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(v1.5.0.9040) removal of isolate_identifier

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dr. M.S. (Matthijs) Berends
2021-03-08 09:44:17 +01:00
parent a7c9b4c295
commit 8d6ceb6a15
30 changed files with 133 additions and 423 deletions
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16
tests/testthat/test-ggplot_rsi.R
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@ -71,5 +71,19 @@ test_that("ggplot_rsi works", {
ggplot(aes(x = ab, y = n)) +
geom_col())$data),
"data.frame")
expect_equal(class((data.frame(ab = as.ab(c("amx", "amc")),
n = c(40, 100)) %>%
ggplot(aes(x = ab, y = n)) +
geom_col())$data),
"data.frame")
# support for manual colours
expect_equal(class((ggplot(data.frame(x = c("Value1", "Value2", "Value3"),
y = c(1, 2, 3),
z = c("Value4", "Value5", "Value6"))) +
geom_col(aes(x = x, y = y, fill = z)) +
scale_rsi_colours(Value4 = "S", Value5 = "I", Value6 = "R"))$data),
"data.frame")
})

44
tests/testthat/test-isolate_identifier.R
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@ -1,44 +0,0 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Data Analysis for R #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2021 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 data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
context("isolate_identifier.R")
test_that("isolate_identifier works", {
x <- suppressMessages(isolate_identifier(example_isolates))
expect_s3_class(x, "isolate_identifier")
expect_s3_class(x, "character")
expect_equal(suppressMessages(
unique(nchar(isolate_identifier(example_isolates, cols_ab = carbapenems(), col_mo = FALSE)))),
2)
expect_warning(isolate_identifier(example_isolates[, 1:3, drop = FALSE])) # without mo and without rsi
expect_warning(isolate_identifier(example_isolates[, 1:9, drop = FALSE])) # only without rsi
expect_output(print(x))
expect_s3_class(unique(c(x, x)), "isolate_identifier")
})