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AMR
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better as.mo handling

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dr. M.S. (Matthijs) Berends 4 years ago
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9 changed files with 204 additions and 50 deletions
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  1. 8
      DESCRIPTION
  2. 3
      NAMESPACE
  3. 18
      NEWS.md
  4. 4
      R/first_isolate.R
  5. 174
      R/mo.R
  6. 9
      R/mo_property.R
  7. 14
      man/mo_failures.Rd
  8. 14
      man/mo_renamed.Rd
  9. 10
      tests/testthat/test-mo.R

8
DESCRIPTION
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@ -1,6 +1,6 @@ @@ -1,6 +1,6 @@
Package: AMR
Version: 0.5.0
Date: 2018-12-01
Version: 0.5.0.9001
Date: 2018-12-05
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(
@ -39,8 +39,8 @@ Authors@R: c( @@ -39,8 +39,8 @@ Authors@R: c(
role = "ths",
comment = c(ORCID = "0000-0003-1634-0010")))
Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) to work with microbial and antimicrobial properties by using
evidence-based methods.
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods.
Depends:
R (>= 3.1.0)
Imports:

3
NAMESPACE
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@ -94,6 +94,7 @@ export(mdro) @@ -94,6 +94,7 @@ export(mdro)
export(mo_TSN)
export(mo_authors)
export(mo_class)
export(mo_failures)
export(mo_family)
export(mo_fullname)
export(mo_genus)
@ -103,6 +104,7 @@ export(mo_order) @@ -103,6 +104,7 @@ export(mo_order)
export(mo_phylum)
export(mo_property)
export(mo_ref)
export(mo_renamed)
export(mo_shortname)
export(mo_species)
export(mo_subkingdom)
@ -175,6 +177,7 @@ importFrom(crayon,blue) @@ -175,6 +177,7 @@ importFrom(crayon,blue)
importFrom(crayon,bold)
importFrom(crayon,green)
importFrom(crayon,italic)
importFrom(crayon,magenta)
importFrom(crayon,red)
importFrom(crayon,silver)
importFrom(crayon,strip_style)

18
NEWS.md
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@ -1,5 +1,19 @@ @@ -1,5 +1,19 @@
# 0.5.0
**Published on CRAN: 2018-12-01**
# 0.5.0.90xx (latest development version)
#### New
* Function `mo_failures` to review values that could not be coerced to a valid MO code, using `as.mo`. This latter function will now only show a maximum of 25 uncoerced values.
#### Changed
* Improvements for `as.mo`:
* Finds better results when input is in other languages
* Better handling for subspecies
* Better handling for *Salmonellae*
* Function `first_isolate` will now use a column named like "patid" for the patient ID, when this parameter was left blank
# 0.5.0 (latest stable release)
**Published on CRAN: 2018-11-30**
#### New
* Repository moved to GitLab: https://gitlab.com/msberends/AMR

4
R/first_isolate.R
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@ -164,8 +164,8 @@ first_isolate <- function(tbl, @@ -164,8 +164,8 @@ first_isolate <- function(tbl,
message("NOTE: Using column `", col_date, "` as input for `col_date`.")
}
# -- patient id
if (is.null(col_patient_id) & any(colnames(tbl) %like% "^patient")) {
col_patient_id <- colnames(tbl)[colnames(tbl) %like% "^patient"][1]
if (is.null(col_patient_id) & any(colnames(tbl) %like% "^(patient|patid)")) {
col_patient_id <- colnames(tbl)[colnames(tbl) %like% "^(patient|patid)"][1]
message("NOTE: Using column `", col_patient_id, "` as input for `col_patient_id`.")
}

