -where: - -- $\bar{W}$ = mean fitness of the population -- $\bar{z}_1, \bar{z}_2$ = population mean phenotypes - -Unlike correlated fitness surfaces (which use individual data), adaptive landscapes require simulation because they represent a theoretical construct—the expected mean fitness for a population with a given mean phenotype. - -**Calculation procedure:** - -For each candidate population mean $\bar{\mathbf{z}}$: - -**1. Simulate individuals around the mean** - -$$ -\mathbf{z}_{\text{ind}} \sim \mathcal{N}(\bar{\mathbf{z}}, \mathbf{P}) -$$ - -where $\mathbf{P}$ is the within-population phenotypic variance–covariance matrix. - -**2. Predict individual fitness** - -$$ -w_{\text{ind}} = \hat{f}(\mathbf{z}_{\text{ind}}) -$$ - -**3. Compute mean fitness** - -$$ -\bar{W}(\bar{\mathbf{z}}) = -\frac{1}{N_{\text{sim}}} -\sum_{j=1}^{N_{\text{sim}}} w_{\text{ind}, j} -$$ - -The resulting surface: - -$$ -\bar{W} = g(\bar{z}_1, \bar{z}_2) -$$ - -is the **adaptive landscape**. - -**Mathematical distinction** - -| Surface | Level | Formula | Interpretation | -|--------|------|--------|----------------| -| Correlated Fitness | Individual | $w = f(\mathbf{z})$ | Current selection pattern | -| Adaptive Landscape | Population | $\bar{W} = g(\bar{\mathbf{z}})$ | Evolutionary potential | - -**File:** `adaptive_landscape.R` - -### 2.8 Model Selection and Comparison - -The framework provides tools to compare correlated fitness surfaces with adaptive landscapes: - -$$ -\text{Comparison} = \text{Correlated Fitness}(\mathbf{z}) \; \text{vs} \; \text{Adaptive Landscape}(\bar{\mathbf{z}}) -$$ - -This comparison highlights the difference between: - -- **Empirical selection** (individual-level fitness) -- **Theoretical evolutionary potential** (population-level mean fitness) - -**File:** `compare_fitness_surfaces.R` - ---- - -## 3. Framework Structure - -### 3.1 Core Scripts and Their Roles - -| Script | Purpose | Key Functions | Mathematical Component | -|--------|--------|--------------|------------------------| -| `prepare_selection_data.R` | Data preprocessing | Standardization, relative fitness, NA handling | $z_i = \frac{x_i - \bar{x}}{s_x}$, $w_i = \frac{W_i}{\bar{W}}$ | -| `detect_family.R` | Fitness type detection | Binary vs continuous | $W_i \in \{0,1\}$ vs $W_i \in \mathbb{R}^+$ | -| `selection_differential.R` | Selection differential | $S = \text{Cov}(z, w)$ | $S = \mathbb{E}[(z - \bar{z})(w - \bar{w})]$ | -| `selection_coefficients.R` | Main wrapper | Complete analysis | Gradient estimation | -| `analyze_linear_selection.R` | Linear gradients | Regression | $w = \alpha + \boldsymbol{\beta}^T \mathbf{z} + \varepsilon$ | -| `analyze_nonlinear_selection.R` | Quadratic gradients | $z^2$ + interactions | $w = \alpha + \boldsymbol{\beta}^T\mathbf{z} + \frac{1}{2}\mathbf{z}^T\boldsymbol{\gamma}\mathbf{z} + \varepsilon$ | -| `analyze_disruptive_selection.R` | Single-trait quadratic | Stabilizing/disruptive test | $\gamma_{ii} = 2\beta_{ii}$ | -| `extract_results.R` | Result extraction | Coefficient parsing | $\beta$, $\gamma$ | -| `univariate_spline.R` | 1D fitness | GAM spline | $w = \alpha + s(z) + \varepsilon$ | -| `correlated_fitness_surface.R` | 2D fitness | GAM / TPS | $w = \alpha + f(z_1, z_2) + \varepsilon$ | -| `adaptive_landscape.R` | Adaptive landscape | Simulation | $\bar{W} = g(\bar{z}_1, \bar{z}_2)$ | -| `compare_fitness_surfaces.R` | Comparison | Surface contrast | Individual vs population | -| `plot_correlated_fitness.R` | Visualization | Contour plots | 2D fitness | -| `plot_univariate_fitness.R` | Visualization | Line + CI | $w \pm 1.96 \times \text{SE}$ | -| `plot_adaptive_landscape.R` | Visualization | Population surface | $\bar{W}(\bar{z})$ | - -### 3.2 Function Dependencies - -```{r, message=FALSE} -library(DiagrammeR) - -grViz(" -digraph workflow { - - graph [layout = dot, rankdir = TB, fontname = 'Helvetica', fontsize = 10] - node [fontname = 'Helvetica', fontsize = 9] - edge [fontname = 'Helvetica', fontsize = 8] - - # ===================== - # DATA PREPARATION - # ===================== - subgraph cluster_data { - label = 'DATA PREPARATION' - style = filled - fillcolor = '#E8F4FD' - color = '#2C7FB8' - - prep [label = 'prepare_selection_data.R\n- z = (x - μ)/σ\n- w = W / W̄\n- NA handling', fillcolor = '#D9EAF7', shape = box] - detect [label = 'detect_family.R\n- Binary vs continuous\n- 0/1 detection', fillcolor = '#D9EAF7', shape = box] - - prep -> detect [label = 'prepared data', color = '#2C7FB8'] - } - - # ===================== - # SELECTION GRADIENTS - # ===================== - subgraph cluster_selection { - label = 'SELECTION GRADIENT ESTIMATION' - style = filled - fillcolor = '#FEF5E7' - color = '#E67E22' - - coeff [label = 'selection_coefficients.R\nMain wrapper\nIntegrates all methods', fillcolor = '#FCE9CF', shape = box] - - linear [label = 'analyze_linear_selection.R\nw ~ β₁z₁ + β₂z₂\nType III ANOVA\nConvergence checks', fillcolor = '#FCE9CF', shape = box] - nonlinear [label = 'analyze_nonlinear_selection.R\nw = β₁z₁ + β₂z₂\n+ ½γ₁₁z₁² + ½γ₂₂z₂²\n+ γ₁₂z₁z₂\nVIF checks', fillcolor = '#FCE9CF', shape = box] - - extract [label = 'extract_results.R\nβ (linear)\nγ = 2β_quad\nγ_ij = β_interaction', fillcolor = '#FCE9CF', shape = box] - diff [label = 'selection_differential.R\nS = Cov(z, w)\n= mean(z × w) when z standardized', fillcolor = '#FCE9CF', shape = box] - disrupt [label = 'analyze_disruptive_selection.R\nSingle trait: w ~ z + z²\nγ = 2β_quad\nγ > 0: disruptive\nγ < 0: stabilizing', fillcolor = '#FCE9CF', shape = box] - - coeff -> linear [label = 'multivariate', color = '#E67E22'] - coeff -> nonlinear [label = 'multivariate', color = '#E67E22'] - coeff -> disrupt [label = 'univariate', color = '#E67E22'] - - linear -> extract [label = 'coefficients', color = '#E67E22'] - nonlinear -> extract [label = 'coefficients', color = '#E67E22'] - disrupt -> extract [label = 'coefficients', color = '#E67E22'] - - extract -> diff [label = 'combined results', color = '#E67E22'] - } - - # ===================== - # FITNESS SURFACES - # ===================== - subgraph cluster_surface { - label = 'NONPARAMETRIC FITNESS SURFACES' - style = filled - fillcolor = '#E8F8F5' - color = '#1ABC9C' - - uni [label = 'univariate_spline.R\nw = α + s(z) + ε\nGAM with mgcv::gam()\nk = basis dimension', fillcolor = '#D5F5E3', shape = box] - uni_plot [label = 'plot_univariate_fitness.R\nLine plot\n95% confidence bands\nw ± 1.96 × SE', fillcolor = '#D5F5E3', shape = box] - - corr [label = 'correlated_fitness_surface.R\nw = α + f(z₁,z₂) + ε\nMethod: GAM (binary)\nMethod: TPS (continuous)\nReturns grid with .fit', fillcolor = '#D5F5E3', shape = box] - corr_plot [label = 'plot_correlated_fitness.R\nContour plots\nEnhanced: + original data\nOptimal point (yellow)', fillcolor = '#D5F5E3', shape = box] - - uni -> uni_plot [label = 'grid with fit/lwr/upr', color = '#1ABC9C'] - corr -> corr_plot [label = 'grid with .fit', color = '#1ABC9C'] - } - - # ===================== - # ADAPTIVE LANDSCAPE - # ===================== - subgraph cluster_adaptive { - label = 'ADAPTIVE LANDSCAPE (Wrightian)' - style = filled - fillcolor = '#FDEDEC' - color = '#C0392B' - - adapt [label = 'adaptive_landscape.R\nW̄ = g(z̄₁,z̄₂)\nPopulation mean fitness\nSimulation: mvrnorm(n, μ = z̄, Σ = P)\nReturns grid with .mean_fit', fillcolor = '#FADBD8', shape = box] - adapt_plot [label = 'plot_adaptive_landscape.R\nContour plots\n3D perspective\nOptimum population phenotype', fillcolor = '#FADBD8', shape = box] - - adapt -> adapt_plot [label = 'grid with .mean_fit', color = '#C0392B'] - } - - # ===================== - # COMPARISON & INFERENCE - # ===================== - subgraph cluster_compare { - label = 'COMPARISON & INFERENCE' - style = filled - fillcolor = '#EBF5FB' - color = '#2980B9' - - compare [label = 'compare_fitness_surfaces.R\nSide-by-side plots\nOverlay comparison\nCorrelation between surfaces', fillcolor = '#D4E6F1', shape = box] - boot [label = 'bootstrap_selection.R\nBootstrap CI for gradients\nResampling with replacement\nReturns: confidence intervals', fillcolor = '#D4E6F1', shape = box] - } - - # ===================== - # FLOW CONNECTIONS - # ===================== - detect -> coeff [label = 'fitness type', color = '#7F8C8D', penwidth = 2] - - # From selection gradients to surfaces - extract -> uni [label = 'gradients', color = '#7F8C8D', style = dashed] - extract -> corr [label = 'gradients', color = '#7F8C8D', style = dashed] - - # Correlated fitness feeds adaptive landscape - corr -> adapt [label = 'fitted model', color = '#C0392B', penwidth = 2, style = bold] - - # Comparison - corr -> compare [label = 'correlated surface', color = '#2980B9', style = dashed] - adapt -> compare [label = 'adaptive landscape', color = '#2980B9', style = dashed] - - # Additional connections - diff -> compare [label = 'selection strength', color = '#7F8C8D', style = dotted] - - # ===================== - # LEGEND - # ===================== - subgraph cluster_legend { - label = 'LEGEND' - style = filled - fillcolor = '#F9F9F9' - color = '#BDC3C7' - - legend1 [label = 'Solid arrows: Data flow', fillcolor = '#F9F9F9', shape = plaintext] - legend2 [label = 'Dashed arrows: Information flow', fillcolor = '#F9F9F9', shape = plaintext] - legend3 [label = 'Dotted arrows: Optional analysis', fillcolor = '#F9F9F9', shape = plaintext] - legend4 [label = 'Bold arrows: Key dependency', fillcolor = '#F9F9F9', shape = plaintext] - - legend1 -> legend2 -> legend3 -> legend4 [style = invis] - } -} -") -``` ---- - -## 4. Installation and Requirements - -### 4.1 Required Packages, functions and scripts - -### Required Packages - -```{r, message=FALSE, warning=FALSE} -required_packages <- c( - "mgcv", # GAM models - "fields", # Thin plate splines - "MASS", # multivariate normal simulation - "Matrix", # matrix operations - "ggplot2", # plotting - "dplyr", # data manipulation - "tidyr", # data tidying - "here", # path handling - "ggrepel", # labels - "viridis", # color scales - "patchwork" -) - -missing <- required_packages[!required_packages %in% installed.packages()[, "Package"]] - -if (length(missing) > 0) { - install.packages(missing) -} - -invisible(lapply(required_packages, library, character.only = TRUE)) -``` - -### Required functions and scripts -```{r, message=FALSE, warning=FALSE} -function_files <- c( - "compare_fitness_surfaces.R", - "correlated_fitness_surface.R", - "detect_family.R", - "extract_results.R", - "selection_analysis.R", - "selection_differential.R", - "selection_coefficients.R", - "univariate_spline.R" -) - -scripts_files <- c( - "1_prepare_selection_data.R", - "2_linear_selection_analysis.R", - "3_nonlinear_selection_analysis.R", - "4_disruptive_selection_analysis.R", - "5_adaptive_landscape_analysis.R" -) - -plotting_files <- c( - "plot_adaptive_landscape.R", - "plot_correlated_fitness.R", - "plot_univariate_fitness.R", - "plot_fitness_surfaces_comparison.R" -) - -all_files <- list( - functions = list(path = c("R", "functions"), files = function_files), - scripts = list(path = c("R", "scripts"), files = scripts_files), - plotting = list(path = c("R", "plotting"), files = plotting_files) -) - -for (group in all_files) { - for (f in group$files) { - file_path <- do.call(here::here, as.list(c(group$path, f))) - - if (file.exists(file_path)) { - source(file_path) - cat("Loaded:", file_path, "\n") - } else { - cat("Missing:", file_path, "\n") - } - } -} -``` - -### 4.2 Package Descriptions - -| Package | Purpose | -|---------|--------| -| `mgcv` | Generalized additive models (GAMs) for flexible spline-based fitness estimation | -| `fields` | Thin-plate spline (TPS) interpolation for bivariate fitness surfaces | -| `MASS` | Multivariate normal simulation (`mvrnorm`) for adaptive landscape generation | -| `Matrix` | Matrix operations and positive-definite corrections (`nearPD`) | -| `car` | Type III ANOVA and variance inflation factor (VIF) diagnostics | -| `ggplot2` | Visualization of fitness functions and contour surfaces | -| `dplyr` | Data manipulation and transformation (filtering, summarizing) | -| `tidyr` | Data reshaping (long/wide format conversion) | -| `ggrepel` | Improved text labeling in plots (avoids overlap) | -| `viridis` | Perceptually uniform color scales for scientific visualization | -| `here` | Robust and reproducible file path management | - ---- - -## 5. Detailed Function Reference - -### 5.1 `prepare_selection_data()` - -**Purpose:** Preprocesses raw data for selection analysis. - -```R -prepare_selection_data( - data, # Data frame - fitness_col, # Name of