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(v0.7.1.9024) eucast_rules() fix, new MOs

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dr. M.S. (Matthijs) Berends 2019-08-06 14:39:22 +02:00
parent 85b62aaf8f
commit 3a1f960f89
23 changed files with 252 additions and 411 deletions
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6
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.7.1.9023 Version: 0.7.1.9024
Date: 2019-08-04 Date: 2019-08-06
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(
@ -67,7 +67,7 @@ Suggests:
VignetteBuilder: knitr VignetteBuilder: knitr
URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR URL: https://msberends.gitlab.io/AMR, https://gitlab.com/msberends/AMR
BugReports: https://gitlab.com/msberends/AMR/issues BugReports: https://gitlab.com/msberends/AMR/issues
License: GPL-2 | file LICENSE License: GPL-2
Encoding: UTF-8 Encoding: UTF-8
LazyData: true LazyData: true
RoxygenNote: 6.1.1 RoxygenNote: 6.1.1

339
LICENSE
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@ -1,339 +0,0 @@
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10
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9023 # AMR 0.7.1.9024
### Breaking ### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too. * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
@ -35,13 +35,17 @@
Since this is a major change, usage of the old `also_single_tested` will throw an informative error that it has been replaced by `only_all_tested`. Since this is a major change, usage of the old `also_single_tested` will throw an informative error that it has been replaced by `only_all_tested`.
### Changed ### Changed
* Fixed a bug in `eucast_rules()` that caused an error when the input was a specific kind of `tibble`
* Removed class `atc` - using `as.atc()` is now deprecated in favour of `ab_atc()` and this will return a character, not the `atc` class anymore * Removed class `atc` - using `as.atc()` is now deprecated in favour of `ab_atc()` and this will return a character, not the `atc` class anymore
* Removed deprecated functions `abname()`, `ab_official()`, `atc_name()`, `atc_official()`, `atc_property()`, `atc_tradenames()`, `atc_trivial_nl()` * Removed deprecated functions `abname()`, `ab_official()`, `atc_name()`, `atc_official()`, `atc_property()`, `atc_tradenames()`, `atc_trivial_nl()`
* Fix and speed improvement for `mo_shortname()` * Fix and speed improvement for `mo_shortname()`
* Fix for `as.mo()` where misspelled input would not be understood * Algorithm improvements for `as.mo()`:
* Some misspelled input were not understood
* These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus
* Added support for unknown yeasts and fungi
* Added the newest taxonomic data from the IJSEM journal (now up to date until August 2019)
* Fix for using `mo_*` functions where the coercion uncertainties and failures would not be available through `mo_uncertainties()` and `mo_failures()` anymore * Fix for using `mo_*` functions where the coercion uncertainties and failures would not be available through `mo_uncertainties()` and `mo_failures()` anymore
* Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country * Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country
* Fix for frequency tables when creating one directly on a group (using `group_by()`)
* The `name` of `RIF` is now Rifampicin instead of Rifampin * The `name` of `RIF` is now Rifampicin instead of Rifampin
* The `antibiotics` data set is now sorted by name * The `antibiotics` data set is now sorted by name
* Using verbose mode with `eucast_rules(..., verbose = TRUE)` returns more informative and readable output * Using verbose mode with `eucast_rules(..., verbose = TRUE)` returns more informative and readable output

10
R/data.R
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@ -55,7 +55,7 @@
#' #'
#' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}. #' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
#' @inheritSection catalogue_of_life Catalogue of Life #' @inheritSection catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 67,906 observations and 16 variables: #' @format A \code{\link{data.frame}} with 68,260 observations and 16 variables:
#' \describe{ #' \describe{
#' \item{\code{mo}}{ID of microorganism as used by this package} #' \item{\code{mo}}{ID of microorganism as used by this package}
#' \item{\code{col_id}}{Catalogue of Life ID} #' \item{\code{col_id}}{Catalogue of Life ID}
@ -72,8 +72,8 @@
#' \item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)} #' \item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
#' \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])} #' \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
#' \item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)} #' \item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)}
#' \item{3 other 'undefined' entries (unknown, unknown Gram negatives and unknown Gram positives)} #' \item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
#' \item{8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life} #' \item{8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
#' } #' }
#' @section About the records from DSMZ (see source): #' @section About the records from DSMZ (see source):
#' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists. #' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
@ -91,14 +91,14 @@ catalogue_of_life <- list(
version = "Catalogue of Life: {year} Annual Checklist", version = "Catalogue of Life: {year} Annual Checklist",
url_CoL = "http://www.catalogueoflife.org/annual-checklist/{year}/", url_CoL = "http://www.catalogueoflife.org/annual-checklist/{year}/",
url_DSMZ = "https://www.dsmz.de/microorganisms/pnu/bacterial_nomenclature_info_mm.php", url_DSMZ = "https://www.dsmz.de/microorganisms/pnu/bacterial_nomenclature_info_mm.php",
yearmonth_DSMZ = "February 2019" yearmonth_DSMZ = "August 2019"
) )
#' Data set with previously accepted taxonomic names #' Data set with previously accepted taxonomic names
#' #'
#' A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by \code{\link{as.mo}}. #' A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by \code{\link{as.mo}}.
#' @inheritSection catalogue_of_life Catalogue of Life #' @inheritSection catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 21,342 observations and 4 variables: #' @format A \code{\link{data.frame}} with 21,743 observations and 4 variables:
#' \describe{ #' \describe{
#' \item{\code{col_id}}{Catalogue of Life ID that was originally given} #' \item{\code{col_id}}{Catalogue of Life ID that was originally given}
#' \item{\code{col_id_new}}{New Catalogue of Life ID that responds to an entry in the \code{\link{microorganisms}} data set} #' \item{\code{col_id_new}}{New Catalogue of Life ID that responds to an entry in the \code{\link{microorganisms}} data set}

