diff --git a/.gitlab-ci.R b/.gitlab-ci.R index ae44cf34..4a2628c5 100644 --- a/.gitlab-ci.R +++ b/.gitlab-ci.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # install_if_needed <- function(pkg, repos, quiet) { diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 95459424..156d744b 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # stages: diff --git a/DESCRIPTION b/DESCRIPTION index f1406b8d..2afed23f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 0.6.1.9001 -Date: 2019-03-29 +Version: 0.6.1.9002 +Date: 2019-04-05 Title: Antimicrobial Resistance Analysis Authors@R: c( person( diff --git a/NAMESPACE b/NAMESPACE index 37afc23d..4ec62f58 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -40,7 +40,6 @@ S3method(summary,mic) S3method(summary,mo) S3method(summary,rsi) export("%like%") -export(EUCAST_rules) export(ab_atc) export(ab_certe) export(ab_name) @@ -82,6 +81,7 @@ export(count_all) export(count_df) export(eucast_exceptional_phenotypes) export(eucast_rules) +export(eucast_rules_file) export(facet_rsi) export(filter_1st_cephalosporins) export(filter_2nd_cephalosporins) @@ -108,11 +108,8 @@ export(get_mo_source) export(ggplot_rsi) export(ggplot_rsi_predict) export(guess_ab_col) -export(guess_atc) -export(guess_mo) export(header) export(inner_join_microorganisms) -export(interpretive_reading) export(is.atc) export(is.mic) export(is.mo) @@ -281,6 +278,7 @@ importFrom(graphics,points) importFrom(graphics,text) importFrom(hms,is.hms) importFrom(knitr,kable) +importFrom(microbenchmark,microbenchmark) importFrom(rlang,as_label) importFrom(rlang,enquos) importFrom(rlang,eval_tidy) diff --git a/NEWS.md b/NEWS.md index e8d65843..f4bf27a5 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,11 @@ # AMR 0.6.1.9001 **Note: latest development version** +#### Changed +* Removed deprecated functions `guess_mo()`, `guess_atc()`, `EUCAST_rules()`, `interpretive_reading()` +* Added more old taxonomic names to the `microorganisms.old` data set, which leads to better results finding when using the `as.mo()` function +* Frequency tables of microbial IDs speed improvement +* Removed all hardcoded EUCAST rules and replaced them with a new reference file: `./inst/eucast/eucast.tsv`. # AMR 0.6.1 diff --git a/R/abname.R b/R/abname.R index a561ae68..87ae33d0 100755 --- a/R/abname.R +++ b/R/abname.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Name of an antibiotic diff --git a/R/age.R b/R/age.R index 0df17e96..0eca8995 100755 --- a/R/age.R +++ b/R/age.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Age in years of individuals diff --git a/R/amr.R b/R/amr.R index bdbc9b5a..3c5edef9 100644 --- a/R/amr.R +++ b/R/amr.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' The \code{AMR} Package @@ -64,4 +64,6 @@ #' \url{https://gitlab.com/msberends/AMR/issues} #' @name AMR #' @rdname AMR +# # prevent NOTE on R >= 3.6 +#' @importFrom microbenchmark microbenchmark NULL diff --git a/R/atc.R b/R/atc.R index b609dceb..626e399b 100755 --- a/R/atc.R +++ b/R/atc.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Transform to ATC code diff --git a/R/atc_online.R b/R/atc_online.R index c201b51a..469c28be 100644 --- a/R/atc_online.R +++ b/R/atc_online.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Get ATC properties from WHOCC website diff --git a/R/atc_property.R b/R/atc_property.R index 36a98486..b3a55ded 100755 --- a/R/atc_property.R +++ b/R/atc_property.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Property of an antibiotic diff --git a/R/availability.R b/R/availability.R index 17b620a7..cec00f1e 100644 --- a/R/availability.R +++ b/R/availability.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Check availability of columns diff --git a/R/catalogue_of_life.R b/R/catalogue_of_life.R index f15d7c80..812e5e0d 100755 --- a/R/catalogue_of_life.R +++ b/R/catalogue_of_life.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' The Catalogue of Life @@ -33,7 +33,7 @@ #' \item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa} #' \item{All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).} #' \item{All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like \emph{Strongyloides} and \emph{Taenia})} -#' \item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed} +#' \item{All ~21,000 previously accepted names of included (sub)species that have been taxonomically renamed} #' \item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies} #' \item{The responsible author(s) and year of scientific publication} #' } diff --git a/R/count.R b/R/count.R index b1036cdc..0d56ce1f 100755 --- a/R/count.R +++ b/R/count.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Count isolates @@ -74,15 +74,15 @@ #' # Count co-resistance between amoxicillin/clav acid and gentamicin, #' # so we can see that combination therapy does a lot more than mono therapy. #' # Please mind that `portion_S` calculates percentages right away instead. -#' count_S(septic_patients$amcl) # S = 1057 (67.1%) -#' count_all(septic_patients$amcl) # n = 1576 +#' count_S(septic_patients$amcl) # S = 1342 (71.4%) +#' count_all(septic_patients$amcl) # n = 1879 #' #' count_S(septic_patients$gent) # S = 1372 (74.0%) #' count_all(septic_patients$gent) # n = 1855 #' #' with(septic_patients, -#' count_S(amcl, gent)) # S = 1396 (92.0%) -#' with(septic_patients, # n = 1517 +#' count_S(amcl, gent)) # S = 1660 (92.3%) +#' with(septic_patients, # n = 1798 #' n_rsi(amcl, gent)) #' #' # Get portions S/I/R immediately of all rsi columns diff --git a/R/data.R b/R/data.R index 68bd43d8..5ca6e1c9 100755 --- a/R/data.R +++ b/R/data.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Data set with ~500 antibiotics @@ -183,14 +183,14 @@ catalogue_of_life <- list( #' #' A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by \code{\link{as.mo}}. #' @inheritSection catalogue_of_life Catalogue of Life -#' @format A \code{\link{data.frame}} with 16,911 observations and 4 variables: +#' @format A \code{\link{data.frame}} with 21,342 observations and 4 variables: #' \describe{ -#' \item{\code{col_id}}{Catalogue of Life ID} -#' \item{\code{tsn_new}}{New Catalogue of Life ID} -#' \item{\code{fullname}}{Old taxonomic name of the microorganism} +#' \item{\code{col_id}}{Catalogue of Life ID that was originally given} +#' \item{\code{col_id_new}}{New Catalogue of Life ID that responds to an entry in the \code{\link{microorganisms}} data set} +#' \item{\code{fullname}}{Old full taxonomic name of the microorganism} #' \item{\code{ref}}{Author(s) and year of concerning scientific publication} #' } -#' @source [3] Catalogue of Life: Annual Checklist (public online database), \url{www.catalogueoflife.org}. +#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}). #' @inheritSection AMR Read more on our website! #' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms}} "microorganisms.old" @@ -261,3 +261,23 @@ catalogue_of_life <- list( #' } #' @inheritSection AMR Read more on our website! "WHONET" + +# transforms data set to data.frame with only ASCII values, to comply with CRAN policies +dataset_UTF8_to_ASCII <- function(df) { + trans <- function(vect) { + iconv(vect, from = "UTF-8", to = "ASCII//TRANSLIT") + } + df <- as.data.frame(df, stringsAsFactors = FALSE) + for (i in 1:NCOL(df)) { + col <- df[, i] + if (is.factor(col)) { + levels(col) <- trans(levels(col)) + } else if (is.character(col)) { + col <- trans(col) + } else { + col + } + df[, i] <- col + } + df +} diff --git a/R/deprecated.R b/R/deprecated.R index ca95703b..a05acce7 100755 --- a/R/deprecated.R +++ b/R/deprecated.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Deprecated functions @@ -47,20 +47,6 @@ ratio <- function(x, ratio) { sum(x, na.rm = TRUE) * (ratio / sum(ratio, na.rm = TRUE)) } -#' @rdname AMR-deprecated -#' @export -guess_mo <- function(...) { - .Deprecated(new = "as.mo", package = "AMR") - as.mo(...) -} - -#' @rdname AMR-deprecated -#' @export -guess_atc <- function(...) { - .Deprecated(new = "as.atc", package = "AMR") - as.atc(...) -} - #' @rdname AMR-deprecated #' @export ab_property <- function(...) { diff --git a/R/eucast_rules.R b/R/eucast_rules.R index d6022f2e..79d160a6 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -16,19 +16,31 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # +# global variables +EUCAST_RULES_FILE_LOCATION <- system.file("eucast/eucast_rules.tsv", package = "AMR") +EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019" +EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016" + #' EUCAST rules #' #' Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables. -#' @param tbl table with antibiotic columns, like e.g. \code{amox} and \code{amcl} +#' @param x data with antibiotic columns, like e.g. \code{amox} and \code{amcl} #' @param info print progress #' @param rules a character vector that specifies which rules should be applied - one or more of \code{c("breakpoints", "expert", "other", "all")} #' @param verbose a logical to indicate whether extensive info should be returned as a \code{data.frame} with info about which rows and columns are effected. It runs all EUCAST rules, but will not be applied to an output - only an informative \code{data.frame} with changes will be returned as output. #' @param amcl,amik,amox,ampi,azit,azlo,aztr,cefa,cfep,cfot,cfox,cfra,cfta,cftr,cfur,chlo,cipr,clar,clin,clox,coli,czol,dapt,doxy,erta,eryt,fosf,fusi,gent,imip,kana,levo,linc,line,mero,mezl,mino,moxi,nali,neom,neti,nitr,norf,novo,oflo,oxac,peni,pipe,pita,poly,pris,qida,rifa,roxi,siso,teic,tetr,tica,tige,tobr,trim,trsu,vanc column name of an antibiotic, see Antibiotics #' @param ... parameters that are passed on to \code{eucast_rules} #' @inheritParams first_isolate +#' @details +#' The file used for applying all EUCAST rules can be retrieved with \code{\link{eucast_rules_file}()}. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by this function can be found when running this command: \cr +#' \code{AMR::EUCAST_RULES_FILE_LOCATION} (without brackets). +#' +#' In the source code it is located under \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{\code{./inst/eucast/eucast_rules.tsv}}. +#' +#' \strong{Note:} When ampicillin (J01CA01) is not available but amoxicillin (J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. #' @section Antibiotics: #' To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning. #' @@ -99,9 +111,9 @@ #' @keywords interpretive eucast reading resistance #' @rdname eucast_rules #' @export -#' @importFrom dplyr %>% select pull mutate_at vars +#' @importFrom dplyr %>% select pull mutate_at vars group_by summarise n #' @importFrom crayon bold bgGreen bgYellow bgRed black green blue italic strip_style -#' @return The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations. +#' @return The input of \code{tbl_}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations. #' @source #' \itemize{ #' \item{ @@ -118,6 +130,8 @@ #' \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx} #' } #' } +#' +#' For editing the reference file (which is available with \code{\link{eucast_rules_file}}), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like amcl. They can be separated by comma: \code{"amcl, fluoroquinolones"}. The mo_property can be any column name from the \code{\link{microorganisms}} data set, or \code{genus_species} or \code{gramstain}. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180). #' @inheritSection AMR Read more on our website! #' @examples #' a <- eucast_rules(septic_patients) @@ -160,7 +174,7 @@ #' # do not apply EUCAST rules, but rather get a a data.frame #' # with 18 rows, containing all details about the transformations: #' c <- eucast_rules(a, verbose = TRUE) -eucast_rules <- function(tbl, +eucast_rules <- function(x, col_mo = NULL, info = TRUE, rules = c("breakpoints", "expert", "other", "all"), @@ -227,116 +241,121 @@ eucast_rules <- function(tbl, tobr = guess_ab_col(), trim = guess_ab_col(), trsu = guess_ab_col(), - vanc = guess_ab_col()) { + vanc = guess_ab_col(), + ...) { - EUCAST_VERSION_BREAKPOINTS <- "9.0, 2019" - EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016" - if (!is.data.frame(tbl)) { - stop("`tbl` must be a data frame.", call. = FALSE) + # support old `tbl` parameter + if ("tbl" %in% names(list(...))) { + x <- list(...)