Apply #86 to many test files

trias-project · Aug 8, 2022 · de195ee · de195ee
1 parent 21411b6
commit de195ee
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Showing 12 changed files with 318 additions and 318 deletions.
diff --git a/tests/testthat/test-gbif_verify_keys.R b/tests/testthat/test-gbif_verify_keys.R
@@ -5,30 +5,30 @@ context("test_gbif_verify_keys")
 testthat::test_that("test several input types", {
   # input contains nothing
   keys_null1 <- list()
-  expect_null(gbif_verify_keys(keys_null1))
+  testthat::expect_null(gbif_verify_keys(keys_null1))
 
   # input contains invalid taxon keys (they contain letters)
   keys_err1 <- c("1", "128", "120391203", "AE", "12k")
-  expect_error(
+  testthat::expect_error(
     gbif_verify_keys(keys_err1),
     "Invalid keys: AE,12k ."
   )
 
   # input contains empty strings
   keys_err2 <- c("", "", "1")
-  expect_error(
+  testthat::expect_error(
     gbif_verify_keys(keys_err2),
     "Invalid keys: \"\"\"\",\"\"\"\" ."
   )
 
   # input contains dates
-  expect_error(
+  testthat::expect_error(
     gbif_verify_keys(as.Date("2018-01-01")),
     "keys should be a vector, a named list or a data.frame."
   )
 
   # input df doesn't contain column with name keys
-  expect_error(gbif_verify_keys(data.frame(bad_col_name = 12)),
+  testthat::expect_error(gbif_verify_keys(data.frame(bad_col_name = 12)),
     paste(
       "Column with keys not found.",
       "Did you forget maybe to pass",
@@ -85,31 +85,31 @@ testthat::test_that("output type and content", {
   )  
 
   # output type is "list"
-  expect_type(output1, "list")
-  expect_type(output2, "list")
-  expect_type(output3, "list")
-  expect_type(output4, "list")
-  expect_null(gbif_verify_keys(keys = c(NA, NA)))
-  expect_null(gbif_verify_keys(keys = c(NA_character_, NA_character_)))
+  testthat::expect_type(output1, "list")
+  testthat::expect_type(output2, "list")
+  testthat::expect_type(output3, "list")
+  testthat::expect_type(output4, "list")
+  testthat::expect_null(gbif_verify_keys(keys = c(NA, NA)))
+  testthat::expect_null(gbif_verify_keys(keys = c(NA_character_, NA_character_)))
 
   # output class is tibble data.frame
-  expect_equal(class(output1), c("tbl_df", "tbl", "data.frame"))
-  expect_equal(class(output2), c("tbl_df", "tbl", "data.frame"))
-  expect_equal(class(output3), c("tbl_df", "tbl", "data.frame"))
-  expect_equal(class(output2), c("tbl_df", "tbl", "data.frame"))
+  testthat::expect_equal(class(output1), c("tbl_df", "tbl", "data.frame"))
+  testthat::expect_equal(class(output2), c("tbl_df", "tbl", "data.frame"))
+  testthat::expect_equal(class(output3), c("tbl_df", "tbl", "data.frame"))
+  testthat::expect_equal(class(output2), c("tbl_df", "tbl", "data.frame"))
 
 
   # output content is the same for all kinds of inputs
-  expect_true(nrow(output1) == nrow(output_keys))
-  expect_true(nrow(output2) == nrow(output_keys))
-  expect_true(nrow(output3) == nrow(output_keys))
-  expect_true(nrow(output4) == nrow(output_keys))
-  expect_true(nrow(gbif_verify_keys(keys = "1")) == 1)
-  expect_equal(output1, output_keys)
-  expect_equal(output2, output_keys)
-  expect_equal(output3, output_keys)
-  expect_equal(output3, output_keys)
-  expect_equal(output4, output_keys)
+  testthat::expect_true(nrow(output1) == nrow(output_keys))
+  testthat::expect_true(nrow(output2) == nrow(output_keys))
+  testthat::expect_true(nrow(output3) == nrow(output_keys))
+  testthat::expect_true(nrow(output4) == nrow(output_keys))
+  testthat::expect_true(nrow(gbif_verify_keys(keys = "1")) == 1)
+  testthat::expect_equal(output1, output_keys)
+  testthat::expect_equal(output2, output_keys)
+  testthat::expect_equal(output3, output_keys)
+  testthat::expect_equal(output3, output_keys)
+  testthat::expect_equal(output4, output_keys)
 })
 