fitness column (character) - trait_cols, # Vector of trait column names - standardize = TRUE, # Standardize traits to mean 0, SD 1 - add_relative = TRUE, # Add relative fitness column - na_action = c("warn", "drop", "none"), # How to handle NAs - name_relative = "relative_fitness" # Name for relative fitness column -) -``` - -**Returns:** Modified data frame with: -- Standardized traits (if `standardize = TRUE`) -- Relative fitness column (if `add_relative = TRUE`) -- Potentially dropped NA rows (if `na_action = "drop"`) - -**Example:** - -```{r, message=FALSE, warning=FALSE} -set.seed(42) - -raw_data <- data.frame( - survival = rbinom(100, 1, 0.6), - size = rnorm(100, 10, 2), - color = rnorm(100, 5, 1) -) - -prepared <- prepare_selection_data( - data = raw_data, - fitness_col = "survival", - trait_cols = c("size", "color"), - standardize = TRUE, - add_relative = TRUE, - na_action = "drop" -) - -cat("size:", nrow(prepared), "\n") -head(prepared) -``` - -### 5.2 `detect_family()` - -**Purpose:** Automatically determines whether fitness is binary or continuous. - -```R -detect_family(y) # y = fitness vector -``` - -**Logic:** -- **Binary** if: ≤ 2 unique values, all in {0,1}, and n ≥ 10 -- **Continuous** otherwise - -**Returns:** List with: -- `$type`: "binary" or "continuous" -- `$family`: Appropriate GLM family object - -**Example:** - -```{r, message=FALSE, warning=FALSE} -# Binary fitness -fitness_binary <- c(1, 0, 1, 1, 0, 1) -detect_family(fitness_binary) - -# Continuous fitness -fitness_cont <- c(2.3, 4.1, 3.2, 5.6, 1.8) -detect_family(fitness_cont) -``` - -### 5.3 `selection_differential()` - -**Purpose:** Calculates the selection differential ($S$) for a single trait. - -```R -selection_differential( - data, - fitness_col, - trait_col, - assume_standardized = TRUE, # Whether trait is already standardized - use_relative = TRUE # Use relative fitness -) -``` - -**Formula:** $ -S = \text{Cov}(z, w) -$ - -When traits are standardized ($\bar{z} = 0$), this simplifies to: -$$S = \mathbb{E}(z \times w) = \frac{1}{n}\sum_{i=1}^n z_i w_i$$ - -**Example:** -```{r, message=FALSE, warning=FALSE} -# Calculate selection differential for size -S_size <- selection_differential( - data = prepared, - fitness_col = "relative_fitness", - trait_col = "size", - assume_standardized = TRUE, - use_relative = TRUE -) - -# Calculate for color -S_color <- selection_differential( - data = prepared, - fitness_col = "relative_fitness", - trait_col = "color", - assume_standardized = TRUE, - use_relative = TRUE -) - -cat("Selection Differentials (S):\n") -cat("Size :", round(S_size, 4), "\n") -cat("Color:", round(S_color, 4), "\n") -``` - -### 5.4 `analyze_linear_selection()` - -**Purpose:** Estimates linear selection gradients ($\boldsymbol{\beta}$) with comprehensive diagnostics. - -```R -analyze_linear_selection( - data, - fitness_col, - trait_cols, - fitness_type # "binary" or "continuous" -) -``` - -**Features:** -- Sample size checks (warning if n < 10) -- Missing data handling -- Convergence checks for GLM -- Type III ANOVA (if `car` package available) -- Separation detection for binary models - -**Returns:** List containing: -- `$model`: Fitted model object (lm or glm) -- `$summary`: Model summary -- `$anova`: Type III ANOVA table (if available) - -**Example:** - -```{r, message=FALSE, warning=FALSE} -linear_results <- analyze_linear_selection( - data = prepared, - fitness_col = "relative_fitness", - trait_cols = c("size", "color"), - fitness_type = "continuous" -) - -# View coefficients -summary(linear_results$model) -``` - -### 5.5 `analyze_nonlinear_selection()` - -**Purpose:** Estimates quadratic ($\gamma_{ii}$) and correlational ($\gamma_{ij}$) selection gradients. - -```R -analyze_nonlinear_selection( - data, - fitness_col, - trait_cols, - fitness_type -) -``` - -**Model specification:** Automatically constructs: -- Linear terms: $z_i$ -- Quadratic terms: $z_i^2$ -- Interaction terms: $z_i \times z_j$ (for i < j) - -**Diagnostics:** -- Sample size checks (n < 20 warning) -- Variance inflation factors (VIF > 10 warning) -- Convergence monitoring for GLM - -**Example:** -```{r, message=FALSE, warning=FALSE} -nonlinear_results <- analyze_nonlinear_selection( - data = prepared, - fitness_col = "relative_fitness", - trait_cols = c("size", "color"), - fitness_type = "continuous" -) - -# Extract quadratic term for size (multiply by 2 for gamma) -coef(summary(nonlinear_results$model))["I(size^2)", ] -``` - -### 5.6 `analyze_disruptive_selection()` - -**Purpose:** Specialized function for detecting disruptive or stabilizing selection on a single trait. - -```R -analyze_disruptive_selection( - data, - fitness_col, - trait_col, - fitness_type = c("binary", "continuous"), - standardize = TRUE -) -``` - -**Model:** $w \sim z + z^2$ - -**Returns:** Data frame with: -- Linear term ($\beta$): Directional selection -- Quadratic term ($\gamma = 2 \times b_2$): Disruptive (positive) or stabilizing (negative) - -**Example:** -```{r, message=FALSE, warning=FALSE} -disruptive_test <- analyze_disruptive_selection( - data = prepared, - fitness_col = "relative_fitness", - trait_col = "size", - fitness_type = "continuous" -) - -print(disruptive_test) -``` - -### 5.7 `univariate_spline()` - -**Purpose:** Fits a flexible nonparametric fitness function using GAMs. - -```R -univariate_spline( - data, - fitness_col, - trait_col, - fitness_type = c("binary", "continuous"), - k = 10 # Basis dimension (smoothness parameter) -) -``` - -**Technical details:** -- Uses penalized regression splines with REML smoothing parameter selection -- For binary fitness: binomial GAM with logit link -- For continuous: Gaussian GAM -- Returns predictions with 95% confidence intervals - -**Example:** -```{r, message=FALSE, warning=FALSE, cache=FALSE} -n_unique <- length(unique(prepared$size[complete.cases(prepared$size)])) -n_obs <- sum(complete.cases(prepared$size)) - -# k should be: -# - At most n_unique - 1 (can't have more basis than unique values) -# - At most n_obs / 2 (to avoid overfitting) -# - At least 3 (minimum for smoothness) -# - At most 8 (cap for interpretability) - -k_val <- min( - 8, - n_unique - 1, - floor(n_obs / 2) # Avoid overfitting -) - -k_val <- max(3, k_val) - -cat("Fitting spline with:\n") -cat(" - Unique values:", n_unique, "\n") -cat(" - Observations:", n_obs, "\n") -cat(" - k =", k_val, "\n") - -spline_fit <- univariate_spline( - data = prepared, - fitness_col = "survival", - trait_col = "size", - fitness_type = "binary", - k = k_val -) - -head(spline_fit$grid) -``` - -### 5.8 `plot_univariate_fitness()` - -**Purpose:** Visualizes univariate correlated fitness functions with confidence bands. - -```R -plot_univariate_fitness( - uni, # Output from univariate_spline() - trait_col, - title = NULL -) -``` - -**Returns:** ggplot2 object with line plot and 95% confidence bands. - -**Example:** -```{r, message=FALSE, warning=FALSE, fig.align="center", out.width="80%", fig.cap="Figure 1. Correlated fitness function for body size"} -p <- plot_univariate_fitness( - spline_fit, - "size", - title = "Correlated Fitness Function: Body Size" -) -print(p) -``` - - -### 5.8 `correlated_fitness_surface()` - -**Purpose:** Estimates 2D fitness surfaces using thin-plate splines (continuous) or GAMs (binary). - -```R -correlated_fitness_surface( - data, - fitness_col, - trait_cols, # Exactly 2 traits - grid_n = 60, # Grid resolution (grid_n × grid_n points) - method = "auto", # "auto", "gam", or "tps" - scale_traits = TRUE, - k = 30 # Basis dimension for GAM method -) -``` - -**Method selection:** -- `"tps"`: Uses `fields::Tps()` for continuous fitness (spline-based) -- `"gam"`: Uses `mgcv::gam()` with tensor product smooth (works for both) -- `"auto"`: Chooses based on fitness type (GAM for binary, TPS for continuous) - -**Returns:** List containing: -- `$model`: Fitted model object -- `$grid`: Data frame with trait values and predicted fitness -- `$method`: Method used -- `$data_type`: "binary" or "continuous" - -**Example:** -```{r, message=FALSE, warning=FALSE} -surface <- correlated_fitness_surface( - data = prepared, - fitness_col = "relative_fitness", - trait_cols = c("size", "color"), - method = "gam", - scale_traits = TRUE -) - -# Find optimum (maximum fitness) -optimum <- surface$grid[which.max(surface$grid$.fit), ] -print(optimum) -``` - -### 5.9 `plot_correlated_fitness()` - -**Purpose:** Visualize 2D fitness surfaces with contour plots. -```R -plot_correlated_fitness( - tps, # Output from univariate_spline() - trait_col, - bins - title = NULL -) - -p <- plot_correlated_fitness_enhanced( - tps, correlated_fitness_surface - trait_cols, - original_data, - fitness_col, - bins = 12 -) -``` - -**Example:** -```{r, message=FALSE, warning=FALSE, fig.width=8, fig.height=6, fig.cap="Correlated fitness surface for size and color"} -p <- plot_correlated_fitness( - tps = surface, - trait_cols = c("size", "color"), - bins = 12 -) - -print(p) -``` - -```{r, message=FALSE, warning=FALSE, fig.width=8, fig.height=6, fig.cap="Correlated fitness surface with original data points"} -p <- plot_correlated_fitness_enhanced( - tps = surface, - trait_cols = c("size", "color"), - original_data = prepared, - fitness_col = "relative_fitness", - bins = 12 -) - -print(p) -``` - -### 5.10 `adaptive_landscape()` - -**Purpose:** Calculates the Wrightian adaptive landscape, which is a population-level concept distinct from correlated fitness surfaces. - -```R -adaptive_landscape( - data, # Individual-level data frame - fitness_model, # Fitted model from correlated_fitness_surface() - trait_cols, # Character vector of length 2 with trait names - group_col = NULL, # Optional grouping column (e.g., "species") - population_variance = NULL,# Within-population variance-covariance matrix - simulation_n = 1000, # Number of individuals to simulate per grid point - grid_n = 50, # Grid resolution (grid_n × grid_n) - custom_range = NULL # Optional custom range for population means -) -``` - -**Calculation Steps:** -- 1. Create grid of possible population means ($\bar{z}_1$, $\bar{z}_2$) across the trait range -- 2. Estimate within-population variance from the data -- 3. Simulate individuals around each population mean: $\mathbf{z} \sim \mathcal{N}(\bar{\mathbf{z}}, \mathbf{P})$ -- 4. Predict fitness for each simulated individual using the fitted model -- 5. Calculate mean fitness $\bar{W} = \frac{1}{N}\sum \hat{w}_{\text{ind}}$ -- 6. Find optimum - the population mean that maximizes $\bar{W}$ - -**Returns:** -- `$grid`: Population means with mean fitness -- `$optimum`: Population mean with highest fitness -- `$actual_population_means`: Actual means (if group_col provided) - -**Example:** -```{r, dev="png", fig.show="hold"} -landscape <- adaptive_landscape( - data = prepared, - fitness_model = surface$model, - trait_cols = c("size", "color"), - grid_n = 50, - simulation_n = 1000 -) - -landscape$optimum -``` - - -### 5.11 `plot_adaptive_landscape.R` - -**Purpose:** Creates a 2D contour map showing how mean fitness varies with population mean phenotypes. - -```R -plot_adaptive_landscape( - landscape, # Output from adaptive_landscape() - trait_cols, # Two trait column names - original_data = NULL, # Optional original data for overlaying points - group_col = NULL, # Optional grouping column for labels - bins = 12, # Number of contour bins - show_optimum = TRUE, # Show optimal population mean (yellow star) - show_actual_means = TRUE # Show actual population means (red points) -) - -plot_adaptive_landscape_3d( - landscape, # Output from adaptive_landscape() - trait_cols, # Two trait column names - theta = -30, # Azimuthal rotation angle - phi = 30, # Colatitude tilt angle - grid_n = 150 # Resolution for interpolation (higher = smoother) -) -``` - -**Example:** -```{r, message=FALSE, warning=FALSE, fig.width=8, fig.height=6, fig.cap="Adaptive landscape showing mean fitness as function of population mean size and color"} -p <- plot_adaptive_landscape( - landscape = landscape, - trait_cols = c("size", "color"), - bins = 12 -) - -print(p) -``` - -```{r, message=FALSE, warning=FALSE, fig.width=10, fig.height=7, fig.cap="3D adaptive landscape showing the shape of mean fitness"} -p <- plot_adaptive_landscape_3d( - landscape = landscape, - trait_cols = c("size", "color"), - theta = -30, - phi = 30, - grid_n = 300 -) - -print(p) -``` - - -### 5.12 `selection_coefficients()` - -**Purpose:** Main wrapper function that runs a complete selection analysis. - -```R -selection_coefficients( - data, - fitness_col, - trait_cols, - fitness_type = c("auto", "binary", "continuous"), - standardize = TRUE, - use_relative_for_fit = TRUE -) -``` - -**Workflow:** -1. Prepares data (standardization, relative fitness) -2. Detects fitness type (if `auto`) -3. Runs linear selection analysis -4. Runs nonlinear selection analysis -5. Extracts all coefficients into a single table - -**Returns:** Data frame with columns: -- `Term`: Coefficient name (e.g., "size", "size²", "size×color") -- `Type`: "Linear", "Quadratic", or "Correlational" -- `Beta_Coefficient`: Estimated selection gradient -- `Standard_Error`: Standard error of estimate -- `P_Value`: Statistical significance -- `Variance`: Square of standard error - -**Example:** -```{r, message=FALSE, warning=FALSE} -results_binary <- selection_coefficients( - data = prepared, - fitness_col = "survival", # Binary 0/1 - trait_cols = c("size", "color"), # Only available traits - fitness_type = "binary", - standardize = TRUE -) - -print(results_binary) -``` - -### 5.13 Extraction Functions - -Internal functions used by `selection_coefficients()`: - -- `extract_linear_coefficients(trait_cols, results)` -- `extract_quadratic_coefficients(trait_cols, results)` -- `extract_interaction_coefficients(trait_cols, results)` - -These functions safely extract coefficients from model objects, handling different column names and missing terms. - -### 5.14 `selection_analysis()` - -**Purpose:** serve as a wrapper function that combines everything in one call. - -```{r, message=FALSE, warning=FALSE} -analysis <- selection_analysis( - data = prepared, - fitness_col = "survival", - trait_cols = c("size", "color") -) - -analysis$coefficients_table -analysis$prepared_data -analysis$fitness_type -analysis$models$linear -analysis$models$nonlinear -``` - - -### 5.15 `compare_fitness_surfaces()` - -**Purpose:** serve as a wrapper function that combines everything in one call. - -```{r, message=FALSE, warning=FALSE} -comparison <- compare_fitness_surfaces_data( - correlated_surface = surface, - adaptive_landscape = landscape, - trait_cols = c("size", "color") -) - -comparison$summary_stats -``` - -```{r, message=FALSE, warning=FALSE, fig.width=12, fig.height=5, fig.cap="Side-by-side comparison"} -plots <- plot_fitness_surfaces_comparison( - comparison_data = comparison, - bins = 15 -) - -print(plots$overlay) -``` - -```{r, message=FALSE, warning=FALSE, fig.width=12, fig.height=5, fig.cap="Side-by-side comparison"} -plots <- plot_fitness_surfaces_comparison( - comparison_data = comparison, - bins = 15 -) - -print(plots$side_by_side) -``` ---- - -## 6. Interpretation Guide - -### 6.1 Statistical Significance - -| P-value | Evidence | -|---------|----------| -| < 0.001 | Strong evidence of selection | -| 0.001-0.01 | Moderate evidence | -| 0.01-0.05 | Weak evidence | -| > 0.05 | No significant selection detected | - -### 6.2 Selection Types - -**Linear Selection ($\beta$):** - -| $\beta$ sign | Interpretation | -|--------------|----------------| -| Positive (+) | Selection favors larger trait values | -| Negative (-) | Selection favors smaller trait values | -| Zero (0) | No directional selection | - -**Quadratic Selection ($\gamma$):** - -| $\gamma$ sign | Interpretation | Shape | -|---------------|----------------|-------| -| Negative (-) | Stabilizing selection | ∩-shaped | -| Positive (+) | Disruptive selection | ∪-shaped | -| Zero (0) | No nonlinear selection | Linear | - -**Correlational Selection ($\gamma_{ij}$):** - -| $\gamma_{ij}$ sign | Interpretation | -|--------------------|----------------| -| Positive (+) | Selection favors positive correlation (both traits high or both low) | -| Negative (-) | Selection favors negative correlation (one high, one low) | -| Zero (0) | Traits evolve independently | - -### 6.3 Effect Sizes - -**For standardized traits ($\mu=0, \sigma=1$):** - -| $|\beta|$ | Effect size | -|-----------|-------------| -| < 0.1 | Weak selection | -| 0.1 - 0.3 | Moderate selection | -| > 0.3 | Strong selection | - -### 6.4 Example Interpretations - -``` -Scenario 1: β_size = 0.25, p = 0.001 -→ "Body size experiences significant positive directional selection. - A one-standard-deviation increase in size increases relative fitness