24
R/eucast_rules.R
View File

@ -184,6 +184,20 @@ eucast_rules <- function(x,
verbose = FALSE, verbose = FALSE,
...) { ...) {
if (verbose == TRUE & interactive()) {
txt <- paste0("WARNING: In Verbose mode, the eucast_rules() function does not apply rules to the data, but instead returns a data set in logbook form: with extensive info about which rows and columns would be effected and in which way.",
"\n\nThis may overwrite your existing data if you use e.g.:",
"\ndata <- eucast_rules(data, verbose = TRUE)\n\nDo you want to continue?")
if ("rstudioapi" %in% rownames(installed.packages())) {
q_continue <- rstudioapi::showQuestion("Using verbose = TRUE with eucast_rules()", txt)
} else {
q_continue <- menu(choices = c("OK", "Cancel"), graphics = TRUE, title = txt)
}
if (q_continue %in% c(FALSE, 2)) {
return(invisible())
}
}
if (!is.data.frame(x)) { if (!is.data.frame(x)) {
stop("`x` must be a data frame.", call. = FALSE) stop("`x` must be a data frame.", call. = FALSE)
} }
@ -381,7 +395,6 @@ eucast_rules <- function(x,
cols <- unique(cols[!is.na(cols) & !is.null(cols)]) cols <- unique(cols[!is.na(cols) & !is.null(cols)])
if (length(rows) > 0 & length(cols) > 0) { if (length(rows) > 0 & length(cols) > 0) {
before_df <- x_original before_df <- x_original
before <- as.character(unlist(as.list(x_original[rows, cols])))
tryCatch( tryCatch(
# insert into original table # insert into original table
@ -402,9 +415,7 @@ eucast_rules <- function(x,
x[rows, cols] <<- x_original[rows, cols] x[rows, cols] <<- x_original[rows, cols]
after <- as.character(unlist(as.list(x_original[rows, cols]))) # before_df might not be a data.frame, but a tibble or data.table instead
# before_df might not be a data.frame, but a tibble of data.table instead
old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows,] old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows,]
no_of_changes_this_run <- 0 no_of_changes_this_run <- 0
for (i in 1:length(cols)) { for (i in 1:length(cols)) {
@ -419,13 +430,14 @@ eucast_rules <- function(x,
stringsAsFactors = FALSE) stringsAsFactors = FALSE)
colnames(verbose_new) <- c("row", "col", "mo_fullname", "old", "new", "rule", "rule_group", "rule_name") colnames(verbose_new) <- c("row", "col", "mo_fullname", "old", "new", "rule", "rule_group", "rule_name")
verbose_new <- verbose_new %>% filter(old != new | is.na(old)) verbose_new <- verbose_new %>% filter(old != new | is.na(old))
# save changes to data set 'verbose_info'
verbose_info <<- rbind(verbose_info, verbose_new) verbose_info <<- rbind(verbose_info, verbose_new)
no_of_changes_this_run <- no_of_changes_this_run + nrow(verbose_new) no_of_changes_this_run <- no_of_changes_this_run + nrow(verbose_new)
} }
# return number of (new) changes # after the applied changes: return number of (new) changes
return(no_of_changes_this_run) return(no_of_changes_this_run)
} }
# return number of (new) changes: none. # no changes were applied: return number of (new) changes: none.
return(0) return(0)
} }

6
R/like.R
View File

@ -76,7 +76,11 @@ like <- function(x, pattern) {
if (is.factor(x)) { if (is.factor(x)) {
as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = TRUE) as.integer(x) %in% base::grep(pattern, levels(x), ignore.case = TRUE)
} else { } else {
base::grepl(pattern, x, ignore.case = TRUE) tryCatch(base::grepl(pattern, x, ignore.case = TRUE),
error = function(e) ifelse(test = grepl("Invalid regexp", e$message),
# try with perl = TRUE:
yes = return(base::grepl(pattern, x, ignore.case = TRUE, perl = TRUE)),
no = stop(e$message)))
} }
} }