$tbl + } + + tbl_ <- x + + if (!is.data.frame(tbl_)) { + stop("`tbl_` must be a data frame.", call. = FALSE) } # try to find columns based on type # -- mo if (is.null(col_mo)) { - col_mo <- search_type_in_df(tbl = tbl, type = "mo") + col_mo <- search_type_in_df(tbl = tbl_, type = "mo") } if (is.null(col_mo)) { stop("`col_mo` must be set.", call. = FALSE) } if (!all(rules %in% c("breakpoints", "expert", "other", "all"))) { - stop("Parameter `rules` must be one or more of: 'breakpoints', 'expert', 'other', 'all'.") + stop("`rules` must be one or more of: 'breakpoints', 'expert', 'other', 'all'.") } if (is.null(col_mo)) { - stop("Parameter `col_mo` must be set") + stop("`col_mo` must be set") } warned <- FALSE - changed_results <- 0 txt_error <- function() { cat("", bgRed(black(" ERROR ")), "\n") } txt_warning <- function() { if (warned == FALSE) { cat("", bgYellow(black(" WARNING ")), "\n") }; warned <<- TRUE } - txt_ok <- function() { + txt_ok <- function(no_of_changes) { if (warned == FALSE) { - if (changed_results > 0) { - if (changed_results == 1) { - cat(blue(" (1 change)\n")) + if (no_of_changes > 0) { + if (no_of_changes == 1) { + cat(blue(" (1 new change)\n")) } else { - cat(blue(paste0(" (", changed_results, " changes)\n"))) + cat(blue(paste0(" (", no_of_changes, " new changes)\n"))) } } else { - cat(green(" (no changes)\n")) + cat(green(" (no new changes)\n")) } warned <<- FALSE } } # check columns - if (identical(amcl, as.name("guess_ab_col"))) { amcl <- guess_ab_col(tbl, "amcl", verbose = verbose) } - if (identical(amik, as.name("guess_ab_col"))) { amik <- guess_ab_col(tbl, "amik", verbose = verbose) } - if (identical(amox, as.name("guess_ab_col"))) { amox <- guess_ab_col(tbl, "amox", verbose = verbose) } - if (identical(ampi, as.name("guess_ab_col"))) { ampi <- guess_ab_col(tbl, "ampi", verbose = verbose) } - if (identical(azit, as.name("guess_ab_col"))) { azit <- guess_ab_col(tbl, "azit", verbose = verbose) } - if (identical(azlo, as.name("guess_ab_col"))) { azlo <- guess_ab_col(tbl, "azlo", verbose = verbose) } - if (identical(aztr, as.name("guess_ab_col"))) { aztr <- guess_ab_col(tbl, "aztr", verbose = verbose) } - if (identical(cefa, as.name("guess_ab_col"))) { cefa <- guess_ab_col(tbl, "cefa", verbose = verbose) } - if (identical(cfep, as.name("guess_ab_col"))) { cfep <- guess_ab_col(tbl, "cfep", verbose = verbose) } - if (identical(cfot, as.name("guess_ab_col"))) { cfot <- guess_ab_col(tbl, "cfot", verbose = verbose) } - if (identical(cfox, as.name("guess_ab_col"))) { cfox <- guess_ab_col(tbl, "cfox", verbose = verbose) } - if (identical(cfra, as.name("guess_ab_col"))) { cfra <- guess_ab_col(tbl, "cfra", verbose = verbose) } - if (identical(cfta, as.name("guess_ab_col"))) { cfta <- guess_ab_col(tbl, "cfta", verbose = verbose) } - if (identical(cftr, as.name("guess_ab_col"))) { cftr <- guess_ab_col(tbl, "cftr", verbose = verbose) } - if (identical(cfur, as.name("guess_ab_col"))) { cfur <- guess_ab_col(tbl, "cfur", verbose = verbose) } - if (identical(chlo, as.name("guess_ab_col"))) { chlo <- guess_ab_col(tbl, "chlo", verbose = verbose) } - if (identical(cipr, as.name("guess_ab_col"))) { cipr <- guess_ab_col(tbl, "cipr", verbose = verbose) } - if (identical(clar, as.name("guess_ab_col"))) { clar <- guess_ab_col(tbl, "clar", verbose = verbose) } - if (identical(clin, as.name("guess_ab_col"))) { clin <- guess_ab_col(tbl, "clin", verbose = verbose) } - if (identical(clox, as.name("guess_ab_col"))) { clox <- guess_ab_col(tbl, "clox", verbose = verbose) } - if (identical(coli, as.name("guess_ab_col"))) { coli <- guess_ab_col(tbl, "coli", verbose = verbose) } - if (identical(czol, as.name("guess_ab_col"))) { czol <- guess_ab_col(tbl, "czol", verbose = verbose) } - if (identical(dapt, as.name("guess_ab_col"))) { dapt <- guess_ab_col(tbl, "dapt", verbose = verbose) } - if (identical(doxy, as.name("guess_ab_col"))) { doxy <- guess_ab_col(tbl, "doxy", verbose = verbose) } - if (identical(erta, as.name("guess_ab_col"))) { erta <- guess_ab_col(tbl, "erta", verbose = verbose) } - if (identical(eryt, as.name("guess_ab_col"))) { eryt <- guess_ab_col(tbl, "eryt", verbose = verbose) } - if (identical(fosf, as.name("guess_ab_col"))) { fosf <- guess_ab_col(tbl, "fosf", verbose = verbose) } - if (identical(fusi, as.name("guess_ab_col"))) { fusi <- guess_ab_col(tbl, "fusi", verbose = verbose) } - if (identical(gent, as.name("guess_ab_col"))) { gent <- guess_ab_col(tbl, "gent", verbose = verbose) } - if (identical(imip, as.name("guess_ab_col"))) { imip <- guess_ab_col(tbl, "imip", verbose = verbose) } - if (identical(kana, as.name("guess_ab_col"))) { kana <- guess_ab_col(tbl, "kana", verbose = verbose) } - if (identical(levo, as.name("guess_ab_col"))) { levo <- guess_ab_col(tbl, "levo", verbose = verbose) } - if (identical(linc, as.name("guess_ab_col"))) { linc <- guess_ab_col(tbl, "linc", verbose = verbose) } - if (identical(line, as.name("guess_ab_col"))) { line <- guess_ab_col(tbl, "line", verbose = verbose) } - if (identical(mero, as.name("guess_ab_col"))) { mero <- guess_ab_col(tbl, "mero", verbose = verbose) } - if (identical(mezl, as.name("guess_ab_col"))) { mezl <- guess_ab_col(tbl, "mezl", verbose = verbose) } - if (identical(mino, as.name("guess_ab_col"))) { mino <- guess_ab_col(tbl, "mino", verbose = verbose) } - if (identical(moxi, as.name("guess_ab_col"))) { moxi <- guess_ab_col(tbl, "moxi", verbose = verbose) } - if (identical(nali, as.name("guess_ab_col"))) { nali <- guess_ab_col(tbl, "nali", verbose = verbose) } - if (identical(neom, as.name("guess_ab_col"))) { neom <- guess_ab_col(tbl, "neom", verbose = verbose) } - if (identical(neti, as.name("guess_ab_col"))) { neti <- guess_ab_col(tbl, "neti", verbose = verbose) } - if (identical(nitr, as.name("guess_ab_col"))) { nitr <- guess_ab_col(tbl, "nitr", verbose = verbose) } - if (identical(norf, as.name("guess_ab_col"))) { norf <- guess_ab_col(tbl, "norf", verbose = verbose) } - if (identical(novo, as.name("guess_ab_col"))) { novo <- guess_ab_col(tbl, "novo", verbose = verbose) } - if (identical(oflo, as.name("guess_ab_col"))) { oflo <- guess_ab_col(tbl, "oflo", verbose = verbose) } - if (identical(oxac, as.name("guess_ab_col"))) { oxac <- guess_ab_col(tbl, "oxac", verbose = verbose) } - if (identical(peni, as.name("guess_ab_col"))) { peni <- guess_ab_col(tbl, "peni", verbose = verbose) } - if (identical(pipe, as.name("guess_ab_col"))) { pipe <- guess_ab_col(tbl, "pipe", verbose = verbose) } - if (identical(pita, as.name("guess_ab_col"))) { pita <- guess_ab_col(tbl, "pita", verbose = verbose) } - if (identical(poly, as.name("guess_ab_col"))) { poly <- guess_ab_col(tbl, "poly", verbose = verbose) } - if (identical(pris, as.name("guess_ab_col"))) { pris <- guess_ab_col(tbl, "pris", verbose = verbose) } - if (identical(qida, as.name("guess_ab_col"))) { qida <- guess_ab_col(tbl, "qida", verbose = verbose) } - if (identical(rifa, as.name("guess_ab_col"))) { rifa <- guess_ab_col(tbl, "rifa", verbose = verbose) } - if (identical(roxi, as.name("guess_ab_col"))) { roxi <- guess_ab_col(tbl, "roxi", verbose = verbose) } - if (identical(siso, as.name("guess_ab_col"))) { siso <- guess_ab_col(tbl, "siso", verbose = verbose) } - if (identical(teic, as.name("guess_ab_col"))) { teic <- guess_ab_col(tbl, "teic", verbose = verbose) } - if (identical(tetr, as.name("guess_ab_col"))) { tetr <- guess_ab_col(tbl, "tetr", verbose = verbose) } - if (identical(tica, as.name("guess_ab_col"))) { tica <- guess_ab_col(tbl, "tica", verbose = verbose) } - if (identical(tige, as.name("guess_ab_col"))) { tige <- guess_ab_col(tbl, "tige", verbose = verbose) } - if (identical(tobr, as.name("guess_ab_col"))) { tobr <- guess_ab_col(tbl, "tobr", verbose = verbose) } - if (identical(trim, as.name("guess_ab_col"))) { trim <- guess_ab_col(tbl, "trim", verbose = verbose) } - if (identical(trsu, as.name("guess_ab_col"))) { trsu <- guess_ab_col(tbl, "trsu", verbose = verbose) } - if (identical(vanc, as.name("guess_ab_col"))) { vanc <- guess_ab_col(tbl, "vanc", verbose = verbose) } + if (identical(amcl, as.name("guess_ab_col"))) { amcl <- guess_ab_col(tbl_, "amcl", verbose = verbose) } + if (identical(amik, as.name("guess_ab_col"))) { amik <- guess_ab_col(tbl_, "amik", verbose = verbose) } + if (identical(amox, as.name("guess_ab_col"))) { amox <- guess_ab_col(tbl_, "amox", verbose = verbose) } + if (identical(ampi, as.name("guess_ab_col"))) { ampi <- guess_ab_col(tbl_, "ampi", verbose = verbose) } + if (identical(azit, as.name("guess_ab_col"))) { azit <- guess_ab_col(tbl_, "azit", verbose = verbose) } + if (identical(azlo, as.name("guess_ab_col"))) { azlo <- guess_ab_col(tbl_, "azlo", verbose = verbose) } + if (identical(aztr, as.name("guess_ab_col"))) { aztr <- guess_ab_col(tbl_, "aztr", verbose = verbose) } + if (identical(cefa, as.name("guess_ab_col"))) { cefa <- guess_ab_col(tbl_, "cefa", verbose = verbose) } + if (identical(cfep, as.name("guess_ab_col"))) { cfep <- guess_ab_col(tbl_, "cfep", verbose = verbose) } + if (identical(cfot, as.name("guess_ab_col"))) { cfot <- guess_ab_col(tbl_, "cfot", verbose = verbose) } + if (identical(cfox, as.name("guess_ab_col"))) { cfox <- guess_ab_col(tbl_, "cfox", verbose = verbose) } + if (identical(cfra, as.name("guess_ab_col"))) { cfra <- guess_ab_col(tbl_, "cfra", verbose = verbose) } + if (identical(cfta, as.name("guess_ab_col"))) { cfta <- guess_ab_col(tbl_, "cfta", verbose = verbose) } + if (identical(cftr, as.name("guess_ab_col"))) { cftr <- guess_ab_col(tbl_, "cftr", verbose = verbose) } + if (identical(cfur, as.name("guess_ab_col"))) { cfur <- guess_ab_col(tbl_, "cfur", verbose = verbose) } + if (identical(chlo, as.name("guess_ab_col"))) { chlo <- guess_ab_col(tbl_, "chlo", verbose = verbose) } + if (identical(cipr, as.name("guess_ab_col"))) { cipr <- guess_ab_col(tbl_, "cipr", verbose = verbose) } + if (identical(clar, as.name("guess_ab_col"))) { clar <- guess_ab_col(tbl_, "clar", verbose = verbose) } + if (identical(clin, as.name("guess_ab_col"))) { clin <- guess_ab_col(tbl_, "clin", verbose = verbose) } + if (identical(clox, as.name("guess_ab_col"))) { clox <- guess_ab_col(tbl_, "clox", verbose = verbose) } + if (identical(coli, as.name("guess_ab_col"))) { coli <- guess_ab_col(tbl_, "coli", verbose = verbose) } + if (identical(czol, as.name("guess_ab_col"))) { czol <- guess_ab_col(tbl_, "czol", verbose = verbose) } + if (identical(dapt, as.name("guess_ab_col"))) { dapt <- guess_ab_col(tbl_, "dapt", verbose = verbose) } + if (identical(doxy, as.name("guess_ab_col"))) { doxy <- guess_ab_col(tbl_, "doxy", verbose = verbose) } + if (identical(erta, as.name("guess_ab_col"))) { erta <- guess_ab_col(tbl_, "erta", verbose = verbose) } + if (identical(eryt, as.name("guess_ab_col"))) { eryt <- guess_ab_col(tbl_, "eryt", verbose = verbose) } + if (identical(fosf, as.name("guess_ab_col"))) { fosf <- guess_ab_col(tbl_, "fosf", verbose = verbose) } + if (identical(fusi, as.name("guess_ab_col"))) { fusi <- guess_ab_col(tbl_, "fusi", verbose = verbose) } + if (identical(gent, as.name("guess_ab_col"))) { gent <- guess_ab_col(tbl_, "gent", verbose = verbose) } + if (identical(imip, as.name("guess_ab_col"))) { imip <- guess_ab_col(tbl_, "imip", verbose = verbose) } + if (identical(kana, as.name("guess_ab_col"))) { kana <- guess_ab_col(tbl_, "kana", verbose = verbose) } + if (identical(levo, as.name("guess_ab_col"))) { levo <- guess_ab_col(tbl_, "levo", verbose = verbose) } + if (identical(linc, as.name("guess_ab_col"))) { linc <- guess_ab_col(tbl_, "linc", verbose = verbose) } + if (identical(line, as.name("guess_ab_col"))) { line <- guess_ab_col(tbl_, "line", verbose = verbose) } + if (identical(mero, as.name("guess_ab_col"))) { mero <- guess_ab_col(tbl_, "mero", verbose = verbose) } + if (identical(mezl, as.name("guess_ab_col"))) { mezl <- guess_ab_col(tbl_, "mezl", verbose = verbose) } + if (identical(mino, as.name("guess_ab_col"))) { mino <- guess_ab_col(tbl_, "mino", verbose = verbose) } + if (identical(moxi, as.name("guess_ab_col"))) { moxi <- guess_ab_col(tbl_, "moxi", verbose = verbose) } + if (identical(nali, as.name("guess_ab_col"))) { nali <- guess_ab_col(tbl_, "nali", verbose = verbose) } + if (identical(neom, as.name("guess_ab_col"))) { neom <- guess_ab_col(tbl_, "neom", verbose = verbose) } + if (identical(neti, as.name("guess_ab_col"))) { neti <- guess_ab_col(tbl_, "neti", verbose = verbose) } + if (identical(nitr, as.name("guess_ab_col"))) { nitr <- guess_ab_col(tbl_, "nitr", verbose = verbose) } + if (identical(norf, as.name("guess_ab_col"))) { norf <- guess_ab_col(tbl_, "norf", verbose = verbose) } + if (identical(novo, as.name("guess_ab_col"))) { novo <- guess_ab_col(tbl_, "novo", verbose = verbose) } + if (identical(oflo, as.name("guess_ab_col"))) { oflo <- guess_ab_col(tbl_, "oflo", verbose = verbose) } + if (identical(oxac, as.name("guess_ab_col"))) { oxac <- guess_ab_col(tbl_, "oxac", verbose = verbose) } + if (identical(peni, as.name("guess_ab_col"))) { peni <- guess_ab_col(tbl_, "peni", verbose = verbose) } + if (identical(pipe, as.name("guess_ab_col"))) { pipe <- guess_ab_col(tbl_, "pipe", verbose = verbose) } + if (identical(pita, as.name("guess_ab_col"))) { pita <- guess_ab_col(tbl_, "pita", verbose = verbose) } + if (identical(poly, as.name("guess_ab_col"))) { poly <- guess_ab_col(tbl_, "poly", verbose = verbose) } + if (identical(pris, as.name("guess_ab_col"))) { pris <- guess_ab_col(tbl_, "pris", verbose = verbose) } + if (identical(qida, as.name("guess_ab_col"))) { qida <- guess_ab_col(tbl_, "qida", verbose = verbose) } + if (identical(rifa, as.name("guess_ab_col"))) { rifa <- guess_ab_col(tbl_, "rifa", verbose = verbose) } + if (identical(roxi, as.name("guess_ab_col"))) { roxi <- guess_ab_col(tbl_, "roxi", verbose = verbose) } + if (identical(siso, as.name("guess_ab_col"))) { siso <- guess_ab_col(tbl_, "siso", verbose = verbose) } + if (identical(teic, as.name("guess_ab_col"))) { teic <- guess_ab_col(tbl_, "teic", verbose = verbose) } + if (identical(tetr, as.name("guess_ab_col"))) { tetr <- guess_ab_col(tbl_, "tetr", verbose = verbose) } + if (identical(tica, as.name("guess_ab_col"))) { tica <- guess_ab_col(tbl_, "tica", verbose = verbose) } + if (identical(tige, as.name("guess_ab_col"))) { tige <- guess_ab_col(tbl_, "tige", verbose = verbose) } + if (identical(tobr, as.name("guess_ab_col"))) { tobr <- guess_ab_col(tbl_, "tobr", verbose = verbose) } + if (identical(trim, as.name("guess_ab_col"))) { trim <- guess_ab_col(tbl_, "trim", verbose = verbose) } + if (identical(trsu, as.name("guess_ab_col"))) { trsu <- guess_ab_col(tbl_, "trsu", verbose = verbose) } + if (identical(vanc, as.name("guess_ab_col"))) { vanc <- guess_ab_col(tbl_, "vanc", verbose = verbose) } col.list <- c(amcl, amik, amox, ampi, azit, azlo, aztr, cefa, cfra, cfep, cfot, cfox, cfta, cftr, cfur, chlo, cipr, clar, clin, clox, coli, czol, dapt, doxy, erta, eryt, fosf, fusi, gent, imip, kana, @@ -348,7 +367,7 @@ eucast_rules <- function(tbl, immediate. = TRUE, call. = FALSE) } - col.list <- check_available_columns(tbl = tbl, col.list = col.list, info = info) + col.list <- check_available_columns(tbl = tbl_, col.list = col.list, info = info) amcl <- col.list[amcl] amik <- col.list[amik] amox <- col.list[amox] @@ -413,22 +432,18 @@ eucast_rules <- function(tbl, trsu <- col.list[trsu] vanc <- col.list[vanc] - number_added_S <- 0 - number_added_I <- 0 - number_added_R <- 0 - number_changed_to_S <- 0 - number_changed_to_I <- 0 - number_changed_to_R <- 0 + ab_missing <- function(ab) { + all(ab %in% c(NULL, NA)) + } - number_affected_rows <- integer(0) verbose_info <- data.frame(row = integer(0), col = character(0), - mo = character(0), mo_fullname = character(0), old = character(0), new = character(0), - rule_source = character(0), + rule = character(0), rule_group = character(0), + rule_name = character(0), stringsAsFactors = FALSE) # helper function for editing the table @@ -454,101 +469,71 @@ eucast_rules <- function(tbl, stop(e, call. = FALSE) } ) - # suppressMessages( - # suppressWarnings( - # tbl[rows, cols] <<- to - # )) + tbl_[rows, cols] <<- tbl_original[rows, cols] after <- as.character(unlist(as.list(tbl_original[rows, cols]))) - tbl[rows, cols] <<- tbl_original[rows, cols] - - number_newly_added_S <- sum(!before %in% c("S", "I", "R") & after == "S", na.rm = TRUE) - number_newly_added_I <- sum(!before %in% c("S", "I", "R") & after == "I", na.rm = TRUE) - number_newly_added_R <- sum(!before %in% c("S", "I", "R") & after == "R", na.rm = TRUE) - number_newly_changed_to_S <- sum(before %in% c("I", "R") & after == "S", na.rm = TRUE) - number_newly_changed_to_I <- sum(before %in% c("S", "R") & after == "I", na.rm = TRUE) - number_newly_changed_to_R <- sum(before %in% c("S", "I") & after == "R", na.rm = TRUE) - - # totals - number_added_S <<- number_added_S + number_newly_added_S - number_added_I <<- number_added_I + number_newly_added_I - number_added_R <<- number_added_R + number_newly_added_R - number_changed_to_S <<- number_changed_to_S + number_newly_changed_to_S - number_changed_to_I <<- number_changed_to_I + number_newly_changed_to_I - number_changed_to_R <<- number_changed_to_R + number_newly_changed_to_R - number_affected_rows <<- unique(c(number_affected_rows, rows)) - - # will be reset at start of every rule - changed_results <<- changed_results + - number_newly_added_S + - number_newly_added_I + - number_newly_added_R + - number_newly_changed_to_S + - number_newly_changed_to_I + - number_newly_changed_to_R - - if (verbose == TRUE) { - old <- as.data.frame(tbl_bak, stringsAsFactors = FALSE)[rows,] - new <- as.data.frame(tbl, stringsAsFactors = FALSE)[rows,] - MOs <- as.data.frame(tbl_original, stringsAsFactors = FALSE)[rows, col_mo][[1]] - for (i in 1:length(cols)) { - verbose_new <- data.frame(row = rows, - col = cols[i], - mo = MOs, - mo_fullname = "", - old = as.character(old[, cols[i]]), - new = as.character(new[, cols[i]]), - rule_source = strip_style(rule[1]), - rule_group = strip_style(rule[2]), - stringsAsFactors = FALSE) - colnames(verbose_new) <- c("row", "col", "mo", "mo_fullname", "old", "new", "rule_source", "rule_group") - verbose_info <<- rbind(verbose_info, verbose_new) - } + # before_df might not be a data.frame, but a tibble of data.table instead + old <- as.data.frame(before_df, stringsAsFactors = FALSE)[rows,] + no_of_changes_this_run <- 0 + for (i in 1:length(cols)) { + verbose_new <- data.frame(row = rows, + col = cols[i], + mo_fullname = tbl_[rows, "fullname"], + old = as.character(old[, cols[i]]), + new = as.character(tbl_[rows, cols[i]]), + rule = strip_style(rule[1]), + rule_group = strip_style(rule[2]), + rule_name = strip_style(rule[3]), + stringsAsFactors = FALSE) + colnames(verbose_new) <- c("row", "col", "mo_fullname", "old", "new", "rule", "rule_group", "rule_name") + verbose_new <- verbose_new %>% filter(old != new | is.na(old)) + verbose_info <<- rbind(verbose_info, verbose_new) + no_of_changes_this_run <- no_of_changes_this_run + nrow(verbose_new) } + # return number of (new) changes + return(no_of_changes_this_run) } - } - - na.rm <- function(col) { - if (is.null(col)) { - "" - } else { - col - } + # return number of (new) changes: none. + return(0) } # save original table - tbl_original <- tbl - tbl_bak <- tbl + tbl_original <- tbl_ # join to microorganisms data set - tbl <- tbl %>% - mutate_at(vars(col_mo), as.mo) %>% - left_join_microorganisms(by = col_mo, suffix = c("_oldcols", "")) %>% - mutate(gramstain = mo_gramstain(pull(., col_mo))) %>% - as.data.frame(stringsAsFactors = FALSE) + suppressWarnings( + tbl_ <- tbl_ %>% + mutate_at(vars(col_mo), as.mo) %>% + left_join_microorganisms(by = col_mo, suffix = c("_oldcols", "")) %>% + mutate(gramstain = mo_gramstain(pull(., col_mo), language = "en"), + genus_species = paste(genus, species)) %>% + as.data.frame(stringsAsFactors = FALSE) + ) if (info == TRUE) { - cat("\nRules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)\n") + cat(paste0( + "\nRules by the ", bold("European Committee on Antimicrobial Susceptibility Testing (EUCAST)"), + "\n", blue("http://eucast.org/"), "\n")) } # since ampicillin ^= amoxicillin, get the first from the latter (not in original EUCAST table) - if (!is.null(ampi) & !is.null(amox)) { + if (!ab_missing(ampi) & !ab_missing(amox)) { if (verbose == TRUE) { cat("\n VERBOSE: transforming", - length(which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R"))), + length(which(tbl_[, amox] == "S" & !tbl_[, ampi] %in% c("S", "I", "R"))), "empty ampicillin fields to 'S' based on amoxicillin. ") cat("\n VERBOSE: transforming", - length(which(tbl[, amox] == "I" & !tbl[, ampi] %in% c("S", "I", "R"))), + length(which(tbl_[, amox] == "I" & !tbl_[, ampi] %in% c("S", "I", "R"))), "empty ampicillin fields to 'I' based on amoxicillin. ") cat("\n VERBOSE: transforming", - length(which(tbl[, amox] == "R" & !tbl[, ampi] %in% c("S", "I", "R"))), + length(which(tbl_[, amox] == "R" & !tbl_[, ampi] %in% c("S", "I", "R"))), "empty ampicillin fields to 'R' based on amoxicillin. \n") } - tbl[which(tbl[, amox] == "S" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "S" - tbl[which(tbl[, amox] == "I" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "I" - tbl[which(tbl[, amox] == "R" & !tbl[, ampi] %in% c("S", "I", "R")), ampi] <- "R" - } else if (is.null(ampi) & !is.null(amox)) { + tbl_[which(tbl_[, amox] == "S" & !tbl_[, ampi] %in% c("S", "I", "R")), ampi] <- "S" + tbl_[which(tbl_[, amox] == "I" & !tbl_[, ampi] %in% c("S", "I", "R")), ampi] <- "I" + tbl_[which(tbl_[, amox] == "R" & !tbl_[, ampi] %in% c("S", "I", "R")), ampi] <- "R" + } else if (ab_missing(ampi) & !ab_missing(amox)) { # ampicillin column is missing, but amoxicillin is available message(blue(paste0("NOTE: Using column `", bold(amox), "` as input for ampicillin (J01CA01) since many EUCAST rules depend on it."))) ampi <- amox @@ -562,1357 +547,283 @@ eucast_rules <- function(tbl, glycopeptides <- c(vanc, teic) streptogramins <- c(qida, pris) # should officially also be quinupristin/dalfopristin cephalosporins <- c(cfep, cfot, cfox, cfra, cfta, cftr, cfur, czol) + cephalosporins_without_cfta <- cephalosporins[cephalosporins != ifelse(is.null(cfta), "", cfta)] carbapenems <- c(erta, imip, mero) aminopenicillins <- c(ampi, amox) ureidopenicillins <- c(pipe, pita, azlo, mezl) fluoroquinolones <- c(oflo, cipr, norf, levo, moxi) - all_betalactam <- c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, amcl, oxac, clox, peni) + all_betalactams <- c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, amcl, oxac, clox, peni) - if (any(c("all", "breakpoints") %in% rules)) { - # BREAKPOINTS ------------------------------------------------------------- - - if (info == TRUE) { - cat(bold(paste0('\nEUCAST Clinical Breakpoints (v', EUCAST_VERSION_BREAKPOINTS, ')\n'))) + # Help function to get available antibiotic column names ------------------ + get_antibiotic_columns <- function(x, df) { + x <- trimws(unlist(strsplit(x, ",", fixed = TRUE))) + y <- character(0) + for (i in 1:length(x)) { + y <- c(y, tryCatch(get(x[i]), error = function(e) "")) } - rule_group <- "Breakpoints" + y[y != "" & y %in% colnames(df)] + } - # Enterobacteriales (Order) ---- - rule <- 'Enterobacteriales (Order)' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) + eucast_rules_df <- eucast_rules_file() + no_of_changes <- 0 + for (i in 1:nrow(eucast_rules_df)) { + + rule_previous <- eucast_rules_df[max(1, i - 1), "reference.rule"] + rule_current <- eucast_rules_df[i, "reference.rule"] + rule_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule"] + rule_group_previous <- eucast_rules_df[max(1, i - 1), "reference.rule_group"] + rule_group_current <- eucast_rules_df[i, "reference.rule_group"] + rule_group_next <- eucast_rules_df[min(nrow(eucast_rules_df), i + 1), "reference.rule_group"] + #no_of_changes <- 0 + if (is.na(eucast_rules_df[i, 4])) { + rule_text <- paste(eucast_rules_df[i, 6], "=", eucast_rules_df[i, 7]) + } else { + rule_text <- paste("if", eucast_rules_df[i, 4], "=", eucast_rules_df[i, 5], + "then", eucast_rules_df[i, 6], "=", eucast_rules_df[i, 7]) + } + if (i == 1) { + rule_previous <- "" + rule_group_previous <- "" + } + if (i == nrow(eucast_rules_df)) { + rule_next <- "" + rule_group_next <- "" } - if (!is.null(ampi)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$order == 'Enterobacteriales' - & tbl[, ampi] == 'S'), - cols = amox) + # don't apply rules if user doesn't want to apply them + if (rule_group_current %like% "breakpoint" & !any(c("all", "breakpoints") %in% rules)) { + next } - if (!is.null(ampi)) { - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$order == 'Enterobacteriales' - & tbl[, ampi] == 'I'), - cols = amox) + if (rule_group_current %like% "expert" & !any(c("all", "expert") %in% rules)) { + next } - if (!is.null(ampi)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$order == 'Enterobacteriales' - & tbl[, ampi] == 'R'), - cols = amox) - } - if (info == TRUE) { - txt_ok() - } - # Staphylococcus ---- - rule <- italic('Staphylococcus') - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(peni) & !is.null(cfox)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, peni] == 'S' - & tbl[, cfox] == 'S'), - cols = c(ampi, amox, pipe, tica)) - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, peni] == 'R' - & tbl[, cfox] == 'S'), - cols = c(oxac, clox)) - } - if (!is.null(cfox)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, cfox] == 'R'), - cols = all_betalactam) - } - if (!is.null(ampi)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Staphylococcus saprophyticus" - & tbl[, ampi] == 'S'), - cols = c(amox, amcl, pipe, pita)) - } - if (!is.null(cfox)) { - # inferred from cefoxitin - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, cfox] == 'S'), - cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)])) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, cfox] == 'I'), - cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)])) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, cfox] == 'R'), - cols = c(carbapenems, cephalosporins[cephalosporins != na.rm(cfta)])) - } - if (!is.null(norf)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, norf] == 'S'), - cols = c(cipr, levo, moxi, oflo)) - } - if (!is.null(eryt)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, eryt] == 'S'), - cols = c(azit, clar, roxi)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, eryt] == 'I'), - cols = c(azit, clar, roxi)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, eryt] == 'R'), - cols = c(azit, clar, roxi)) - } - if (!is.null(tetr)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Staphylococcus" - & tbl[, tetr] == 'S'), - cols = c(doxy, mino)) - } - if (info == TRUE) { - txt_ok() - } - # Enterococcus ---- - rule <- italic('Enterococcus') - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(ampi)) { # penicillin group - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Enterococcus faecium" - & tbl[, ampi] == 'R'), - cols = all_betalactam) - } - if (!is.null(ampi)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Enterococcus" - & tbl[, ampi] == 'S'), - cols = c(amox, amcl, pipe, pita)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Enterococcus" - & tbl[, ampi] == 'I'), - cols = c(amox, amcl, pipe, pita)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Enterococcus" - & tbl[, ampi] == 'R'), - cols = c(amox, amcl, pipe, pita)) - } - if (!is.null(norf)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Enterococcus" - & tbl[, norf] == 'S'), - cols = c(cipr, levo)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Enterococcus" - & tbl[, norf] == 'I'), - cols = c(cipr, levo)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Enterococcus" - & tbl[, norf] == 'R'), - cols = c(cipr, levo)) - } - if (info == TRUE) { - txt_ok() - } - # Streptococcus groups A, B, C, G---- - rule <- paste(italic('Streptococcus'), 'groups A, B, C, G') - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(peni)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)" - & tbl[, peni] == 'S'), - cols = c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)" - & tbl[, peni] == 'I'), - cols = c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)" - & tbl[, peni] == 'R'), - cols = c(aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl)) - } - if (!is.null(norf)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)" - & tbl[, norf] == 'S'), - cols = c(levo, moxi)) - } - if (!is.null(eryt)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)" - & tbl[, eryt] == 'S'), - cols = c(azit, clar, roxi)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)" - & tbl[, eryt] == 'I'), - cols = c(azit, clar, roxi)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)" - & tbl[, eryt] == 'R'), - cols = c(azit, clar, roxi)) - } - if (!is.null(tetr)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)" - & tbl[, tetr] == 'S'), - cols = c(doxy, mino)) - } - if (info == TRUE) { - txt_ok() - } - # Streptococcus pneumoniae ---- - rule <- italic('Streptococcus pneumoniae') - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(peni)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus pneumoniae" - & tbl[, peni] == 'S'), - cols = c(ampi, amox, amcl, pipe, pita)) - } - if (!is.null(ampi)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus pneumoniae" - & tbl[, ampi] == 'S'), - cols = c(amox, amcl, pipe, pita)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus pneumoniae" - & tbl[, ampi] == 'I'), - cols = c(amox, amcl, pipe, pita)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus pneumoniae" - & tbl[, ampi] == 'R'), - cols = c(amox, amcl, pipe, pita)) - } - if (!is.null(norf)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus pneumoniae" - & tbl[, norf] == 'S'), - cols = c(levo, moxi)) - } - if (!is.null(eryt)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus pneumoniae" - & tbl[, eryt] == 'S'), - cols = c(azit, clar, roxi)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus pneumoniae" - & tbl[, eryt] == 'I'), - cols = c(azit, clar, roxi)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus pneumoniae" - & tbl[, eryt] == 'R'), - cols = c(azit, clar, roxi)) - } - if (!is.null(tetr)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Streptococcus pneumoniae" - & tbl[, tetr] == 'S'), - cols = c(doxy, mino)) - } - if (info == TRUE) { - txt_ok() - } - # Viridans group streptococci ---- - rule <- 'Viridans group