mirror of https://github.com/msberends/AMR.git
(v1.5.0.9022) mo properties speed improvement
This commit is contained in:
parent
5ef8cb41a7
commit
062c49fca1
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@ -53,9 +53,11 @@ jobs:
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- {os: macOS-latest, r: 'devel', allowfail: false}
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- {os: macOS-latest, r: 'release', allowfail: false}
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- {os: macOS-latest, r: 'oldrel', allowfail: false}
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- {os: windows-latest, r: 'devel', allowfail: false}
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- {os: windows-latest, r: 'release', allowfail: false}
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- {os: windows-latest, r: 'oldrel', allowfail: false}
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- {os: ubuntu-20.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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@ -66,7 +68,8 @@ jobs:
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- {os: ubuntu-20.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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# - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-20.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
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- {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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@ -77,7 +80,7 @@ jobs:
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- {os: ubuntu-16.04, r: '3.3', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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# - {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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- {os: ubuntu-16.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.5.0.9021
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Version: 1.5.0.9022
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Date: 2021-02-21
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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5
NEWS.md
5
NEWS.md
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@ -1,4 +1,4 @@
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# AMR 1.5.0.9021
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# AMR 1.5.0.9022
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## <small>Last updated: 21 February 2021</small>
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### New
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@ -58,7 +58,8 @@
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* Functions `print()` and `summary()` on a Principal Components Analysis object (`pca()`) now print additional group info if the original data was grouped using `dplyr::group_by()`
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* Improved speed and reliability of `guess_ab_col()`. As this also internally improves the reliability of `first_isolate()` and `mdro()`, this might have a slight impact on the results of those functions.
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* Fix for `mo_name()` when used in other languages than English
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* The `like()` function (and its fast alias `%like%`) now always use Perl compatibility, improving speed for many functions in this package
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* The `like()` function (and its fast alias `%like%`) now always use Perl compatibility, improving speed for many functions in this package (e.g., `as.mo()` is now up to 4 times faster)
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* *Staphylococcus cornubiensis* is now correctly categorised as coagulase-positive
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### Other
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* Big documentation updates
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@ -112,7 +112,7 @@ check_dataset_integrity <- function() {
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require("AMR")
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})
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stop_if(!valid_microorganisms | !valid_antibiotics,
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"the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object names was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
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"the data set `microorganisms` or `antibiotics` was overwritten in your environment because another package with the same object name(s) was loaded _after_ the AMR package, preventing the AMR package from working correctly. Please load the AMR package last.")
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invisible(TRUE)
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}
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@ -538,7 +538,7 @@ meet_criteria <- function(object,
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if (!is.null(pkg_env$meet_criteria_error_txt)) {
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error_txt <- pkg_env$meet_criteria_error_txt
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pkg_env$meet_criteria_error_txt <- NULL
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stop(error_txt, call. = FALSE)
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stop(error_txt, call. = FALSE) # don't use stop_() here, pkg may not be loaded yet
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}
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pkg_env$meet_criteria_error_txt <- NULL
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@ -867,7 +867,13 @@ font_grey <- function(..., collapse = " ") {
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try_colour(..., before = "\033[38;5;249m", after = "\033[39m", collapse = collapse)
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}
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font_grey_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = collapse)
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if (tryCatch(rstudioapi::getThemeInfo()$dark == TRUE, error = function(e) FALSE)) {
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# similar to HTML #444444
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try_colour(..., before = "\033[48;5;238m", after = "\033[49m", collapse = collapse)
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} else {
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# similar to HTML #eeeeee
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try_colour(..., before = "\033[48;5;254m", after = "\033[49m", collapse = collapse)
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}
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}
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font_green_bg <- function(..., collapse = " ") {
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try_colour(..., before = "\033[42m", after = "\033[49m", collapse = collapse)
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25
R/mo.R
25
R/mo.R
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@ -178,13 +178,6 @@ as.mo <- function(x,
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return(set_clean_class(x, new_class = c("mo", "character")))
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}
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if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
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& isFALSE(Becker)
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& isFALSE(Lancefield), error = function(e) FALSE)) {
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# to improve speed, special case for taxonomically correct full names (case-insensitive)
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return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
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}
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# start off with replaced language-specific non-ASCII characters with ASCII characters
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x <- parse_and_convert(x)
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# replace mo codes used in older package versions
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@ -198,6 +191,13 @@ as.mo <- function(x,
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x[trimws2(x) %like% translate_AMR("no .*growth", language = language)] <- NA_character_
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x[trimws2(x) %like% paste0("^(", translate_AMR("no|not", language = language), ") [a-z]+")] <- "UNKNOWN"
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uncertainty_level <- translate_allow_uncertain(allow_uncertain)
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if (tryCatch(all(x == "" | gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE) %in% MO_lookup$fullname_lower, na.rm = TRUE)
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& isFALSE(Becker)