by 0.25 units." - -Scenario 2: γ_size = -0.15, p = 0.02 -→ "Body size shows significant stabilizing selection. - Intermediate sizes have highest fitness; extremes are disadvantageous." - -Scenario 3: γ_size x beak = 0.32, p = 0.004 -→ "Significant positive correlational selection between size and beak depth. - Selection favors individuals that are either both large or both small." -``` - ---- - -## 7. Troubleshooting and Common Issues - -### 7.1 Sample Size Recommendations - -| Analysis | Minimum n | Recommended n | -|----------|-----------|---------------| -| Linear selection (continuous) | 10 | > 30 | -| Linear selection (binary) | 20 per group | > 50 per group | -| Nonlinear selection | 20 | > 100 | -| Bivariate TPS | 30 | > 200 | - -### 7.2 Convergence Issues in Binary Models - -**Symptoms:** -- Very large coefficients (> 10) -- Extremely large standard errors -- Warning about "complete separation" - -**Solutions:** -```R -# 1. Check for complete separation -table(data$fitness, cut(data$trait, 5)) - -# 2. Use Firth's penalized likelihood -if (!require("logistf")) install.packages("logistf") -library(logistf) -fit <- logistf(fitness ~ trait, data = data) - -# 3. Collect more data -# 4. Simplify model (fewer traits) -``` - -### 7.3 Missing Data Handling - -```R -# Check missing data pattern -library(naniar) -gg_miss_upset(data) - -# Option 1: Drop rows with missing (if < 5%) -prepared <- prepare_selection_data(..., na_action = "drop") - -# Option 2: Impute missing values -library(mice) -imp <- mice(data, m = 5) -data_complete <- complete(imp, 1) - -# Option 3: Use na_action = "warn" to investigate -prepared <- prepare_selection_data(..., na_action = "warn") -``` - -### 7.4 Multicollinearity - -High correlations between traits can inflate standard errors: - -```R -# Check correlations -cor(data[, trait_cols]) - -# Calculate VIF -if (requireNamespace("car", quietly = TRUE)) { - vif_vals <- car::vif(model) - # VIF > 10 indicates problematic collinearity -} -``` - -**Solutions:** -- Use ridge regression -- Collect more data - ---- - -## 8. Output Formats and Reporting - -### 8.1 Table Format for Publications - -```R - -library(knitr) - -results_table <- results %>% - mutate( - Beta = sprintf("%.3f", Beta_Coefficient), - SE = sprintf("%.3f", Standard_Error), - P = case_when( - P_Value < 0.001 ~ "<0.001", - P_Value < 0.01 ~ sprintf("%.3f", P_Value), - TRUE ~ sprintf("%.3f", P_Value) - ), - Sig = case_when( - P_Value < 0.001 ~ "***", - P_Value < 0.01 ~ "**", - P_Value < 0.05 ~ "*", - TRUE ~ "" - ) - ) %>% - select(Term, Type, Beta, SE, P, Sig) - -kable(results_table, caption = "Table 1. Selection gradients (±SE)") -``` - -### 8.2 Visualization for Reports - -```R -library(ggplot2) - -ggplot(results, aes(x = Term, y = Beta_Coefficient, fill = Type)) + - geom_col(position = position_dodge()) + - geom_errorbar( - aes( - ymin = Beta_Coefficient - 1.96 * Standard_Error, - ymax = Beta_Coefficient + 1.96 * Standard_Error - ), - width = 0.2, position = position_dodge(0.9) - ) + - geom_hline(yintercept = 0, linetype = "dashed") + - labs(x = "Trait", y = "Selection Gradient (β or γ)") + - theme_minimal() + - theme(axis.text.x = element_text(angle = 45, hjust = 1)) -``` - ---- - -## 9. References - -1. Lande, R., & Arnold, S. J. (1983). The measurement of selection on correlated characters. *Evolution*, 37(6), 1210-1226. - -2. Arnold, S. J., & Wade, M. J. (1984). On the measurement of natural and sexual selection: Theory. *Evolution*, 38(4), 709-719. - -3. Brodie, E. D., Moore, A. J., & Janzen, F. J. (1995). Visualizing and quantifying natural selection. *Trends in Ecology & Evolution*, 10(8), 313-318. - -4. Schluter, D. (1988). Estimating the form of natural selection on a quantitative trait. *Evolution*, 42(5), 849-861. - -5. Wood, S. N. (2017). Generalized Additive Models: An Introduction with R (2nd ed.). Chapman and Hall/CRC. - -6. Kingsolver, J. G., et al. (2001). The strength of phenotypic selection in natural populations. *The American Naturalist*, 157(3), 245-261. - -7. Hereford, J., Hansen, T. F., & Houle, D. (2004). Comparing strengths of directional selection: How strong is strong? *Evolution*, 58(10), 2133-2143. -