(v1.3.0.9036) documentation fix

tests/testthat/test-_misc.R

@@ -0,0 +1,89 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis                              #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+#                                                                      #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+# Visit our website for more info: https://msberends.github.io/AMR.    #
+# ==================================================================== #
+
+context("aa_helper_functions.R")
+
+test_that("percentages works", {
+  skip_on_cran()
+  expect_equal(percentage(0.25), "25%")
+  expect_equal(percentage(0.5), "50%")
+  expect_equal(percentage(0.500, digits = 1), "50.0%")
+  expect_equal(percentage(0.1234), "12.3%")
+  # round up 0.5
+  expect_equal(percentage(0.0054), "0.5%")
+  expect_equal(percentage(0.0055), "0.6%")
+})
+
+test_that("functions missing in older R versions work", {
+  skip_on_cran()
+  expect_equal(strrep("A", 5), "AAAAA")
+  expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
+  expect_equal(trimws(" test "), "test")
+  expect_equal(trimws(" test ", "l"), "test ")
+  expect_equal(trimws(" test ", "r"), " test")
+})
+
+test_that("looking up ab columns works", {
+  skip_on_cran()
+  expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
+  expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
+  expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))
+  expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS"))
+  expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
+  expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
+})
+
+test_that("imports work", {
+  skip_on_cran()
+  
+  import_functions <- c(
+    "anti_join" = "dplyr",
+    "cur_column" = "dplyr",
+    "freq.default" = "cleaner",
+    "full_join" = "dplyr",
+    "has_internet" = "curl",
+    "html_attr" = "rvest",
+    "html_children" = "rvest",
+    "html_node" = "rvest",
+    "html_nodes" = "rvest",
+    "html_table" = "rvest",
+    "html_text" = "rvest",
+    "inline_hist" = "skimr",
+    "inner_join" = "dplyr",
+    "insertText" = "rstudioapi",
+    "left_join" = "dplyr",
+    "new_pillar_shaft_simple" = "pillar",
+    "peek_mask" = "dplyr",
+    "peek_vars" = "tidyselect",
+    "read_excel" = "readxl",
+    "read_html" = "xml2",
+    "right_join" = "dplyr",
+    "semi_join" = "dplyr",
+    "sfl" = "skimr",
+    "showQuestion" = "rstudioapi")
+  
+  for (i in seq_len(length(import_functions))) {
+    fn <- names(import_functions)[i]
+    pkg <- unname(import_functions[i])
+    expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
+           failure_message = paste0("Function ", pkg, "::", fn, "() does not exist"))
+  }
+})