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Support for German and Spanish microorganism properties, cleanup

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-09-04 11:33:30 +02:00
parent 5405002119
commit b388e3fee7
20 changed files with 256 additions and 157 deletions
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3
tests/testthat/test-ab_property.R
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@ -8,4 +8,7 @@ test_that("ab_property works", {
expect_equal(ab_umcg("amox"), "AMOX")
expect_equal(class(ab_tradenames("amox")), "character")
expect_equal(class(ab_tradenames(c("amox", "amox"))), "list")
expect_equal(ab_atc("amox"), as.character(as.atc("amox")))
expect_error(ab_property("amox", "invalid property"))
})

6
tests/testthat/test-deprecated.R
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@ -16,9 +16,11 @@ test_that("deprecated functions work", {
old_mo <- "ESCCOL"
class(old_mo) <- "bactid"
df_oldmo <- data.frame(test = old_mo)
# print
expect_output(print(old_mo))
# test data.frame and pull
expect_equal(as.character(dplyr::pull(data.frame(test = old_mo), test)), "ESCCOL")
# test pull
library(dplyr)
expect_identical(df_oldmo %>% pull(test), old_mo)
})

51
tests/testthat/test-mo.R
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@ -12,7 +12,7 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("klpn")), "KLEPNE")
expect_equal(as.character(as.mo("Klebsiella")), "KLE")
expect_equal(as.character(as.mo("K. pneu rhino")), "KLEPNERH") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("coagulase negative")), "STACNS")
expect_equal(as.character(as.mo("Bartonella")), "BAR")
expect_equal(as.character(as.mo("P. aer")), "PSEAER") # not Pasteurella aerogenes
@ -30,16 +30,21 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("VISP")), "STCPNE")
expect_equal(as.character(as.mo("VRSP")), "STCPNE")
expect_equal(as.character(as.mo("CNS")), "STACNS")
expect_equal(as.character(as.mo("CoNS")), "STACNS")
expect_equal(as.character(as.mo("CPS")), "STACPS")
expect_equal(as.character(as.mo("CoPS")), "STACPS")
expect_identical(
as.character(
as.mo(c("stau",
"STAU",
"staaur",
"S. aureus",
"S aureus",
"Staphylococcus aureus",
"MRSA",
"VISA"))),
"STAU",
"staaur",
"S. aureus",
"S aureus",
"Staphylococcus aureus",
"MRSA",
"VISA"))),
rep("STAAUR", 8))
# check for Becker classification
@ -55,19 +60,23 @@ test_that("as.mo works", {
expect_identical(as.character(guess_mo("STAAUR", Becker = "all")), "STACPS")
# check for Lancefield classification
expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = FALSE)), "STCPYO")
expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = TRUE)), "STCGRA")
expect_identical(as.character(guess_mo("STCPYO", Lancefield = TRUE)), "STCGRA")
expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = FALSE)), "STCAGA")
expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = TRUE)), "STCGRB") # group B
expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = FALSE)), "STCEQS")
expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = TRUE)), "STCGRC") # group C
expect_identical(as.character(guess_mo("S. anginosus", Lancefield = FALSE)), "STCANG")
expect_identical(as.character(guess_mo("S. anginosus", Lancefield = TRUE)), "STCGRF") # group F
expect_identical(as.character(guess_mo("S. sanguis", Lancefield = FALSE)), "STCSAN")
expect_identical(as.character(guess_mo("S. sanguis", Lancefield = TRUE)), "STCGRH") # group H
expect_identical(as.character(guess_mo("S. salivarius", Lancefield = FALSE)), "STCSAL")
expect_identical(as.character(guess_mo("S. salivarius", Lancefield = TRUE)), "STCGRK") # group K
expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = FALSE)), "STCPYO")
expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = TRUE)), "STCGRA")
expect_identical(as.character(guess_mo("STCPYO", Lancefield = TRUE)), "STCGRA") # group A
expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = FALSE)), "STCAGA")
expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = TRUE)), "STCGRB") # group B
expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = FALSE)), "STCEQS")
expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = TRUE)), "STCGRC") # group C
# Enterococci must only be influenced if Lancefield = "all"
expect_identical(as.character(guess_mo("E. faecium", Lancefield = FALSE)), "ENCFAC")
expect_identical(as.character(guess_mo("E. faecium", Lancefield = TRUE)), "ENCFAC")
expect_identical(as.character(guess_mo("E. faecium", Lancefield = "all")), "STCGRD") # group D
expect_identical(as.character(guess_mo("S. anginosus", Lancefield = FALSE)), "STCANG")
expect_identical(as.character(guess_mo("S. anginosus", Lancefield = TRUE)), "STCGRF") # group F
expect_identical(as.character(guess_mo("S. sanguis", Lancefield = FALSE)), "STCSAN")
expect_identical(as.character(guess_mo("S. sanguis", Lancefield = TRUE)), "STCGRH") # group H
expect_identical(as.character(guess_mo("S. salivarius", Lancefield = FALSE)), "STCSAL")
expect_identical(as.character(guess_mo("S. salivarius", Lancefield = TRUE)), "STCGRK") # group K
library(dplyr)

10
tests/testthat/test-mo_property.R
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@ -9,6 +9,12 @@ test_that("mo_property works", {
expect_equal(mo_type("E. coli"), "Bacteria")
expect_equal(mo_gramstain("E. coli"), "Negative rods")
expect_equal(mo_aerobic("E. coli"), TRUE)
expect_equal(mo_type_nl("E. coli"), "Bacterie")
expect_equal(mo_gramstain_nl("E. coli"), "Negatieve staven")
expect_equal(mo_type("E. coli", language = "de"), "Bakterien")
expect_equal(mo_gramstain("E. coli", language = "de"), "Negative Staebchen")
expect_equal(mo_type("E. coli", language = "nl"), "Bacterie")
expect_equal(mo_gramstain("E. coli", language = "nl"), "Negatieve staven")
expect_error(mo_type("E. coli", language = "INVALID"))
})