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guess_mo deprecation

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dr. M.S. (Matthijs) Berends
2019-01-06 16:40:55 +01:00
parent 5c6ff1bbda
commit 0205b6178d
6 changed files with 46 additions and 107 deletions
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54
tests/testthat/test-mo.R
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@ -102,36 +102,36 @@ test_that("as.mo works", {
c(NA_character_, NA_character_, "B_STNTR_MAL", "B_KLBSL_PNE_RHI", "B_ESCHR_COL"))
# check for Becker classification
expect_identical(as.character(guess_mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI")
expect_identical(as.character(guess_mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CNS")
expect_identical(as.character(guess_mo("STAEPI", Becker = TRUE)), "B_STPHY_CNS")
expect_identical(as.character(guess_mo("S. intermedius", Becker = FALSE)), "B_STRPTC_INT") # Strep (!) intermedius
expect_identical(as.character(guess_mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INT")
expect_identical(as.character(guess_mo("Sta intermedius",Becker = TRUE)), "B_STPHY_CPS")
expect_identical(as.character(guess_mo("STAINT", Becker = TRUE)), "B_STPHY_CPS")
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI")
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CNS")
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CNS")
expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STRPTC_INT") # Strep (!) intermedius
expect_identical(as.character(as.mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INT")
expect_identical(as.character(as.mo("Sta intermedius",Becker = TRUE)), "B_STPHY_CPS")
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_CPS")
# aureus must only be influenced if Becker = "all"
expect_identical(as.character(guess_mo("STAAUR", Becker = FALSE)), "B_STPHY_AUR")
expect_identical(as.character(guess_mo("STAAUR", Becker = TRUE)), "B_STPHY_AUR")
expect_identical(as.character(guess_mo("STAAUR", Becker = "all")), "B_STPHY_CPS")
expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AUR")
expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AUR")
expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_CPS")
# check for Lancefield classification
expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = FALSE)), "B_STRPTC_PYO")
expect_identical(as.character(guess_mo("S. pyogenes", Lancefield = TRUE)), "B_STRPTC_GRA")
expect_identical(as.character(guess_mo("STCPYO", Lancefield = TRUE)), "B_STRPTC_GRA") # group A
expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = FALSE)), "B_STRPTC_AGA")
expect_identical(as.character(guess_mo("S. agalactiae", Lancefield = TRUE)), "B_STRPTC_GRB") # group B
expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = FALSE)), "B_STRPTC_DYS_EQU")
expect_identical(as.character(guess_mo("S. equisimilis", Lancefield = TRUE)), "B_STRPTC_GRC") # group C
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPTC_PYO")
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPTC_GRA")
expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPTC_GRA") # group A
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPTC_AGA")
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPTC_GRB") # group B
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPTC_DYS_EQU")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPTC_GRC") # group C
# Enterococci must only be influenced if Lancefield = "all"
expect_identical(as.character(guess_mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_IUM")
expect_identical(as.character(guess_mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_IUM")
expect_identical(as.character(guess_mo("E. faecium", Lancefield = "all")), "B_STRPTC_GRD") # group D
expect_identical(as.character(guess_mo("S. anginosus", Lancefield = FALSE)), "B_STRPTC_ANG")
expect_identical(as.character(guess_mo("S. anginosus", Lancefield = TRUE)), "B_STRPTC_GRF") # group F
expect_identical(as.character(guess_mo("S. sanguinis", Lancefield = FALSE)), "B_STRPTC_SAN")
expect_identical(as.character(guess_mo("S. sanguinis", Lancefield = TRUE)), "B_STRPTC_GRH") # group H
expect_identical(as.character(guess_mo("S. salivarius", Lancefield = FALSE)), "B_STRPTC_SAL")
expect_identical(as.character(guess_mo("S. salivarius", Lancefield = TRUE)), "B_STRPTC_GRK") # group K
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_IUM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_IUM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPTC_GRD") # group D
expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPTC_ANG")
expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPTC_GRF") # group F
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPTC_SAN")
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPTC_GRH") # group H
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPTC_SAL")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPTC_GRK") # group K
library(dplyr)
@ -166,7 +166,7 @@ test_that("as.mo works", {
# helper function
expect_identical(as.mo("B_ESCHR_COL"),
guess_mo("B_ESCHR_COL"))
as.mo("B_ESCHR_COL"))
# test pull
expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),