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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
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202
tests/testthat/test-ggplot_sir.R
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@ -27,111 +27,113 @@
# 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
test_that("ggplot_sir works", {
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())$data %>%
summarise_all(resistance) %>%
as.double(),
example_isolates %>%
select(AMC, CIP) %>%
summarise_all(resistance) %>%
as.double()
)
# data should be equal
expect_equal(
(example_isolates %>%
select(AMC, CIP) %>%
ggplot_sir())$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_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"))$data %>%
summarise_all(resistance) %>%
as.double(),
example_isolates %>%
select(AMC, CIP) %>%
summarise_all(resistance) %>%
as.double()
)
expect_equal(
(example_isolates %>%
select(AMC, CIP) %>%
ggplot_sir(x = "interpretation", facet = "antibiotic"))$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(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"))$data %>%
summarise_all(count_resistant) %>%
as.double(),
example_isolates %>%
select(AMC, CIP) %>%
summarise_all(count_resistant) %>%
as.double()
)
expect_equal(
(example_isolates %>%
select(AMC, CIP) %>%
ggplot_sir(x = "antibiotic", facet = "interpretation"))$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"
)
# 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())$data,
"data.frame"
)
expect_inherits(
(data.frame(
ab = as.ab(c("amx", "amc")),
n = c(40, 100)
) %>%
ggplot(aes(x = ab, y = n)) +
geom_col())$data,
"data.frame"
)
# support for manual colours
expect_inherits(
suppressWarnings((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(aesthetics = "fill", Value4 = "S", Value5 = "I", Value6 = "R"))$data),
"data.frame"
)
}
# support for manual colours
expect_inherits(
suppressWarnings((ggplot(data.frame(
x = c("Value1", "Value2", "Value3"),
y = c(1, 2, 3),
z = c("Value4", "Value5", "Value6")
)) +
geom_col(aes(x = x, y = y, fill = z)) +
scale_sir_colours(aesthetics = "fill", Value4 = "S", Value5 = "I", Value6 = "R"))$data),
"data.frame"
)
}
})