Warn of duplicate names

Close #48
llrs · Mar 27, 2024 · 736e1cd · 736e1cd
1 parent 817cf57
commit 736e1cd
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Showing 3 changed files with 123 additions and 106 deletions.
diff --git a/R/utils.R b/R/utils.R
@@ -141,6 +141,10 @@ evaluations <- function(num, eval_cat = 4, eval_num = 3) {
 
 add_column <- function(x, values, name) {
   # Add the column and rename it
+  if (name %in% colnames(x)) {
+    msg <- paste("Column", name, "is already present. Did you meant this?")
+    warning(msg, call. = FALSE)
+  }
   out <- cbind(x, values)
   colnames(out)[ncol(out)] <- name
   rownames(out) <- NULL

diff --git a/tests/testthat/test-follow_up.R b/tests/testthat/test-follow_up.R
@@ -1,106 +1,106 @@
-test_that("follow_up works", {
-  data(survey, package = "MASS")
-  survey1 <- survey[1:118, ]
-  survey2 <- survey[119:nrow(survey), ]
-  expect_warning(
-    expect_warning(
-      expect_warning(
-        expect_warning(
-          fu <- follow_up(survey1, survey2, size_subset = 50, iterations = 10)
-        )
-      )
-    )
-  )
-  expect_s3_class(fu, "data.frame")
-})
-
-test_that("follow_up2 works", {
-  data(survey, package = "MASS")
-  expect_error(follow_up2(survey, iterations = 10))
-
-  old_n <- 118
-  # old vs new
-  survey$batch <- c(rep("old", old_n), rep(NA, nrow(survey) - old_n))
-  expect_warning(
-    expect_warning(
-      expect_warning(
-        expect_warning(
-          fu1 <- follow_up2(survey, iterations = 10),
-          "with the data."),
-        "with the new samples"),
-      "some problems with the new data."),
-    "some problems with the old data.")
-  expect_type(fu1, "character")
-  # old vs new with confounding effects
-  survey$batch <- ifelse(survey$Clap %in% "Right", "old", NA)
-  expect_error(
-    expect_warning(
-      expect_warning(
-        expect_warning(
-          expect_warning(
-            follow_up2(survey, iterations = 10)
-          )
-        )
-      )
-    )
-  )
-
-  # old with batches vs new
-  bn <- batch_names(create_subset(old_n, 20))
-  survey$batch <- c(bn, rep(NA, nrow(survey) - old_n))
-  expect_warning(
-    expect_warning(
-      expect_warning(
-        expect_warning(
-          fu3 <- follow_up2(survey, iterations = 10)
-        )
-      )
-    )
-  )
-  expect_type(fu3, "character")
-  # old with batches and confounding effect vs new
-  survey$batch <- ifelse(survey$Clap %in% "Right", "old", NA)
-  bn <- batch_names(create_subset(sum(survey$Clap %in% "Right", na.rm = TRUE), 20))
-  survey$batch[survey$batch %in% "old"] <- bn
-  expect_warning(
-    expect_warning(
-      expect_warning(
-        expect_warning(
-          fu4 <- follow_up2(survey, iterations = 10)
-        )
-      )
-    )
-  )
-  expect_type(fu4, "character")
-})
-
-
-test_that("valid_followup works", {
-  data(survey, package = "MASS")
-  survey1 <- survey[1:118, ]
-  survey2 <- survey[119:nrow(survey), ]
-
-  expect_warning(
-    expect_warning(
-      expect_warning(
-        expect_warning(
-          out <- valid_followup(survey1, survey2)
-        )
-      )
-    )
-  )
-  expect_false(out)
-  survey$batch <- NA
-  survey$batch[1:118]  <- "old"
-
-  expect_warning(
-    expect_warning(
-      expect_warning(
-        expect_warning(
-          out <- valid_followup(all_data = survey)
-        )
-      )
-    )
-  )
-  expect_false(out)
-})