streptococci' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - viridans_group <- c("anginosus", "australis", "bovis", "constellatus", "cristatus", - "equinus", "gallolyticus", "gordonii", "infantarius", "infantis", - "intermedius", "mitis", "mutans", "oligofermentans", "oralis", - "parasanguinis", "peroris", "pseudopneumoniae", "salivarius", - "sanguinis", "sinensis", "sobrinus", "thermophilus", "vestibularis") - if (!is.null(peni)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group - & tbl[, peni] == 'S'), - cols = c(ampi, amox, amcl, pipe, pita)) - } - if (!is.null(ampi)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group - & tbl[, ampi] == 'S'), - cols = c(amox, amcl, pipe, pita)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group - & tbl[, ampi] == 'I'), - cols = c(amox, amcl, pipe, pita)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == "Streptococcus" & tbl$species %in% viridans_group - & tbl[, ampi] == 'R'), - cols = c(amox, amcl, pipe, pita)) - } - if (info == TRUE) { - txt_ok() - } - # Haemophilus influenzae ---- - rule <- italic('Haemophilus influenzae') - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(ampi)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Haemophilus influenzae" - & tbl[, ampi] == 'S'), - cols = c(amox, pipe)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Haemophilus influenzae" - & tbl[, ampi] == 'I'), - cols = c(amox, pipe)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Haemophilus influenzae" - & tbl[, ampi] == 'R'), - cols = c(amox, pipe)) - } - if (!is.null(peni)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Haemophilus influenzae" - & tbl[, peni] == 'S'), - cols = c(ampi, amox, amcl, pipe, pita)) - } - if (!is.null(amcl)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Haemophilus influenzae" - & tbl[, amcl] == 'S'), - cols = pita) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Haemophilus influenzae" - & tbl[, amcl] == 'I'), - cols = pita) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Haemophilus influenzae" - & tbl[, amcl] == 'R'), - cols = pita) - } - if (!is.null(nali)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Haemophilus influenzae" - & tbl[, nali] == 'S'), - cols = c(cipr, levo, moxi, oflo)) - } - if (!is.null(tetr)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Haemophilus influenzae" - & tbl[, tetr] == 'S'), - cols = c(doxy, mino)) - } - if (info == TRUE) { - txt_ok() - } - # Moraxella catarrhalis ---- - rule <- italic('Moraxella catarrhalis') - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(amcl)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Moraxella catarrhalis" - & tbl[, amcl] == 'S'), - cols = pita) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Moraxella catarrhalis" - & tbl[, amcl] == 'I'), - cols = pita) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Moraxella catarrhalis" - & tbl[, amcl] == 'R'), - cols = pita) - } - if (!is.null(nali)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Moraxella catarrhalis" - & tbl[, nali] == 'S'), - cols = c(cipr, levo, moxi, oflo)) - } - if (!is.null(eryt)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Moraxella catarrhalis" - & tbl[, eryt] == 'S'), - cols = c(azit, clar, roxi)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Moraxella catarrhalis" - & tbl[, eryt] == 'I'), - cols = c(azit, clar, roxi)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Moraxella catarrhalis" - & tbl[, eryt] == 'R'), - cols = c(azit, clar, roxi)) - } - if (!is.null(tetr)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Moraxella catarrhalis" - & tbl[, tetr] == 'S'), - cols = c(doxy, mino)) - } - if (info == TRUE) { - txt_ok() - } - # Anaerobic Gram positives ---- - rule <- 'Anaerobic Gram positives' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(peni)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium", - "Cutibacterium", # new name of Propionibacterium - "Bifidobacterium", "Eggerthella", "Eubacterium", - "Lactobacillus ", "Actinomyces") - & tbl[, peni] == 'S'), - cols = c(ampi, amox, pipe, pita, tica)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium", - "Cutibacterium", # new name of Propionibacterium - "Bifidobacterium", "Eggerthella", "Eubacterium", - "Lactobacillus ", "Actinomyces") - & tbl[, peni] == 'I'), - cols = c(ampi, amox, pipe, pita, tica)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus %in% c("Clostridium", "Actinomyces", "Propionibacterium", - "Cutibacterium", # new name of Propionibacterium - "Bifidobacterium", "Eggerthella", "Eubacterium", - "Lactobacillus ", "Actinomyces") - & tbl[, peni] == 'R'), - cols = c(ampi, amox, pipe, pita, tica)) - } - if (info == TRUE) { - txt_ok() - } - # Anaerobic Gram negatives ---- - rule <- 'Anaerobic Gram negatives' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(peni)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas", - "Fusobacterium", "Bilophila ", "Mobiluncus") - & tbl[, peni] == 'S'), - cols = c(ampi, amox, pipe, pita, tica)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas", - "Fusobacterium", "Bilophila ", "Mobiluncus") - & tbl[, peni] == 'I'), - cols = c(ampi, amox, pipe, pita, tica)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus %in% c("Bacteroides", "Prevotella", "Porphyromonas", - "Fusobacterium", "Bilophila ", "Mobiluncus") - & tbl[, peni] == 'R'), - cols = c(ampi, amox, pipe, pita, tica)) - } - if (info == TRUE) { - txt_ok() - } - # Pasteurella multocida ---- - rule <- italic('Pasteurella multocida') - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(peni)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Pasteurella multocida" - & tbl[, peni] == 'S'), - cols = c(ampi, amox)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Pasteurella multocida" - & tbl[, peni] == 'I'), - cols = c(ampi, amox)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Pasteurella multocida" - & tbl[, peni] == 'R'), - cols = c(ampi, amox)) - } - if (info == TRUE) { - txt_ok() - } - # Campylobacter jejuni and coli ---- - rule <- paste(italic('Campylobacter jejuni'), 'and', italic('C. coli')) - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(eryt)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)" - & tbl[, eryt] == 'S'), - cols = c(azit, clar)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)" - & tbl[, eryt] == 'I'), - cols = c(azit, clar)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)" - & tbl[, eryt] == 'R'), - cols = c(azit, clar)) - } - if (!is.null(tetr)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)" - & tbl[, tetr] == 'S'), - cols = doxy) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)" - & tbl[, tetr] == 'I'), - cols = doxy) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Campylobacter (jejuni|coli)" - & tbl[, tetr] == 'R'), - cols = doxy) - } - if (info == TRUE) { - txt_ok() - } - # Aerococcus sanguinicola/urinae ---- - rule <- paste(italic('Aerococcus sanguinicola'), 'and', italic('A. urinae')) - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(norf)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)" - & tbl[, norf] == 'S'), - cols = fluoroquinolones) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)" - & tbl[, norf] == 'I'), - cols = fluoroquinolones) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)" - & tbl[, norf] == 'R'), - cols = fluoroquinolones) - } - if (!is.null(cipr)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)" - & tbl[, cipr] == 'S'), - cols = levo) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)" - & tbl[, cipr] == 'I'), - cols = levo) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Aerococcus (sanguinicola|urinae)" - & tbl[, cipr] == 'R'), - cols = levo) - } - if (info == TRUE) { - txt_ok() - } - # Kingella kingae ---- - rule <- italic('Kingella kingae') - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(peni)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Kingella kingae" - & tbl[, peni] == 'S'), - cols = c(ampi, amox)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Kingella kingae" - & tbl[, peni] == 'I'), - cols = c(ampi, amox)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Kingella kingae" - & tbl[, peni] == 'R'), - cols = c(ampi, amox)) - } - if (!is.null(eryt)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Kingella kingae" - & tbl[, eryt] == 'S'), - cols = c(azit, clar)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Kingella kingae" - & tbl[, eryt] == 'I'), - cols = c(azit, clar)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Kingella kingae" - & tbl[, eryt] == 'R'), - cols = c(azit, clar)) - } - if (!is.null(tetr)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% "^Kingella kingae" - & tbl[, tetr] == 'S'), - cols = doxy) - } - if (info == TRUE) { - txt_ok() - } - - } # end of breakpoints - if (any(c("all", "expert") %in% rules)) { - - # EXPERT RULES AND INTRINSIC RESISTANCE ----------------------------------- - - if (info == TRUE) { - cat(bold(paste0('\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v', EUCAST_VERSION_EXPERT_RULES, ')\n'))) - } - rule_group <- "Expert Rules" - - # Table 1: Intrinsic resistance in Enterobacteriaceae ---- - rule <- paste('Table 1: Intrinsic resistance in', italic('Enterobacteriaceae')) - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - # Intrinsic R for this group - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$family == 'Enterobacteriaceae'), - cols = c(peni, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line)) - # Citrobacter - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium)'), - cols = c(aminopenicillins, tica)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae)'), - cols = c(aminopenicillins, amcl, czol, cfox)) - # Enterobacter - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Enterobacter cloacae'), - cols = c(aminopenicillins, amcl, czol, cfox)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Enterobacter aerogenes'), - cols = c(aminopenicillins, amcl, czol, cfox)) - # Escherichia - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Escherichia hermanni'), - cols = c(aminopenicillins, tica)) - # Hafnia - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Hafnia alvei'), - cols = c(aminopenicillins, amcl, czol, cfox)) - # Klebsiella - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Klebsiella'), - cols = c(aminopenicillins, tica)) - # Morganella / Proteus - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Morganella morganii'), - cols = c(aminopenicillins, amcl, czol, tetracyclines, polymyxins, nitr)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Proteus mirabilis'), - cols = c(tetracyclines, tige, polymyxins, nitr)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Proteus penneri'), - cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Proteus vulgaris'), - cols = c(aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr)) - # Providencia - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Providencia rettgeri'), - cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Providencia stuartii'), - cols = c(aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr)) - # Raoultella - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Raoultella'), - cols = c(aminopenicillins, tica)) - # Serratia - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Serratia marcescens'), - cols = c(aminopenicillins, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != na.rm(mino)], polymyxins, nitr)) - # Yersinia - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Yersinia enterocolitica'), - cols = c(aminopenicillins, amcl, tica, czol, cfox)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Yersinia pseudotuberculosis'), - cols = c(poly, coli)) - if (info == TRUE) { - txt_ok() - } - - # Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria ---- - rule <- 'Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - # Intrinsic R for this group - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus %in% c('Achromobacter', - 'Acinetobacter', - 'Alcaligenes', - 'Bordatella', - 'Burkholderia', - 'Elizabethkingia', - 'Flavobacterium', - 'Ochrobactrum', - 'Pseudomonas', - 'Stenotrophomonas')), - cols = c(peni, cfox, cfur, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line)) - # Acinetobacter - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Acinetobacter (baumannii|pittii|nosocomialis|calcoaceticus)'), - cols = c(aminopenicillins, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, tetracyclines[tetracyclines != na.rm(mino)])) - # Achromobacter - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Achromobacter (xylosoxydans|xylosoxidans)'), - cols = c(aminopenicillins, czol, cfot, cftr, erta)) - # Burkholderia - edit_rsi(to = 'R', - rule = c(rule_group, rule), - # the 'Burkholderia cepacia complex' are all these species: (PMID 16217180) - rows = which(tbl$fullname %like% '^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis)'), - cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosides, trim, fosf, polymyxins)) - # Elizabethkingia - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Elizabethkingia meningoseptic(a|um)'), - cols = c(aminopenicillins, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxins)) - # Ochrobactrum - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Ochrobactrum anthropi'), - cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, cfta, cfep, aztr, erta)) - # Pseudomonas - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Pseudomonas aeruginosa'), - cols = c(aminopenicillins, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige)) - # Stenotrophomonas - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Stenotrophomonas maltophilia'), - cols = c(aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosides, trim, fosf, tetr)) - if (info == TRUE) { - txt_ok() - } - - # Table 3: Intrinsic resistance in other Gram-negative bacteria ---- - rule <- 'Table 3: Intrinsic resistance in other Gram-negative bacteria' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - # Intrinsic R for this group - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus %in% c('Haemophilus', - 'Moraxella', - 'Neisseria', - 'Campylobacter')), - cols = c(glycopeptides, linc, dapt, line)) - # Haemophilus - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Haemophilus