P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-11 17:02:00 +02:00
Code Releases Activity

(v2.1.1.9131) implement testthat

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-01-27 21:43:10 +01:00
parent 92166c16e8
commit f03933940c
63 changed files with 172 additions and 267 deletions
Download Patch File Download Diff File Expand all files Collapse all files

133
tests/testthat/test-ggplot_sir.R Normal file
View File

@ -0,0 +1,133 @@
# ==================================================================== #
# 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("dplyr", min_version = "1.0.0", also_load = TRUE) &&
AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
pdf(NULL) # prevent Rplots.pdf being created
# data should be equal
expect_equal(
(example_isolates %>%
select(AMC, CIP) %>%
ggplot_sir())$data %>%
summarise_all(resistance) %>%
as.double(),
example_isolates %>%
select(AMC, CIP) %>%
summarise_all(resistance) %>%
as.double()
)
expect_inherits(example_isolates %>%
select(AMC, CIP) %>%
ggplot_sir(x = "interpretation", facet = "antibiotic"),
"gg")
expect_inherits(example_isolates %>%
select(AMC, CIP) %>%
ggplot_sir(x = "antibiotic", facet = "interpretation"),
"gg")
expect_equal(
(example_isolates %>%
select(AMC, CIP) %>%
ggplot_sir(x = "interpretation", facet = "antibiotic"))$data %>%
summarise_all(resistance) %>%
as.double(),
example_isolates %>%
select(AMC, CIP) %>%
summarise_all(resistance) %>%
as.double()
)
expect_equal(
(example_isolates %>%
select(AMC, CIP) %>%
ggplot_sir(x = "antibiotic", facet = "interpretation"))$data %>%
summarise_all(resistance) %>%
as.double(),
example_isolates %>%
select(AMC, CIP) %>%
summarise_all(resistance) %>%
as.double()
)
expect_equal(
(example_isolates %>%
select(AMC, CIP) %>%
ggplot_sir(x = "antibiotic", facet = "interpretation"))$data %>%
summarise_all(count_resistant) %>%
as.double(),
example_isolates %>%
select(AMC, CIP) %>%
summarise_all(count_resistant) %>%
as.double()
)
# support for scale_type ab and mo
expect_inherits(
(data.frame(
mo = as.mo(c("e. coli", "s aureus")),
n = c(40, 100)
) %>%
ggplot(aes(x = mo, y = n)) +
geom_col())$data,
"data.frame"
)
expect_inherits(
(data.frame(
ab = as.ab(c("amx", "amc")),
n = c(40, 100)
) %>%
ggplot(aes(x = ab, y = n)) +
geom_col())$data,
"data.frame"
)
expect_inherits(
(data.frame(
ab = as.ab(c("amx", "amc")),
n = c(40, 100)
) %>%
ggplot(aes(x = ab, y = n)) +
geom_col())$data,
"data.frame"
)
# support for manual colours
expect_inherits(
(ggplot(data.frame(
x = c("Value1", "Value2", "Value3"),
y = c(1, 2, 3),
z = c("Value4", "Value5", "Value6")
)) +
geom_col(aes(x = x, y = y, fill = z)) +
scale_sir_colours(Value4 = "S", Value5 = "I", Value6 = "R"))$data,
"data.frame"
)
}