P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 11:51:59 +02:00
Code Releases Activity

update dependencies

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-04-02 16:05:09 +02:00
parent cee64ef050
commit 07bdd61241
15 changed files with 172 additions and 221 deletions
Download Patch File Download Diff File Expand all files Collapse all files

1
tests/testthat/test-atc.R
View File

@ -9,6 +9,7 @@ test_that("atc_property works", {
test_that("abname works", {
expect_equal(abname("AMOX"), "Amoxicillin")
expect_equal(abname(c("AMOX", "GENT")), c("Amoxicillin", "Gentamicin"))
expect_equal(abname(c("AMOX+GENT")), "Amoxicillin + gentamicin")
expect_equal(abname("AMOX", from = 'umcg'), "Amoxicillin")
expect_equal(abname("amox", from = 'molis'), "Amoxicillin")
expect_equal(abname("J01CA04", from = 'atc'), "Amoxicillin")

22
tests/testthat/test-classes.R
View File

@ -5,11 +5,14 @@ test_that("rsi works", {
expect_true(as.rsi("I") < as.rsi("R"))
expect_true(as.rsi("R") > as.rsi("S"))
expect_true(is.rsi(as.rsi("S")))
# print plots, should not raise errors
barplot(as.rsi(c("S", "I", "R")))
plot(as.rsi(c("S", "I", "R")))
print(as.rsi(c("S", "I", "R")))
expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
expect_equal(class(barplot(as.rsi(c("S", "I", "R")))), "numeric")
expect_equal(summary(as.rsi(c("S", "R"))), c("Mode" = 'rsi',
"<NA>" = "0",
"Sum S" = "1",
@ -23,13 +26,16 @@ test_that("mic works", {
expect_true(as.mic("1") > as.mic("<=0.0625"))
expect_true(as.mic("1") < as.mic(">=32"))
expect_true(is.mic(as.mic(8)))
expect_equal(as.double(as.mic(">=32")), 32)
expect_equal(as.integer(as.mic(">=32")), 32)
expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
expect_equal(class(plot(as.mic(c(1, 2, 4, 8)))), "numeric")
# print plots, should not raise errors
barplot(as.mic(c(1, 2, 4, 8)))
plot(as.mic(c(1, 2, 4, 8)))
print(as.mic(c(1, 2, 4, 8)))
expect_equal(summary(as.mic(c(2, 8))), c("Mode" = 'mic',
"<NA>" = "0",
"Min." = "2",

4
tests/testthat/test-eucast.R
View File

@ -12,8 +12,8 @@ test_that("EUCAST rules work", {
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
expect_equal(EUCAST_rules(a, info = FALSE), b)
expect_equal(interpretive_reading(a, info = FALSE), b)
expect_equal(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
a <- data.frame(bactid = c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
coli = "-", # Colistin

25
tests/testthat/test-first_isolates.R
View File

@ -7,7 +7,6 @@ test_that("keyantibiotics work", {
expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
})
test_that("guess_bactid works", {
expect_equal(guess_bactid("E. coli"), "ESCCOL")
expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
@ -15,9 +14,23 @@ test_that("guess_bactid works", {
test_that("first isolates work", {
# septic_patients contains 1960 out of 2000 first isolates
expect_equal(sum(first_isolate(septic_patients,
"date",
"patient_id",
"bactid",
info = FALSE)), 1960)
septic_ptns <- septic_patients
expect_equal(sum(first_isolate(tbl = septic_ptns,
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
info = FALSE)), 1960)
# septic_patients contains 1962 out of 2000 first weighted isolates
septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
expect_equal(
suppressWarnings(sum(
first_isolate(tbl = septic_ptns,
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_keyantibiotics = "keyab",
type = "keyantibiotics",
info = TRUE))),
1962)
})

6
tests/testthat/test-misc.R
View File

@ -12,9 +12,3 @@ test_that("percentages works", {
expect_equal(percent(0.5), "50%")
expect_equal(percent(0.1234), "12.3%")
})
test_that("quasiquotation works", {
expect_equal(quasiquotate(deparse(substitute("test")), "test"), "test")
expect_equal(quasiquotate(deparse(substitute('test')), "'test'"), "test")
expect_equal(quasiquotate(deparse(substitute(test)), test), "test")
})