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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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180
tests/testthat/test-resistance_predict.R
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@ -27,94 +27,96 @@
# 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)) {
expect_stdout(AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
sir_predict(
col_ab = "AMX",
col_date = "date",
model = "binomial",
minimum = 10,
info = TRUE
) %>%
pull("value"))
# AMX resistance will increase according to data set `example_isolates`
expect_true(AMX_R[3] < AMX_R[20])
}
test_that("resistance_predict works", {
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
expect_output(AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
sir_predict(
col_ab = "AMX",
col_date = "date",
model = "binomial",
minimum = 10,
info = TRUE
) %>%
pull("value"))
# AMX resistance will increase according to data set `example_isolates`
expect_true(AMX_R[3] < AMX_R[20])
}
expect_stdout(x <- suppressMessages(resistance_predict(example_isolates,
col_ab = "AMX",
year_min = 2010,
model = "binomial",
info = TRUE
)))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
if (AMR:::pkg_is_available("ggplot2")) {
expect_silent(ggplot_sir_predict(x))
expect_silent(ggplot2::autoplot(x))
expect_error(ggplot_sir_predict(example_isolates))
}
expect_stdout(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_stdout(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "loglin",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_stdout(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "lin",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_output(x <- suppressMessages(resistance_predict(example_isolates,
col_ab = "AMX",
year_min = 2010,
model = "binomial",
info = TRUE
)))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
if (AMR:::pkg_is_available("ggplot2")) {
expect_silent(ggplot_sir_predict(x))
expect_silent(ggplot2::autoplot(x))
expect_error(ggplot_sir_predict(example_isolates))
}
expect_output(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_output(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "loglin",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_output(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "lin",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "INVALID MODEL",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE
))
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE
))
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE
))
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "date",
info = TRUE
))
# almost all E. coli are MEM S in the Netherlands :)
expect_error(resistance_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "MEM",
col_date = "date",
info = TRUE
))
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "INVALID MODEL",
col_ab = "AMX",
col_date = "date",
info = TRUE
))
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE
))
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE
))
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE
))
expect_error(sir_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "date",
info = TRUE
))
# almost all E. coli are MEM S in the Netherlands :)
expect_error(resistance_predict(
x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "MEM",
col_date = "date",
info = TRUE
))
})