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(v0.7.1.9075) new microorganism codes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-09-18 15:46:09 +02:00
parent f553a08a7b
commit e2aa4f996b
53 changed files with 636 additions and 475 deletions
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6
tests/testthat/test-first_isolate.R
View File

@ -190,19 +190,19 @@ test_that("first isolates work", {
# unknown MOs
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", "UNKNOWN", mo)) %>%
mutate(mo = ifelse(mo == "B_ESCHR_COLI", "UNKNOWN", mo)) %>%
mutate(first = first_isolate(., include_unknown = FALSE)) %>%
.$first %>%
sum(),
1062)
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", "UNKNOWN", mo)) %>%
mutate(mo = ifelse(mo == "B_ESCHR_COLI", "UNKNOWN", mo)) %>%
mutate(first = first_isolate(., include_unknown = TRUE)) %>%
.$first %>%
sum(),
1529)
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", NA, mo)) %>%
mutate(mo = ifelse(mo == "B_ESCHR_COLI", NA, mo)) %>%
mutate(first = first_isolate(.)) %>%
.$first %>%
sum(),

4
tests/testthat/test-freq.R
View File

@ -26,8 +26,8 @@ test_that("frequency table works", {
# mo
expect_true(is.freq(freq(example_isolates$mo)))
# for this to work, the output of mo_gramstain() is to be expected as follows:
expect_equal(mo_gramstain("B_ESCHR_COL", language = NULL), "Gram-negative")
expect_equal(mo_gramstain("B_STPHY_AUR", language = NULL), "Gram-positive")
expect_equal(mo_gramstain("B_ESCHR_COLI", language = NULL), "Gram-negative")
expect_equal(mo_gramstain("B_STPHY_AURS", language = NULL), "Gram-positive")
# rsi
expect_true(is.freq(freq(example_isolates$AMX)))

14
tests/testthat/test-join_microorganisms.R
View File

@ -45,17 +45,17 @@ test_that("joins work", {
expect_true(nrow(unjoined) < nrow(full))
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COL")), 1)
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COL", by = c("mo" = "mo"))), 1)
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI")), 1)
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI", by = c("mo" = "mo"))), 1)
expect_warning(inner_join_microorganisms("Escherichia", by = c("mo" = "genus")))
expect_equal(nrow(left_join_microorganisms("B_ESCHR_COL")), 1)
expect_equal(nrow(left_join_microorganisms("B_ESCHR_COLI")), 1)
expect_warning(left_join_microorganisms("Escherichia", by = c("mo" = "genus")))
expect_equal(nrow(semi_join_microorganisms("B_ESCHR_COL")), 1)
expect_equal(nrow(anti_join_microorganisms("B_ESCHR_COL")), 0)
expect_equal(nrow(semi_join_microorganisms("B_ESCHR_COLI")), 1)
expect_equal(nrow(anti_join_microorganisms("B_ESCHR_COLI")), 0)
expect_warning(right_join_microorganisms("B_ESCHR_COL"))
expect_warning(full_join_microorganisms("B_ESCHR_COL"))
expect_warning(right_join_microorganisms("B_ESCHR_COLI"))
expect_warning(full_join_microorganisms("B_ESCHR_COLI"))
})

2
tests/testthat/test-mdro.R
View File

@ -40,7 +40,7 @@ test_that("mdro works", {
# example_isolates should have these finding using Dutch guidelines
expect_equal(outcome %>% freq() %>% pull(count),
c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
c(1972, 22, 6)) # 1969 neg, 25 unconfirmed, 6 pos
expect_equal(brmo(example_isolates, info = FALSE),
mdro(example_isolates, guideline = "BRMO", info = FALSE))