123
R/mo.R
View File

@ -472,7 +472,9 @@ exec_as.mo <- function(x,
x_backup_without_spp <- x x_backup_without_spp <- x
x_species <- paste(x, "species") x_species <- paste(x, "species")
# translate to English for supported languages of mo_property # translate to English for supported languages of mo_property
x <- gsub("(Gruppe|gruppe|groep|grupo|gruppo|groupe)", "group", x, ignore.case = TRUE) x <- gsub("(gruppe|groep|grupo|gruppo|groupe)", "group", x, ignore.case = TRUE)
x <- gsub("(hefe|gist|gisten|levadura|lievito|fermento|levure)[a-z]*", "yeast", x, ignore.case = TRUE)
x <- gsub("(schimmels?|mofo|molde|stampo|moisissure)[a-z]*", "fungus", x, ignore.case = TRUE)
# remove non-text in case of "E. coli" except dots and spaces # remove non-text in case of "E. coli" except dots and spaces
x <- gsub("[^.a-zA-Z0-9/ \\-]+", "", x) x <- gsub("[^.a-zA-Z0-9/ \\-]+", "", x)
# replace minus by a space # replace minus by a space
@ -483,7 +485,7 @@ exec_as.mo <- function(x,
x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x) x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x)
# remove genus as first word # remove genus as first word
x <- gsub("^Genus ", "", x) x <- gsub("^Genus ", "", x)
# allow characters that resemble others, but not on first try # allow characters that resemble others ----
if (initial_search == FALSE) { if (initial_search == FALSE) {
x <- tolower(x) x <- tolower(x)
x <- gsub("[iy]+", "[iy]+", x) x <- gsub("[iy]+", "[iy]+", x)
@ -493,15 +495,17 @@ exec_as.mo <- function(x,
x <- gsub("a+", "a+", x) x <- gsub("a+", "a+", x)
x <- gsub("u+", "u+", x) x <- gsub("u+", "u+", x)
# allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica and -a (needs perl for the negative backward lookup): # allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica and -a (needs perl for the negative backward lookup):
x <- gsub("(u\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+)(?![a-z[])", x <- gsub("(u\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+)(?![a-z])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, ignore.case = TRUE, perl = TRUE) "(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, ignore.case = TRUE, perl = TRUE)
x <- gsub("(\\[iy\\]\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+a\\+)(?![a-z[])", x <- gsub("(\\[iy\\]\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+a\\+)(?![a-z])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, ignore.case = TRUE, perl = TRUE) "(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, ignore.case = TRUE, perl = TRUE)
x <- gsub("(\\[iy\\]\\+u\\+m)(?![a-z[])", x <- gsub("(\\[iy\\]\\+u\\+m)(?![a-z])",
"(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, ignore.case = TRUE, perl = TRUE) "(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, ignore.case = TRUE, perl = TRUE)
x <- gsub("e+", "e+", x, ignore.case = TRUE) x <- gsub("e+", "e+", x, ignore.case = TRUE)
x <- gsub("o+", "o+", x, ignore.case = TRUE) x <- gsub("o+", "o+", x, ignore.case = TRUE)
x <- gsub("(.)\\1+", "\\1+", x) x <- gsub("(.)\\1+", "\\1+", x)
# allow ending in -en or -us
x <- gsub("e\\+n(?![a-z[])", "(e+n|u+(c|k|q|qu|s|z|x|ks)+)", x, ignore.case = TRUE, perl = TRUE)
} }
x <- strip_whitespace(x) x <- strip_whitespace(x)
@ -519,7 +523,7 @@ exec_as.mo <- function(x,
x_withspaces_end_only <- paste0(x_withspaces, '$') x_withspaces_end_only <- paste0(x_withspaces, '$')
x_withspaces_start_end <- paste0('^', x_withspaces, '$') x_withspaces_start_end <- paste0('^', x_withspaces, '$')
if (debug == TRUE) { if (isTRUE(debug)) {
cat(paste0('x "', x, '"\n')) cat(paste0('x "', x, '"\n'))
cat(paste0('x_species "', x_species, '"\n')) cat(paste0('x_species "', x_species, '"\n'))
cat(paste0('x_withspaces_start_only "', x_withspaces_start_only, '"\n')) cat(paste0('x_withspaces_start_only "', x_withspaces_start_only, '"\n'))
@ -725,6 +729,14 @@ exec_as.mo <- function(x,
} }
next next
} }
if (x_backup_without_spp[i] %like% 'haemoly.*strept') {
# Haemolytic streptococci in different languages
x[i] <- microorganismsDT[mo == 'B_STRPT_HAE', ..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
next
}
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ---- # CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
if (x_backup_without_spp[i] %like% '[ck]oagulas[ea] negatie?[vf]' if (x_backup_without_spp[i] %like% '[ck]oagulas[ea] negatie?[vf]'
| x_trimmed[i] %like% '[ck]oagulas[ea] negatie?[vf]' | x_trimmed[i] %like% '[ck]oagulas[ea] negatie?[vf]'
@ -787,6 +799,32 @@ exec_as.mo <- function(x,
} }
next next
} }
# trivial names known to the field:
if ("meningococcus" %like% x_trimmed[i]) {
# coerce S. coagulase positive
x[i] <- microorganismsDT[mo == 'B_NESSR_MEN', ..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
next
}
if ("gonococcus" %like% x_trimmed[i]) {
# coerce S. coagulase positive
x[i] <- microorganismsDT[mo == 'B_NESSR_GON', ..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
next
}
if ("pneumococcus" %like% x_trimmed[i]) {
# coerce S. coagulase positive
x[i] <- microorganismsDT[mo == 'B_STRPT_PNE', ..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
next
}
} }
# FIRST TRY FULLNAMES AND CODES ---- # FIRST TRY FULLNAMES AND CODES ----
@ -1006,6 +1044,9 @@ exec_as.mo <- function(x,
if (uncertainty_level >= 1) { if (uncertainty_level >= 1) {
# (1) look again for old taxonomic names, now for G. species ---- # (1) look again for old taxonomic names, now for G. species ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 1] (1) look again for old taxonomic names, now for G. species\n")
}
found <- microorganisms.oldDT[fullname %like% c.x_withspaces_start_end found <- microorganisms.oldDT[fullname %like% c.x_withspaces_start_end
| fullname %like% d.x_withspaces_start_only] | fullname %like% d.x_withspaces_start_only]
if (NROW(found) > 0 & nchar(g.x_backup_without_spp) >= 6) { if (NROW(found) > 0 & nchar(g.x_backup_without_spp) >= 6) {
@ -1035,7 +1076,10 @@ exec_as.mo <- function(x,
# (2) Try with misspelled input ---- # (2) Try with misspelled input ----
# just rerun with initial_search = FALSE will used the extensive regex part above # just rerun with initial_search = FALSE will used the extensive regex part above
found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup, initial_search = FALSE, allow_uncertain = FALSE))) if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 1] (2) Try with misspelled input\n")
}
found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup, initial_search = FALSE, allow_uncertain = FALSE, debug = debug)))
if (!empty_result(found)) { if (!empty_result(found)) {
found_result <- found found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]] found <- microorganismsDT[mo == found, ..property][[1]]
@ -1054,6 +1098,9 @@ exec_as.mo <- function(x,
if (uncertainty_level >= 2) { if (uncertainty_level >= 2) {
# (3) look for genus only, part of name ---- # (3) look for genus only, part of name ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (3) look for genus only, part of name\n")
}
if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like% " ") { if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like% " ") {
if (!grepl("^[A-Z][a-z]+", b.x_trimmed, ignore.case = FALSE)) { if (!grepl("^[A-Z][a-z]+", b.x_trimmed, ignore.case = FALSE)) {
