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added prevalence column and alterted as.mo algorith to use it, added ab_name as alias

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-09-16 16:43:29 +02:00
parent b0ca49d68d
commit b792a2754e
16 changed files with 101 additions and 79 deletions
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26
tests/testthat/test-mo.R
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@ -3,7 +3,7 @@ context("mo.R")
test_that("as.mo works", {
library(dplyr)
MOs <- AMR::microorganisms %>% filter(!is.na(mo))
MOs <- AMR::microorganisms %>% filter(!is.na(mo), nchar(mo) > 3)
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
expect_identical(
@ -12,18 +12,20 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL")
expect_equal(as.character(as.mo("Escherichia coli")), "ESCCOL")
expect_equal(as.character(as.mo("Escherichia species")), "ESC")
expect_equal(as.character(as.mo("Escherichia species")), "ESCSPP")
expect_equal(as.character(as.mo("Escherichia")), "ESCSPP")
expect_equal(as.character(as.mo(" ESCCOL ")), "ESCCOL")
expect_equal(as.character(as.mo("coli")), "ESCCOL") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "KLEPNE")
expect_equal(as.character(as.mo("Klebsiella")), "KLE")
expect_equal(as.character(as.mo("Klebsiella")), "KLESPP")
expect_equal(as.character(as.mo("K. pneu rhino")), "KLEPNERH") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "BAR")
expect_equal(as.character(as.mo("Bartonella")), "BARSPP")
expect_equal(as.character(as.mo("C. difficile")), "CLODIF")
expect_equal(as.character(as.mo("L. pneumophila")), "LEGPNE")
expect_equal(as.character(as.mo("L. non pneumophila")), "LEGNON")
expect_equal(as.character(as.mo("S. beta-haemolytic")), "STCHAE")
expect_equal(as.character(as.mo("Strepto")), "STC") # not Streptobacillus
expect_equal(as.character(as.mo("Streptococcus")), "STC") # not Peptostreptoccus
expect_equal(as.character(as.mo("Strepto")), "STCSPP")
expect_equal(as.character(as.mo("Streptococcus")), "STCSPP") # not Peptostreptoccus
expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("STCGRA", "STCGRB"))
@ -39,7 +41,7 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("bctfgr")), "BACFRA")
expect_equal(as.character(as.mo("MRSE")), "STAEPI")
expect_equal(as.character(as.mo("VRE")), "ENC")
expect_equal(as.character(as.mo("VRE")), "ENCSPP")
expect_equal(as.character(as.mo("MRPA")), "PSEAER")
expect_equal(as.character(as.mo("PISP")), "STCPNE")
expect_equal(as.character(as.mo("PRSP")), "STCPNE")
@ -67,8 +69,9 @@ test_that("as.mo works", {
expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "STAEPI")
expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)), "STACNS")
expect_identical(as.character(guess_mo("STAEPI", Becker = TRUE)), "STACNS")
expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "STAINT")
expect_identical(as.character(guess_mo("S. intermedius", Becker = TRUE)), "STACPS")
expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "STCINT") # Strep (!) intermedius
expect_identical(as.character(guess_mo("Sta intermedius",Becker = FALSE)), "STAINT")
expect_identical(as.character(guess_mo("Sta intermedius",Becker = TRUE)), "STACPS")
expect_identical(as.character(guess_mo("STAINT", Becker = TRUE)), "STACPS")
# aureus must only be influenced if Becker = "all"
expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "STAAUR")
@ -103,8 +106,9 @@ test_that("as.mo works", {
select(genus) %>%
as.mo() %>%
as.character(),
c("ESC", "ESC", "STA", "STA", "STA",
"STA", "STA", "STA", "STA", "STA"))
paste0(c("ESC", "ESC", "STA", "STA", "STA",
"STA", "STA", "STA", "STA", "STA"),
"SPP"))
# select with two columns
expect_identical(