174
R/mo.R
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@ -137,10 +137,10 @@ @@ -137,10 +137,10 @@
#' mutate(mo = as.mo(paste(genus, species)))
#' }
as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE, reference_df = NULL) {
structure(mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = allow_uncertain, reference_df = reference_df),
class = "mo")
mo <- mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = allow_uncertain, reference_df = reference_df)
structure(.Data = mo, class = "mo")
}
#' @rdname as.mo
@ -155,9 +155,12 @@ is.mo <- function(x) { @@ -155,9 +155,12 @@ is.mo <- function(x) {
#' @export
guess_mo <- as.mo
#' @importFrom dplyr %>% pull left_join
#' @importFrom dplyr %>% pull left_join n_distinct
#' @importFrom data.table data.table as.data.table setkey
exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = FALSE, reference_df = NULL, property = "mo") {
#' @importFrom crayon magenta red italic
exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
allow_uncertain = FALSE, reference_df = NULL,
property = "mo", clear_options = TRUE) {
if (!"AMR" %in% base::.packages()) {
library("AMR")
@ -168,6 +171,11 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -168,6 +171,11 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
# microorganisms.oldDT # old taxonomic names, sorted by name (genus+species), TSN
}
if (clear_options == TRUE) {
options(mo_failures = NULL)
options(mo_renamed = NULL)
}
if (NCOL(x) == 2) {
# support tidyverse selection like: df %>% select(colA, colB)
# paste these columns together
@ -231,10 +239,10 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -231,10 +239,10 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x_backup <- trimws(x, which = "both")
# remove spp and species
x <- gsub(" +(spp.?|species)", "", x_backup)
x <- trimws(gsub(" +(spp.?|ssp.?|subsp.?|species)", " ", x_backup, ignore.case = TRUE), which = "both")
x_species <- paste(x, "species")
# translate to English for supported languages of mo_property
x <- gsub("(Gruppe|gruppe|groep|grupo|gruppo|groupe)", "group", x)
x <- gsub("(Gruppe|gruppe|groep|grupo|gruppo|groupe)", "group", x, ignore.case = TRUE)
# remove 'empty' genus and species values
x <- gsub("(no MO)", "", x, fixed = TRUE)
# remove non-text in case of "E. coli" except dots and spaces
@ -244,6 +252,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -244,6 +252,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x <- trimws(x, which = "both")
x_trimmed <- x
x_trimmed_species <- paste(x_trimmed, "species")
x_trimmed_without_group <- gsub(" group$", "", x_trimmed, ignore.case = TRUE)
# remove last part from "-" or "/"
x_trimmed_without_group <- gsub("(.*)[-/].*", "\\1", x_trimmed_without_group)
# replace space and dot by regex sign
x_withspaces <- gsub("[ .]+", ".* ", x)
x <- gsub("[ .]+", ".*", x)
@ -252,13 +263,14 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -252,13 +263,14 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x_withspaces_start <- paste0('^', x_withspaces)
x_withspaces <- paste0('^', x_withspaces, '$')
# cat(paste0('x "', x, '"\n'))
# cat(paste0('x_species "', x_species, '"\n'))
# cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
# cat(paste0('x_withspaces "', x_withspaces, '"\n'))
# cat(paste0('x_backup "', x_backup, '"\n'))
# cat(paste0('x_trimmed "', x_trimmed, '"\n'))
# cat(paste0('x_trimmed_species "', x_trimmed_species, '"\n'))
# cat(paste0('x "', x, '"\n'))
# cat(paste0('x_species "', x_species, '"\n'))
# cat(paste0('x_withspaces_start "', x_withspaces_start, '"\n'))
# cat(paste0('x_withspaces "', x_withspaces, '"\n'))
# cat(paste0('x_backup "', x_backup, '"\n'))
# cat(paste0('x_trimmed "', x_trimmed, '"\n'))
# cat(paste0('x_trimmed_species "', x_trimmed_species, '"\n'))
# cat(paste0('x_trimmed_without_group "', x_trimmed_without_group, '"\n'))
for (i in 1:length(x)) {
if (identical(x_trimmed[i], "")) {
@ -302,7 +314,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -302,7 +314,8 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x[i] <- microorganismsDT[mo == 'B_STPHY_EPI', ..property][[1]][1L]
next
}
if (toupper(x_trimmed[i]) == 'VRE') {
if (toupper(x_trimmed[i]) == "VRE"
| x_trimmed[i] %like% '(enterococci|enterokok|enterococo)[a-z]*?$') {
x[i] <- microorganismsDT[mo == 'B_ENTRC', ..property][[1]][1L]
next
}