# not when input is like Genustext, because then Neospora would lead to Actinokineospora # not when input is like Genustext, because then Neospora would lead to Actinokineospora
@ -1074,9 +1121,12 @@ exec_as.mo <- function(x,
} }
# (4) strip values between brackets ---- # (4) strip values between brackets ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (4) strip values between brackets\n")
}
a.x_backup_stripped <- gsub("( *[(].*[)] *)", " ", a.x_backup) a.x_backup_stripped <- gsub("( *[(].*[)] *)", " ", a.x_backup)
a.x_backup_stripped <- trimws(gsub(" +", " ", a.x_backup_stripped)) a.x_backup_stripped <- trimws(gsub(" +", " ", a.x_backup_stripped))
found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup_stripped, initial_search = FALSE, allow_uncertain = FALSE))) found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup_stripped, initial_search = FALSE, allow_uncertain = FALSE, debug = debug)))
if (!empty_result(found) & nchar(g.x_backup_without_spp) >= 6) { if (!empty_result(found) & nchar(g.x_backup_without_spp) >= 6) {
found_result <- found found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]] found <- microorganismsDT[mo == found, ..property][[1]]
@ -1092,6 +1142,9 @@ exec_as.mo <- function(x,
} }
# (5a) try to strip off half an element from end and check the remains ---- # (5a) try to strip off half an element from end and check the remains ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (5a) try to strip off half an element from end and check the remains\n")
}
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist() x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
if (length(x_strip) > 1) { if (length(x_strip) > 1) {
for (i in 1:(length(x_strip) - 1)) { for (i in 1:(length(x_strip) - 1)) {
@ -1100,7 +1153,7 @@ exec_as.mo <- function(x,
# remove last half of the second term # remove last half of the second term
x_strip_collapsed <- paste(c(x_strip[1:(length(x_strip) - i)], lastword_half), collapse = " ") x_strip_collapsed <- paste(c(x_strip[1:(length(x_strip) - i)], lastword_half), collapse = " ")
if (nchar(x_strip_collapsed) >= 4) { if (nchar(x_strip_collapsed) >= 4) {
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE))) found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE, debug = debug)))
if (!empty_result(found)) { if (!empty_result(found)) {
found_result <- found found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]] found <- microorganismsDT[mo == found, ..property][[1]]
@ -1118,11 +1171,14 @@ exec_as.mo <- function(x,
} }
} }
# (5b) try to strip off one element from end and check the remains ---- # (5b) try to strip off one element from end and check the remains ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (5b) try to strip off one element from end and check the remains\n")
}
if (length(x_strip) > 1) { if (length(x_strip) > 1) {
for (i in 1:(length(x_strip) - 1)) { for (i in 1:(length(x_strip) - 1)) {
x_strip_collapsed <- paste(x_strip[1:(length(x_strip) - i)], collapse = " ") x_strip_collapsed <- paste(x_strip[1:(length(x_strip) - i)], collapse = " ")
if (nchar(x_strip_collapsed) >= 4) { if (nchar(x_strip_collapsed) >= 4) {
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE))) found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE, debug = debug)))
if (!empty_result(found)) { if (!empty_result(found)) {
found_result <- found found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]] found <- microorganismsDT[mo == found, ..property][[1]]
@ -1139,12 +1195,47 @@ exec_as.mo <- function(x,
} }
} }
} }
# (5c) check for unknown yeasts/fungi ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (5b) check for unknown yeasts/fungi\n")
}
if (b.x_trimmed %like% "yeast") {
found <- "F_YEAST"
found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]]
uncertainties <<- rbind(uncertainties,
data.frame(uncertainty = 2,
input = a.x_backup,
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
}
return(found[1L])
}
if (b.x_trimmed %like% "fungus") {
found <- "F_FUNGUS"
found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]]
uncertainties <<- rbind(uncertainties,
data.frame(uncertainty = 2,
input = a.x_backup,
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
}
return(found[1L])
}
# (6) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ---- # (6) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (6) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n")
}
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist() x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) { if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
for (i in 2:(length(x_strip))) { for (i in 2:(length(x_strip))) {
x_strip_collapsed <- paste(x_strip[i:length(x_strip)], collapse = " ") x_strip_collapsed <- paste(x_strip[i:length(x_strip)], collapse = " ")
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE))) found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE, debug = debug)))
if (!empty_result(found)) { if (!empty_result(found)) {
found_result <- found found_result <- found
found <- microorganismsDT[mo == found_result[1L], ..property][[1]] found <- microorganismsDT[mo == found_result[1L], ..property][[1]]
@ -1167,11 +1258,14 @@ exec_as.mo <- function(x,
if (uncertainty_level >= 3) { if (uncertainty_level >= 3) {
# (7) try to strip off one element from start and check the remains ---- # (7) try to strip off one element from start and check the remains ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 3] (7) try to strip off one element from start and check the remains\n")
}
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist() x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) { if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
for (i in 2:(length(x_strip))) { for (i in 2:(length(x_strip))) {
x_strip_collapsed <- paste(x_strip[i:length(x_strip)], collapse = " ") x_strip_collapsed <- paste(x_strip[i:length(x_strip)], collapse = " ")
found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE))) found <- suppressMessages(suppressWarnings(exec_as.mo(x_strip_collapsed, initial_search = FALSE, allow_uncertain = FALSE, debug = debug)))
if (!empty_result(found)) { if (!empty_result(found)) {
found_result <- found found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]] found <- microorganismsDT[mo == found, ..property][[1]]
@ -1189,6 +1283,9 @@ exec_as.mo <- function(x,
} }
# (8) part of a name (very unlikely match) ---- # (8) part of a name (very unlikely match) ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 3] (8) part of a name (very unlikely match)\n")
}
found <- microorganismsDT[fullname %like% f.x_withspaces_end_only] found <- microorganismsDT[fullname %like% f.x_withspaces_end_only]
if (nrow(found) > 0) { if (nrow(found) > 0) {
found_result <- found[["mo"]] found_result <- found[["mo"]]
@ -1217,7 +1314,7 @@ exec_as.mo <- function(x,
x_withspaces_end_only[i], x_withspaces_end_only[i],
x_backup_without_spp[i]) x_backup_without_spp[i])
if (!empty_result(x[i])) { if (!empty_result(x[i])) {
# no set_mo_history: is already set in uncertain_fn() # no set_mo_history here - it is already set in uncertain_fn()
next next
} }