177
tests/testthat/test-mo.R
View File

@ -31,49 +31,50 @@ test_that("as.mo works", {
expect_identical(
as.character(as.mo(c("E. coli", "H. influenzae"))),
c("B_ESCHR_COL", "B_HMPHL_INF"))
c("B_ESCHR_COLI", "B_HMPHL_INFL"))
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COL")
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COL")
expect_equal(as.character(as.mo(22242416)), "B_ESCHR_COL")
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo(22242416)), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
expect_equal(as.character(as.mo("Esch spp.")), "B_ESCHR")
expect_equal(as.character(as.mo(" B_ESCHR_COL ")), "B_ESCHR_COL")
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COL") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNE")
expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNE_RHI") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
expect_equal(as.character(as.mo("C. difficile")), "B_CLSTR_DIF")
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNE")
expect_equal(as.character(as.mo("C. difficile")), "B_CTRDM_DFFC")
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRB")
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRB")
expect_equal(as.character(as.mo("B_STRPTC")), "B_STRPT") # old MO code (<=v0.5.0)
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
expect_equal(as.character(suppressWarnings(as.mo("B_STRPTC"))), "B_STRPT") # old MO code (<=v0.5.0)
expect_equal(as.character(suppressWarnings(as.mo("B_STRPT_PNE"))), "B_STRPT_PNMN") # old MO code (<=v0.8.0)
expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPT_GRA", "B_STRPT_GRB"))
expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPT_GRPA", "B_STRPT_GRPB"))
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYO") # not Actinomyces pyogenes
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYGN") # not Actinomyces pyogenes
# GLIMS
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRA")
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRGL")
expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPI")
expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPDR")
expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_AER")
expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_ARGN")
expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNMN")
expect_equal(as.character(as.mo("CNS")), "B_STPHY_CNS")
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CNS")
expect_equal(as.character(as.mo("CPS")), "B_STPHY_CPS")
expect_equal(as.character(as.mo("CoPS")), "B_STPHY_CPS")
expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIR")
expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MIL")
expect_equal(as.character(as.mo("CNS")), "B_STPHY_CONS")
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CONS")
expect_equal(as.character(as.mo("CPS")), "B_STPHY_COPS")
expect_equal(as.character(as.mo("CoPS")), "B_STPHY_COPS")
expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIRI")
expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MILL")
expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))
@ -90,11 +91,11 @@ test_that("as.mo works", {
"Staphylococcus aureus",
"MRSA",
"VISA")))),
rep("B_STPHY_AUR", 9))
rep("B_STPHY_AURS", 9))
expect_identical(
as.character(
as.mo(c('EHEC', 'EPEC', 'EIEC', 'STEC', 'ATEC', 'UPEC'))),
rep("B_ESCHR_COL", 6))
rep("B_ESCHR_COLI", 6))
# unprevalent MO
expect_identical(
as.character(
@ -102,7 +103,7 @@ test_that("as.mo works", {
"B. nodosa",
"B nodosa",
"Burkholderia nodosa"))),
rep("B_BRKHL_NOD", 4))
rep("B_BRKHL_NODS", 4))
# empty values
expect_identical(as.character(as.mo(c("", NA, NaN))), rep(NA_character_, 3))
@ -110,40 +111,40 @@ test_that("as.mo works", {
expect_warning(as.mo("ab"))
expect_equal(suppressWarnings(as.character(as.mo(c("Qq species", "", "CRS", "K. pneu rhino", "esco")))),
c("UNKNOWN", NA_character_, "B_STNTR_MAL", "B_KLBSL_PNE_RHI", "B_ESCHR_COL"))
c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI"))
# check for Becker classification
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_STPHY_INT")
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")
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STPHY_INTR")
expect_identical(as.character(as.mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INTR")
expect_identical(as.character(as.mo("Sta intermedius",Becker = TRUE)), "B_STPHY_COPS")
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
# aureus must only be influenced if Becker = "all"
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")
expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_COPS")
# check for Lancefield classification
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYO")
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRA")
expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRA") # group A
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGA")
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRB") # group B
expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRB")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYS_EQU")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRC") # group C
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYGN")
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRPA")
expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRPA") # group A
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGLC")
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRPB") # group B
expect_identical(as.character(suppressWarnings(as.mo("estreptococos grupo B"))), "B_STRPT_GRPB")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYSG_EQSM")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRPC") # group C
# Enterococci must only be influenced if Lancefield = "all"
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_STRPT_GRD") # group D
expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANG")
expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRF") # group F
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SAN")
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRH") # group H
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SAL")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRK") # group K