influenzae'), - cols = c(fusi, streptogramins)) - # Moraxella - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Moraxella catarrhalis'), - cols = trim) - # Neisseria - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == 'Neisseria'), - cols = trim) - # Campylobacter - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Campylobacter fetus'), - cols = c(fusi, streptogramins, trim, nali)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Campylobacter (jejuni|coli)'), - cols = c(fusi, streptogramins, trim)) - if (info == TRUE) { - txt_ok() - } - - # Table 4: Intrinsic resistance in Gram-positive bacteria ---- - rule <- 'Table 4: Intrinsic resistance in Gram-positive bacteria' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - # Intrinsic R for this group - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$gramstain == "Gram positive"), - cols = c(aztr, polymyxins, nali)) - # Staphylococcus - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Staphylococcus saprophyticus'), - cols = c(fusi, cfta, fosf, novo)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Staphylococcus (cohnii|xylosus)'), - cols = c(cfta, novo)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Staphylococcus capitis'), - cols = c(cfta, fosf)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Staphylococcus (aureus|epidermidis|coagulase negatief|hominis|haemolyticus|intermedius|pseudointermedius)'), - cols = cfta) - # Streptococcus - # rule 4.5 - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == 'Streptococcus'), - cols = c(fusi, aminoglycosides)) - # Enterococcus - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Enterococcus faecalis'), - cols = c(fusi, cfta, cephalosporins[cephalosporins != na.rm(cfta)], aminoglycosides, macrolides, clin, qida, trim, trsu)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Enterococcus (gallinarum|casseliflavus)'), - cols = c(fusi, cfta, cephalosporins[cephalosporins != na.rm(cfta)], aminoglycosides, macrolides, clin, qida, vanc, trim, trsu)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Enterococcus faecium'), - cols = c(fusi, cfta, cephalosporins[cephalosporins != na.rm(cfta)], aminoglycosides, macrolides, trim, trsu)) - # Corynebacterium - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == 'Corynebacterium'), - cols = fosf) - # Listeria - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Listeria monocytogenes'), - cols = c(cfta, cephalosporins[cephalosporins != na.rm(cfta)])) - # other - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus %in% c('Leuconostoc', 'Pediococcus')), - cols = glycopeptides) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == 'Lactobacillus'), - cols = glycopeptides) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Clostridium (ramosum|innocuum)'), - cols = vanc) - if (info == TRUE) { - txt_ok() - } - - # Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci ---- - rule <- 'Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - # rule 8.3 - if (!is.null(peni)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)' - & tbl[, peni] == 'S'), - cols = c(aminopenicillins, cephalosporins, carbapenems)) - } - # rule 8.6 - if (!is.null(ampi)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == 'Enterococcus' - & tbl[, ampi] == 'R'), - cols = c(ureidopenicillins, carbapenems)) - } - if (!is.null(amox)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == 'Enterococcus' - & tbl[, amox] == 'R'), - cols = c(ureidopenicillins, carbapenems)) - } - if (info == TRUE) { - txt_ok() - } - - # Table 9: Interpretive rules for B-lactam agents and Gram-negative rods ---- - rule <- 'Table 9: Interpretive rules for B-lactam agents and Gram-negative rods' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - # rule 9.3 - if (!is.null(tica) & !is.null(pipe)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$family == 'Enterobacteriaceae' - & tbl[, tica] == 'R' - & tbl[, pipe] == 'S'), - cols = pipe) - } - if (info == TRUE) { - txt_ok() - } - - # Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria ---- - rule <- 'Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - # rule 10.2 - # if (!is.null(ampi)) { - # you should know first if the are B-lactamase positive, so do not run for now - # edit_rsi(to = 'R', - # rule = c(rule_group, rule), - # rows = which(tbl$fullname %like% '^Haemophilus influenza' - # & tbl[, ampi] == 'R'), - # cols = c(ampi, amox, amcl, pipe, pita, cfur)) - # } - if (info == TRUE) { - txt_ok() - } - - # Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins ---- - rule <- 'Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - # rule 11.1 - if (!is.null(eryt)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl[, eryt] == 'S'), - cols = c(azit, clar)) - edit_rsi(to = 'I', - rule = c(rule_group, rule), - rows = which(tbl[, eryt] == 'I'), - cols = c(azit, clar)) - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl[, eryt] == 'R'), - cols = c(azit, clar)) - } - if (info == TRUE) { - txt_ok() - } - - # Table 12: Interpretive rules for aminoglycosides ---- - rule <- 'Table 12: Interpretive rules for aminoglycosides' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - # rule 12.2 - if (!is.null(tobr)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == 'Staphylococcus' - & tbl[, tobr] == 'R'), - cols = c(kana, amik)) - } - # rule 12.3 - if (!is.null(gent)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == 'Staphylococcus' - & tbl[, gent] == 'R'), - cols = aminoglycosides) - } - # rule 12.8 - if (!is.null(gent) & !is.null(tobr)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$family == 'Enterobacteriaceae' - & tbl[, gent] == 'I' - & tbl[, tobr] == 'S'), - cols = gent) - } - # rule 12.9 - if (!is.null(gent) & !is.null(tobr)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$family == 'Enterobacteriaceae' - & tbl[, tobr] == 'I' - & tbl[, gent] == 'R'), - cols = tobr) - } - if (info == TRUE) { - txt_ok() + if (rule_group_current %like% "other" & !any(c("all", "other") %in% rules)) { + next } - # Table 13: Interpretive rules for quinolones ---- - rule <- 'Table 13: Interpretive rules for quinolones' if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - # rule 13.2 - if (!is.null(moxi)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$genus == 'Staphylococcus' - & tbl[, moxi] == 'R'), - cols = fluoroquinolones) - } - # rule 13.4 - if (!is.null(moxi)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Streptococcus pneumoniae' - & tbl[, moxi] == 'R'), - cols = fluoroquinolones) - } - # rule 13.5 - if (!is.null(cipr)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$family == 'Enterobacteriaceae' - & tbl[, cipr] == 'R'), - cols = fluoroquinolones) - } - # rule 13.8 - if (!is.null(cipr)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl$fullname %like% '^Neisseria gonorrhoeae' - & tbl[, cipr] == 'R'), - cols = fluoroquinolones) - } - if (info == TRUE) { - txt_ok() + # Print rule (group) ------------------------------------------------------ + if (rule_group_current != rule_group_previous) { + # is new rule group, one of Breakpoints, Expert Rules and Other + cat(bold( + case_when( + rule_group_current %like% "breakpoint" ~ + paste0("\nEUCAST Clinical Breakpoints (v", EUCAST_VERSION_BREAKPOINTS, ")\n"), + rule_group_current %like% "expert" ~ + paste0("\nEUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v", EUCAST_VERSION_EXPERT_RULES, ")\n"), + TRUE ~ + "\nOther rules\n" + ) + )) + } + # Print rule ------------------------------------------------------------- + if (rule_current != rule_previous) { + # is new rule within group, print its name + if (rule_current %in% c(AMR::microorganisms$family, + AMR::microorganisms$fullname)) { + cat(italic(rule_current)) + } else { + cat(rule_current) + } + warned <- FALSE + } } - } # end of expert rules - if (any(c("all", "other") %in% rules)) { + # Get rule from file ------------------------------------------------------ + col_mo_property <- eucast_rules_df[i, 1] + like_is_one_of <- eucast_rules_df[i, 2] - # OTHER RULES ------------------------------------------------------------- - - if (info == TRUE) { - cat(bold('\nOther rules\n')) - } - rule_group <- "Other rules" - - rule <- 'Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(amcl)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl[, amcl] == 'R'), - cols = ampi) - } - if (info == TRUE) { - txt_ok() - } - rule <- 'Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(pita)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl[, pita] == 'R'), - cols = pipe) - } - if (info == TRUE) { - txt_ok() - } - rule <- 'Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(trsu)) { - edit_rsi(to = 'R', - rule = c(rule_group, rule), - rows = which(tbl[, trsu] == 'R'), - cols = trim) - } - if (info == TRUE) { - txt_ok() - } - rule <- 'Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(ampi)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl[, ampi] == 'S'), - cols = amcl) - } - if (info == TRUE) { - txt_ok() - } - rule <- 'Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(pipe)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl[, pipe] == 'S'), - cols = pita) - } - if (info == TRUE) { - txt_ok() - } - rule <- 'Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S' - if (info == TRUE) { - warned <- FALSE - changed_results <- 0 - cat(rule) - } - if (!is.null(trim)) { - edit_rsi(to = 'S', - rule = c(rule_group, rule), - rows = which(tbl[, trim] == 'S'), - cols = trsu) - } - if (info == TRUE) { - txt_ok() + # be sure to comprise all coagulase-negative/-positive Staphylococci when they are mentioned + if (eucast_rules_df[i, 3] %like% "coagulase-") { + suppressWarnings( + all_staph <- AMR::microorganisms %>% + filter(genus == "Staphylococcus") %>% + mutate(CNS_CPS = mo_fullname(mo, Becker = "all")) + ) + if (eucast_rules_df[i, 3] %like% "coagulase-") { + eucast_rules_df[i, 3] <- paste0("^(", + paste0(all_staph %>% + filter(CNS_CPS %like% "coagulase-negative") %>% + pull(fullname), + collapse = "|"), + ")$") + } else { + eucast_rules_df[i, 3] <- paste0("^(", + paste0(all_staph %>% + filter(CNS_CPS %like% "coagulase-positive") %>% + pull(fullname), + collapse = "|"), + ")$") + } + like_is_one_of <- "like" } - } # end of other rules + if (like_is_one_of == "is") { + mo_value <- paste0("^", eucast_rules_df[i, 3], "$") + } else if (like_is_one_of == "one_of") { + # "Clostridium, Actinomyces, ..." -> "^(Clostridium|Actinomyces|...)$" + mo_value <- paste0("^(", + paste(trimws(unlist(strsplit(eucast_rules_df[i, 3], ",", fixed = TRUE))), + collapse = "|"), + ")$") + } else if (like_is_one_of == "like") { + mo_value <- eucast_rules_df[i, 3] + } else { + stop("invalid like_is_one_of", call. = FALSE) + } - # restore old col_mo values if needed - # if (!is.null(col_mo_original)) { - # tbl_original[, col_mo] <- col_mo_original - # } + source_antibiotics <- eucast_rules_df[i, 4] + source_value <- trimws(unlist(strsplit(eucast_rules_df[i, 5], ",", fixed = TRUE))) + target_antibiotics <- eucast_rules_df[i, 6] + target_value <- eucast_rules_df[i, 7] + if (is.na(source_antibiotics)) { + rows <- tryCatch(which(tbl_[, col_mo_property] %like% mo_value), + error = function(e) integer(0)) + } else { + source_antibiotics <- get_antibiotic_columns(source_antibiotics, tbl_) + if (length(source_value) == 1 & length(source_antibiotics) > 1) { + source_value <- rep(source_value, length(source_antibiotics)) + } + if (length(source_antibiotics) == 0) { + rows <- integer(0) + } else if (length(source_antibiotics) == 1) { + rows <- tryCatch(which(tbl_[, col_mo_property] %like% mo_value + & tbl_[, source_antibiotics[1L]] == source_value[1L]), + error = function(e) integer(0)) + } else if (length(source_antibiotics) == 2) { + rows <- tryCatch(which(tbl_[, col_mo_property] %like% mo_value + & tbl_[, source_antibiotics[1L]] == source_value[1L] + & tbl_[, source_antibiotics[2L]] == source_value[2L]), + error = function(e) integer(0)) + } else if (length(source_antibiotics) == 3) { + rows <- tryCatch(which(tbl_[, col_mo_property] %like% mo_value + & tbl_[, source_antibiotics[1L]] == source_value[1L] + & tbl_[, source_antibiotics[2L]] == source_value[2L] + & tbl_[, source_antibiotics[3L]] == source_value[3L]), + error = function(e) integer(0)) + } else { + stop("only 3 antibiotics supported for source_antibiotics ", call. = FALSE) + } + } + + cols <- get_antibiotic_columns(target_antibiotics, tbl_) + + # Apply rule on data ------------------------------------------------------ + # this will return the unique number of changes + no_of_changes <- no_of_changes + edit_rsi(to = target_value, + rule = c(rule_text, rule_group_current, rule_current), + rows = rows, + cols = cols) + + # Print number of new changes --------------------------------------------- + if (info == TRUE & rule_next != rule_current) { + # print only on last one of rules in this group + txt_ok(no_of_changes = no_of_changes) + no_of_changes <- 0 + } + } + + # Print overview ---------------------------------------------------------- if (info == TRUE) { if (verbose == TRUE) { wouldve <- "would have " } else { wouldve <- "" } - if (sum(number_added_S, number_added_I, number_added_R, - number_changed_to_S, number_changed_to_I, number_changed_to_R, - na.rm = TRUE) == 0) { - colour <- green # is function - } else { - colour <- blue # is function - } + + verbose_info <- verbose_info %>% + arrange(row, rule_group, rule_name, col) + decimal.mark <- getOption("OutDec") big.mark <- ifelse(decimal.mark != ",", ",", ".") formatnr <- function(x) { - format(x, big.mark = big.mark, decimal.mark = decimal.mark) + trimws(format(x, big.mark = big.mark, decimal.mark = decimal.mark)) } - cat(bold(paste('\n=> EUCAST rules', paste0(wouldve, 'affected'), - number_affected_rows %>% length() %>% formatnr(), - 'out of', nrow(tbl_original) %>% formatnr(), - 'rows\n'))) - total_added <- number_added_S + number_added_I + number_added_R - total_changed <- number_changed_to_S + number_changed_to_I + number_changed_to_R - cat(colour(paste0(" -> ", wouldve, "added ", - bold(formatnr(total_added), "test results"), - if(total_added > 0) - paste0(" (", formatnr(number_added_S), " as S; ", - formatnr(number_added_I), " as I; ", - formatnr(number_added_R), " as R)"), + + cat(paste0("\n", silver(strrep("-", options()$width - 1)), "\n")) + cat(bold(paste('EUCAST rules', paste0(wouldve, 'affected'), + formatnr(n_distinct(verbose_info$row)), + 'out of', formatnr(nrow(tbl_original)), + 'rows, making a total of', formatnr(nrow(verbose_info)), 'edits\n'))) + + # print added values ---- + if (verbose_info %>% filter(is.na(old)) %>% nrow() == 0) { + colour <- cat # is function + } else { + colour <- blue # is function + } + cat(colour(paste0("=> ", wouldve, "added ", + bold(formatnr(verbose_info %>% + filter(is.na(old)) %>% + nrow()), "test results"), "\n"))) - cat(colour(paste0(" -> ", wouldve, "changed ", - bold(formatnr(total_changed), "test results"), - if(total_changed > 0) - paste0(" (", formatnr(number_changed_to_S), " to S; ", - formatnr(number_changed_to_I), " to I; ", - formatnr(number_changed_to_R), " to R)"), + if (verbose_info %>% filter(is.na(old)) %>% nrow() > 0) { + verbose_info %>% + filter(is.na(old)) %>% + # sort it well: S < I < R + mutate(new = as.rsi(new)) %>% + group_by(new) %>% + summarise(n = n()) %>% + mutate(plural = ifelse(n > 1, "s", ""), + txt = paste0(formatnr(n), " test result", plural, " added as ", new)) %>% + pull(txt) %>% + paste(" -", ., collapse = "\n") %>% + cat() + } + + # print changed values ---- + if (verbose_info %>% filter(!is.na(old)) %>% nrow() == 0) { + colour <- cat # is function + } else { + colour <- blue # is function + } + cat(colour(paste0("\n=> ", wouldve, "changed ", + bold(formatnr(verbose_info %>% + filter(!is.na(old)) %>% + nrow()), "test results"), "\n"))) - if (verbose == FALSE) { - cat(paste("Use", bold("verbose = TRUE"), "to get a data.frame with all specified edits.