StreamCatTools 0.11.0 release

.github/workflows/coverage.yaml

@@ -30,6 +30,7 @@ jobs:
         with:
           extra-packages: any::covr, any::xml2
           needs: coverage
+          cache-version: 2  # Increment this to bust the cache
 
       - name: Test coverage
         run: |

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: StreamCatTools
 Type: Package
 Title: 'StreamCatTools'
-Version: 0.10.0
+Version: 0.11.0
 Authors@R: c(person(given = "Marc", 
                     family = "Weber", 
                     role = c("aut", "cre"), 
@@ -52,7 +52,7 @@ Imports:
     patchwork,
     cowplot,
     tigris,
-    ggplot2
+    ggplot2,
 Suggests: 
   dplyr,
   mapview,
@@ -67,7 +67,12 @@ Suggests:
   stringr,
   purrr,
   lifecycle,
-  tidyselect
+  tidyselect,
+  DBI, 
+  duckdb,
+  tictoc,
+  stats,
+  wk
 Encoding: UTF-8
 URL: https://usepa.github.io/StreamCatTools/, https://github.com/USEPA/StreamCatTools
 BugReports: https://github.com/USEPA/StreamCatTools/issues

NAMESPACE

@@ -7,7 +7,7 @@ export(lc_get_metric_names)
 export(lc_get_nlcd)
 export(lc_get_nni)
 export(lc_get_params)
-export(lc_nlcd)
+export(lc_get_watershed)
 export(lc_plotnni)
 export(sc_fullname)
 export(sc_get_comid)
@@ -16,7 +16,6 @@ export(sc_get_metric_names)
 export(sc_get_nlcd)
 export(sc_get_nni)
 export(sc_get_params)
-export(sc_nlcd)
 export(sc_plotnni)
 import(ggpattern)
 import(ggplot2)

NEWS.md

@@ -1,3 +1,11 @@
+# StreamCatTools 0.11.0
+
+-   Adds new `lc_get_watershed` function to return a lake watershed as an `sf`
+    feature for a LakeCat (NHDPlusV2 Waterbody) COMID from an S3-hosted, 
+    HUC2-partitioned GeoParquet dataset
+-   Uses optional HUC2 query as well as retries, multi-threading and `duckdb`
+    to speed up retrieval of spatial data from AWS S3 bucket
+
 # StreamCatTools 0.10.0
 
 -   Adds new functions `sc_get_nni()` and `lc_get_nni()` for ease of access to 

R/lc_get_data.R

@@ -191,6 +191,21 @@ lc_get_data <- function(comid = NULL,
 #' @param comid Return metric information for specific COMIDs
 #' Syntax: comid=<comid1>,<comid2>
 #'
+#' @param state Return metric information for COMIDs within a specific state. Use a state's abbreviation to
+#' query for a given state.
+#' Syntax: state=<state1>,<state2>
+#'
+#' @param county Return metric information for COMIDs within a specific county.
+#' Users must use the FIPS code, not county name, as a way to disambiguate counties.
+#' Syntax: county=<county1>,<county1>
+#'
+#' @param region Return metric information for COMIDs within a specified hydroregion.
+#' Syntax: region=<regionid1>,<regionid2>
+#'
+#' @param conus Return all COMIDs in the conterminous United States.
+#' The default value is false.
+#' Values: true|false
+#'
 #' @param showAreaSqKm Return the area in square kilometers of a given area of interest.
 #' The default value is false.
 #' Values: true|false
@@ -207,7 +222,7 @@ lc_get_data <- function(comid = NULL,
 #' @examples
 #' \dontrun{
 #'
-#' df <- lc_nlcd(comid='23783629', year='2019', aoi='ws')  # Will show a deprecation warning
+#' df <- lc_get_nlcd(comid='23783629', year='2019', aoi='ws')  # Will show a deprecation warning
 #' 
 #' df <- lc_get_nlcd(comid='23783629', year='2019', aoi='ws')
 #' 
@@ -294,31 +309,6 @@ lc_get_nlcd <- function(year = '2019',
   return(final_df)
 }
 
-#' @rdname lc_get_nlcd
-#' @export
-#' @keywords internal
-lc_nlcd <- function(year = '2019',
-                    comid = NULL,
-                    aoi = NULL,
-                    showAreaSqKm = NULL,
-                    showPctFull = NULL,
-                    state = NULL,
-                    county = NULL,
-                    region = NULL,
-                    conus = NULL,
-                    countOnly = NULL) {
-  lifecycle::deprecate_warn("0.10.0", "lc_nlcd()", "lc_get_nlcd()")
-  lc_get_nlcd(year = '2019',
-              comid = NULL,
-              aoi = NULL,
-              showAreaSqKm = NULL,
-              showPctFull = NULL,
-              state = NULL,
-              county = NULL,
-              region = NULL,
-              conus = NULL,
-              countOnly = NULL)
-}
 
