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(v2.1.1.9159) new approach as.ab()

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-02-26 19:23:54 +01:00
parent 122bca0f95
commit 0c3ea4b538
18 changed files with 130 additions and 284 deletions
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7
tests/testthat/test-ab.R
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@ -27,20 +27,21 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
ab_reset_session()
expect_equal(
as.character(as.ab(c(
"J01FA01",
"J 01 FA 01",
"Erythromycin",
"eryt",
" eryt 123",
"ERYT",
"ERY",
"erytromicine",
"Erythrocin",
"Romycin"
))),
rep("ERY", 10)
rep("ERY", 9)
)
expect_identical(class(as.ab("amox")), c("ab", "character"))
@ -49,7 +50,7 @@ expect_true(is.ab(as.ab("amox")))
expect_stdout(print(as.ab("amox")))
expect_stdout(print(data.frame(a = as.ab("amox"))))
# expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
# expect_warning(as.ab("UNKNOWN"))
expect_stdout(print(as.ab("amox")))

14
tests/testthat/test-ab_from_text.R
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@ -27,20 +27,22 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
ab_reset_session()
expect_identical(
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")[[1]],
ab_from_text("28/03/2020 amoxicilliin 500mg po tds")[[1]],
as.ab("Amoxicillin")
)
expect_identical(
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", thorough_search = TRUE)[[1]],
ab_from_text("28/03/2020 amoxicilliin 500mg po tds", thorough_search = TRUE)[[1]],
as.ab("Amoxicillin")
)
expect_identical(
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", thorough_search = FALSE)[[1]],
ab_from_text("28/03/2020 amoxicilliin 500mg po tds", thorough_search = FALSE)[[1]],
as.ab("Amoxicillin")
)
expect_identical(
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", translate_ab = TRUE)[[1]],
ab_from_text("28/03/2020 amoxicilliin 500mg po tds", translate_ab = TRUE)[[1]],
"Amoxicillin"
)
expect_identical(
@ -49,10 +51,10 @@ expect_identical(
)
expect_identical(
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", type = "dose")[[1]],
ab_from_text("28/03/2020 amoxicilliin 500mg po tds", type = "dose")[[1]],
500
)
expect_identical(
ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds", type = "admin")[[1]],
ab_from_text("28/03/2020 amoxicilliin 500mg po tds", type = "admin")[[1]],
"oral"
)

3
tests/testthat/test-ab_property.R
View File

@ -27,6 +27,8 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
ab_reset_session()
expect_identical(ab_name("AMX", language = NULL), "Amoxicillin")
expect_identical(ab_atc("AMX"), "J01CA04")
expect_identical(ab_cid("AMX"), as.integer(33613))
@ -94,3 +96,4 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
set_ab_names(NIT:VAN) %>%
colnames())))
}