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Catalogue of Life, replaces ITIS

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-02-18 02:33:37 +01:00
parent 9209787a53
commit 54f8258f8c
88 changed files with 607 additions and 590 deletions
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22
tests/testthat/test-first_isolate.R
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@ -22,7 +22,7 @@
context("first_isolate.R")
test_that("first isolates work", {
# septic_patients contains 1317 out of 2000 first isolates
# first isolates
expect_equal(
sum(
first_isolate(tbl = septic_patients,
@ -31,9 +31,9 @@ test_that("first isolates work", {
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1317)
1274)
# septic_patients contains 1413 out of 2000 first *weighted* isolates
# first *weighted* isolates
expect_equal(
suppressWarnings(
sum(
@ -46,7 +46,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1413)
1369)
# should be same for tibbles
expect_equal(
suppressWarnings(
@ -60,8 +60,8 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1413)
# and 1436 when not ignoring I
1369)
# when not ignoring I
expect_equal(
suppressWarnings(
sum(
@ -74,8 +74,8 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1436)
# and 1417 when using points
1392)
# when using points
expect_equal(
suppressWarnings(
sum(
@ -87,9 +87,9 @@ test_that("first isolates work", {
type = "points",
info = TRUE),
na.rm = TRUE)),
1417)
1372)
# septic_patients contains 1163 out of 2000 first non-ICU isolates
# first non-ICU isolates
expect_equal(
sum(
first_isolate(septic_patients,
@ -100,7 +100,7 @@ test_that("first isolates work", {
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
1163)
1129)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)

78
tests/testthat/test-mo.R
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@ -41,27 +41,25 @@ test_that("as.mo works", {
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("Bartonella")), "B_BRTNL")
expect_equal(as.character(as.mo("C. difficile")), "B_CTRDM_DIF")
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("Strepto")), "B_STRPTC")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPTC") # not Peptostreptoccus
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(c("GAS", "GBS"))), c("B_STRPTC_GRA", "B_STRPTC_GRB"))
expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPT_GRA", "B_STRPT_GRB"))
expect_equal(as.character(as.mo("S. pyo")), "B_STRPTC_PYO") # not Actinomyces pyogenes
expect_equal(as.character(as.mo("P. aer")), "B_PDMNS_AER") # not Pasteurella aerogenes
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYO") # not Actinomyces pyogenes
# GLIMS
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRA")
expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPI")
expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
expect_equal(as.character(as.mo("MRPA")), "B_PDMNS_AER")
expect_equal(as.character(as.mo("PISP")), "B_STRPTC_PNE")
expect_equal(as.character(as.mo("PRSP")), "B_STRPTC_PNE")
expect_equal(as.character(as.mo("VISP")), "B_STRPTC_PNE")
expect_equal(as.character(as.mo("VRSP")), "B_STRPTC_PNE")
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("CNS")), "B_STPHY_CNS")
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CNS")
@ -85,13 +83,11 @@ test_that("as.mo works", {
# unprevalent MO
expect_identical(
as.character(
as.mo(c("buno",
"BUNO",
"burnod",
as.mo(c("burnod",
"B. nodosa",
"B nodosa",
"Burkholderia nodosa"))),
rep("B_BRKHL_NOD", 6))
rep("B_BRKHL_NOD", 4))
# empty values
expect_identical(as.character(as.mo(c("", NA, NaN))), rep(NA_character_, 3))
@ -105,7 +101,7 @@ test_that("as.mo works", {
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("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")
@ -115,23 +111,23 @@ test_that("as.mo works", {
expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_CPS")
# check for Lancefield classification
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
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(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
# 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_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
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
library(dplyr)
@ -164,10 +160,6 @@ test_that("as.mo works", {
# print
expect_output(print(as.mo(c("B_ESCHR_COL", NA))))
# helper function
expect_identical(as.mo("B_ESCHR_COL"),
as.mo("B_ESCHR_COL"))
# test pull
expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),
2000)
@ -192,11 +184,11 @@ test_that("as.mo works", {
# check old names
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLA")
# - Didymosphaeria spartinae (unprevalent)
expect_warning(suppressMessages(as.mo("D spartin", allow_uncertain = TRUE)))
# - was renamed to Leptosphaeria obiones
expect_equal(suppressWarnings(suppressMessages(as.character(as.mo("D spartin", allow_uncertain = TRUE)))),
"F_LPTSP_OBI")
# # - Didymosphaeria spartinae (unprevalent)
# expect_warning(suppressMessages(as.mo("D spartin", allow_uncertain = TRUE)))
# # - was renamed to Leptosphaeria obiones
# expect_equal(suppressWarnings(suppressMessages(as.character(as.mo("D spartin", allow_uncertain = TRUE)))),
# "F_LPTSP_OBI")
# check uncertain names
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), NA_character_)
@ -217,10 +209,6 @@ test_that("as.mo works", {
expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
c("B_ESCHR_COL", "B_ESCHR_COL"))
# TSN of prevalent and non prevalent ones
expect_equal(mo_TSN(c("Gomphosphaeria aponina delicatula", "Escherichia coli")),
c(717, 285))
# expect_equal(mo_fullname(c("E. spp.",
# "E. spp",
# "E. species")),
@ -236,7 +224,7 @@ test_that("as.mo works", {
c("Microbacterium paraoxidans",
"Streptococcus suis (bovis gr)",
"Raoultella (here some text) terrigena")))),
c("B_MCRBC", "B_STRPTC_SUI", "B_RLTLL_TER"))
c("B_MCRBC", "B_STRPT_SUI", "B_RLTLL_TER"))
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(as.character(suppressMessages(as.mo("Salmonella Goettingen"))),

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

@ -23,31 +23,29 @@ context("mo_property.R")
test_that("mo_property works", {
expect_equal(mo_kingdom("E. coli"), "Bacteria")
expect_equal(mo_subkingdom("E. coli"), "Negibacteria")
expect_equal(mo_phylum("E. coli"), "Proteobacteria")
expect_equal(mo_class("E. coli"), "Gammaproteobacteria")
expect_equal(mo_order("E. coli"), "Enterobacteriales")
expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
expect_equal(mo_genus("E. coli"), "Escherichia")
expect_equal(mo_species("E. coli"), "coli")
expect_equal(mo_subspecies("E. coli"), NA_character_)
expect_equal(mo_subspecies("E. coli"), "")
expect_equal(mo_fullname("E. coli"), "Escherichia coli")
expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
expect_equal(mo_TSN("E. coli"), 285)
expect_equal(class(mo_taxonomy("E. coli")), "list")
expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "subkingdom", "phylum", "class", "order",
expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies"))
expect_equal(mo_ref("E. coli"), "Castellani and Chalmers, 1919")
expect_equal(mo_authors("E. coli"), "Castellani and Chalmers")
expect_equal(mo_ref("E. coli"), "(Migula, 1895) Castellani and Chalmers, 1919")
expect_equal(mo_authors("E. coli"), "(Migula) Castellani and Chalmers")
expect_equal(mo_year("E. coli"), 1919)
expect_equal(mo_shortname("MRSA"), "S. aureus")
expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
expect_equal(mo_shortname("MRSA", Becker = "all", language = "en"), "CoPS")
expect_equal(mo_shortname("S. aga"), "S. agalactiae")
expect_equal(mo_shortname("S. aga", Lancefield = TRUE), "GBS")
expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")
# test integrity
MOs <- AMR::microorganisms