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_FACM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_FACM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRPD") # group D
expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANGN")
expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRPF") # group F
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SNGN")
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRPH") # group H
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K
library(dplyr)
@ -173,14 +174,14 @@ test_that("as.mo works", {
expect_error(example_isolates %>% select(1:3) %>% as.mo())
# print
expect_output(print(as.mo(c("B_ESCHR_COL", NA))))
expect_output(print(as.mo(c("B_ESCHR_COLI", NA))))
# test pull
expect_equal(nrow(example_isolates %>% mutate(mo = as.mo(mo))),
2000)
# test data.frame
expect_equal(nrow(data.frame(test = as.mo("B_ESCHR_COL"))),
expect_equal(nrow(data.frame(test = as.mo("B_ESCHR_COLI"))),
1)
# check empty values
@ -188,40 +189,40 @@ test_that("as.mo works", {
NA_character_)
# check less prevalent MOs
expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APO_DEL")
expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APO_DEL")
expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APO_DEL")
expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APO")
expect_equal(as.character(as.mo("Gomphosphaeria aponina delicatula")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("Gomphosphaeria apo del")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("G apo deli")), "B_GMPHS_APNN_DLCT")
expect_equal(as.character(as.mo("Gomphosphaeria aponina")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("Gomphosphaeria species")), "B_GMPHS")
expect_equal(as.character(as.mo("Gomphosphaeria")), "B_GMPHS")
expect_equal(as.character(as.mo(" B_GMPHS_APO ")), "B_GMPHS_APO")
expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APO")
expect_equal(as.character(as.mo(" B_GMPHS_APNN ")), "B_GMPHS_APNN")
expect_equal(as.character(as.mo("g aponina")), "B_GMPHS_APNN")
# check old names
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLA")
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLTT")
print(mo_renamed())
# check uncertain names
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AUR")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AURS")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE))
expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AUR")
expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
expect_equal(suppressWarnings(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
expect_equal(suppressWarnings(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AUR")
expect_equal(suppressWarnings(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AURS")
# predefined reference_df
expect_equal(as.character(as.mo("TestingOwnID",
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COL"))),
"B_ESCHR_COL")
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI"))),
"B_ESCHR_COLI")
expect_equal(as.character(as.mo(c("TestingOwnID", "E. coli"),
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COL"))),
c("B_ESCHR_COL", "B_ESCHR_COL"))
reference_df = data.frame(mycol = "TestingOwnID", mo = "B_ESCHR_COLI"))),
c("B_ESCHR_COLI", "B_ESCHR_COLI"))
expect_warning(as.mo("TestingOwnID", reference_df = NULL))
expect_error(as.mo("E. coli", reference_df = data.frame(mycol = "TestingOwnID")))
# combination of existing mo and other code
expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
c("B_ESCHR_COL", "B_ESCHR_COL"))
expect_identical(suppressWarnings(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL")))),
c("B_ESCHR_COLI", "B_ESCHR_COLI"))
# expect_equal(mo_fullname(c("E. spp.",
# "E. spp",
@ -230,24 +231,24 @@ test_that("as.mo works", {
# from different sources
expect_equal(as.character(as.mo(
c("PRTMIR", "bclcer", "B_ESCHR_COL"))),
c("B_PROTS_MIR", "B_BCLLS_CER", "B_ESCHR_COL"))
c("PRTMIR", "bclcer", "B_ESCHR_COLI"))),
c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI"))
# hard to find
expect_equal(as.character(suppressWarnings(as.mo(
c("Microbacterium paraoxidans",
"Streptococcus suis (bovis gr)",
"Raoultella (here some text) terrigena")))),
c("B_MCRBC_PAR", "B_STRPT_SUI", "B_RLTLL_TER"))
print(mo_uncertainties())
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG"))
expect_output(print(mo_uncertainties()))
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(as.character(suppressWarnings(as.mo("Salmonella Goettingen"))),
"B_SLMNL_ENT")
"B_SLMNL_ENTR")
expect_equal(as.character(as.mo("Salmonella Group A")), "B_SLMNL")
# no virusses
expect_warning(as.mo("Virus"))
expect_equal(as.character(as.mo("Virus")), NA_character_)
# summary
expect_equal(length(summary(example_isolates$mo)), 6)
@ -257,7 +258,7 @@ test_that("as.mo works", {
rep(NA_character_, 3))
expect_equal(as.character(as.mo("con")), "UNKNOWN")
expect_equal(as.character(as.mo("xxx")), NA_character_)
expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COL"))
expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COLI"))
expect_equal(as.character(as.mo(c("other", "none", "unknown"))),
rep("UNKNOWN", 3))
@ -271,21 +272,21 @@ test_that("as.mo works", {
expect_error(translate_allow_uncertain(5))
# very old MO codes (<= v0.5.0)
expect_equal(as.character(as.mo("F_CCCCS_NEO")), "F_CRYPT_NEO")
expect_equal(as.character(as.mo("F_CANDD_GLB")), "F_CANDD_GLA")
expect_equal(suppressWarnings(as.character(as.mo("F_CCCCS_NEO"))), "F_CRYPT_NFRM")
expect_equal(suppressWarnings(as.character(as.mo("F_CANDD_GLB"))), "F_CANDD_GLBR")
# debug mode
expect_output(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
# ..coccus
expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
c("B_NESSR_MEN", "B_NESSR_GON", "B_STRPT_PNE"))
c("B_NESSR_MNNG", "B_NESSR_GNRR", "B_STRPT_PNMN"))
# yeasts and fungi
expect_equal(suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
c("F_YEAST", "F_FUNGUS"))
# print tibble
expect_output(print(tibble(mo = as.mo("B_STRPT_PNE"))))
expect_output(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
# assigning and subsetting
x <- example_isolates$mo

