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(v2.1.1.9146) new scale_*_sir() functions

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dr. M.S. (Matthijs) Berends
2025-02-13 19:47:57 +01:00
parent 5ff9210c12
commit bd2887bcd4
16 changed files with 460 additions and 81 deletions
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tests/testthat/test-plotting.R Normal file
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# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# 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/ #
# ==================================================================== #
if (AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
pdf(NULL) # prevent Rplots.pdf being created
# scale_*_mic
aesthetics <- c("x", "y", "colour", "fill")
expected_methods <- c("transform", "transform_df", "breaks", "labels", "limits")
for (aest in aesthetics) {
scale_fn_name <- paste0("scale_", aest, "_continuous")
scale_obj <- getExportedValue("ggplot2", scale_fn_name)()
for (method in expected_methods) {
expect_true(is.function(scale_obj[[method]]) || method %in% names(scale_obj),
info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name))
}
}
# scale_*_sir
aesthetics <- c("colour", "fill")
expected_methods <- c("transform", "transform_df", "labels", "limits")
for (aest in aesthetics) {
scale_fn_name <- "scale_discrete_manual"
scale_obj <- getExportedValue("ggplot2", scale_fn_name)(aesthetics = aest)
for (method in expected_methods) {
expect_true(is.function(scale_obj[[method]]) || method %in% names(scale_obj),
info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name))
}
}
for (method in expected_methods) {
expect_true(is.function(ggplot2::scale_x_discrete()[[method]]) || method %in% names(ggplot2::scale_x_discrete()),
info = paste0("Method '", method, "' is missing in ggplot2::", "scale_x_discrete"))
}
expect_inherits(ggplot(data.frame(count = c(1,2,3, 4),
sir = c("S", "I", "R", "SDD")),
aes(x = sir, y = count, fill = sir)) +
geom_col() +
scale_x_sir(eucast_I = F, language = "el") +
scale_fill_sir(eucast_I = T, language = "nl"),
"gg")
expect_inherits(ggplot(data.frame(mic = as.mic(c(2,4,8, 16)),
sir = as.sir(c("S", "I", "R", "SDD"))),
aes(x = sir, y = mic)) +
geom_point() +
scale_y_mic(),
"gg")
expect_inherits(ggplot(data.frame(mic = as.mic(c(2,4,8, 16)),
sir = as.sir(c("S", "I", "R", "SDD"))),
aes(x = sir, y = mic)) +
geom_col() +
scale_y_mic(),
"gg")
expect_inherits(ggplot(data.frame(mic = as.mic(c(2,4,8, 16)),
sir = as.sir(c("S", "I", "R", "SDD"))),
aes(x = sir, y = mic)) +
geom_col() +
scale_y_mic(mic_range = c(4,16)) +
scale_x_sir(),
"gg")
}