@ -323,7 +336,18 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -323,7 +336,18 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
next
}
if (toupper(x_trimmed[i]) %like% '^G[ABCDFGHK]S$') {
x[i] <- microorganismsDT[mo == gsub("G([ABCDFGHK])S", "B_STRPTC_GR\\1", x_trimmed[i]), ..property][[1]][1L]
# Streptococci, like GBS = Group B Streptococci (B_STRPTC_GRB)
x[i] <- microorganismsDT[mo == gsub("G([ABCDFGHK])S", "B_STRPTC_GR\\1", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
next
}
if (toupper(x_trimmed[i]) %like% '(streptococc|streptokok).* [ABCDFGHK]$') {
# Streptococci in different languages, like "estreptococos grupo B"
x[i] <- microorganismsDT[mo == gsub(".*(streptococ|streptokok|estreptococ).* ([ABCDFGHK])$", "B_STRPTC_GR\\2", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
next
}
if (toupper(x_trimmed[i]) %like% 'group [ABCDFGHK] (streptococ|streptokok|estreptococ)') {
# Streptococci in different languages, like "Group A Streptococci"
x[i] <- microorganismsDT[mo == gsub(".*group ([ABCDFGHK]) (streptococ|streptokok|estreptococ).*", "B_STRPTC_GR\\1", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
next
}
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
@ -341,18 +365,24 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -341,18 +365,24 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x[i] <- microorganismsDT[mo == 'B_STPHY_CPS', ..property][[1]][1L]
next
}
if (tolower(x[i]) %like% '^gram[ -]+nega.*'
| tolower(x_trimmed[i]) %like% '^gram[ -]+nega.*') {
if (tolower(x[i]) %like% 'gram[ -]?neg.*'
| tolower(x_trimmed[i]) %like% 'gram[ -]?neg.*') {
# coerce S. coagulase positive
x[i] <- microorganismsDT[mo == 'B_GRAMN', ..property][[1]][1L]
next
}
if (tolower(x[i]) %like% '^gram[ -]+posi.*'
| tolower(x_trimmed[i]) %like% '^gram[ -]+posi.*') {
if (tolower(x[i]) %like% 'gram[ -]?pos.*'
| tolower(x_trimmed[i]) %like% 'gram[ -]?pos.*') {
# coerce S. coagulase positive
x[i] <- microorganismsDT[mo == 'B_GRAMP', ..property][[1]][1L]
next
}
if (grepl("[sS]almonella [A-Z][a-z]+ ?.*", x_trimmed[i])) {
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
x[i] <- microorganismsDT[mo == 'B_SLMNL_ENT', ..property][[1]][1L]
base::message(magenta(paste0("Note: ", italic(x_trimmed[i]), " is a subspecies of ", italic("Salmonella enterica"), " (B_SLMNL_ENT)")))
next
}
}
# FIRST TRY FULLNAMES AND CODES
@ -424,6 +454,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -424,6 +454,12 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x[i] <- found[1L]
next
}
found <- microorganisms.prevDT[tolower(fullname) == tolower(x_trimmed_without_group[i]), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
# try any match keeping spaces ----
found <- microorganisms.prevDT[fullname %like% x_withspaces[i], ..property][[1]]
@ -495,28 +531,29 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -495,28 +531,29 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x[i] <- found[1L]
next
}
found <- microorganisms.unprevDT[tolower(fullname) == tolower(x_trimmed_without_group[i]), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
# try any match keeping spaces ----
found <- microorganisms.unprevDT[fullname %like% x_withspaces[i], ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
# try any match keeping spaces, not ending with $ ----
found <- microorganisms.unprevDT[fullname %like% x_withspaces_start[i], ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
# try any match diregarding spaces ----
found <- microorganisms.unprevDT[fullname %like% x[i], ..property][[1]]
if (length(found) > 0) {
if (length(found) > 0 & nchar(x_trimmed[i]) >= 6) {
x[i] <- found[1L]
next
}
# try splitting of characters in the middle and then find ID ----
# only when text length is 6 or lower
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
@ -568,15 +605,15 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -568,15 +605,15 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
found <- microorganisms.oldDT[name %like% x_withspaces[i]
| name %like% x_withspaces_start[i]
| name %like% x[i],]
if (NROW(found) > 0) {
if (NROW(found) > 0 & nchar(x_trimmed[i]) >= 6) {
if (property == "ref") {
x[i] <- found[1, ref]
} else {
x[i] <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
}
warning("Uncertain interpretation: '",
x_backup[i], "' -> '", found[1, name], "'",
call. = FALSE, immediate. = TRUE)
warning(red(paste0("UNCERTAIN - '",