\n")) + if (verbose_info %>% filter(!is.na(old)) %>% nrow() > 0) { + verbose_info %>% + filter(!is.na(old)) %>% + # sort it well: S < I < R + mutate(old = as.rsi(old), + new = as.rsi(new)) %>% + group_by(old, new) %>% + summarise(n = n()) %>% + mutate(plural = ifelse(n > 1, "s", ""), + txt = paste0(formatnr(n), " test result", plural, " changed from ", old, " to ", new)) %>% + pull(txt) %>% + paste(" -", ., collapse = "\n") %>% + cat() + cat("\n") + } + cat(paste0(silver(strrep("-", options()$width - 1)), "\n")) + + if (verbose == FALSE & nrow(verbose_info) > 0) { + cat(paste("\nUse", bold("verbose = TRUE"), "to get a data.frame with all specified edits instead.\n")) } } + # Return data set --------------------------------------------------------- if (verbose == TRUE) { - suppressWarnings( - suppressMessages( - verbose_info$mo_fullname <- mo_fullname(verbose_info$mo) - ) - ) - verbose_info <- verbose_info %>% - filter(!is.na(new) & !identical(old, new)) %>% - arrange(row) - return(verbose_info) + verbose_info + } else { + tbl_original } - - tbl_original } #' @rdname eucast_rules +#' @importFrom dplyr %>% arrange #' @export -EUCAST_rules <- function(...) { - .Deprecated("eucast_rules") - eucast_rules(...) +eucast_rules_file <- function() { + utils::read.delim(file = EUCAST_RULES_FILE_LOCATION, + sep = "\t", + stringsAsFactors = FALSE, + header = TRUE, + strip.white = TRUE, + na = c(NA, "", NULL)) %>% + arrange(reference.rule_group, + reference.rule) } - -#' @rdname eucast_rules -#' @export -interpretive_reading <- function(...) { - .Deprecated("eucast_rules") - eucast_rules(...) -} - diff --git a/R/filter_ab_class.R b/R/filter_ab_class.R index 5d4c71a9..9b7c4631 100644 --- a/R/filter_ab_class.R +++ b/R/filter_ab_class.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Filter isolates on result in antibiotic class diff --git a/R/first_isolate.R b/R/first_isolate.R index deb9da10..7993694a 100755 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Determine first (weighted) isolates diff --git a/R/freq.R b/R/freq.R index ac3e1655..a4ef129c 100755 --- a/R/freq.R +++ b/R/freq.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Frequency table diff --git a/R/g.test.R b/R/g.test.R index 3d05d079..10a70572 100755 --- a/R/g.test.R +++ b/R/g.test.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' \emph{G}-test for Count Data diff --git a/R/get_locale.R b/R/get_locale.R index e67f6fd4..fc6584ad 100755 --- a/R/get_locale.R +++ b/R/get_locale.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Get language for AMR diff --git a/R/ggplot_rsi.R b/R/ggplot_rsi.R index 9a2d8730..988c99b2 100755 --- a/R/ggplot_rsi.R +++ b/R/ggplot_rsi.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' AMR plots with \code{ggplot2} diff --git a/R/globals.R b/R/globals.R index 9590ebc4..df54682c 100755 --- a/R/globals.R +++ b/R/globals.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # globalVariables(c(".", @@ -28,6 +28,7 @@ globalVariables(c(".", "authors", "Becker", "certe", + "CNS_CPS", "cnt", "col_id", "count", @@ -46,8 +47,8 @@ globalVariables(c(".", "genus", "gramstain", "index", - "Interpretation", "input", + "Interpretation", "item", "key_ab", "key_ab_lag", @@ -81,6 +82,7 @@ globalVariables(c(".", "Pasted", "patient_id", "phylum", + "plural", "prevalence", "prevalent", "property", @@ -88,6 +90,10 @@ globalVariables(c(".", "R", "real_first_isolate", "ref", + "reference.rule", + "reference.rule_group", + "rule_group", + "rule_name", "S", "se_max", "se_min", @@ -101,6 +107,7 @@ globalVariables(c(".", "transmute", "tsn", "tsn_new", + "txt", "umcg", "value", "Value", diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R index a94a971a..095ad469 100755 --- a/R/guess_ab_col.R +++ b/R/guess_ab_col.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Guess antibiotic column diff --git a/R/join_microorganisms.R b/R/join_microorganisms.R index 15b4cf64..7121f613 100755 --- a/R/join_microorganisms.R +++ b/R/join_microorganisms.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Join a table with \code{microorganisms} diff --git a/R/key_antibiotics.R b/R/key_antibiotics.R index 17310e5f..67527eeb 100755 --- a/R/key_antibiotics.R +++ b/R/key_antibiotics.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Key antibiotics for first \emph{weighted} isolates diff --git a/R/kurtosis.R b/R/kurtosis.R index aa9daf3e..cc715be6 100755 --- a/R/kurtosis.R +++ b/R/kurtosis.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Kurtosis of the sample diff --git a/R/like.R b/R/like.R index f606c986..c46595e9 100755 --- a/R/like.R +++ b/R/like.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Pattern Matching diff --git a/R/mdro.R b/R/mdro.R index 1602db3d..24aac652 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Determine multidrug-resistant organisms (MDRO) diff --git a/R/mic.R b/R/mic.R index 374fe55b..502eaebf 100755 --- a/R/mic.R +++ b/R/mic.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Class 'mic' diff --git a/R/misc.R b/R/misc.R index 2217b850..43ee9dc9 100755 --- a/R/misc.R +++ b/R/misc.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # # No export, no Rd @@ -76,18 +76,18 @@ check_available_columns <- function(tbl, col.list, info = TRUE) { # are they available as upper case or lower case then? for (i in 1:length(col.list)) { if (is.null(col.list[i]) | isTRUE(is.na(col.list[i]))) { - col.list[i] <- NULL + col.list[i] <- NA } else if (toupper(col.list[i]) %in% colnames(tbl)) { col.list[i] <- toupper(col.list[i]) } else if (tolower(col.list[i]) %in% colnames(tbl)) { col.list[i] <- tolower(col.list[i]) } else if (!col.list[i] %in% colnames(tbl)) { - col.list[i] <- NULL + col.list[i] <- NA } } if (!all(col.list %in% colnames(tbl))) { if (info == TRUE) { - warning('These columns do not exist and will be ignored: ', + warning('Some columns do not exist and will be ignored: ', col.list.bak[!(col.list %in% colnames(tbl))] %>% toString(), '.\nTHIS MAY STRONGLY INFLUENCE THE OUTCOME.', immediate. = TRUE, diff --git a/R/mo.R b/R/mo.R index b30aed52..860a6bec 100755 --- a/R/mo.R +++ b/R/mo.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Transform to microorganism ID @@ -229,7 +229,6 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, & isFALSE(Lancefield)) { y <- x - } else if (!any(is.na(mo_hist)) & isFALSE(Becker) & isFALSE(Lancefield)) { diff --git a/R/mo_history.R b/R/mo_history.R index b6a9e0f3..54098efc 100644 --- a/R/mo_history.R +++ b/R/mo_history.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # # print successful as.mo coercions to AMR environment diff --git a/R/mo_property.R b/R/mo_property.R index 1d3faccb..1cf4e6e3 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Property of a microorganism @@ -136,7 +136,7 @@ mo_fullname <- function(x, language = get_locale(), ...) { } #' @rdname mo_property -#' @importFrom dplyr %>% left_join mutate pull +#' @importFrom dplyr %>% mutate pull #' @export mo_shortname <- function(x, language = get_locale(), ...) { dots <- list(...) @@ -247,7 +247,12 @@ mo_phylum <- function(x, language = get_locale(), ...) { #' @rdname mo_property #' @export mo_kingdom <- function(x, language = get_locale(), ...) { - mo_translate(mo_validate(x = x, property = "kingdom", ...), language = language) + kngdm <- mo_validate(x = x, property = "kingdom", ...) + if (language != "en") { + unknowns <- as.mo(x, ...) == "UNKOWN" + kngdm[unknowns] <- mo_translate(kngdm[unknowns], language = language) + } + kngdm } #' @rdname mo_property @@ -260,14 +265,14 @@ mo_type <- function(x, language = get_locale(), ...) { #' @export mo_gramstain <- function(x, language = get_locale(), ...) { x.bak <- x - x.mo <- as.mo(x, ...) - x.phylum <- mo_phylum(x.mo) + x.mo <- as.mo(x, language = "en", ...) + x.phylum <- mo_phylum(x.mo, language = "en") x[x.phylum %in% c("Actinobacteria", "Chloroflexi", "Firmicutes", "Tenericutes")] <- "Gram positive" x[x != "Gram positive"] <- "Gram negative" - x[mo_kingdom(x.mo) != "Bacteria"] <- NA_character_ + x[mo_kingdom(x.mo, language = "en") != "Bacteria"] <- NA_character_ x[x.mo == "B_GRAMP"] <- "Gram positive" x[x.mo == "B_GRAMN"] <- "Gram negative" diff --git a/R/mo_source.R b/R/mo_source.R index cd1f2365..28659607 100644 --- a/R/mo_source.R +++ b/R/mo_source.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Use predefined reference data set diff --git a/R/p.symbol.R b/R/p.symbol.R index b5d67367..ffd4c8a2 100755 --- a/R/p.symbol.R +++ b/R/p.symbol.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Symbol of a p value diff --git a/R/portion.R b/R/portion.R index 278c9723..31a73caf 100755 --- a/R/portion.R +++ b/R/portion.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Calculate resistance of isolates @@ -100,14 +100,14 @@ #' #' # Calculate co-resistance between amoxicillin/clav acid and gentamicin, #' # so we can see that combination therapy does a lot more than mono therapy: -#' septic_patients %>% portion_S(amcl) # S = 67.1% -#' septic_patients %>% count_all(amcl) # n = 1576 +#' septic_patients %>% portion_S(amcl) # S = 71.4% +#' septic_patients %>% count_all(amcl) # n = 1879 #' #' septic_patients %>% portion_S(gent) # S = 74.0% #' septic_patients %>% count_all(gent) # n = 1855 #' -#' septic_patients %>% portion_S(amcl, gent) # S = 92.0% -#' septic_patients %>% count_all(amcl, gent) # n = 1517 +#' septic_patients %>% portion_S(amcl, gent) # S = 92.3% +#' septic_patients %>% count_all(amcl, gent) # n = 1798 #' #' #' septic_patients %>% diff --git a/R/read.4d.R b/R/read.4d.R index d6f7bb4e..693a32d6 100755 --- a/R/read.4d.R +++ b/R/read.4d.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Read data from 4D database diff --git a/R/resistance_predict.R b/R/resistance_predict.R index 55e60d92..12249939 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Predict antimicrobial resistance diff --git a/R/rsi.R b/R/rsi.R index cdbdf93b..a7cde301 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Class 'rsi' @@ -114,7 +114,12 @@ mic_like <- function(x) { gsub("[^0-9.,]+", "", .) %>% unique() mic_valid <- suppressWarnings(as.mic(mic)) - sum(!is.na(mic_valid)) / length(mic) + result <- sum(!is.na(mic_valid)) / length(mic) + if (is.na(result)) { + 0 + } else { + result + } } #' @rdname as.rsi diff --git a/R/rsi_calc.R b/R/rsi_calc.R index ca5a8843..a579a1ad 100755 --- a/R/rsi_calc.R +++ b/R/rsi_calc.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' @importFrom dplyr %>% pull all_vars any_vars filter_all funs mutate_all diff --git a/R/skewness.R b/R/skewness.R index 2cf6c5a4..b3cad0a0 100755 --- a/R/skewness.R +++ b/R/skewness.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' Skewness of the sample diff --git a/R/whocc.R b/R/whocc.R index 846e7990..61ac3808 100755 --- a/R/whocc.R +++ b/R/whocc.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' WHOCC: WHO Collaborating Centre for Drug Statistics Methodology diff --git a/R/zzz.R b/R/zzz.R index 6d4a87df..24f915a2 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # #' @importFrom data.table as.data.table setkey @@ -44,6 +44,15 @@ assign(x = "mo_codes_v0.5.0", value = make_trans_tbl(), envir = asNamespace("AMR")) + + assign(x = "mo_history", + value = data.frame(x = character(0), + mo = character(0), + uncertainty_level = integer(0), + package_v = character(0), + stringsAsFactors = FALSE), + envir = asNamespace("AMR")) + } #' @importFrom dplyr mutate case_when diff --git a/_pkgdown.yml b/_pkgdown.yml index 5052090d..e2b69889 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # url: 'https://msberends.gitlab.io/AMR' diff --git a/appveyor.yml b/appveyor.yml index a241a40d..f82022c8 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # # Download script file from GitHub diff --git a/data/WHONET.rda b/data/WHONET.rda index 9a079c86..144c0cb2 100644 Binary files a/data/WHONET.rda and b/data/WHONET.rda differ diff --git a/data/microorganisms.old.rda b/data/microorganisms.old.rda index a6082ecb..bfa33f47 100644 Binary files a/data/microorganisms.old.rda and b/data/microorganisms.old.rda differ diff --git a/data/microorganisms.rda b/data/microorganisms.rda index d2e4c1d1..1269a0b3 100755 Binary files a/data/microorganisms.rda and b/data/microorganisms.rda differ diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 3cf55fe5..ae2c6d42 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002 diff --git a/docs/articles/AMR.html b/docs/articles/AMR.html index d2cef62d..0f2d78dd 100644 --- a/docs/articles/AMR.html +++ b/docs/articles/AMR.html @@ -40,7 +40,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002 @@ -192,7 +192,7 @@

