From 85e2fbe4a3905a851e62526db0646facea232e1a Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Wed, 19 Oct 2022 11:47:57 +0200 Subject: [PATCH] remove warnings from unit tests --- DESCRIPTION | 2 +- NEWS.md | 2 +- R/aa_helper_functions.R | 6 ++-- R/ab.R | 7 ++-- R/ab_property.R | 2 +- R/ab_selectors.R | 4 +-- R/custom_eucast_rules.R | 30 ++++++++-------- R/disk.R | 4 +-- R/eucast_rules.R | 4 +-- R/first_isolate.R | 2 +- R/guess_ab_col.R | 4 +-- R/key_antimicrobials.R | 2 +- R/mdro.R | 4 +-- R/mic.R | 12 +++---- R/mo.R | 4 +-- R/mo_property.R | 58 +++++++++++++++---------------- R/mo_source.R | 6 ++-- R/random.R | 2 +- R/rsi.R | 12 +++---- R/rsi_calc.R | 6 ++-- inst/tinytest/test-mdro.R | 2 +- inst/tinytest/test-mo.R | 2 +- inst/tinytest/test-mo_property.R | 5 +-- man/antibiotic_class_selectors.Rd | 2 +- man/as.ab.Rd | 5 +-- man/as.disk.Rd | 2 +- man/as.mic.Rd | 10 +++--- man/as.rsi.Rd | 6 ++-- man/eucast_rules.Rd | 2 +- man/first_isolate.Rd | 2 +- man/guess_ab_col.Rd | 2 +- man/key_antimicrobials.Rd | 2 +- man/mdro.Rd | 2 +- man/mo_source.Rd | 6 ++-- man/random.Rd | 2 +- 35 files changed, 115 insertions(+), 110 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ef9e683f..c3645be8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9022 +Version: 1.8.2.9023 Date: 2022-10-19 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index e5fba191..9641e4f0 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9022 +# AMR 1.8.2.9023 This version will eventually become v2.0! We're happy to reach a new major milestone soon! diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R index be625615..9ee870ad 100755 --- a/R/aa_helper_functions.R +++ b/R/aa_helper_functions.R @@ -226,7 +226,7 @@ search_type_in_df <- function(x, type, info = TRUE) { # -- mo if (type == "mo") { if (any(vapply(FUN.VALUE = logical(1), x, is.mo))) { - # take first column + # take first 'mo' column found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)] } else if ("mo" %in% colnames_formatted && suppressWarnings(all(x$mo %in% c(NA, AMR::microorganisms$mo)))) { @@ -664,7 +664,7 @@ vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_ca return(paste0(quotes, v, quotes)) } if (identical(v, c("I", "R", "S"))) { - # class should be sorted like this + # class 'rsi' should be sorted like this v <- c("R", "S", "I") } # all commas except for last item, so will become '"val1", "val2", "val3" or "val4"' @@ -1434,7 +1434,7 @@ s3_register <- function(generic, class, method = NULL) { # see here for the full list: https://github.com/r-lib/backports if (getRversion() < "3.1.0") { # R-3.0 does not contain these functions, set them here to prevent installation failure - # (required for extension of the class) + # (required for extension of the 'mic' class) cospi <- function(...) 1 sinpi <- function(...) 1 tanpi <- function(...) 1 diff --git a/R/ab.R b/R/ab.R index b6bfda04..23c077bb 100755 --- a/R/ab.R +++ b/R/ab.R @@ -84,12 +84,13 @@ #' # they use as.ab() internally: #' ab_name("J01FA01") # "Erythromycin" #' ab_name("eryt") # "Erythromycin" +#' #' \donttest{ #' if (require("dplyr")) { #' -#' # you can quickly rename columns using dplyr >= 1.0.0: +#' # you can quickly rename 'rsi' columns using set_ab_names() with dplyr: #' example_isolates %>% -#' rename_with(as.ab, where(is.rsi)) +#' set_ab_names(where(is.rsi), property = "atc") #' } #' } as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) { @@ -548,7 +549,7 @@ type_sum.ab <- function(x, ...) { #' @export #' @noRd print.ab <- function(x, ...) { - cat("Class \n") + cat("Class 'ab'\n") print(as.character(x), quote = FALSE) } diff --git a/R/ab_property.R b/R/ab_property.R index b0ae2882..e2b77669 100644 --- a/R/ab_property.R +++ b/R/ab_property.R @@ -453,7 +453,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale ab_validate <- function(x, property, ...) { if (tryCatch(all(x[!is.na(x)] %in% AMR_env$AB_lookup$ab), error = function(e) FALSE)) { - # special case for ab_* functions where class is already + # special case for ab_* functions where class is already 'ab' x <- AMR_env$AB_lookup[match(x, AMR_env$AB_lookup$ab), property, drop = TRUE] } else { # try to catch an error when inputting an invalid argument diff --git a/R/ab_selectors.R b/R/ab_selectors.R index 54f0c4a0..8edcc389 100644 --- a/R/ab_selectors.R +++ b/R/ab_selectors.R @@ -32,7 +32,7 @@ #' These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by [cephalosporins()]. #' @param ab_class an antimicrobial class or a part of it, such as `"carba"` and `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value. #' @param filter an [expression] to be evaluated in the [antibiotics] data set, such as `name %like% "trim"` -#' @param only_rsi_columns a [logical] to indicate whether only columns of class `` must be selected (defaults to `FALSE`), see [as.rsi()] +#' @param only_rsi_columns a [logical] to indicate whether only columns of class `rsi` must be selected (defaults to `FALSE`), see [as.rsi()] #' @param only_treatable a [logical] to indicate whether agents that are only for laboratory tests should be excluded (defaults to `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`) #' @param ... ignored, only in place to allow future extensions #' @details @@ -575,7 +575,7 @@ ab_select_exec <- function(function_name, } else if (isTRUE(function_name == "antimycobacterials")) { abx <- AMR_env$AB_lookup$ab[which(AMR_env$AB_lookup$group == "Antimycobacterials")] } else { - # their upper case equivalent are vectors with class , created in data-raw/_pre_commit_hook.R + # their upper case equivalent are