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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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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)