BIN
R/sysdata.rda
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Binary file not shown.

12
data-raw/eucast_rules.tsv
View File

@ -1,4 +1,14 @@
if_mo_property like_is_one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group # ---------------------------------------------------------------------------------------------------
# For editing this EUCAST reference file, these values can all be used for target antibiotics:
# all_betalactams, aminoglycosides, carbapenems, cephalosporins, cephalosporins_without_CAZ, fluoroquinolones,
# glycopeptides, macrolides, minopenicillins, polymyxins, streptogramins, tetracyclines, ureidopenicillins
# and all separate EARS-Net letter codes like AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
# The if_mo_property column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
# The like.is.one_of column must contain one of: like, is, one_of ('like' will read the first column as regular expression)
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in: LiPuma J, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
# >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
# ---------------------------------------------------------------------------------------------------
if_mo_property like.is.one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group
order is Enterobacteriales AMP S AMX S Enterobacteriales (Order) Breakpoints order is Enterobacteriales AMP S AMX S Enterobacteriales (Order) Breakpoints
order is Enterobacteriales AMP I AMX I Enterobacteriales (Order) Breakpoints order is Enterobacteriales AMP I AMX I Enterobacteriales (Order) Breakpoints
order is Enterobacteriales AMP R AMX R Enterobacteriales (Order) Breakpoints order is Enterobacteriales AMP R AMX R Enterobacteriales (Order) Breakpoints

Can't render this file because it contains an unexpected character in line 6 and column 94.

20
data-raw/internals.R
View File

@ -1,14 +1,16 @@
# EUCAST rules ---- # ---------------------------------------------------------------------------------------------------
# For editing the reference file, these values can all be used for target antibiotics: # For editing this EUCAST reference file, these values can all be used for target antibiotics:
# "aminoglycosides", "tetracyclines", "polymyxins", "macrolides", "glycopeptides", # all_betalactams, aminoglycosides, carbapenems, cephalosporins, cephalosporins_without_CAZ, fluoroquinolones,
# "streptogramins", "cephalosporins", "cephalosporins_without_CAZ", "carbapenems", # glycopeptides, macrolides, minopenicillins, polymyxins, streptogramins, tetracyclines, ureidopenicillins
# "minopenicillins", "ureidopenicillins", "fluoroquinolones", "all_betalactams", # and all separate EARS-Net letter codes like AMC. They can be separated by comma: 'AMC, fluoroquinolones'.
# and all separate EARS-Net letter codes like "AMC". They can be separated by comma: "AMC, fluoroquinolones". # The if_mo_property column can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain".
# The mo_property can be any column name from the AMR::microorganisms data set, or "genus_species" or "gramstain". # The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. All species in this group can be found in:
# The EUCAST guideline contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: # LiPuma J, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180).
# LiPuma JJ, Curr Opin Pulm Med. 2005 Nov;11(6):528-33. (PMID 16217180). # >>>>> IF YOU WANT TO IMPORT THIS FILE INTO YOUR OWN SOFTWARE, HAVE THE FIRST 10 LINES SKIPPED <<<<<
# ---------------------------------------------------------------------------------------------------
eucast_rules_file <- dplyr::arrange( eucast_rules_file <- dplyr::arrange(
.data = utils::read.delim(file = "data-raw/eucast_rules.tsv", .data = utils::read.delim(file = "data-raw/eucast_rules.tsv",
skip = 10,
sep = "\t", sep = "\t",
stringsAsFactors = FALSE, stringsAsFactors = FALSE,
header = TRUE, header = TRUE,

