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atc and bactid functions, readme update

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-08-25 22:01:14 +02:00
parent 460dee789f
commit 2acdb1981c
30 changed files with 761 additions and 449 deletions
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2
tests/testthat/test-abname.R
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@ -5,7 +5,7 @@ test_that("abname works", {
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', tolower = TRUE), "amoxicillin")
expect_equal(abname("amox", from = 'certe', tolower = TRUE), "amoxicillin")
expect_equal(abname("J01CA04", from = 'atc'), "Amoxicillin")
expect_equal(abname(c("amox", "J01CA04", "Trimox", "dispermox", "Amoxil")),
rep("Amoxicillin", 5))

15
tests/testthat/test-atc.R
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@ -22,14 +22,25 @@ test_that("atc_property works", {
})
test_that("guess_atc works", {
expect_equal(guess_atc(c("J01FA01",
expect_equal(as.character(guess_atc(c("J01FA01",
"Erythromycin",
"eryt",
"ERYT",
"ERY",
"Erythrocin",
"Eryzole",
"Pediamycin")),
"Pediamycin"))),
rep("J01FA01", 8))
expect_identical(class(as.atc("amox")), "atc")
})
test_that("atc.property works", {
expect_equal(atc.certe("J01CA04"), "amox")
expect_equal(atc.umcg("J01CA04"), "AMOX")
expect_equal(atc.official("J01CA04"), "Amoxicillin")
expect_equal(atc.official_nl("J01CA04"), "Amoxicilline")
expect_equal(atc.trivial_nl("J01CA04"), "Amoxicilline")
})

13
tests/testthat/test-bactid.R
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@ -108,3 +108,16 @@ test_that("as.bactid works", {
NA_character_)
})
test_that("bactid.property works", {
expect_equal(bactid.family("E. coli"), "Enterobacteriaceae")
expect_equal(bactid.genus("E. coli"), "Escherichia")
expect_equal(bactid.species("E. coli"), "coli")
expect_equal(bactid.subspecies("E. coli"), NA_character_)
expect_equal(bactid.fullname("E. coli"), "Escherichia coli")
expect_equal(bactid.type("E. coli"), "Bacteria")
expect_equal(bactid.gramstain("E. coli"), "Negative rods")
expect_equal(bactid.aerobic("E. coli"), TRUE)
expect_equal(bactid.type_nl("E. coli"), "Bacterie")
expect_equal(bactid.gramstain_nl("E. coli"), "Negatieve staven")
})

5
tests/testthat/test-eucast.R
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@ -32,8 +32,3 @@ test_that("EUCAST rules work", {
stringsAsFactors = FALSE)
expect_equal(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
})
test_that("MO properties work", {
expect_equal(mo_property("ESCCOL"), "Escherichia coli")
expect_equal(mo_property("STAAUR"), "Staphylococcus aureus")
})

23
tests/testthat/test-classes.R → tests/testthat/test-mic.R
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@ -1,25 +1,4 @@
context("classes.R")
test_that("rsi works", {
expect_true(as.rsi("S") < as.rsi("I"))
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(summary(as.rsi(c("S", "R"))), c("Mode" = 'rsi',
"<NA>" = "0",
"Sum S" = "1",
"Sum IR" = "1",
"-Sum R" = "1",
"-Sum I" = "0"))
})
context("mic.R")
test_that("mic works", {
expect_true(as.mic(8) == as.mic("8"))

22
tests/testthat/test-rsi.R Normal file
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@ -0,0 +1,22 @@
context("rsi.R")
test_that("rsi works", {
expect_true(as.rsi("S") < as.rsi("I"))
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(summary(as.rsi(c("S", "R"))), c("Mode" = 'rsi',
"<NA>" = "0",
"Sum S" = "1",
"Sum IR" = "1",
"-Sum R" = "1",
"-Sum I" = "0"))
})