AMR/tests/testthat/test-_misc.R

# ==================================================================== #
# 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"))
  }
})