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(v1.3.0.9036) documentation fix

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-09-30 10:24:53 +02:00
parent 4e0374af29
commit ac1c78c793
19 changed files with 86 additions and 106 deletions
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7
tests/testthat/test-_all_examples.R → tests/testthat/test-_deprecated.R Executable file → Normal file
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@ -18,3 +18,10 @@
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
context("deprecated.R")
test_that("deprecated functions work", {
skip_on_cran()
# if some functions get deprecated, put the tests here
})

39
tests/testthat/test-misc.R → tests/testthat/test-_misc.R
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@ -19,7 +19,7 @@
# Visit our website for more info: https://msberends.github.io/AMR. #
# ==================================================================== #
context("misc.R")
context("aa_helper_functions.R")
test_that("percentages works", {
skip_on_cran()
@ -50,3 +50,40 @@ test_that("looking up ab columns works", {
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"))
}
})

31
tests/testthat/test-deprecated.R
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@ -1,31 +0,0 @@
# ==================================================================== #
# 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("deprecated.R")
test_that("deprecated functions work", {
skip_on_cran()
expect_equal(suppressWarnings(portion_S(example_isolates$AMX)), proportion_S(example_isolates$AMX))
expect_equal(suppressWarnings(portion_SI(example_isolates$AMX)), proportion_SI(example_isolates$AMX))
expect_equal(suppressWarnings(portion_I(example_isolates$AMX)), proportion_I(example_isolates$AMX))
expect_equal(suppressWarnings(portion_IR(example_isolates$AMX)), proportion_IR(example_isolates$AMX))
expect_equal(suppressWarnings(portion_R(example_isolates$AMX)), proportion_R(example_isolates$AMX))
})

49
tests/testthat/test-import_fn.R
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@ -1,49 +0,0 @@
# ==================================================================== #
# 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("import_fn.R")
test_that("imports work", {
skip_on_cran()
import_functions <- c(
cleaner = "freq.default",
curl = "has_internet",
dplyr = "cur_column",
dplyr = "peek_mask",
readxl = "read_excel",
rstudioapi = "showQuestion",
rvest = "html_attr",
rvest = "html_children",
rvest = "html_node",
rvest = "html_nodes",
rvest = "html_table",
rvest = "html_text",
tidyselect = "peek_vars",
xml2 = "read_html")
for (i in seq_len(length(import_functions))) {
pkg <- names(import_functions)[i]
fn <- 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"))
}
})

1
tests/testthat/test-mic.R
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@ -40,6 +40,7 @@ test_that("mic works", {
expect_s3_class(c(x[1], x[9]), "mic")
expect_s3_class(unique(x[1], x[9]), "mic")
expect_warning(as.mic("INVALID VALUE"))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.mic(c(1, 2, 4, 8))))