vectors with class 'ab', created in data-raw/_pre_commit_hook.R # carbapenems() gets its codes from AMR:::AB_CARBAPENEMS abx <- get(paste0("AB_", toupper(function_name)), envir = asNamespace("AMR")) # manually added codes from add_custom_antimicrobials() must also be supported diff --git a/R/custom_eucast_rules.R b/R/custom_eucast_rules.R index 6f50d9a6..ea9ec849 100644 --- a/R/custom_eucast_rules.R +++ b/R/custom_eucast_rules.R @@ -253,20 +253,22 @@ print.custom_eucast_rules <- function(x, ...) { } format_custom_query_rule <- function(query, colours = has_colour()) { - query <- gsub(" & ", font_black(font_bold(" and ")), query, fixed = TRUE) - query <- gsub(" | ", font_black(" or "), query, fixed = TRUE) - query <- gsub(" + ", font_black(" plus "), query, fixed = TRUE) - query <- gsub(" - ", font_black(" minus "), query, fixed = TRUE) - query <- gsub(" / ", font_black(" divided by "), query, fixed = TRUE) - query <- gsub(" * ", font_black(" times "), query, fixed = TRUE) - query <- gsub(" == ", font_black(" is "), query, fixed = TRUE) - query <- gsub(" > ", font_black(" is higher than "), query, fixed = TRUE) - query <- gsub(" < ", font_black(" is lower than "), query, fixed = TRUE) - query <- gsub(" >= ", font_black(" is higher than or equal to "), query, fixed = TRUE) - query <- gsub(" <= ", font_black(" is lower than or equal to "), query, fixed = TRUE) - query <- gsub(" ^ ", font_black(" to the power of "), query, fixed = TRUE) - query <- gsub(" %in% ", font_black(" is one of "), query, fixed = TRUE) - query <- gsub(" %like% ", font_black(" resembles "), query, fixed = TRUE) + # font_black() is very expensive in RStudio because it checks if the theme is dark, so do it once: + txt <- font_black("{text}") + query <- gsub(" & ", sub("{text}", font_bold(" and "), txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" | ", sub("{text}", " or ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" + ", sub("{text}", " plus ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" - ", sub("{text}", " minus ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" / ", sub("{text}", " divided by ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" * ", sub("{text}", " times ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" == ", sub("{text}", " is ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" > ", sub("{text}", " is higher than ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" < ", sub("{text}", " is lower than ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" >= ", sub("{text}", " is higher than or equal to ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" <= ", sub("{text}", " is lower than or equal to ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" ^ ", sub("{text}", " to the power of ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" %in% ", sub("{text}", " is one of ", txt, fixed = TRUE), query, fixed = TRUE) + query <- gsub(" %like% ", sub("{text}", " resembles ", txt, fixed = TRUE), query, fixed = TRUE) if (colours == TRUE) { query <- gsub('"R"', font_red_bg(" R "), query, fixed = TRUE) query <- gsub('"S"', font_green_bg(" S "), query, fixed = TRUE) diff --git a/R/disk.R b/R/disk.R index 463522c4..5081a2ba 100644 --- a/R/disk.R +++ b/R/disk.R @@ -139,7 +139,7 @@ all_valid_disks <- function(x) { } #' @rdname as.disk -#' @details `NA_disk_` is a missing value of the new `` class. +#' @details `NA_disk_` is a missing value of the new `disk` class. #' @export NA_disk_ <- set_clean_class(as.integer(NA_real_), new_class = c("disk", "integer") @@ -167,7 +167,7 @@ type_sum.disk <- function(x, ...) { #' @export #' @noRd print.disk <- function(x, ...) { - cat("Class \n") + cat("Class 'disk'\n") print(as.integer(x), quote = FALSE) } diff --git a/R/eucast_rules.R b/R/eucast_rules.R index d89674d1..2cd8b6c8 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -69,7 +69,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) { #' @param ... column name of an antibiotic, see section *Antibiotics* below #' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()] #' @param administration route of administration, either `r vector_or(dosage$administration)` -#' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `` (see [as.rsi()]) on beforehand (defaults to `FALSE`) +#' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `rsi` (see [as.rsi()]) on beforehand (defaults to `FALSE`) #' @param custom_rules custom rules to apply, created with [custom_eucast_rules()] #' @inheritParams first_isolate #' @details @@ -1023,7 +1023,7 @@ eucast_rules <- function(x, warn_lacking_rsi_class <- warn_lacking_rsi_class[order(colnames(x.bak))] warn_lacking_rsi_class <- warn_lacking_rsi_class[!is.na(warn_lacking_rsi_class)] warning_( - "in `eucast_rules()`: not all columns with antimicrobial results are of class . Transform them on beforehand, with e.g.:\n", + "in `eucast_rules()`: not all columns with antimicrobial results are of class 'rsi'. Transform them on beforehand, with e.g.:\n", " - ", x_deparsed, " %>% as.rsi(", ifelse(length(warn_lacking_rsi_class) == 1, warn_lacking_rsi_class, paste0(warn_lacking_rsi_class[1], ":", warn_lacking_rsi_class[length(warn_lacking_rsi_class)]) diff --git a/R/first_isolate.R b/R/first_isolate.R index 4a3dc0da..056d2a77 100755 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -48,7 +48,7 @@ #' @param points_threshold minimum number of points to require before differences in the antibiogram will lead to inclusion of an isolate when `type = "points"`, see *Details* #' @param info a [logical] to indicate info should be