Updated iscamsummary

Author: VisruthSK

R/iscamsummary.R

@@ -16,17 +16,19 @@
 #' @examples
 #' set.seed(0)
 #' fake_data <- rnorm(30) # simulating some data
+#' groups <- sample(c("group1","group2"), 30, TRUE)
 #' summary(fake_data)
-#' summary(fake_data, sample(c("group1","group2"), 30, TRUE)) # with groups
+#' summary(fake_data, explanatory = groups, digits = 2) # with groups
 summary <- function(x, explanatory = NULL, digits = 3) {
   if (is.null(explanatory)) {
-    round(.getSummaryStats(x), digits)
+    output <- .getSummaryStats(x)
   } else {
-    as.data.frame(round(
-      do.call(rbind, tapply(x, explanatory, .getSummaryStats)),
-      digits = digits
+    output <- as.data.frame(do.call(
+      rbind,
+      tapply(x, explanatory, .getSummaryStats)
     ))
   }
+  round(output, digits)
 }
 
 .getSummaryStats <- function(x) {
@@ -38,7 +40,7 @@ summary <- function(x, explanatory = NULL, digits = 3) {
     n = length(x) - sum(is.na(x)),
     Min = min(x, na.rm = TRUE),
     Q1 = curried_quantile(0.25),
-    Median = curried_quantile(0.5),
+    Median = median(x, na.rm = TRUE),
     Q3 = curried_quantile(0.75),
     Max = max(x, na.rm = TRUE),
     Mean = mean(x, na.rm = TRUE),

tests/testthat/_snaps/iscamsummary.md

@@ -0,0 +1,35 @@
+# summary without explanatory works
+
+    Code
+      summary(fake_data)
+    Output
+        Missing  n   Min     Q1 Median    Q3   Max  Mean    SD
+      1       0 30 -1.54 -0.621 -0.031 0.487 2.405 0.022 0.914
+
+---
+
+    Code
+      summary(fake_data, digits = 5)
+    Output
+        Missing  n      Min       Q1   Median      Q3     Max    Mean      SD
+      1       0 30 -1.53995 -0.62109 -0.03144 0.48663 2.40465 0.02195 0.91414
+
+# summary with explanatory works
+
+    Code
+      summary(fake_data, groups)
+    Output
+             Missing  n    Min     Q1 Median    Q3   Max   Mean    SD
+      group1       0 13 -1.238 -0.326 -0.057 0.436 1.263 -0.020 0.655
+      group2       0 17 -1.540 -0.892  0.133 0.764 2.405  0.054 1.091
+
+---
+
+    Code
+      summary(fake_data, groups)
+    Output
+             Missing  n    Min     Q1 Median    Q3   Max   Mean    SD
+      group1       0 10 -1.540 -0.298 -0.148 0.676 2.405  0.173 1.103
+      group2       0 10 -1.285 -1.093 -0.089 0.360 1.330 -0.207 0.919
+      group3       0 10 -0.892 -0.390  0.098 0.472 1.272  0.101 0.736
+

tests/testthat/test-hypergeometric.R

@@ -0,0 +1,54 @@
+set.seed(0)
+fake_data <- rnorm(30)
+groups <- sample(c("group1", "group2"), 30, TRUE)
+raw_summary <- data.frame(
+  Missing = sum(is.na(fake_data)),
+  n = length(fake_data),
+  Min = min(fake_data),
+  Q1 = quantile(fake_data, probs = 0.25),
+  Median = median(fake_data),
+  Q3 = quantile(fake_data, probs = 0.75),
+  Max = max(fake_data),
+  Mean = mean(fake_data),
+  SD = sd(fake_data),
+  row.names = NULL
+)
+
+test_that("summary without explanatory works", {
+  expect_equal(
+    summary(fake_data),
+    raw_summary |> round(3)
+  )
+
+  expect_equal(
+    summary(fake_data, digits = 5),
+    raw_summary |> round(5)
+  )
+
+  expect_snapshot(summary(fake_data))
+  expect_snapshot(summary(fake_data, digits = 5))
+})
+
+test_that("summary with explanatory works", {
+  group1 <- fake_data[groups == "group1"]
+  group2 <- fake_data[groups == "group2"]
+
+  expect_equal(
+    summary(fake_data, groups),
+    rbind(summary(group1), summary(group2)) |>
+      structure(row.names = c("group1", "group2"))
+  )
+  expect_snapshot(summary(fake_data, groups))
+
+  groups <- sample(c("group1", "group2", "group3"), 30, TRUE)
+  group1 <- fake_data[groups == "group1"]
+  group2 <- fake_data[groups == "group2"]
+  group3 <- fake_data[groups == "group3"]
+
+  expect_equal(
+    summary(fake_data, groups),
+    rbind(summary(group1), summary(group2), summary(group3)) |>
+      structure(row.names = c("group1", "group2", "group3"))
+  )
+  expect_snapshot(summary(fake_data, groups))
+})