How to conduct AMR analysis

Matthijs S. Berends

-

27 March 2019

+

05 April 2019

@@ -201,7 +201,7 @@ -

Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 27 March 2019.

+

Note: values on this page will change with every website update since they are based on randomly created values and the page was written in R Markdown. However, the methodology remains unchanged. This page was generated on 05 April 2019.

Introduction

@@ -217,21 +217,21 @@ -2019-03-27 +2019-04-05 abcd Escherichia coli S S -2019-03-27 +2019-04-05 abcd Escherichia coli S R -2019-03-27 +2019-04-05 efgh Escherichia coli R @@ -327,30 +327,19 @@ -2015-10-28 -A4 +2015-03-05 +Z5 Hospital B Escherichia coli S R S S -M - - -2011-07-22 -Y8 -Hospital C -Streptococcus pneumoniae -S -S -S -S F - -2014-09-30 -N3 + +2017-08-05 +K5 Hospital B Streptococcus pneumoniae S @@ -359,38 +348,49 @@ S M + +2012-08-31 +V4 +Hospital A +Klebsiella pneumoniae +R +S +R +S +F + -2013-02-14 -Z6 +2013-07-07 +G5 +Hospital A +Escherichia coli +R +S +R +S +M + + +2015-09-03 +O2 Hospital A Escherichia coli S S -R +S S F - -2015-02-01 -D5 -Hospital C -Escherichia coli -S -I -S -S -M - -2013-12-28 -V6 -Hospital B -Staphylococcus aureus -R +2014-03-20 +K9 +Hospital D +Escherichia coli +S S R S -F +M @@ -411,8 +411,8 @@ #> #> Item Count Percent Cum. Count Cum. Percent #> --- ----- ------- -------- ----------- ------------- -#> 1 M 10,344 51.7% 10,344 51.7% -#> 2 F 9,656 48.3% 20,000 100.0% +#> 1 M 10,405 52.0% 10,405 52.0% +#> 2 F 9,595 48.0% 20,000 100.0%

So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values M and F. From a researcher perspective: there are slightly more men. Nothing we didn’t already know.