printed, defaults to `TRUE` only in interactive mode #' @param include_unknown a [logical] to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate. -#' @param include_untested_rsi a [logical] to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use `include_untested_rsi = FALSE` to always return `FALSE` for such rows. This checks the data set for columns of class `` and consequently requires transforming columns with antibiotic results using [as.rsi()] first. +#' @param include_untested_rsi a [logical] to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use `include_untested_rsi = FALSE` to always return `FALSE` for such rows. This checks the data set for columns of class `rsi` and consequently requires transforming columns with antibiotic results using [as.rsi()] first. #' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], otherwise arguments passed on to [key_antimicrobials()] (such as `universal`, `gram_negative`, `gram_positive`) #' @details #' To conduct epidemiological analyses on antimicrobial resistance data, only so-called first isolates should be included to prevent overestimation and underestimation of antimicrobial resistance. Different methods can be used to do so, see below. diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R index 361d64f5..d772a621 100755 --- a/R/guess_ab_col.R +++ b/R/guess_ab_col.R @@ -33,7 +33,7 @@ #' @param x a [data.frame] #' @param search_string a text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x` #' @param verbose a [logical] to indicate whether additional info should be printed -#' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `` (see [as.rsi()]) on beforehand (defaults to `FALSE`) +#' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `rsi` (see [as.rsi()]) on beforehand (defaults to `FALSE`) #' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antibiotics] data set for any column containing a name or code of that antibiotic. #' @return A column name of `x`, or `NULL` when no result is found. #' @export @@ -171,7 +171,7 @@ get_column_abx <- function(x, } # only check columns that are a valid AB code, ATC code, name, abbreviation or synonym, - # or already have the class (as.rsi) + # or already have the 'rsi' class (as.rsi) # and that they have no more than 50% invalid values vectr_antibiotics <- unlist(AMR_env$AB_lookup$generalised_all) vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3] diff --git a/R/key_antimicrobials.R b/R/key_antimicrobials.R index d330ddd1..dbdc508b 100755 --- a/R/key_antimicrobials.R +++ b/R/key_antimicrobials.R @@ -37,7 +37,7 @@ #' @param gram_negative names of antibiotic agents for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents. #' @param gram_positive names of antibiotic agents for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents. #' @param antifungal names of antifungal agents for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents. -#' @param only_rsi_columns a [logical] to indicate whether only columns must be included that were transformed to class `` (see [as.rsi()]) on beforehand (defaults to `FALSE`) +#' @param only_rsi_columns a [logical] to indicate whether only columns must be included that were transformed to class `rsi` (see [as.rsi()]) on beforehand (defaults to `FALSE`) #' @param ... ignored, only in place to allow future extensions #' @details #' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*. diff --git a/R/mdro.R b/R/mdro.R index 136e7bb9..32a70557 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -1941,9 +1941,9 @@ print.custom_mdro_guideline <- function(x, ...) { cat(" ", i + 1, ". ", font_bold("Otherwise: "), font_red(paste0("Negative")), "\n", sep = "") cat("\nUnmatched rows will return ", font_red("NA"), ".\n", sep = "") if (isTRUE(attributes(x)$as_factor)) { - cat("Results will be of class , with ordered levels: ", paste0(attributes(x)$values, collapse = " < "), "\n", sep = "") + cat("Results will be of class 'factor', with ordered levels: ", paste0(attributes(x)$values, collapse = " < "), "\n", sep = "") } else { - cat("Results will be of class .\n") + cat("Results will be of class 'character'.\n") } } diff --git a/R/mic.R b/R/mic.R index 6357504a..13e9ba2c 100755 --- a/R/mic.R +++ b/R/mic.R @@ -84,7 +84,7 @@ valid_mic_levels <- c( #' ``` #' x <- random_mic(10) #' x -#' #> Class +#' #> Class 'mic' #' #> [1] 16 1 8 8 64 >=128 0.0625 32 32 16 #' #' is.factor(x) @@ -101,7 +101,7 @@ valid_mic_levels <- c( #' #' ``` #' x[x > 4] -#' #> Class +#' #> Class 'mic' #' #> [1] 16 8 8 64 >=128 32 32 16 #' #' df <- data.frame(x, hospital = "A") @@ -119,7 +119,7 @@ valid_mic_levels <- c( #' #' Using [as.double()] or [as.numeric()] on MIC values will remove the operators and return a numeric vector. Do **not** use [as.integer()] on MIC values as by the \R convention on [factor]s, it will return the index of the factor levels (which is often useless for regular users). #' -#' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `` class. +#' Use [droplevels()] to drop unused levels. At default, it will return a plain factor. Use `droplevels(..., as.mic = TRUE)` to maintain the `mic` class. #' @return Ordered [factor] with additional class [`mic`], that in mathematical operations acts as decimal numbers. Bare in mind that the outcome of any mathematical operation on MICs will return a [numeric] value. #' @aliases mic #' @export @@ -253,7 +253,7 @@ all_valid_mics <- function(x) { } #' @rdname as.mic -#' @details `NA_mic_` is a missing value of the new `` class, analogous to e.g. base \R's [`NA_character_`][base::NA]. +#' @details `NA_mic_` is a missing value of the new `mic` class, analogous to e.g. base \R's [`NA_character_`][base::NA]. #' @format NULL #' @export NA_mic_ <- set_clean_class(factor(NA, levels = valid_mic_levels, ordered = TRUE), @@ -282,7 +282,7 @@ as.numeric.mic <- function(x, ...) { #' @rdname as.mic #' @method droplevels mic -#' @param as.mic a [logical] to indicate whether the `` class should be kept, defaults to `FALSE` +#' @param as.mic a [logical] to indicate whether the `mic` class should be kept, defaults to `FALSE` #' @export droplevels.mic <- function(x, as.mic = FALSE, ...) { x <- droplevels.factor(x, ...) @@ -313,7 +313,7 @@ type_sum.mic <- function(x, ...) { #' @export #' @noRd print.mic <- function(x, ...) { - cat("Class ", + cat("Class 'mic'", ifelse(length(levels(x)) < length(valid_mic_levels), font_red(" with dropped levels"), ""), "\n", sep = "" diff --git a/R/mo.R b/R/mo.R index 7d7646d0..87e640f9 100755 --- a/R/mo.R +++ b/R/mo.R @@ -408,7 +408,7 @@ as.mo <- function(x, } } - # 'MO_CONS' and 'MO_COPS' are vectors created in R/_pre_commit_hook.R + # 'MO_CONS' and 'MO_COPS' are 'mo' vectors created in R/_pre_commit_hook.R out[out %in% MO_CONS] <- "B_STPHY_CONS" out[out %in% MO_COPS] <- "B_STPHY_COPS" if (Becker == "all") { @@ -635,7 +635,7 @@ get_skimmers.mo <- function(column) { #' @export #' @noRd print.mo <- function(x, print.shortnames = FALSE, ...) { - cat("Class \n") + cat("Class 'mo'\n") x_names <- names(x) if (is.null(x_names) & print.shortnames == TRUE) { x_names <- tryCatch(mo_shortname(x, ...), error = function(e) NULL) diff --git a/R/mo_property.R b/R/mo_property.R index 63891798..20a15911 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -172,7 +172,7 @@ #' } mo_name <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_name") } meet_criteria(x, allow_NA = TRUE) @@ -194,7 +194,7 @@ mo_fullname <- mo_name #' @export mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_shortname") } meet_criteria(x, allow_NA = TRUE) @@ -235,7 +235,7 @@ mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti #' @export mo_subspecies <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_subspecies") } meet_criteria(x, allow_NA = TRUE) @@ -249,7 +249,7 @@ mo_subspecies <- function(x, language = get_AMR_locale(), keep_synonyms = getOpt #' @export mo_species <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_species") } meet_criteria(x, allow_NA = TRUE) @@ -263,7 +263,7 @@ mo_species <- function(x, language = get_AMR_locale(), keep_synonyms = getOption #' @export mo_genus <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_genus") } meet_criteria(x, allow_NA = TRUE) @@ -277,7 +277,7 @@ mo_genus <- function(x, language = get_AMR_locale(), keep_synonyms = getOption(" #' @export mo_family <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_family") } meet_criteria(x, allow_NA = TRUE) @@ -291,7 +291,7 @@ mo_family <- function(x, language = get_AMR_locale(), keep_synonyms = getOption( #' @export mo_order <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_order") } meet_criteria(x, allow_NA = TRUE) @@ -305,7 +305,7 @@ mo_order <- function(x, language = get_AMR_locale(), keep_synonyms = getOption(" #' @export mo_class <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_class") } meet_criteria(x, allow_NA = TRUE) @@ -319,7 +319,7 @@ mo_class <- function(x, language = get_AMR_locale(), keep_synonyms = getOption(" #' @export mo_phylum <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_phylum") } meet_criteria(x, allow_NA = TRUE) @@ -333,7 +333,7 @@ mo_phylum <- function(x, language = get_AMR_locale(), keep_synonyms = getOption( #' @export mo_kingdom <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_kingdom") } meet_criteria(x, allow_NA = TRUE) @@ -351,7 +351,7 @@ mo_domain <- mo_kingdom #' @export mo_type <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_type") } meet_criteria(x, allow_NA = TRUE) @@ -368,7 +368,7 @@ mo_type <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A #' @export mo_status <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_status") } meet_criteria(x, allow_NA = TRUE) @@ -382,7 +382,7 @@ mo_status <- function(x, language = get_AMR_locale(), keep_synonyms = getOption( #' @export mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_gramstain") } meet_criteria(x, allow_NA = TRUE) @@ -417,7 +417,7 @@ mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti #' @export mo_is_gram_negative <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_is_gram_negative") } meet_criteria(x, allow_NA = TRUE) @@ -437,7 +437,7 @@ mo_is_gram_negative <- function(x, language = get_AMR_locale(), keep_synonyms = #' @export mo_is_gram_positive <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_is_gram_positive") } meet_criteria(x, allow_NA = TRUE) @@ -457,7 +457,7 @@ mo_is_gram_positive <- function(x, language = get_AMR_locale(), keep_synonyms = #' @export mo_is_yeast <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_is_yeast") } meet_criteria(x, allow_NA = TRUE) @@ -482,7 +482,7 @@ mo_is_yeast <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio #' @export mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_is_intrinsic_resistant") } meet_criteria(x, allow_NA = TRUE) @@ -519,7 +519,7 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), keep_s #' @export mo_snomed <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_snomed") } meet_criteria(x, allow_NA = TRUE) @@ -533,7 +533,7 @@ mo_snomed <- function(x, language = get_AMR_locale(), keep_synonyms = getOption( #' @export mo_ref <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_ref") } meet_criteria(x, allow_NA = TRUE) @@ -547,7 +547,7 @@ mo_ref <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AM #' @export mo_authors <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_authors") } meet_criteria(x, allow_NA = TRUE) @@ -564,7 +564,7 @@ mo_authors <- function(x, language = get_AMR_locale(), keep_synonyms = getOption #' @export mo_year <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_year") } meet_criteria(x, allow_NA = TRUE) @@ -581,7 +581,7 @@ mo_year <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A #' @export mo_lpsn <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_lpsn") } meet_criteria(x, allow_NA = TRUE) @@ -595,7 +595,7 @@ mo_lpsn <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A #' @export mo_gbif <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_gbif") } meet_criteria(x, allow_NA = TRUE) @@ -609,7 +609,7 @@ mo_gbif <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A #' @export mo_rank <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_rank") } meet_criteria(x, allow_NA = TRUE) @@ -623,7 +623,7 @@ mo_rank <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A #' @export mo_taxonomy <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_taxonomy") } meet_criteria(x, allow_NA = TRUE) @@ -652,7 +652,7 @@ mo_taxonomy <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio #' @export mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_synonyms") } meet_criteria(x, allow_NA = TRUE) @@ -698,7 +698,7 @@ mo_current <- function(x, language = get_AMR_locale(), ...) { #' @export mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_info") } meet_criteria(x, allow_NA = TRUE) @@ -736,7 +736,7 @@ mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A #' @export mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_url") } meet_criteria(x, allow_NA = TRUE) @@ -775,7 +775,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms = #' @export mo_property <- function(x, property = "fullname", language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) { if (missing(x)) { - # this tries to find the data and an column + # this tries to find the data and an 'mo' column x <- find_mo_col(fn = "mo_property") } meet_criteria(x, allow_NA = TRUE) diff --git a/R/mo_source.R b/R/mo_source.R index 609e9731..4ea9ff1e 100644 --- a/R/mo_source.R +++ b/R/mo_source.R @@ -75,7 +75,7 @@ #' #' ``` #' as.mo("lab_mo_ecoli") -#' #> Class +#' #> Class 'mo' #' #> [1] B_ESCHR_COLI #' #' mo_genus("lab_mo_kpneumoniae") @@ -85,7 +85,7 @@ #' as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli")) #' #> NOTE: Translation to one microorganism was guessed with uncertainty. #' #> Use mo_uncertainties() to review it. -#' #> Class +#' #> Class 'mo' #' #> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI #' ``` #' @@ -108,7 +108,7 @@ #' #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from #' #> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns #' #> "Organisation XYZ" and "mo" -#' #> Class +#' #> Class 'mo' #' #> [1] B_ESCHR_COLI #' #' mo_genus("lab_Staph_aureus") diff --git a/R/random.R b/R/random.R index 32df979a..e13c4a92 100644 --- a/R/random.R +++ b/R/random.R @@ -38,7 +38,7 @@ #' @details The base \R function [sample()] is used for generating values. #' #' Generated values are based on the EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` guideline as implemented in the [rsi_translation] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument. -#' @return class `` for [random_mic()] (see [as.mic()]) and class `` for [random_disk()] (see [as.disk()]) +#' @return class `mic` for [random_mic()] (see [as.mic()]) and class `disk` for [random_disk()] (see [as.disk()]) #' @name random #' @rdname random #' @export diff --git a/R/rsi.R b/R/rsi.R index a230ba57..9b218b48 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -82,7 +82,7 @@ #' #' ### Other #' -#' The function [is.rsi()] detects if the input contains class ``. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector. +#' The function [is.rsi()] detects if the input contains class `rsi`. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector. #' #' The function [is.rsi.eligible()] returns `TRUE` when a columns contains at most 5% invalid antimicrobial interpretations (not S and/or I and/or R), and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` argument. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector. #' @section Interpretation of R and S/I: @@ -96,7 +96,7 @@ #' A microorganism is categorised as *Susceptible, Increased exposure* when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. #' #' This AMR package honours this (new) insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates. -#' @return Ordered [factor] with new class `` +#' @return Ordered [factor] with new class `rsi` #' @aliases rsi #' @export #' @seealso [as.mic()], [as.disk()], [as.mo()] @@ -198,7 +198,7 @@ as.rsi <- function(x, ...) { } #' @rdname as.rsi -#' @details `NA_rsi_` is a missing value of the new `` class, analogous to e.g. base \R's [`NA_character_`][base::NA]. +#' @details `NA_rsi_` is a missing value of the new `rsi` class, analogous to e.g. base \R's [`NA_character_`][base::NA]. #' @export NA_rsi_ <- set_clean_class(factor(NA, levels = c("S", "I", "R"), ordered = TRUE), new_class = c("rsi", "ordered", "factor") @@ -609,7 +609,7 @@ as.rsi.data.frame <- function(x, } else if (!is.rsi(x.bak[, ab_cols[i], drop = TRUE])) { show_message <- TRUE # only print message if class not already set - message_("=> Assigning class to already clean column '", font_bold(ab), "' (", + message_("=> Assigning class 'rsi' to already clean column '", font_bold(ab), "' (", ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""), ab_name(ab_coerced, tolower = TRUE), ")... ", appendLF = FALSE, @@ -702,7 +702,7 @@ as_rsi_method <- function(method_short, ) } if (is.null(mo)) { - stop_("No information was supplied about the microorganisms (missing argument `mo` and no column of class found). See ?as.rsi.