 testthat::test_that("function works even with duplicated taxon keys", {
@@ -139,5 +139,5 @@ testthat::test_that("function works even with duplicated taxon keys", {
       is_synonym = rep(c(NA, NA, TRUE, FALSE), 2)
     )
 
-  expect_equal(output_with_duplicates, expected_output_with_duplicates)
+  testthat::expect_equal(output_with_duplicates, expected_output_with_duplicates)
 })
diff --git a/tests/testthat/test-indicator_introduction_year.R b/tests/testthat/test-indicator_introduction_year.R
@@ -120,7 +120,7 @@ testthat::test_that("Param: labels", {
 })
 
 testthat::test_that("Test warnings", {
-  expect_warning(indicator_introduction_year(input_test_df),
+  testthat::expect_warning(indicator_introduction_year(input_test_df),
     paste0(
       nrow_no_first_obs,
       " records have no information about year of introduction ",

diff --git a/tests/testthat/test-input_apply_decision_rules.R b/tests/testthat/test-input_apply_decision_rules.R
@@ -1,34 +1,34 @@
 context("test_input_decision_rules")
 
-df_dr <- tibble(
+df_dr <- dplyr::tibble(
   taxonID = c(rep(1008955, 10), rep(2493598, 3)),
   y = c(seq(2009, 2018), seq(2016, 2018)),
   obs = c(1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 3, 0)
 )
 
-df_duplicate <- tibble(taxonID = c(1, 1), y = c(2001, 2001), obs = c(5, 3))
+df_duplicate <- dplyr::tibble(taxonID = c(1, 1), y = c(2001, 2001), obs = c(5, 3))
 
-df_duplicates <- tibble(
+df_duplicates <- dplyr::tibble(
   taxonID = c(1, 1, 2, 2, 3),
   y = c(2000, 2001, 2001, 2001, 2000),
   obs = c(0, 0, 1, 0, 1)
 )
 
-df_hole <- tibble(
+df_hole <- dplyr::tibble(
   taxonID = c(rep(1234, 3)),
   y = c(2010, 2011, 2018),
   obs = c(1, 2, 5)
 )
 
-df_holes <- tibble(
+df_holes <- dplyr::tibble(
   taxonID = c(rep(1234, 3), rep(1256, 4)),
   y = c(2010, 2011, 2018, 2014, 2016, 2018, 2020),
   obs = c(1, 2, 3, 5, 1, 2, 5)
 )
 
 testthat::test_that("Test inputs' types.", {
   # df
-  expect_error(apply_decision_rules(
+  testthat::expect_error(apply_decision_rules(
     df = 3,
     y_var = "n_observations",
     eval_year = 2018
@@ -40,7 +40,7 @@ testthat::test_that("Test inputs' types.", {
   fixed = TRUE
   )
   # y_var
-  expect_error(apply_decision_rules(
+  testthat::expect_error(apply_decision_rules(
     df = df_dr,
     y_var = 3,
     eval_year = 2018
@@ -52,7 +52,7 @@ testthat::test_that("Test inputs' types.", {
   fixed = TRUE
   )
   # eval_year
-  expect_error(apply_decision_rules(
+  testthat::expect_error(apply_decision_rules(
     df = df_dr,
     y_var = "n_observations",
     eval_year = "yyyy"
@@ -63,7 +63,7 @@ testthat::test_that("Test inputs' types.", {
   ),
   fixed = TRUE
   )
-  expect_error(apply_decision_rules(
+  testthat::expect_error(apply_decision_rules(
     df = df_dr,
     y_var = "n_observations",
     eval_year = list(a = 2018)
@@ -75,7 +75,7 @@ testthat::test_that("Test inputs' types.", {
   fixed = TRUE
   )
   # year
-  expect_error(apply_decision_rules(
+  testthat::expect_error(apply_decision_rules(
     df = df_dr,
     y_var = "n_observations",
     year = 3,
@@ -88,7 +88,7 @@ testthat::test_that("Test inputs' types.", {
   fixed = TRUE
   )
   # taxonKey
-  expect_error(apply_decision_rules(
+  testthat::expect_error(apply_decision_rules(
     df = df_dr,
     y_var = "n_observations",
     eval_year = 2018,
@@ -103,15 +103,15 @@ testthat::test_that("Test inputs' types.", {
 })
 
