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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
140 changed files with 4870 additions and 4702 deletions
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84
tests/testthat/test-pca.R
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@@ -27,51 +27,53 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
resistance_data <- structure(
list(
order = c("Bacillales", "Enterobacterales", "Enterobacterales"),
genus = c("Staphylococcus", "Escherichia", "Klebsiella"),
AMC = c(0.00425, 0.13062, 0.10344),
CXM = c(0.00425, 0.05376, 0.10344),
CTX = c(0.00000, 0.02396, 0.05172),
TOB = c(0.02325, 0.02597, 0.10344),
TMP = c(0.08387, 0.39141, 0.18367)
),
class = c("grouped_df", "tbl_df", "tbl", "data.frame"),
row.names = c(NA, -3L),
groups = structure(
test_that("pca works", {
resistance_data <- structure(
list(
order = c("Bacillales", "Enterobacterales"),
.rows = list(1L, 2:3)
order = c("Bacillales", "Enterobacterales", "Enterobacterales"),
genus = c("Staphylococcus", "Escherichia", "Klebsiella"),
AMC = c(0.00425, 0.13062, 0.10344),
CXM = c(0.00425, 0.05376, 0.10344),
CTX = c(0.00000, 0.02396, 0.05172),
TOB = c(0.02325, 0.02597, 0.10344),
TMP = c(0.08387, 0.39141, 0.18367)
),
row.names = c(NA, -2L),
class = c("tbl_df", "tbl", "data.frame"),
.drop = TRUE
class = c("grouped_df", "tbl_df", "tbl", "data.frame"),
row.names = c(NA, -3L),
groups = structure(
list(
order = c("Bacillales", "Enterobacterales"),
.rows = list(1L, 2:3)
),
row.names = c(NA, -2L),
class = c("tbl_df", "tbl", "data.frame"),
.drop = TRUE
)
)
)
pca_model <- pca(resistance_data)
expect_inherits(pca_model, "pca")
pca_model <- pca(resistance_data)
expect_inherits(pca_model, "pca")
pdf(NULL) # prevent Rplots.pdf being created
if (AMR:::pkg_is_available("ggplot2")) {
ggplot_pca(pca_model, ellipse = TRUE)
ggplot_pca(pca_model, arrows_textangled = FALSE)
}
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
resistance_data <- example_isolates %>%
group_by(
order = mo_order(mo),
genus = mo_genus(mo)
) %>%
summarise_if(is.sir, resistance, minimum = 0)
pca_result <- resistance_data %>%
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, "SXT")
expect_inherits(pca_result, "prcomp")
pdf(NULL) # prevent Rplots.pdf being created
if (AMR:::pkg_is_available("ggplot2")) {
ggplot_pca(pca_result, ellipse = TRUE)
ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
ggplot_pca(pca_model, ellipse = TRUE)
ggplot_pca(pca_model, arrows_textangled = FALSE)
}
}
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
resistance_data <- example_isolates %>%
group_by(
order = mo_order(mo),
genus = mo_genus(mo)
) %>%
summarise_if(is.sir, resistance, minimum = 0)
pca_result <- resistance_data %>%
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, "SXT")
expect_inherits(pca_result, "prcomp")
if (AMR:::pkg_is_available("ggplot2")) {
ggplot_pca(pca_result, ellipse = TRUE)
ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
}
}
})