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(v1.4.0.9001) is_gram_positive(), is_gram_negative(), parameter hardening

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-10-19 17:09:19 +02:00
parent 833a1be36d
commit 4e9ccb4435
76 changed files with 969 additions and 491 deletions
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3
tests/testthat/test-_deprecated.R
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@ -27,5 +27,6 @@ context("deprecated.R")
test_that("deprecated functions work", {
skip_on_cran()
# if some functions get deprecated, put the tests here
expect_identical(suppressWarnings(p_symbol(c(0.001, 0.01, 0.05, 0.1, 1, NA, 3))),
c("***", "**", "*", ".", " ", NA, NA))
})

5
tests/testthat/test-mo_property.R
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@ -112,4 +112,9 @@ test_that("mo_property works", {
stringsAsFactors = FALSE)
expect_equal(nrow(subset(x, f1 != f2)), 0)
# is gram pos/neg (also return FALSE for all non-bacteria)
expect_equal(is_gram_negative(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
c(TRUE, FALSE, FALSE))
expect_equal(is_gram_positive(c("Escherichia coli", "Staphylococcus aureus", "Candida albicans")),
c(FALSE, TRUE, FALSE))
})

32
tests/testthat/test-p_symbol.R
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@ -1,32 +0,0 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# 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 the full manual and a complete tutorial about #
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
context("p_symbol.R")
test_that("P symbol works", {
skip_on_cran()
expect_identical(p_symbol(c(0.001, 0.01, 0.05, 0.1, 1, NA, 3)),
c("***", "**", "*", ".", " ", NA, NA))
})