2
tests/testthat/test-mo_property.R
View File

@ -57,7 +57,7 @@ test_that("mo_property works", {
expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
#expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
# test integrity
MOs <- AMR::microorganisms

2
tests/testthat/test-read.4d.R
View File

@ -45,7 +45,7 @@ test_that("read 4D works", {
expect_equal(ncol(x), 11)
expect_equal(class(x$date_received), "Date")
expect_equal(class(x$mo), "mo")
expect_equal(as.character(x$mo), "B_ESCHR_COL")
expect_equal(as.character(x$mo), "B_ESCHR_COLI")
expect_equal(is.rsi(x$peni), TRUE)
})

20
tests/testthat/test-resistance_predict.R
View File

@ -23,7 +23,7 @@ context("resistance_predict.R")
test_that("prediction of rsi works", {
AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COL") %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",
col_date = "date",
model = "binomial",
@ -40,47 +40,47 @@ test_that("prediction of rsi works", {
library(dplyr)
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "loglin",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_output(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "lin",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "INVALID MODEL",
col_ab = "AMX",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "NOT EXISTING COLUMN",
col_date = "date",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "NOT EXISTING COLUMN",
info = TRUE))
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(rsi_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
col_ab = "AMX",
col_date = "date",
info = TRUE))
# almost all E. coli are MEM S in the Netherlands :)
expect_error(resistance_predict(x = filter(example_isolates, mo == "B_ESCHR_COL"),
expect_error(resistance_predict(x = filter(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "MEM",
col_date = "date",

10
tests/testthat/test-rsi.R
View File

@ -58,13 +58,13 @@ test_that("rsi works", {
test_that("mic2rsi works", {
expect_equal(as.character(
as.rsi(x = as.mic(0.125),
mo = "B_STRPT_PNE",
mo = "B_STRPT_PNMN",
ab = "AMX",
guideline = "EUCAST")),
"S")
expect_equal(as.character(
as.rsi(x = as.mic(4),
mo = "B_STRPT_PNE",
mo = "B_STRPT_PNMN",
ab = "AMX",
guideline = "EUCAST")),
"R")
@ -80,19 +80,19 @@ test_that("mic2rsi works", {
test_that("disk2rsi works", {
expect_equal(as.character(
as.rsi(x = as.disk(22),
mo = "B_STRPT_PNE",
mo = "B_STRPT_PNMN",
ab = "ERY",
guideline = "CLSI")),
"S")
expect_equal(as.character(
as.rsi(x = as.disk(18),
mo = "B_STRPT_PNE",
mo = "B_STRPT_PNMN",
ab = "ERY",
guideline = "CLSI")),
"I")
expect_equal(as.character(
as.rsi(x = as.disk(10),
mo = "B_STRPT_PNE",
mo = "B_STRPT_PNMN",
ab = "ERY",
guideline = "CLSI")),
"R")