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(v2.1.1.9064) unit tests

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dr. M.S. (Matthijs) Berends 2024-07-16 15:55:58 +02:00
parent 640888f408
commit 7f344836ea
7 changed files with 60 additions and 15 deletions
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38
.github/prehooks/pre-commit vendored Executable file
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@ -0,0 +1,38 @@
#!/bin/bash
# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# always add these:
git add data-raw/*
git add man/*
git add R/sysdata.rda
git add NAMESPACE
git add DESCRIPTION
git add NEWS.md

2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 2.1.1.9063
Version: 2.1.1.9064
Date: 2024-07-16
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9063
# AMR 2.1.1.9064
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*

19
R/mo.R
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@ -420,17 +420,21 @@ as.mo <- function(x,
# Keep or replace synonyms ----
lpsn_matches <- AMR_env$MO_lookup$lpsn_renamed_to[match(out, AMR_env$MO_lookup$mo)]
lpsn_matches[!lpsn_matches %in% AMR_env$MO_lookup$lpsn] <- NA
# GBIF only for non-bacteria, since we use LPSN as primary source for bacteria
mycobank_matches <- AMR_env$MO_lookup$mycobank_renamed_to[match(out, AMR_env$MO_lookup$mo)]
mycobank_matches[!mycobank_matches %in% AMR_env$MO_lookup$mycobank] <- NA
# GBIF only for non-bacteria and non-fungi, since we use LPSN as primary source for bacteria and MycoBank for fungi
# (an example is Strep anginosus, renamed according to GBIF, not according to LPSN)
gbif_matches <- AMR_env$MO_lookup$gbif_renamed_to[AMR_env$MO_lookup$kingdom != "Bacteria"][match(out, AMR_env$MO_lookup$mo[AMR_env$MO_lookup$kingdom != "Bacteria"])]
gbif_matches <- AMR_env$MO_lookup$gbif_renamed_to[!AMR_env$MO_lookup$kingdom %in% c("Bacteria", "Fungi")][match(out, AMR_env$MO_lookup$mo[!AMR_env$MO_lookup$kingdom %in% c("Bacteria", "Fungi")])]
gbif_matches[!gbif_matches %in% AMR_env$MO_lookup$gbif] <- NA
AMR_env$mo_renamed <- list(
old = out[!is.na(gbif_matches) | !is.na(lpsn_matches)],
gbif_matches = gbif_matches[!is.na(gbif_matches) | !is.na(lpsn_matches)],
lpsn_matches = lpsn_matches[!is.na(gbif_matches) | !is.na(lpsn_matches)]
old = out[!is.na(gbif_matches) | !is.na(lpsn_matches) | !is.na(mycobank_matches)],
gbif_matches = gbif_matches[!is.na(gbif_matches) | !is.na(lpsn_matches) | !is.na(mycobank_matches)],
mycobank_matches = mycobank_matches[!is.na(gbif_matches) | !is.na(lpsn_matches) | !is.na(mycobank_matches)],
lpsn_matches = lpsn_matches[!is.na(gbif_matches) | !is.na(lpsn_matches) | !is.na(mycobank_matches)]
)
if (isFALSE(keep_synonyms)) {
out[which(!is.na(gbif_matches))] <- AMR_env$MO_lookup$mo[match(gbif_matches[which(!is.na(gbif_matches))], AMR_env$MO_lookup$gbif)]
out[which(!is.na(mycobank_matches))] <- AMR_env$MO_lookup$mo[match(mycobank_matches[which(!is.na(mycobank_matches))], AMR_env$MO_lookup$mycobank)]
out[which(!is.na(lpsn_matches))] <- AMR_env$MO_lookup$mo[match(lpsn_matches[which(!is.na(lpsn_matches))], AMR_env$MO_lookup$lpsn)]
if (isTRUE(info) && length(AMR_env$mo_renamed$old) > 0) {
print(mo_renamed(), extra_txt = " (use `keep_synonyms = TRUE` to leave uncorrected)")
@ -1040,13 +1044,14 @@ convert_colloquial_input <- function(x) {
out[x %like_case% "anaerob[a-z]+ .*gram[ -]?neg.*"] <- "B_ANAER-NEG"
out[x %like_case% "anaerob[a-z]+ .*gram[ -]?pos.*"] <- "B_ANAER-POS"
out[is.na(out) & x %like_case% "anaerob[a-z]+ (micro)?.*organism"] <- "B_ANAER"
out[is.na(out) & x %like_case% "anaerob[a-z]+ bacter"] <- "B_ANAER"
# coryneform bacteria
out[x %like_case% "^coryneform"] <- "B_CORYNF"
# yeasts and fungi
out[x %like_case% "^yeast?"] <- "F_YEAST"
out[x %like_case% "^fung(us|i)"] <- "F_FUNGUS"
out[x %like_case% "(^| )yeast?"] <- "F_YEAST"
out[x %like_case% "(^| )fung(us|i)"] <- "F_FUNGUS"
# trivial names known to the field
out[x %like_case% "meningo[ck]o[ck]"] <- "B_NESSR_MNNG"

3
data-raw/_pre_commit_checks.R
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@ -122,7 +122,8 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
"vitulinus", "vitulus", "warneri", "xylosus",
"caledonicus", "canis",
"durrellii", "lloydii",
"ratti", "taiwanensis", "veratri", "urealyticus"
"ratti", "taiwanensis", "veratri", "urealyticus",
"americanisciuri", "marylandisciuri", "shinii", "brunensis"
) |
# old, now renamed to S. schleiferi (but still as synonym in our data of course):
(MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),

2
inst/tinytest/test-mo.R
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@ -265,7 +265,7 @@ expect_equal(
"Raoultella (here some text) terrigena"
)
))),
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG")
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_KLBSL_TRRG")
)
expect_stdout(print(mo_uncertainties()))
x <- as.mo("Sta. aur")

9
inst/tinytest/test-mo_property.R
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@ -104,10 +104,10 @@ expect_true(length(mo_group_members("B_HACEK")) > 1)
expect_inherits(mo_group_members(c("Candida albicans", "Escherichia coli")), "list")
expect_identical(mo_oxygen_tolerance(c("Klebsiella pneumoniae", "Clostridioides difficile")),
c("aerobe", "anaerobe"))
c("facultative anaerobe", "anaerobe"))
expect_equal(as.character(table(mo_pathogenicity(example_isolates$mo))),
c("1874", "109", "1", "16"))
c("1911", "72", "1", "16"))
expect_equal(mo_ref("Escherichia coli"), "Castellani et al., 1919")
expect_equal(mo_authors("Escherichia coli"), "Castellani et al.")
@ -116,8 +116,9 @@ expect_equal(mo_year("Escherichia coli"), 1919)
expect_true(mo_url("Candida albicans") %like% "gbif.org")
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
# test integrity
expect_identical(microorganisms$fullname, mo_fullname(microorganisms$fullname, language = "en", keep_synonyms = TRUE))
# test integrity of getting back full names
expect_identical(microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"],
suppressWarnings(mo_fullname(microorganisms$fullname[microorganisms$fullname %unlike% "(Fungi|{)"], language = "en", keep_synonyms = TRUE)))
# check languages
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")