55
data-raw/reproduction_of_microorganisms.R
View File

@ -99,7 +99,7 @@ MOs <- data_total %>%
# and not all fungi: Aspergillus, Candida, Trichphyton and Pneumocystis are the most important, # and not all fungi: Aspergillus, Candida, Trichphyton and Pneumocystis are the most important,
# so only keep these orders from the fungi: # so only keep these orders from the fungi:
& !(kingdom == "Fungi" & !(kingdom == "Fungi"
& !order %in% c("Eurotiales", "Saccharomycetales", "Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales")) & !order %in% c("Eurotiales", "Mucorales", "Saccharomycetales", "Schizosaccharomycetales", "Tremellales", "Onygenales", "Pneumocystales"))
) )
# or the genus has to be one of the genera we found in our hospitals last decades (Northern Netherlands, 2002-2018) # or the genus has to be one of the genera we found in our hospitals last decades (Northern Netherlands, 2002-2018)
| genus %in% c("Absidia", "Acremonium", "Actinotignum", "Alternaria", "Anaerosalibacter", "Ancylostoma", "Anisakis", "Apophysomyces", | genus %in% c("Absidia", "Acremonium", "Actinotignum", "Alternaria", "Anaerosalibacter", "Ancylostoma", "Anisakis", "Apophysomyces",
@ -123,7 +123,7 @@ MOs <- MOs %>%
MOs <- MOs %>% MOs <- MOs %>%
# remove text if it contains 'Not assigned' like phylum in viruses # remove text if it contains 'Not assigned' like phylum in viruses
mutate_all(~gsub("Not assigned", "", .)) mutate_all(~gsub("(Not assigned|\\[homonym\\]|\\[mistake\\])", "", ., ignore.case = TRUE))
MOs <- MOs %>% MOs <- MOs %>%
# Only keep first author, e.g. transform 'Smith, Jones, 2011' to 'Smith et al., 2011': # Only keep first author, e.g. transform 'Smith, Jones, 2011' to 'Smith et al., 2011':
@ -167,7 +167,9 @@ MOs <- MOs %>%
# Remove non-ASCII characters (these are not allowed by CRAN) # Remove non-ASCII characters (these are not allowed by CRAN)
MOs <- MOs %>% MOs <- MOs %>%
lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>% lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>%
as_tibble(stringsAsFactors = FALSE) as_tibble(stringsAsFactors = FALSE) %>%
# remove invalid characters
mutate_all(~gsub("[\"'`]+", "", .))
# Split old taxonomic names - they refer in the original data to a new `taxonID` with `acceptedNameUsageID` # Split old taxonomic names - they refer in the original data to a new `taxonID` with `acceptedNameUsageID`
MOs.old <- MOs %>% MOs.old <- MOs %>%
@ -219,6 +221,9 @@ MOs <- MOs %>%
!(source == "DSMZ" & fullname %in% (MOs %>% filter(source == "CoL") %>% pull(fullname)))) %>% !(source == "DSMZ" & fullname %in% (MOs %>% filter(source == "CoL") %>% pull(fullname)))) %>%
distinct(fullname, .keep_all = TRUE) distinct(fullname, .keep_all = TRUE)
# what characters are in the fullnames?
paste(unique(sort(unlist(strsplit(x = paste(MOs$fullname, collapse = ""), split = "")))), collapse = "")
# Add abbreviations so we can easily know which ones are which ones. # Add abbreviations so we can easily know which ones are which ones.
# These will become valid and unique microbial IDs for the AMR package. # These will become valid and unique microbial IDs for the AMR package.
MOs <- MOs %>% MOs <- MOs %>%
@ -295,7 +300,6 @@ MOs <- MOs %>%
# put `mo` in front, followed by the rest # put `mo` in front, followed by the rest
select(mo, everything(), -abbr_other, -abbr_genus, -abbr_species, -abbr_subspecies) select(mo, everything(), -abbr_other, -abbr_genus, -abbr_species, -abbr_subspecies)
# add non-taxonomic entries # add non-taxonomic entries
MOs <- MOs %>% MOs <- MOs %>%
bind_rows( bind_rows(
@ -348,6 +352,38 @@ MOs <- MOs %>%
species_id = "", species_id = "",
source = "manually added", source = "manually added",
stringsAsFactors = FALSE), stringsAsFactors = FALSE),
data.frame(mo = "F_YEAST",
col_id = NA_integer_,
fullname = "(unknown yeast)",
kingdom = "Fungi",
phylum = "(unknown phylum)",
class = "(unknown class)",
order = "(unknown order)",
family = "(unknown family)",
genus = "(unknown genus)",
species = "(unknown species)",
subspecies = "(unknown subspecies)",
rank = "species",
ref = NA_character_,
species_id = "",
source = "manually added",
stringsAsFactors = FALSE),
data.frame(mo = "F_FUNGUS",
col_id = NA_integer_,
fullname = "(unknown fungus)",
kingdom = "Fungi",
phylum = "(unknown phylum)",
class = "(unknown class)",
order = "(unknown order)",
family = "(unknown family)",
genus = "(unknown genus)",
species = "(unknown species)",
subspecies = "(unknown subspecies)",
rank = "species",
ref = NA_character_,
species_id = "",
source = "manually added",
stringsAsFactors = FALSE),
# CoNS # CoNS
MOs %>% MOs %>%
filter(genus == "Staphylococcus", species == "epidermidis") %>% .[1,] %>% filter(genus == "Staphylococcus", species == "epidermidis") %>% .[1,] %>%
@ -488,6 +524,11 @@ MOs <- MOs %>%
sum(duplicated(MOs$mo)) sum(duplicated(MOs$mo))
colnames(MOs) colnames(MOs)
# here we welcome the new ones:
MOs %>% filter(!fullname %in% AMR::microorganisms$fullname) %>% View()
# and the ones we lost:
AMR::microorganisms %>% filter(!fullname %in% MOs$fullname) %>% View()
# set prevalence per species # set prevalence per species
MOs <- MOs %>% MOs <- MOs %>%
mutate(prevalence = case_when( mutate(prevalence = case_when(
@ -534,12 +575,16 @@ MOs.old$col_id <- as.integer(MOs.old$col_id)
MOs.old$col_id_new <- as.integer(MOs.old$col_id_new) MOs.old$col_id_new <- as.integer(MOs.old$col_id_new)
# save # save
### for other server
saveRDS(MOs, "microorganisms.rds") saveRDS(MOs, "microorganisms.rds")
saveRDS(MOs.old, "microorganisms.old.rds") saveRDS(MOs.old, "microorganisms.old.rds")
### for same server
microorganisms <- MOs
microorganisms.old <- MOs.old
# on the server, do: # on the server, do:
usethis::use_data(microorganisms, overwrite = TRUE, version = 2) usethis::use_data(microorganisms, overwrite = TRUE, version = 2)
usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2) usethis::use_data(microorganisms.old, overwrite = TRUE, version = 2)
rm(microorganisms) rm(microorganisms)
rm(microorganisms.old) rm(microorganisms.old)
# and update the year in R/data.R # and update the year and dimensions in R/data.R

