mirror of
https://github.com/msberends/AMR.git
synced 2025-07-09 17:02:03 +02:00
Support for German and Spanish microorganism properties, cleanup
This commit is contained in:
@ -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)
|
||||
|
||||
|
Reference in New Issue
Block a user