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& isFALSE(Lancefield), error = function(e) FALSE)) {
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# to improve speed, special case for taxonomically correct full names (case-insensitive)
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return(MO_lookup[match(gsub(".*(unknown ).*", "unknown name", tolower(x), perl = TRUE), MO_lookup$fullname_lower), "mo", drop = TRUE])
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}
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if (!is.null(reference_df)
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&& check_validity_mo_source(reference_df)
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@ -481,11 +481,11 @@ exec_as.mo <- function(x,
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# Fill in fullnames and MO codes at once
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known_names <- tolower(x_backup) %in% MO_lookup$fullname_lower
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x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname), property, drop = TRUE]
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x[known_names] <- MO_lookup[match(tolower(x_backup)[known_names], MO_lookup$fullname_lower), property, drop = TRUE]
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known_codes <- toupper(x_backup) %in% MO_lookup$mo
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x[known_codes] <- MO_lookup[match(toupper(x_backup)[known_codes], MO_lookup$mo), property, drop = TRUE]
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already_known <- known_names | known_codes
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# now only continue where the right taxonomic output is not already known
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if (any(!already_known)) {
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x_known <- x[already_known]
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@ -984,7 +984,6 @@ exec_as.mo <- function(x,
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g.x_backup_without_spp %pm>% substr(1, x_length / 2),
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".* ",
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g.x_backup_without_spp %pm>% substr((x_length / 2) + 1, x_length))
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print(x_split)
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found <- lookup(fullname_lower %like_case% x_split,
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haystack = data_to_check)
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if (!is.na(found)) {
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@ -1977,13 +1976,13 @@ parse_and_convert <- function(x) {
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if (NCOL(x) > 2) {
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stop("a maximum of two columns is allowed", call. = FALSE)
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} else if (NCOL(x) == 2) {
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# support Tidyverse selection like: df %pm>% select(colA, colB)
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# support Tidyverse selection like: df %>% select(colA, colB)
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# paste these columns together
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x <- as.data.frame(x, stringsAsFactors = FALSE)
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colnames(x) <- c("A", "B")
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x <- paste(x$A, x$B)
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} else {
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# support Tidyverse selection like: df %pm>% select(colA)
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# support Tidyverse selection like: df %>% select(colA)
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x <- as.data.frame(x, stringsAsFactors = FALSE)[[1]]
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}
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}
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@ -1991,6 +1990,8 @@ parse_and_convert <- function(x) {
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parsed <- iconv(x, to = "UTF-8")
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parsed[is.na(parsed) & !is.na(x)] <- iconv(x[is.na(parsed) & !is.na(x)], from = "Latin1", to = "ASCII//TRANSLIT")
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parsed <- gsub('"', "", parsed, fixed = TRUE)
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parsed <- gsub(" +", " ", parsed, perl = TRUE)
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parsed <- trimws(parsed)
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}, error = function(e) stop(e$message, call. = FALSE)) # this will also be thrown when running `as.mo(no_existing_object)`
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parsed
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}
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@ -694,22 +694,22 @@ mo_property <- function(x, property = "fullname", language = get_locale(), ...)
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mo_validate <- function(x, property, language, ...) {
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check_dataset_integrity()
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if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & length(list(...)) == 0, error = function(e) FALSE)) {
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# special case for mo_* functions where class is already <mo>
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return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
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}
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dots <- list(...)
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Becker <- dots$Becker
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if (is.null(Becker)) {
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if (is.null(Becker) | property %in% c("kingdom", "phylum", "class", "order", "family", "genus")) {
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Becker <- FALSE
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}
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Lancefield <- dots$Lancefield
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if (is.null(Lancefield)) {
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if (is.null(Lancefield) | property %in% c("kingdom", "phylum", "class", "order", "family", "genus")) {
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Lancefield <- FALSE
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}
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has_Becker_or_Lancefield <- Becker %in% c(TRUE, "all") | Lancefield %in% c(TRUE, "all")
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if (tryCatch(all(x[!is.na(x)] %in% MO_lookup$mo) & !has_Becker_or_Lancefield, error = function(e) FALSE)) {
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# special case for mo_* functions where class is already <mo>
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return(MO_lookup[match(x, MO_lookup$mo), property, drop = TRUE])
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}
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# try to catch an error when inputting an invalid argument
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# so the 'call.' can be set to FALSE
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tryCatch(x[1L] %in% MO_lookup[1, property, drop = TRUE],
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# because it's already a valid MO
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x <- exec_as.mo(x, property = property, initial_search = FALSE, language = language, ...)
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} else if (!all(x %in% MO_lookup[, property, drop = TRUE])
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| Becker %in% c(TRUE, "all")
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| Lancefield %in% c(TRUE, "all")) {
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| has_Becker_or_Lancefield) {
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accepted_args <- names(as.list(args("as.mo")))
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accepted_args <- accepted_args[!accepted_args %in% c("", "...", "x", "property")]
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stop_if(!all(names(dots) %in% names(as.list(args("as.mo")))),
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"invalid argument(s): ", vector_and(names(dots)[!names(dots) %in% names(as.list(args("as.mo")))], quotes = "'"),
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".\nAccepted arguments are ", vector_and(accepted_args, quotes = "'"), ".",
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call = FALSE)
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x <- exec_as.mo(x, property = property, language = language, ...)
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}
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BIN
R/sysdata.rda
BIN
R/sysdata.rda
Binary file not shown.
Binary file not shown.
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@ -51,18 +51,19 @@ create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
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"lentus", "lugdunensis", "massiliensis", "microti",
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"muscae", "nepalensis", "pasteuri", "petrasii",
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"pettenkoferi", "piscifermentans", "pseudoxylosus",
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"rostri", "saccharolyticus", "saprophyticus",
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"pulvereri", "rostri", "saccharolyticus", "saprophyticus",
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"sciuri", "simulans", "stepanovicii", "succinus",
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"vitulinus", "warneri", "xylosus")
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"vitulinus", "vitulus", "warneri", "xylosus")
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| (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
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"mo", drop = TRUE]
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} else if (type == "CoPS") {
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MO_staph[which(MO_staph$species %in% c("coagulase-positive",
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"simiae", "agnetis",
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"agnetis", "argenteus",
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"cornubiensis",
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"delphini", "lutrae",
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"hyicus", "intermedius",
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"pseudintermedius", "pseudointermedius",
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"schweitzeri", "argenteus")
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"schweitzeri", "simiae")
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| (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
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"mo", drop = TRUE]
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}
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
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</span>
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</div>
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@ -43,7 +43,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
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</span>
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</div>
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@ -81,7 +81,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9021</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
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</span>
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</div>
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@ -236,9 +236,9 @@
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<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
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</div>
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<div id="amr-1509021" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0.9021">
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<a href="#amr-1509021" class="anchor"></a>AMR 1.5.0.9021<small> Unreleased </small>
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<div id="amr-1509022" class="section level1">
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<h1 class="page-header" data-toc-text="1.5.0.9022">
|
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<a href="#amr-1509022" class="anchor"></a>AMR 1.5.0.9022<small> Unreleased </small>
|
||||
</h1>
|
||||
<div id="last-updated-21-february-2021" class="section level2">
|
||||
<h2 class="hasAnchor">
|
||||
|
|
@ -326,7 +326,9 @@
|
|||
</li>
|
||||
<li>Improved speed and reliability of <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code>. As this also internally improves the reliability of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>, this might have a slight impact on the results of those functions.</li>
|
||||
<li>Fix for <code><a href="../reference/mo_property.html">mo_name()</a></code> when used in other languages than English</li>
|
||||
<li>The <code><a href="../reference/like.html">like()</a></code> function (and its fast alias <code><a href="../reference/like.html">%like%</a></code>) now always use Perl compatibility, improving speed for many functions in this package</li>
|
||||
<li>The <code><a href="../reference/like.html">like()</a></code> function (and its fast alias <code><a href="../reference/like.html">%like%</a></code>) now always use Perl compatibility, improving speed for many functions in this package (e.g., <code><a href="../reference/as.mo.html">as.mo()</a></code> is now up to 4 times faster)</li>
|
||||
<li>
|
||||
<em>Staphylococcus cornubiensis</em> is now correctly categorised as coagulase-positive</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="other" class="section level3">
|
||||
|
|
|
|||
|
|
@ -12,7 +12,7 @@ articles:
|
|||
datasets: datasets.html
|
||||
resistance_predict: resistance_predict.html
|
||||
welcome_to_AMR: welcome_to_AMR.html
|
||||
last_built: 2021-02-21T19:14Z
|
||||
last_built: 2021-02-21T21:55Z
|
||||
urls:
|
||||
reference: https://msberends.github.io/AMR//reference
|
||||
article: https://msberends.github.io/AMR//articles
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -81,7 +81,7 @@
|
|||
</button>
|
||||
<span class="navbar-brand">
|
||||
<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">1.5.0.9021</span>
|
||||
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9022</span>
|
||||
</span>
|
||||
</div>
|
||||
|
||||
|
|
|
|||
|
|
@ -86,3 +86,13 @@ test_that("CoL version info works", {
|
|||
|
||||
expect_output(print(catalogue_of_life_version()))
|
||||
})
|
||||
|
||||
test_that("CoNS/CoPS are up to date", {
|
||||
uncategorised <- subset(microorganisms,
|
||||
genus == "Staphylococcus" &
|
||||
!species %in% c("", "aureus") &
|
||||
!mo %in% c(MO_CONS, MO_COPS))
|
||||
expect(NROW(uncategorised) == 0,
|
||||
failure_message = paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
|
||||
uncategorised$species, " (", uncategorised$mo, ")"))
|
||||
})
|
||||
|
|
|
|||
Loading…
Reference in New Issue