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2
docs/articles/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9024</span>
</span> </span>
</div> </div>

2
docs/authors.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9024</span>
</span> </span>
</div> </div>

6
docs/index.html
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@ -42,7 +42,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a> <a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9024</span>
</span> </span>
</div> </div>
@ -377,9 +377,7 @@
<div class="license"> <div class="license">
<h2>License</h2> <h2>License</h2>
<ul class="list-unstyled"> <ul class="list-unstyled">
<li> <li><a href="https://www.r-project.org/Licenses/GPL-2">GPL-2</a></li>
<a href="https://www.r-project.org/Licenses/GPL-2">GPL-2</a> | file <a href="LICENSE-text.html">LICENSE</a>
</li>
</ul> </ul>
</div> </div>
<div class="developers"> <div class="developers">

20
docs/news/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9024</span>
</span> </span>
</div> </div>
@ -225,9 +225,9 @@
</div> </div>
<div id="amr-0-7-1-9023" class="section level1"> <div id="amr-0-7-1-9024" class="section level1">
<h1 class="page-header"> <h1 class="page-header">
<a href="#amr-0-7-1-9023" class="anchor"></a>AMR 0.7.1.9023<small> Unreleased </small> <a href="#amr-0-7-1-9024" class="anchor"></a>AMR 0.7.1.9024<small> Unreleased </small>
</h1> </h1>
<div id="breaking" class="section level3"> <div id="breaking" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">
@ -273,15 +273,23 @@
<h3 class="hasAnchor"> <h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3> <a href="#changed" class="anchor"></a>Changed</h3>
<ul> <ul>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> that caused an error when the input was a specific kind of <code>tibble</code>
</li>
<li>Removed class <code>atc</code> - using <code><a href="../reference/AMR-deprecated.html">as.atc()</a></code> is now deprecated in favour of <code><a href="../reference/ab_property.html">ab_atc()</a></code> and this will return a character, not the <code>atc</code> class anymore</li> <li>Removed class <code>atc</code> - using <code><a href="../reference/AMR-deprecated.html">as.atc()</a></code> is now deprecated in favour of <code><a href="../reference/ab_property.html">ab_atc()</a></code> and this will return a character, not the <code>atc</code> class anymore</li>
<li>Removed deprecated functions <code>abname()</code>, <code>ab_official()</code>, <code>atc_name()</code>, <code>atc_official()</code>, <code>atc_property()</code>, <code>atc_tradenames()</code>, <code>atc_trivial_nl()</code> <li>Removed deprecated functions <code>abname()</code>, <code>ab_official()</code>, <code>atc_name()</code>, <code>atc_official()</code>, <code>atc_property()</code>, <code>atc_tradenames()</code>, <code>atc_trivial_nl()</code>
</li> </li>
<li>Fix and speed improvement for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> <li>Fix and speed improvement for <code><a href="../reference/mo_property.html">mo_shortname()</a></code>
</li> </li>
<li>Fix for <code><a href="../reference/as.mo.html">as.mo()</a></code> where misspelled input would not be understood</li> <li>Algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul>
<li>Some misspelled input were not understood</li>
<li>These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus</li>
<li>Added support for unknown yeasts and fungi</li>
</ul>
</li>
<li>Added the newest taxonomic data from the IJSEM journal (now up to date until August 2019)</li>
<li>Fix for using <code>mo_*</code> functions where the coercion uncertainties and failures would not be available through <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> and <code><a href="../reference/as.mo.html">mo_failures()</a></code> anymore</li> <li>Fix for using <code>mo_*</code> functions where the coercion uncertainties and failures would not be available through <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> and <code><a href="../reference/as.mo.html">mo_failures()</a></code> anymore</li>
<li>Deprecated the <code>country</code> parameter of <code><a href="../reference/mdro.html">mdro()</a></code> in favour of the already existing <code>guideline</code> parameter to support multiple guidelines within one country</li> <li>Deprecated the <code>country</code> parameter of <code><a href="../reference/mdro.html">mdro()</a></code> in favour of the already existing <code>guideline</code> parameter to support multiple guidelines within one country</li>
<li>Fix for frequency tables when creating one directly on a group (using <code>group_by()</code>)</li>
<li>The <code>name</code> of <code>RIF</code> is now Rifampicin instead of Rifampin</li> <li>The <code>name</code> of <code>RIF</code> is now Rifampicin instead of Rifampin</li>
<li>The <code>antibiotics</code> data set is now sorted by name</li> <li>The <code>antibiotics</code> data set is now sorted by name</li>
<li>Using verbose mode with <code><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code> returns more informative and readable output</li> <li>Using verbose mode with <code><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code> returns more informative and readable output</li>
@ -1198,7 +1206,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav"> <div id="tocnav">
<h2>Contents</h2> <h2>Contents</h2>
<ul class="nav nav-pills nav-stacked"> <ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9023">0.7.1.9023</a></li> <li><a href="#amr-0-7-1-9024">0.7.1.9024</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li> <li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li> <li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li> <li><a href="#amr-0-6-1">0.6.1</a></li>