\n\n", + stop_("No information was supplied about the microorganisms (missing argument `mo` and no column of class 'mo' found). See ?as.rsi.\n\n", "To transform certain columns with e.g. mutate(), use `data %>% mutate(across(..., as.rsi, mo = x))`, where x is your column with microorganisms.\n", "To tranform all ", method_long, " in a data set, use `data %>% as.rsi()` or `data %>% mutate(across(where(is.", method_short, "), as.rsi))`.", call = FALSE @@ -1086,7 +1086,7 @@ get_skimmers.rsi <- function(column) { #' @export #' @noRd print.rsi <- function(x, ...) { - cat("Class \n") + cat("Class 'rsi'\n") print(as.character(x), quote = FALSE) } diff --git a/R/rsi_calc.R b/R/rsi_calc.R index b9a98279..92b48843 100755 --- a/R/rsi_calc.R +++ b/R/rsi_calc.R @@ -120,7 +120,7 @@ rsi_calc <- function(..., if (is.data.frame(x)) { rsi_integrity_check <- character(0) for (i in seq_len(ncol(x))) { - # check integrity of columns: force class + # check integrity of columns: force 'rsi' class if (!is.rsi(x[, i, drop = TRUE])) { rsi_integrity_check <- c(rsi_integrity_check, as.character(x[, i, drop = TRUE])) x[, i] <- suppressWarnings(as.rsi(x[, i, drop = TRUE])) # warning will be given later @@ -160,7 +160,7 @@ rsi_calc <- function(..., if (print_warning == TRUE) { if (message_not_thrown_before("rsi_calc")) { - warning_("Increase speed by transforming to class on beforehand:\n", + warning_("Increase speed by transforming to class 'rsi' on beforehand:\n", " your_data %>% mutate_if(is.rsi.eligible, as.rsi)\n", " your_data %>% mutate(across(where(is.rsi.eligible), as.rsi))", call = FALSE @@ -344,7 +344,7 @@ rsi_calc_df <- function(type, # "proportion", "count" or "both" } else if (isTRUE(combine_IR)) { out$interpretation <- factor(out$interpretation, levels = c("S", "IR"), ordered = TRUE) } else { - # don't use as.rsi() here, as it would add the class and we would like + # don't use as.rsi() here, as it would add the class 'rsi' and we would like # the same data structure as output, regardless of input out$interpretation <- factor(out$interpretation, levels = c("S", "I", "R"), ordered = TRUE) } diff --git a/inst/tinytest/test-mdro.R b/inst/tinytest/test-mdro.R index c8ee9dcd..19b37fae 100755 --- a/inst/tinytest/test-mdro.R +++ b/inst/tinytest/test-mdro.R @@ -281,6 +281,6 @@ expect_warning(mdro(example_isolates, # print groups if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) { - expect_stdout(x <- mdro(example_isolates %>% group_by(ward), info = TRUE)) + expect_stdout(x <- mdro(example_isolates %>% group_by(ward), info = TRUE, pct_required_classes = 0)) expect_stdout(x <- mdro(example_isolates %>% group_by(ward), guideline = custom, info = TRUE)) } diff --git a/inst/tinytest/test-mo.R b/inst/tinytest/test-mo.R index 4a3b2f1f..66ca08a9 100644 --- a/inst/tinytest/test-mo.R +++ b/inst/tinytest/test-mo.R @@ -297,7 +297,7 @@ expect_equal(as.character(as.mo("con")), "UNKNOWN") expect_equal(as.character(as.mo("xxx")), NA_character_) expect_equal(as.character(as.mo(c("xxx", "con", "eco"))), c(NA_character_, "UNKNOWN", "B_ESCHR_COLI")) expect_equal( - as.character(as.mo(c("other", "none", "unknown"))), + as.character(suppressWarnings(as.mo(c("other", "none", "unknown")))), rep("UNKNOWN", 3) ) diff --git a/inst/tinytest/test-mo_property.R b/inst/tinytest/test-mo_property.R index 4419895d..615a0c1a 100644 --- a/inst/tinytest/test-mo_property.R +++ b/inst/tinytest/test-mo_property.R @@ -84,9 +84,10 @@ for (l in AMR:::LANGUAGES_SUPPORTED[-1]) { expect_false(mo_gramstain("Escherichia coli", language = l) == gr, info = paste("Gram-stain in language", l)) } +# test languages expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN")) -dutch <- mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")], language = "nl", keep_synonyms = TRUE) # should be transformable to English again -expect_identical(mo_name(dutch, language = NULL, keep_synonyms = TRUE), +dutch <- suppressWarnings(mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")], language = "nl", keep_synonyms = TRUE)) # should be transformable to English again +expect_identical(suppressWarnings(mo_name(dutch, language = NULL, keep_synonyms = TRUE)), microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase|Fungi")]) # gigantic test - will run ALL names # manual property function diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index d4ddf7c2..ca691254 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -102,7 +102,7 @@ not_intrinsic_resistant( \arguments{ \item{ab_class}{an antimicrobial class or a part of it, such as \code{"carba"} and \code{"carbapenems"}. The columns \code{group}, \code{atc_group1} and \code{atc_group2} of the \link{antibiotics} data set will be searched (case-insensitive) for this value.