 #' @title Get NNI
 #' 
@@ -365,8 +355,8 @@ lc_nlcd <- function(year = '2019',
 #' }
 
 lc_get_nni <- function(year, aoi = NULL, comid = NULL,
-                    showAreaSqKm = TRUE, showPctFull = NULL,
-                    countOnly = NULL) {
+                       showAreaSqKm = TRUE, showPctFull = NULL,
+                       countOnly = NULL) {
   # year must be a character string.
   year_chr <-  as.character(year)
   # split multiple years supplied as a single string into
@@ -412,29 +402,29 @@ lc_get_nni <- function(year, aoi = NULL, comid = NULL,
   )
   # Vector of NNI metric names.
   nni <- c(
-      'n_leg_',
-      'n_ags_',
-      'n_ff_',
-      'n_uf_',
-      'n_cf_',
-      'n_cr_',
-      'n_hw_',
-      'n_lw_',
-      'p_leg_',
-      'p_ags_',
-      'p_ff_',
-      'p_uf_',
-      'p_cr_',
-      'p_hw_',
-      'p_lw_'
-    )
+    'n_leg_',
+    'n_ags_',
+    'n_ff_',
+    'n_uf_',
+    'n_cf_',
+    'n_cr_',
+    'n_hw_',
+    'n_lw_',
+    'p_leg_',
+    'p_ags_',
+    'p_ff_',
+    'p_uf_',
+    'p_cr_',
+    'p_hw_',
+    'p_lw_'
+  )
   # Add n_dep for available years
   ndep_year_vec <- year_vec[!year_vec %in% c('1987', '1988', '1989')]
   ndep_comb <- expand.grid('n_dep_', ndep_year_vec)
   ndep_mets <- paste0(ndep_comb$Var1,
-                     ndep_comb$Var2,
-                     collapse = ",",
-                     recycle0 = TRUE)
+                      ndep_comb$Var2,
+                      collapse = ",",
+                      recycle0 = TRUE)
   # Add p_dep for available years
   pdep_year_vec <- year_vec[!year_vec %in% c('1987', '1988', '1989', '1990', '1991', '1992', '1993', '1994', '1995', '1996',
                                              '2014', '2015', '2016', '2017')]
@@ -447,17 +437,17 @@ lc_get_nni <- function(year, aoi = NULL, comid = NULL,
   ww_year_vec <- year_vec[year_vec %in% c('1988', '1990', '1992', '1996', '2000', '2004', '2008', '2012')]
   ww_comb <- expand.grid(c('p_usgsww_', 'n_usgsww_'), ww_year_vec)
   ww_mets <- paste0(ww_comb$Var1,
-                      ww_comb$Var2,
-                      collapse = ",",
-                      recycle0 = TRUE)
+                    ww_comb$Var2,
+                    collapse = ",",
+                    recycle0 = TRUE)
   # Create a data frame of all NNI Metric and year combinations.
   all_comb <- expand.grid(nni, year_vec)
   # Concatenate the NLCD metric name with the supplied year(s) to create
   # valid metric names to submit to the API.
   nni_mets <- paste0(all_comb$Var1,
-                      all_comb$Var2,
-                      collapse = ",",
-                      recycle0 = TRUE)
+                     all_comb$Var2,
+                     collapse = ",",
+                     recycle0 = TRUE)
   # Combine all NNI metrics
   nni_mets_all <- paste0(nni_mets, ",", ndep_mets, ",", pdep_mets, ",", ww_mets)
 
@@ -472,5 +462,4 @@ lc_get_nni <- function(year, aoi = NULL, comid = NULL,
   )
   # End of function. Return a data frame.
   return(final_df)
-}
-
+}

R/lc_get_params.R

@@ -46,7 +46,7 @@ lc_get_params <- function(param = NULL) {
     } else if(param == 'variable_info') {
       params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |>
         httr2::req_perform() |>
-        httr2::resp_body_string() |>
+        httr2::resp_body_raw() |>
         readr::read_csv(show_col_types = FALSE) |>
         dplyr::select(-UUID,-DATE_DOWNLOADED,-METADATA) |>
         dplyr::rename(dataset=FINAL_TABLE,category=INDICATOR_CATEGORY,
@@ -57,14 +57,14 @@ lc_get_params <- function(param = NULL) {
     } else if(param == 'categories'){
       params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |>
         httr2::req_perform() |>
-        httr2::resp_body_string() |>
+        httr2::resp_body_raw() |>
         readr::read_csv(show_col_types = FALSE) |>
         dplyr::select(INDICATOR_CATEGORY)
       params <- sort(unique(params$INDICATOR_CATEGORY))
     } else if(param == 'datasets'){
       params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |>
         httr2::req_perform() |>
-        httr2::resp_body_string() |>
+        httr2::resp_body_raw() |>
         readr::read_csv(show_col_types = FALSE) |>
         dplyr::select(DSNAME)
       params <- sort(unique(params$DSNAME[!is.na(params$DSNAME)]))
@@ -80,7 +80,7 @@ lc_get_params <- function(param = NULL) {
     } else if(param == 'county'){
       params <- resp$county_options[[1]]
       params$fips <- as.character(params$fips)
-      params <- params |> dplyr::select(-fips_str)
+      params <- params |> dplyr::select(-dplyr::any_of("fips_str"))
       params$fips[nchar(params$fips) < 5] <- paste0('0',params$fips[nchar(params$fips) < 5])
       params <- params[with(params,order(state,county_name)),]
     }
@@ -168,7 +168,7 @@ lc_get_metric_names <- function(category = NULL,
   resp <- tryCatch({
     params <- httr2::request('https://api.epa.gov/StreamCat/lakes/variable_info') |>
     httr2::req_perform() |>
-    httr2::resp_body_string() |>
+    httr2::resp_body_raw() |>
     readr::read_csv(show_col_types = FALSE)
   },error = function(e) {
     message("An error occurred during req_perform(); the service may be down or function parameters may be mis-specified: ", e$message)