x_backup[i], "' -> ", italic(found[1, name]))),
call. = FALSE, immediate. = TRUE)
renamed_note(name_old = found[1, name],
name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
ref_old = found[1, ref],
@ -584,14 +621,38 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -584,14 +621,38 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
next
}
# (2) try to strip off one element and check the remains
x_strip <- x_backup[i] %>% strsplit(" ") %>% unlist()
x_strip <- x_strip[1:length(x_strip) - 1]
x[i] <- suppressWarnings(suppressMessages(as.mo(x_strip)))
# (2) strip values between brackets ----
found <- microorganismsDT[fullname %like% gsub("( [(].*[)]) ", " ", x_withspaces[i])
| fullname %like% gsub("( [(].*[)]) ", " ", x_backup[i])
| fullname %like% gsub("( [(].*[)]) ", " ", x[i]),]
if (NROW(found) > 0 & nchar(x_trimmed[i]) >= 6) {
x[i] <- found[1, ..property][[1]]
warning(red(paste0("UNCERTAIN - '",
x_backup[i], "' -> ", italic(found[1, fullname][[1]]), " (", found[1, mo][[1]], ")")),
call. = FALSE, immediate. = TRUE)
next
}
# (3) try to strip off one element and check the remains ----
look_for_part <- function(z) {
x_strip <- z %>% strsplit(" ") %>% unlist()
if (length(x_strip) > 1 & nchar(x_trimmed[i]) >= 6) {
for (i in 1:(length(x_strip) - 1)) {
x_strip_collapsed <- paste(x_strip[1:(length(x_strip) - i)], collapse = " ")
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, clear_options = FALSE)))
if (!is.na(found)) {
found <- microorganismsDT[mo == found, ..property][[1]]
warning(red(paste0("UNCERTAIN - '",
z, "' -> ", italic(microorganismsDT[mo == found[1L], fullname][[1]]), " (", found[1L], ")")),
call. = FALSE, immediate. = TRUE)
return(found[1L])
}
}
}
return(NA_character_)
}
x[i] <- look_for_part(x_backup[i])
if (!is.na(x[i])) {
warning("Uncertain interpretation: '",
x_backup[i], "' -> '", microorganismsDT[mo == x[i], fullname], "' (", x[i], ")",
call. = FALSE, immediate. = TRUE)
next
}
}
@ -605,10 +666,16 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -605,10 +666,16 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
failures <- failures[!failures %in% c(NA, NULL, NaN)]
if (length(failures) > 0) {
warning("These ", length(failures) , " values could not be coerced to a valid MO code: ",
paste('"', unique(failures), '"', sep = "", collapse = ', '),
".",
call. = FALSE)
options(mo_failures = sort(unique(failures)))
if (n_distinct(failures) > 25) {
warning(n_distinct(failures), " different values could not be coerced to a valid MO code. See mo_failures() to review them.",
call. = FALSE)
} else {
warning("These ", length(failures) , " values could not be coerced to a valid MO code: ",
paste('"', unique(failures), '"', sep = "", collapse = ', '),
". See mo_failures() to review them.",
call. = FALSE)
}
}
# Becker ----
@ -687,6 +754,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = @@ -687,6 +754,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
x
}
#' @importFrom crayon blue
renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") {
if (!is.na(ref_old)) {
ref_old <- paste0(" (", ref_old, ")")
@ -698,7 +766,11 @@ renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") { @@ -698,7 +766,11 @@ renamed_note <- function(name_old, name_new, ref_old = "", ref_new = "") {
} else {
ref_new <- ""
}
base::message(paste0("Note: '", name_old, "'", ref_old, " was renamed '", name_new, "'", ref_new))
msg <- paste0("'", name_old, "'", ref_old, " was renamed '", name_new, "'", ref_new)
msg_plain <- paste0(name_old, ref_old, " -> ", name_new, ref_new)
msg_plain <- c(getOption("mo_renamed", character(0)), msg_plain)
options(mo_renamed = sort(msg_plain))
base::message(blue(paste("Note:", msg)))
}
#' @exportMethod print.mo
@ -733,3 +805,21 @@ as.data.frame.mo <- function (x, ...) { @@ -733,3 +805,21 @@ as.data.frame.mo <- function (x, ...) {
pull.mo <- function(.data, ...) {
pull(as.data.frame(.data), ...)
}
#' Vector of failed coercion attempts
#'
#' Returns a vector of all failed attempts to coerce values to a valid MO code with \code{\link{as.mo}}.
#' @seealso \code{\link{as.mo}}
#' @export
mo_failures <- function() {
getOption("mo_failures")
}
#' Vector of taxonomic renamed items
#'
#' Returns a vector of all renamed items of the last coercion to valid MO codes with \code{\link{as.mo}}.
#' @seealso \code{\link{as.mo}}
#' @export
mo_renamed <- function() {
getOption("mo_renamed")
}