} -\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \verb{} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}} +\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \code{rsi} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}} \item{only_treatable}{a \link{logical} to indicate whether agents that are only for laboratory tests should be excluded (defaults to \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})} diff --git a/man/as.ab.Rd b/man/as.ab.Rd index 04faf07c..7e2e8b4e 100644 --- a/man/as.ab.Rd +++ b/man/as.ab.Rd @@ -89,12 +89,13 @@ ab_atc("seephthriaaksone") # and even this works # they use as.ab() internally: ab_name("J01FA01") # "Erythromycin" ab_name("eryt") # "Erythromycin" + \donttest{ if (require("dplyr")) { - # you can quickly rename columns using dplyr >= 1.0.0: + # you can quickly rename 'rsi' columns using set_ab_names() with dplyr: example_isolates \%>\% - rename_with(as.ab, where(is.rsi)) + set_ab_names(where(is.rsi), property = "atc") } } } diff --git a/man/as.disk.Rd b/man/as.disk.Rd index 050da92d..ff486be4 100644 --- a/man/as.disk.Rd +++ b/man/as.disk.Rd @@ -31,7 +31,7 @@ This transforms a vector to a new class \code{\link{disk}}, which is a disk diff \details{ Interpret disk values as RSI values with \code{\link[=as.rsi]{as.rsi()}}. It supports guidelines from EUCAST and CLSI. -\code{NA_disk_} is a missing value of the new \verb{} class. +\code{NA_disk_} is a missing value of the new \code{disk} class. } \examples{ # transform existing disk zones to the `disk` class (using base R) diff --git a/man/as.mic.Rd b/man/as.mic.Rd index 0596798f..bcb67cb0 100755 --- a/man/as.mic.Rd +++ b/man/as.mic.Rd @@ -22,7 +22,7 @@ is.mic(x) \item{na.rm}{a \link{logical} indicating whether missing values should be removed} -\item{as.mic}{a \link{logical} to indicate whether the \verb{} class should be kept, defaults to \code{FALSE}} +\item{as.mic}{a \link{logical} to indicate whether the \code{mic} class should be kept, defaults to \code{FALSE}} \item{...}{arguments passed on to methods} } @@ -39,7 +39,7 @@ This class for MIC values is a quite a special data type: formally it is an orde \if{html}{\out{
}}\preformatted{x <- random_mic(10) x -#> Class +#> Class 'mic' #> [1] 16 1 8 8 64 >=128 0.0625 32 32 16 is.factor(x) @@ -55,7 +55,7 @@ median(x) This makes it possible to maintain operators that often come with MIC values, such ">=" and "<=", even when filtering using \link{numeric} values in data analysis, e.g.: \if{html}{\out{
}}\preformatted{x[x > 4] -#> Class +#> Class 'mic' #> [1] 16 8 8 64 >=128 32 32 16 df <- data.frame(x, hospital = "A") @@ -73,9 +73,9 @@ The following \link[=groupGeneric]{generic functions} are implemented for the MI Using \code{\link[=as.double]{as.double()}} or \code{\link[=as.numeric]{as.numeric()}} on MIC values will remove the operators and return a numeric vector. Do \strong{not} use \code{\link[=as.integer]{as.integer()}} on MIC values as by the \R convention on \link{factor}s, it will return the index of the factor levels (which is often useless for regular users). -Use \code{\link[=droplevels]{droplevels()}} to drop unused levels. At default, it will return a plain factor. Use \code{droplevels(..., as.mic = TRUE)} to maintain the \verb{} class. +Use \code{\link[=droplevels]{droplevels()}} to drop unused levels. At default, it will return a plain factor. Use \code{droplevels(..., as.mic = TRUE)} to maintain the \code{mic} class. -\code{NA_mic_} is a missing value of the new \verb{} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}. +\code{NA_mic_} is a missing value of the new \code{mic} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}. } \examples{ mic_data <- as.mic(c(">=32", "1.0", "1", "1.00", 8, "<=0.128", "8", "16", "16")) diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd index dd947756..befe3c12 100755 --- a/man/as.rsi.Rd +++ b/man/as.rsi.Rd @@ -86,7 +86,7 @@ rsi_interpretation_history(clean = FALSE) \item{clean}{a \link{logical} to indicate whether previously stored results should be forgotten after returning the 'logbook' with results} } \value{ -Ordered \link{factor} with new class \verb{} +Ordered \link{factor} with new class \code{rsi} } \description{ Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class \code{\link{rsi}}, which is an ordered \link{factor} with levels \verb{S < I < R}. @@ -139,12 +139,12 @@ The repository of this package \href{https://github.com/msberends/AMR/blob/main/ \subsection{Other}{ -The function \code{\link[=is.rsi]{is.rsi()}} detects if the input contains class \verb{}. If the input is a \link{data.frame}, it iterates over all columns and returns a \link{logical} vector. +The function \code{\link[=is.rsi]{is.rsi()}} detects if the input contains class \code{rsi}. If the input is a \link{data.frame}, it iterates over all columns and returns a \link{logical} vector. The function \code{\link[=is.rsi.eligible]{is.rsi.eligible()}} returns \code{TRUE} when a columns contains at most 5\% invalid antimicrobial interpretations (not S and/or I and/or R), and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} argument. If the input is a \link{data.frame}, it iterates over all columns and returns a \link{logical} vector. } -\code{NA_rsi_} is a missing value of the new \verb{} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}. +\code{NA_rsi_} is a missing value of the new \code{rsi} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}. } \section{Interpretation of R and S/I}{ diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index b530088f..922410ca 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -52,7 +52,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11) \item{ampc_cephalosporin_resistance}{a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these version of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of \code{NA} (the default) for this argument will remove results for these three agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.