 testthat::test_that("Test input length.", {
-  expect_error(
+  testthat::expect_error(
     apply_decision_rules(
       df = df_dr,
       y_var = c("n_observations", "why a second col?"),
       eval_year = 2018
     ),
     paste("Multiple values for argument y_var provided.")
   )
-  expect_error(
+  testthat::expect_error(
     apply_decision_rules(
       df = df_dr,
       y_var = c("n_observations"),
@@ -120,7 +120,7 @@ testthat::test_that("Test input length.", {
     ),
     paste("Multiple values for argument year provided.")
   )
-  expect_error(
+  testthat::expect_error(
     apply_decision_rules(
       df = df_dr,
       y_var = c("n_observations"),
@@ -132,7 +132,7 @@ testthat::test_that("Test input length.", {
 })
 
 testthat::test_that("Test df contains all needed columns and information.", {
-  expect_error(apply_decision_rules(
+  testthat::expect_error(apply_decision_rules(
     df = df_dr,
     y_var = "y_var_wrong",
     eval_year = 2018,
@@ -145,7 +145,7 @@ testthat::test_that("Test df contains all needed columns and information.", {
   ),
   fixed = TRUE
   )
-  expect_error(
+  testthat::expect_error(
     apply_decision_rules(
       df = df_dr,
       taxonKey = "taxonID",
@@ -158,7 +158,7 @@ testthat::test_that("Test df contains all needed columns and information.", {
       "Check value of argument year."
     )
   )
-  expect_error(apply_decision_rules(
+  testthat::expect_error(apply_decision_rules(
     df = df_dr,
     y_var = "obs",
     year = "y",
@@ -171,7 +171,7 @@ testthat::test_that("Test df contains all needed columns and information.", {
   ),
   fixed = TRUE
   )
-  expect_error(
+  testthat::expect_error(
     apply_decision_rules(
       df = df_dr,
       y_var = "obs",
@@ -184,7 +184,7 @@ testthat::test_that("Test df contains all needed columns and information.", {
       "Check value of argument eval_year."
     )
   )
-  expect_error(
+  testthat::expect_error(
     apply_decision_rules(
       df = df_duplicate,
       y_var = "obs",
@@ -197,7 +197,7 @@ testthat::test_that("Test df contains all needed columns and information.", {
       "of one or more taxa contain duplicates."
     )
   )
-  expect_error(
+  testthat::expect_error(
     apply_decision_rules(
       df = df_duplicates,
       y_var = "obs",
@@ -210,7 +210,7 @@ testthat::test_that("Test df contains all needed columns and information.", {
       "of one or more taxa contain duplicates."
     )
   )
-  expect_error(
+  testthat::expect_error(
     apply_decision_rules(
       df = df_hole,
       y_var = "obs",
@@ -222,7 +222,7 @@ testthat::test_that("Test df contains all needed columns and information.", {
       "as they contain missing time values: 1234."
     )
   )
-  expect_error(
+  testthat::expect_error(
     apply_decision_rules(
       df = df_holes,
       y_var = "obs",