9
R/mo_property.R
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@ -461,6 +461,15 @@ mo_validate <- function(x, property, ...) { @@ -461,6 +461,15 @@ mo_validate <- function(x, property, ...) {
Lancefield <- FALSE
}
if (!"AMR" %in% base::.packages()) {
library("AMR")
# These data.tables are available as data sets when the AMR package is loaded:
# microorganismsDT # this one is sorted by kingdom (B<F<P), prevalence, TSN
# microorganisms.prevDT # same as microorganismsDT, but with prevalence != 9999
# microorganisms.unprevDT # same as microorganismsDT, but with prevalence == 9999
# microorganisms.oldDT # old taxonomic names, sorted by name (genus+species), TSN
}
if (!all(x %in% microorganismsDT[[property]])
| Becker %in% c(TRUE, "all")
| Lancefield %in% c(TRUE, "all")) {

14
man/mo_failures.Rd
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@ -0,0 +1,14 @@ @@ -0,0 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo.R
\name{mo_failures}
\alias{mo_failures}
\title{Vector of failed coercion attempts}
\usage{
mo_failures()
}
\description{
Returns a vector of all failed attempts to coerce values to a valid MO code with \code{\link{as.mo}}.
}
\seealso{
\code{\link{as.mo}}
}

14
man/mo_renamed.Rd
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@ -0,0 +1,14 @@ @@ -0,0 +1,14 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mo.R
\name{mo_renamed}
\alias{mo_renamed}
\title{Vector of taxonomic renamed items}
\usage{
mo_renamed()
}
\description{
Returns a vector of all renamed items of the last coercion to valid MO codes with \code{\link{as.mo}}.
}
\seealso{
\code{\link{as.mo}}
}

10
tests/testthat/test-mo.R
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@ -210,4 +210,14 @@ test_that("as.mo works", { @@ -210,4 +210,14 @@ test_that("as.mo works", {
c("PRTMIR", "bclcer", "B_ESCHR_COL"))),
c("B_PROTS_MIR", "B_BCLLS_CER", "B_ESCHR_COL"))
# hard to find
expect_equal(as.character(suppressWarnings(as.mo(
c("Microbacterium paraoxidans",
"Streptococcus suis (bovis gr)",
"Raoultella (here some text) terrigena"), allow_uncertain = TRUE))),
c("B_MCRBC", "B_STRPTC_SUI", "B_RLTLL_TER"))
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(as.character(suppressMessages(as.mo("Salmonella Goettingen", allow_uncertain = TRUE))),
"B_SLMNL_ENT")
})

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