} -\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \verb{} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})} +\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})} \item{custom_rules}{custom rules to apply, created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}} diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd index 6616c55a..0c68c8e2 100755 --- a/man/first_isolate.Rd +++ b/man/first_isolate.Rd @@ -82,7 +82,7 @@ filter_first_isolate( \item{include_unknown}{a \link{logical} to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code \code{"UNKNOWN"}, which defaults to \code{FALSE}. For WHONET users, this means that all records with organism code \code{"con"} (\emph{contamination}) will be excluded at default. Isolates with a microbial ID of \code{NA} will always be excluded as first isolate.} -\item{include_untested_rsi}{a \link{logical} to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use \code{include_untested_rsi = FALSE} to always return \code{FALSE} for such rows. This checks the data set for columns of class \verb{} and consequently requires transforming columns with antibiotic results using \code{\link[=as.rsi]{as.rsi()}} first.} +\item{include_untested_rsi}{a \link{logical} to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use \code{include_untested_rsi = FALSE} to always return \code{FALSE} for such rows. This checks the data set for columns of class \code{rsi} and consequently requires transforming columns with antibiotic results using \code{\link[=as.rsi]{as.rsi()}} first.} \item{...}{arguments passed on to \code{\link[=first_isolate]{first_isolate()}} when using \code{\link[=filter_first_isolate]{filter_first_isolate()}}, otherwise arguments passed on to \code{\link[=key_antimicrobials]{key_antimicrobials()}} (such as \code{universal}, \code{gram_negative}, \code{gram_positive})} } diff --git a/man/guess_ab_col.Rd b/man/guess_ab_col.Rd index 7cd7d6ea..c411d669 100644 --- a/man/guess_ab_col.Rd +++ b/man/guess_ab_col.Rd @@ -18,7 +18,7 @@ guess_ab_col( \item{verbose}{a \link{logical} to indicate whether additional info should be printed} -\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \verb{} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})} +\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})} } \value{ A column name of \code{x}, or \code{NULL} when no result is found. diff --git a/man/key_antimicrobials.Rd b/man/key_antimicrobials.Rd index 63b7a32f..00022635 100644 --- a/man/key_antimicrobials.Rd +++ b/man/key_antimicrobials.Rd @@ -45,7 +45,7 @@ antimicrobials_equal( \item{antifungal}{names of antifungal agents for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.} -\item{only_rsi_columns}{a \link{logical} to indicate whether only columns must be included that were transformed to class \verb{} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})} +\item{only_rsi_columns}{a \link{logical} to indicate whether only columns must be included that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})} \item{...}{ignored, only in place to allow future extensions} diff --git a/man/mdro.Rd b/man/mdro.Rd index 965350d0..56b3d696 100644 --- a/man/mdro.Rd +++ b/man/mdro.Rd @@ -58,7 +58,7 @@ eucast_exceptional_phenotypes(x = NULL, only_rsi_columns = FALSE, ...) \item{verbose}{a \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.} -\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \verb{} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})} +\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})} \item{...}{in case of \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}: a set of rules, see section \emph{Using Custom Guidelines} below. Otherwise: column name of an antibiotic, see section \emph{Antibiotics} below.} diff --git a/man/mo_source.Rd b/man/mo_source.Rd index 790cb52c..04ad0276 100644 --- a/man/mo_source.Rd +++ b/man/mo_source.Rd @@ -60,7 +60,7 @@ It has now created a file \code{"~/mo_source.rds"} with the contents of our Exce And now we can use it in our functions: \if{html}{\out{
}}\preformatted{as.mo("lab_mo_ecoli") -#> Class +#> Class 'mo' #> [1] B_ESCHR_COLI mo_genus("lab_mo_kpneumoniae") @@ -70,7 +70,7 @@ mo_genus("lab_mo_kpneumoniae") as.mo(c("Escherichia coli", "E. coli", "lab_mo_ecoli")) #> NOTE: Translation to one microorganism was guessed with uncertainty. #> Use mo_uncertainties() to review it. -#> Class +#> Class 'mo' #> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI }\if{html}{\out{
}} @@ -91,7 +91,7 @@ If we edit the Excel file by, let's say, adding row 4 like this: #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from #> '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns #> "Organisation XYZ" and "mo" -#> Class +#> Class 'mo' #> [1] B_ESCHR_COLI mo_genus("lab_Staph_aureus") diff --git a/man/random.Rd b/man/random.Rd index c9207c52..36acd13d 100644 --- a/man/random.Rd +++ b/man/random.Rd @@ -25,7 +25,7 @@ random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...) \item{prob_RSI}{a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)} } \value{ -class \verb{} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[=as.mic]{as.mic()}}) and class \verb{} for \code{\link[=random_disk]{random_disk()}} (see \code{\link[=as.disk]{as.disk()}}) +class \code{mic} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[=as.mic]{as.mic()}}) and class \code{disk} for \code{\link[=random_disk]{random_disk()}} (see \code{\link[=as.disk]{as.disk()}}) } \description{ These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible.