AMR/tests/testthat/test-ggplot_rsi.R

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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
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# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
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# 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. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
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context("ggplot_rsi.R")
test_that("ggplot_rsi works", {
skip_if_not("ggplot2" %in% rownames(installed.packages()))
library(dplyr)
library(ggplot2)
# data should be equal
expect_equal(
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(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi())$data %>%
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summarise_all(portion_IR) %>% as.double(),
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septic_patients %>% select(AMC, CIP) %>%
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summarise_all(portion_IR) %>% as.double()
)
expect_equal(
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(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "Interpretation", facet = "Antibiotic"))$data %>%
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summarise_all(portion_IR) %>% as.double(),
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septic_patients %>% select(AMC, CIP) %>%
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summarise_all(portion_IR) %>% as.double()
)
expect_equal(
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(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "Antibiotic", facet = "Interpretation"))$data %>%
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summarise_all(portion_IR) %>% as.double(),
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septic_patients %>% select(AMC, CIP) %>%
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summarise_all(portion_IR) %>% as.double()
)
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expect_equal(
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(septic_patients %>% select(AMC, CIP) %>% ggplot_rsi(x = "Antibiotic",
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facet = "Interpretation",
fun = count_df))$data %>%
summarise_all(count_IR) %>% as.double(),
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septic_patients %>% select(AMC, CIP) %>%
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summarise_all(count_IR) %>% as.double()
)
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expect_error(ggplot_rsi(septic_patients, fun = "invalid"))
expect_error(geom_rsi(septic_patients, fun = "invalid"))
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# support for scale_type ab and mo
expect_equal(class((data.frame(mo = as.mo(c("e. coli", "s aureus")),
n = c(40, 100)) %>%
ggplot(aes(x = mo, y = n)) +
geom_col())$data),
"data.frame")
expect_equal(class((data.frame(ab = as.ab(c("amx", "amc")),
n = c(40, 100)) %>%
ggplot(aes(x = ab, y = n)) +
geom_col())$data),
"data.frame")
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})