diff --git a/DESCRIPTION b/DESCRIPTION index 6fc68885..2a0ae261 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 0.7.1.9087 -Date: 2019-09-23 +Version: 0.7.1.9088 +Date: 2019-09-25 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 7405bd0e..1ad0fad6 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 0.7.1.9087 -Last updated: 23-Sep-2019 +# AMR 0.7.1.9088 +Last updated: 25-Sep-2019 ### Breaking * Determination of first isolates now **excludes** all 'unknown' microorganisms at default, i.e. microbial code `"UNKNOWN"`. They can be included with the new parameter `include_unknown`: diff --git a/R/bug_drug_combinations.R b/R/bug_drug_combinations.R index e2addec3..73f438ef 100644 --- a/R/bug_drug_combinations.R +++ b/R/bug_drug_combinations.R @@ -21,15 +21,17 @@ #' Determine bug-drug combinations #' -#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a printable format, see Examples. +#' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{format} on the result to prettify it to a publicable/printable format, see Examples. #' @inheritParams eucast_rules #' @param combine_IR logical to indicate whether values R and I should be summed #' @param add_ab_group logical to indicate where the group of the antimicrobials must be included as a first column +#' @param remove_intrinsic_resistant logical to indicate that rows with 100\% resistance for all tested antimicrobials must be removed from the table #' @param FUN the function to call on the \code{mo} column to transform the microorganism IDs, defaults to \code{\link{mo_shortname}} -#' @param ... argumments passed on to \code{FUN} +#' @param translate_ab a character of length 1 containing column names of the \code{\link{antibiotics}} data set +#' @param ... arguments passed on to \code{FUN} #' @inheritParams rsi_df #' @inheritParams base::formatC -#' @importFrom dplyr rename +#' @importFrom dplyr %>% rename group_by select mutate filter pull #' @importFrom tidyr spread #' @importFrom clean freq #' @details The function \code{format} calculates the resistance per bug-drug combination. Use \code{combine_IR = FALSE} (default) to test R vs. S+I and \code{combine_IR = TRUE} to test R+I vs. S. @@ -74,9 +76,9 @@ bug_drug_combinations <- function(x, x <- x %>% mutate(mo = x %>% pull(col_mo) %>% FUN(...)) %>% - filter(mo %in% (clean::freq(mo) %>% - filter(count >= minimum) %>% - pull(item))) %>% + filter(mo %in% (freq(mo) %>% + filter(count >= minimum) %>% + pull(item))) %>% group_by(mo) %>% AMR::rsi_df(translate_ab = FALSE, combine_SI = FALSE) %>% select(-value) %>% @@ -88,41 +90,73 @@ bug_drug_combinations <- function(x, structure(.Data = x, class = c("bug_drug_combinations", class(x))) } -#' @importFrom dplyr everything rename +#' @importFrom dplyr everything rename %>% ungroup group_by summarise mutate_all arrange everything lag #' @importFrom tidyr spread #' @exportMethod format.bug_drug_combinations #' @export #' @rdname bug_drug_combinations -format.bug_drug_combinations <- function(x, - combine_IR = FALSE, +format.bug_drug_combinations <- function(x, + translate_ab = "name (ab, atc)", + language = get_locale(), + minimum = 30, + combine_SI = TRUE, + combine_IR = FALSE, add_ab_group = TRUE, + remove_intrinsic_resistant = FALSE, decimal.mark = getOption("OutDec"), big.mark = ifelse(decimal.mark == ",", ".", ","), ...) { - if (combine_IR == FALSE) { + if (remove_intrinsic_resistant == TRUE) { + x <- x %>% filter(R != total) + } + if (combine_IR == FALSE | combine_SI == TRUE) { x$isolates <- x$R } else { x$isolates <- x$R + x$I } + + give_ab_name <- function(ab, format, language) { + format <- tolower(format) + ab_txt <- rep(format, length(ab)) + for (i in 1:length(ab_txt)) { + ab_txt[i] <- gsub("ab", ab[i], ab_txt[i]) + ab_txt[i] <- gsub("cid", ab_cid(ab[i]), ab_txt[i]) + ab_txt[i] <- gsub("group", ab_group(ab[i], language = language), ab_txt[i]) + ab_txt[i] <- gsub("atc_group1", ab_atc_group1(ab[i], language = language), ab_txt[i]) + ab_txt[i] <- gsub("atc_group2", ab_atc_group2(ab[i], language = language), ab_txt[i]) + ab_txt[i] <- gsub("atc", ab_atc(ab[i]), ab_txt[i]) + ab_txt[i] <- gsub("name", ab_name(ab[i], language = language), ab_txt[i]) + ab_txt[i] + } + ab_txt + } + y <- x %>% + filter(total >= minimum) %>% + mutate(ab = as.ab(ab), + ab_txt = give_ab_name(ab = ab, format = translate_ab, language = language)) %>% + group_by(ab, ab_txt, mo) %>% + summarise(isolates = sum(isolates, na.rm = TRUE), + total = sum(total, na.rm = TRUE)) %>% + ungroup() %>% mutate(txt = paste0(percent(isolates / total, force_zero = TRUE, decimal.mark = decimal.mark, big.mark = big.mark), " (", trimws(format(isolates, big.mark = big.mark)), "/", trimws(format(total, big.mark = big.mark)), ")")) %>% - select(ab, mo, txt) %>% + select(ab, ab_txt, mo, txt) %>% spread(mo, txt) %>% mutate_all(~ifelse(is.na(.), "", .)) %>% - mutate(ab_group = ab_group(ab), - ab = paste0(ab_name(ab), " (", as.ab(ab), ", ", ab_atc(ab), ")")) %>% - select(ab_group, ab, everything()) %>% - arrange(ab_group, ab) %>% + mutate(ab_group = ab_group(ab, language = language), + ab_txt) %>% + select(ab_group, ab_txt, everything(), -ab) %>% + arrange(ab_group, ab_txt) %>% mutate(ab_group = ifelse(ab_group != lag(ab_group) | is.na(lag(ab_group)), ab_group, "")) if (add_ab_group == FALSE) { - y <- y %>% select(-ab_group) %>% rename("Antibiotic" = ab) + y <- y %>% select(-ab_group) %>% rename("Drug" = ab_txt) colnames(y)[1] <- translate_AMR(colnames(y)[1], language = get_locale(), only_unknown = FALSE) } else { y <- y %>% rename("Group" = ab_group, - "Antibiotic" = ab) + "Drug" = ab_txt) colnames(y)[1:2] <- translate_AMR(colnames(y)[1:2], language = get_locale(), only_unknown = FALSE) } y @@ -133,5 +167,5 @@ format.bug_drug_combinations <- function(x, #' @importFrom crayon blue print.bug_drug_combinations <- function(x, ...) { print(as.data.frame(x, stringsAsFactors = FALSE)) - message(blue("NOTE: Use 'format()' on this result to get a format that is ready for export or printing.")) + message(blue("NOTE: Use 'format()' on this result to get a publicable/printable format.")) } diff --git a/R/globals.R b/R/globals.R index 9485920a..5db2422b 100755 --- a/R/globals.R +++ b/R/globals.R @@ -22,6 +22,7 @@ globalVariables(c(".", "..property", "ab", + "ab_txt", "abbreviations", "antibiotic", "CNS_CPS", diff --git a/R/sysdata.rda b/R/sysdata.rda index 0bc537ee..cbb2ef76 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/data-raw/translations.tsv b/data-raw/translations.tsv index 58fa076b..85e2cd3f 100644 --- a/data-raw/translations.tsv +++ b/data-raw/translations.tsv @@ -54,6 +54,8 @@ nl ([([ ]*?)group \\1groep FALSE FALSE nl ([([ ]*?)Group \\1Groep FALSE FALSE nl antibiotic antibioticum FALSE FALSE nl Antibiotic Antibioticum FALSE FALSE +nl Drug Middel FALSE FALSE +nl drug middel FALSE FALSE es Coagulase-negative Staphylococcus Staphylococcus coagulasa negativo FALSE FALSE es Coagulase-positive Staphylococcus Staphylococcus coagulasa positivo FALSE FALSE es Beta-haemolytic Streptococcus Streptococcus Beta-hemolítico FALSE FALSE diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 00000000..3531b3d3 --- /dev/null +++ b/docs/404.html @@ -0,0 +1,276 @@ + + + + + + + + +Page not found (404) • AMR (for R) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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