+test_that("follow_up works", {
+  data(survey, package = "MASS")
+  survey1 <- survey[1:118, ]
+  survey2 <- survey[119:nrow(survey), ]
+  expect_warning(
+    expect_warning(
+      expect_warning(
+        expect_warning(
+          fu <- follow_up(survey1, survey2, size_subset = 50, iterations = 10, old_new = "batch2")
+        )
+      )
+    )
+  )
+  expect_s3_class(fu, "data.frame")
+})
+
+test_that("follow_up2 works", {
+  data(survey, package = "MASS")
+  expect_error(follow_up2(survey, iterations = 10))
+
+  old_n <- 118
+  # old vs new
+  survey$batch <- c(rep("old", old_n), rep(NA, nrow(survey) - old_n))
+  expect_warning(
+    expect_warning(
+      expect_warning(
+        expect_warning(
+          fu1 <- follow_up2(survey, iterations = 10),
+          "with the data."),
+        "with the new samples"),
+      "some problems with the new data."),
+    "some problems with the old data.")
+  expect_type(fu1, "character")
+  # old vs new with confounding effects
+  survey$batch <- ifelse(survey$Clap %in% "Right", "old", NA)
+  expect_error(
+    expect_warning(
+      expect_warning(
+        expect_warning(
+          expect_warning(
+            follow_up2(survey, iterations = 10)
+          )
+        )
+      )
+    )
+  )
+
+  # old with batches vs new
+  bn <- batch_names(create_subset(old_n, 20))
+  survey$batch <- c(bn, rep(NA, nrow(survey) - old_n))
+  expect_warning(
+    expect_warning(
+      expect_warning(
+        expect_warning(
+          fu3 <- follow_up2(survey, iterations = 10)
+        )
+      )
+    )
+  )
+  expect_type(fu3, "character")
+  # old with batches and confounding effect vs new
+  survey$batch <- ifelse(survey$Clap %in% "Right", "old", NA)
+  bn <- batch_names(create_subset(sum(survey$Clap %in% "Right", na.rm = TRUE), 20))
+  survey$batch[survey$batch %in% "old"] <- bn
+  expect_warning(
+    expect_warning(
+      expect_warning(
+        expect_warning(
+          fu4 <- follow_up2(survey, iterations = 10)
+        )
+      )
+    )
+  )
+  expect_type(fu4, "character")
+})
+
+
+test_that("valid_followup works", {
+  data(survey, package = "MASS")
+  survey1 <- survey[1:118, ]
+  survey2 <- survey[119:nrow(survey), ]
+
+  expect_warning(
+    expect_warning(
+      expect_warning(
+        expect_warning(
+          out <- valid_followup(survey1, survey2)
+        )
+      )
+    )
+  )
+  expect_false(out)
+  survey$batch <- NA
+  survey$batch[1:118]  <- "old"
+
+  expect_warning(
+    expect_warning(
+      expect_warning(
+        expect_warning(
+          out <- valid_followup(all_data = survey)
+        )
+      )
+    )
+  )
+  expect_false(out)
+})
diff --git a/tests/testthat/test-inspect.R b/tests/testthat/test-inspect.R
@@ -40,3 +40,16 @@ test_that("inspect with translate_index", {
   i2 <- inspect(index2, i1, index_name = "spatial")
   expect_true(all(table(i2$batch, i2$spatial)<= 1))
 })
+
+  test_that("Warning on duplidate names", {
+  data(survey, package = "MASS")
+  columns <- c("Sex", "Age", "Smoke")
+  expect_warning(index <- design(pheno = survey[, columns], size_subset = 70,
+                  iterations = 10))
+  batches <- inspect(index, survey[, columns])
+
+  expect_warning(index2 <- design(pheno = batches, size_subset = 70,
+                   iterations = 10))
+  expect_warning(inspect(index2, batches))
+  expect_no_warning(inspect(index2, batches, index_name = "batch2"))
+})