2
docs/reference/index.html
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@ -78,7 +78,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9023</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9024</span>
</span> </span>
</div> </div>

8
docs/reference/microorganisms.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9024</span>
</span> </span>
</div> </div>
@ -238,7 +238,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 67,906 observations and 16 variables:</p><dl class='dl-horizontal'> <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 68,260 observations and 16 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd> <dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd> <dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd> <dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd>
@ -261,8 +261,8 @@
<li><p>9 entries of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li> <li><p>9 entries of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
<li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li> <li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
<li><p>3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)</p></li> <li><p>3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)</p></li>
<li><p>3 other 'undefined' entries (unknown, unknown Gram negatives and unknown Gram positives)</p></li> <li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
<li><p>8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life</p></li> <li><p>8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life</p></li>
</ul> </ul>
<h2 class="hasAnchor" id="about-the-records-from-dsmz-see-source-"><a class="anchor" href="#about-the-records-from-dsmz-see-source-"></a>About the records from DSMZ (see source)</h2> <h2 class="hasAnchor" id="about-the-records-from-dsmz-see-source-"><a class="anchor" href="#about-the-records-from-dsmz-see-source-"></a>About the records from DSMZ (see source)</h2>

4
docs/reference/microorganisms.old.html
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@ -80,7 +80,7 @@
</button> </button>
<span class="navbar-brand"> <span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a> <a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9015</span> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9024</span>
</span> </span>
</div> </div>
@ -238,7 +238,7 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 21,342 observations and 4 variables:</p><dl class='dl-horizontal'> <p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 21,743 observations and 4 variables:</p><dl class='dl-horizontal'>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID that was originally given</p></dd> <dt><code>col_id</code></dt><dd><p>Catalogue of Life ID that was originally given</p></dd>
<dt><code>col_id_new</code></dt><dd><p>New Catalogue of Life ID that responds to an entry in the <code><a href='microorganisms.html'>microorganisms</a></code> data set</p></dd> <dt><code>col_id_new</code></dt><dd><p>New Catalogue of Life ID that responds to an entry in the <code><a href='microorganisms.html'>microorganisms</a></code> data set</p></dd>
<dt><code>fullname</code></dt><dd><p>Old full taxonomic name of the microorganism</p></dd> <dt><code>fullname</code></dt><dd><p>Old full taxonomic name of the microorganism</p></dd>

6
man/microorganisms.Rd
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@ -4,7 +4,7 @@
\name{microorganisms} \name{microorganisms}
\alias{microorganisms} \alias{microorganisms}
\title{Data set with ~65,000 microorganisms} \title{Data set with ~65,000 microorganisms}
\format{A \code{\link{data.frame}} with 67,906 observations and 16 variables: \format{A \code{\link{data.frame}} with 68,260 observations and 16 variables:
\describe{ \describe{
\item{\code{mo}}{ID of microorganism as used by this package} \item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID} \item{\code{col_id}}{Catalogue of Life ID}
@ -33,8 +33,8 @@ Manually added were:
\item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)} \item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
\item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])} \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)} \item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)}
\item{3 other 'undefined' entries (unknown, unknown Gram negatives and unknown Gram positives)} \item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
\item{8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life} \item{8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
} }
} }
\section{About the records from DSMZ (see source)}{ \section{About the records from DSMZ (see source)}{

2
man/microorganisms.old.Rd
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@ -4,7 +4,7 @@
\name{microorganisms.old} \name{microorganisms.old}
\alias{microorganisms.old} \alias{microorganisms.old}
\title{Data set with previously accepted taxonomic names} \title{Data set with previously accepted taxonomic names}
\format{A \code{\link{data.frame}} with 21,342 observations and 4 variables: \format{A \code{\link{data.frame}} with 21,743 observations and 4 variables:
\describe{ \describe{
\item{\code{col_id}}{Catalogue of Life ID that was originally given} \item{\code{col_id}}{Catalogue of Life ID that was originally given}
\item{\code{col_id_new}}{New Catalogue of Life ID that responds to an entry in the \code{\link{microorganisms}} data set} \item{\code{col_id_new}}{New Catalogue of Life ID that responds to an entry in the \code{\link{microorganisms}} data set}

2
tests/testthat/test-eucast_rules.R
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@ -25,7 +25,7 @@ test_that("EUCAST rules work", {
# thoroughly check input table # thoroughly check input table
expect_equal(colnames(eucast_rules_file), expect_equal(colnames(eucast_rules_file),
c("if_mo_property", "like_is_one_of", "this_value", c("if_mo_property", "like.is.one_of", "this_value",
"and_these_antibiotics", "have_these_values", "and_these_antibiotics", "have_these_values",
"then_change_these_antibiotics", "to_value", "then_change_these_antibiotics", "to_value",
"reference.rule", "reference.rule_group")) "reference.rule", "reference.rule_group"))