The data is already quite clean, but we still need to transform some variables. The bacteria column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The mutate() function of the dplyr package makes this really easy:

data <- data %>%
@@ -425,46 +425,59 @@
 
data <- eucast_rules(data, col_mo = "bacteria")
 #> 
 #> Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
-#> 
-#> EUCAST Clinical Breakpoints (v9.0, 2019)
-#> Enterobacteriales (Order) (no changes)
-#> Staphylococcus (no changes)
-#> Enterococcus (no changes)
-#> Streptococcus groups A, B, C, G (no changes)
-#> Streptococcus pneumoniae (no changes)
-#> Viridans group streptococci (no changes)
-#> Haemophilus influenzae (no changes)
-#> Moraxella catarrhalis (no changes)
-#> Anaerobic Gram positives (no changes)
-#> Anaerobic Gram negatives (no changes)
-#> Pasteurella multocida (no changes)
-#> Campylobacter jejuni and C. coli (no changes)
-#> Aerococcus sanguinicola and A. urinae (no changes)
-#> Kingella kingae (no changes)
-#> 
-#> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
-#> Table 1:  Intrinsic resistance in Enterobacteriaceae (1342 changes)
-#> Table 2:  Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)
-#> Table 3:  Intrinsic resistance in other Gram-negative bacteria (no changes)
-#> Table 4:  Intrinsic resistance in Gram-positive bacteria (2726 changes)
-#> Table 8:  Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)
-#> Table 9:  Interpretive rules for B-lactam agents and Gram-negative rods (no changes)
-#> Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)
-#> Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)
-#> Table 12: Interpretive rules for aminoglycosides (no changes)
-#> Table 13: Interpretive rules for quinolones (no changes)
-#> 
-#> Other rules
-#> Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (no changes)
-#> Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)
-#> Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)
-#> Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (no changes)
-#> Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)
-#> Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)
-#> 
-#> => EUCAST rules affected 7,400 out of 20,000 rows
-#>    -> added 0 test results
-#>    -> changed 4,068 test results (0 to S; 0 to I; 4,068 to R)

+#> http://eucast.org/
+#> 
+#> EUCAST Clinical Breakpoints (v9.0, 2019)
+#> Aerococcus sanguinicola (no new changes)
+#> Aerococcus urinae (no new changes)
+#> Anaerobic Gram negatives (no new changes)
+#> Anaerobic Gram positives (no new changes)
+#> Campylobacter coli (no new changes)
+#> Campylobacter jejuni (no new changes)
+#> Enterobacteriales (Order) (no new changes)
+#> Enterococcus (no new changes)
+#> Haemophilus influenzae (no new changes)
+#> Kingella kingae (no new changes)
+#> Moraxella catarrhalis (no new changes)
+#> Pasteurella multocida (no new changes)
+#> Staphylococcus (no new changes)
+#> Streptococcus groups A, B, C, G (no new changes)
+#> Streptococcus pneumoniae (1476 new changes)
+#> Viridans group streptococci (no new changes)
+#> 
+#> EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)
+#> Table 01: Intrinsic resistance in Enterobacteriaceae (1290 new changes)
+#> Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no new changes)
+#> Table 03: Intrinsic resistance in other Gram-negative bacteria (no new changes)
+#> Table 04: Intrinsic resistance in Gram-positive bacteria (2758 new changes)
+#> Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no new changes)
+#> Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no new changes)
+#> Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no new changes)
+#> Table 12: Interpretive rules for aminoglycosides (no new changes)
+#> Table 13: Interpretive rules for quinolones (no new changes)
+#> 
+#> Other rules
+#> Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2311 new changes)
+#> Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (107 new changes)
+#> Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no new changes)
+#> Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no new changes)
+#> Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no new changes)
+#> Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no new changes)
+#> 
+#> --------------------------------------------------------------------------
+#> EUCAST rules affected 6,584 out of 20,000 rows, making a total of 7,942 edits
+#> => added 0 test results
+#> 
+#> => changed 7,942 test results
+#>    - 125 test results changed from S to I
+#>    - 4,719 test results changed from S to R
+#>    - 1,093 test results changed from I to S
+#>    - 299 test results changed from I to R
+#>    - 1,682 test results changed from R to S
+#>    - 24 test results changed from R to I
+#> --------------------------------------------------------------------------
+#> 
+#> Use verbose = TRUE to get a data.frame with all specified edits instead.

@@ -489,8 +502,8 @@ #> NOTE: Using column `bacteria` as input for `col_mo`. #> NOTE: Using column `date` as input for `col_date`. #> NOTE: Using column `patient_id` as input for `col_patient_id`. -#> => Found 5,665 first isolates (28.3% of total)

-

So only 28.3% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:

+#> => Found 5,681 first isolates (28.4% of total) +

So only 28.4% is suitable for resistance analysis! We can now filter on it with the filter() function, also from the dplyr package:

data_1st <- data %>% 
   filter(first == TRUE)

For future use, the above two syntaxes can be shortened with the filter_first_isolate() function:

@@ -516,87 +529,87 @@ 1 -2010-09-11 -L7 +2010-01-24 +N5 B_ESCHR_COL -R -I +S +S S S TRUE 2 -2010-11-07 -L7 +2010-07-22 +N5 B_ESCHR_COL S S S -R +S FALSE 3 -2011-01-16 -L7 +2010-07-29 +N5 B_ESCHR_COL -S R S S +S FALSE 4 -2011-02-25 -L7 +2010-09-17 +N5 B_ESCHR_COL R -S +I S S FALSE 5 -2011-08-07 -L7 +2011-02-27 +N5 B_ESCHR_COL S S S S -FALSE - - -6 -2011-08-16 -L7 -B_ESCHR_COL -S -S -R -S -FALSE - - -7 -2011-10-08 -L7 -B_ESCHR_COL -S -R -S -S TRUE -8 -2011-10-26 -L7 +6 +2011-04-25 +N5 B_ESCHR_COL -R +S +S +S +S +FALSE + + +7 +2011-04-30 +N5 +B_ESCHR_COL +S +S +S +S +FALSE + + +8 +2011-05-27 +N5 +B_ESCHR_COL +S S S S @@ -604,23 +617,23 @@ 9 -2012-01-15 -L7 +2011-06-24 +N5 B_ESCHR_COL -S -I R S +S +S FALSE 10 -2012-02-08 -L7 +2011-10-29 +N5 B_ESCHR_COL +R S -S -S +R S FALSE @@ -637,7 +650,7 @@ #> NOTE: Using column `patient_id` as input for `col_patient_id`. #> NOTE: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this. #> [Criterion] Inclusion based on key antibiotics, ignoring I. -#> => Found 15,729 first weighted isolates (78.6% of total) +#> => Found 15,059 first weighted isolates (75.3% of total) @@ -654,11 +667,11 @@ - - + + - - + + @@ -666,119 +679,119 @@ - - + + - + + - - - + + - + - - + + - + - + - - + + - + - - + + - + - + - - + + - - - - - - - - - - - - - + + + + + + + + + + + + + - - + + - - + + - - + + + - - +
isolate
12010-09-11L72010-01-24N5 B_ESCHR_COLRISS S S TRUE
22010-11-07L72010-07-22N5 B_ESCHR_COL S S SRSFALSE FALSETRUE
32011-01-16L72010-07-29N5 B_ESCHR_COLS R S SS FALSE TRUE
42011-02-25L72010-09-17N5 B_ESCHR_COL RSI S S FALSETRUEFALSE
52011-08-07L72011-02-27N5 B_ESCHR_COL S S S SFALSETRUE TRUE
62011-08-16L72011-04-25N5 B_ESCHR_COL S SRS S FALSETRUEFALSE
72011-10-08L72011-04-30N5 B_ESCHR_COL SRSSTRUETRUE
82011-10-26L7B_ESCHR_COLR S S S FALSETRUEFALSE
82011-05-27N5B_ESCHR_COLSSSSFALSEFALSE
92012-01-15L72011-06-24N5 B_ESCHR_COLSI R SSS FALSE TRUE
102012-02-08L72011-10-29N5 B_ESCHR_COLR SSSR S FALSE TRUE
-

Instead of 2, now 10 isolates are flagged. In total, 78.6% of all isolates are marked ‘first weighted’ - 50.3% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.

+

Instead of 2, now 5 isolates are flagged. In total, 75.3% of all isolates are marked ‘first weighted’ - 46.9% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.

As with filter_first_isolate(), there’s a shortcut for this new algorithm too:

data_1st <- data %>% 
   filter_first_weighted_isolate()
-

So we end up with 15,729 isolates for analysis.

+

So we end up with 15,059 isolates for analysis.

We can remove unneeded columns:

data_1st <- data_1st %>% 
   select(-c(first, keyab))
@@ -802,13 +815,58 @@ -2015-10-28 -A4 +2015-03-05 +Z5 Hospital B B_ESCHR_COL S +S +S +S +F +Gram negative +Escherichia +coli +TRUE + + +2017-08-05 +K5 +Hospital B +B_STRPT_PNE +S +S +S +R +M +Gram positive +Streptococcus +pneumoniae +TRUE + + +2012-08-31 +V4 +Hospital A +B_KLBSL_PNE R S +R +S +F +Gram negative +Klebsiella +pneumoniae +TRUE + + +2013-07-07 +G5 +Hospital A +B_ESCHR_COL +R +S +R S M Gram negative @@ -816,44 +874,14 @@ coli TRUE - -2011-07-22 -Y8 -Hospital C -B_STRPT_PNE -S -S -S -R -F -Gram positive -Streptococcus -pneumoniae -TRUE - -2014-09-30 -N3 -Hospital B -B_STRPT_PNE -S -S -S -R -M -Gram positive -Streptococcus -pneumoniae -TRUE - - -2013-02-14 -Z6 +2015-09-03 +O2 Hospital A B_ESCHR_COL S S -R +S S F Gram negative @@ -861,34 +889,19 @@ coli TRUE - -2015-02-01 -D5 -Hospital C -B_ESCHR_COL -S -I -S -S -M -Gram negative -Escherichia -coli -TRUE - -2013-12-28 -V6 -Hospital B -B_STPHY_AUR -R +2014-03-20 +K9 +Hospital D +B_ESCHR_COL +S S R S -F -Gram positive -Staphylococcus -aureus +M +Gram negative +Escherichia +coli TRUE @@ -908,9 +921,9 @@ 
freq(paste(data_1st$genus, data_1st$species))

Or can be used like the dplyr way, which is easier readable:

data_1st %>% freq(genus, species)
-

Frequency table of genus and species from a data.frame (15,729 x 13)

+

Frequency table of genus and species from a data.frame (15,059 x 13)

Columns: 2
-Length: 15,729 (of which NA: 0 = 0.00%)
+Length: 15,059 (of which NA: 0 = 0.00%)
Unique: 4

Shortest: 16
Longest: 24

@@ -927,33 +940,33 @@ Longest: 24

1 Escherichia coli -7,807 -49.6% -7,807 -49.6% +7,494 +49.8% +7,494 +49.8% 2 Staphylococcus aureus -3,919 -24.9% -11,726 -74.6% +3,673 +24.4% +11,167 +74.2% 3 Streptococcus pneumoniae -2,426 +2,325 15.4% -14,152 -90.0% +13,492 +89.6% 4 Klebsiella pneumoniae -1,577 -10.0% -15,729 +1,567 +10.4% +15,059 100.0% @@ -964,7 +977,7 @@ Longest: 24

Resistance percentages

The functions portion_S(), portion_SI(), portion_I(), portion_IR() and portion_R() can be used to determine the portion of a specific antimicrobial outcome. They can be used on their own:

data_1st %>% portion_IR(amox)
-#> [1] 0.4796236
+#> [1] 0.4999668

Or can be used in conjuction with group_by() and summarise(), both from the dplyr package:

data_1st %>% 
   group_by(hospital) %>% 
@@ -977,19 +990,19 @@ Longest: 24

 
 
 Hospital A
-0.4841779
+0.5037963
 
 
 Hospital B
-0.4800215
+0.5007457
 
 
 Hospital C
-0.4663419
+0.5111524
 
 
 Hospital D
-0.4815057
+0.4851550
 
 
 
@@ -1007,23 +1020,23 @@ Longest: 24

 
 
 Hospital A
-0.4841779
-4835
+0.5037963
+4478
 
 
 Hospital B
-0.4800215
-5581
+0.5007457
+5364
 
 
 Hospital C
-0.4663419
-2258
+0.5111524
+2152
 
 
 Hospital D
-0.4815057
-3055
+0.4851550
+3065
 
 
 
@@ -1043,27 +1056,27 @@ Longest: 24

 
 
 Escherichia
-0.7376713
-0.8986807
-0.9754067
+0.8796370
+0.8973846
+0.9902589
 
 
 Klebsiella
-0.7305010
-0.8953710
-0.9727330
+0.7172942
+0.9081047
+0.9821315
 
 
 Staphylococcus
-0.7305435
-0.9275325
-0.9793315
+0.8829295
+0.9221345
+0.9918323
 
 
 Streptococcus
-0.7320692
+0.5767742
 0.0000000
-0.7320692
+0.5767742
 
 
 
diff --git a/docs/articles/AMR_files/figure-html/plot 1-1.png b/docs/articles/AMR_files/figure-html/plot 1-1.png
index b76ef17b..e19ff0cd 100644
Binary files a/docs/articles/AMR_files/figure-html/plot 1-1.png and b/docs/articles/AMR_files/figure-html/plot 1-1.png differ
diff --git a/docs/articles/AMR_files/figure-html/plot 3-1.png b/docs/articles/AMR_files/figure-html/plot 3-1.png
index a6b86eeb..ddcb0034 100644
Binary files a/docs/articles/AMR_files/figure-html/plot 3-1.png and b/docs/articles/AMR_files/figure-html/plot 3-1.png differ
diff --git a/docs/articles/AMR_files/figure-html/plot 4-1.png b/docs/articles/AMR_files/figure-html/plot 4-1.png
index 9bc0d924..0f6db905 100644
Binary files a/docs/articles/AMR_files/figure-html/plot 4-1.png and b/docs/articles/AMR_files/figure-html/plot 4-1.png differ
diff --git a/docs/articles/AMR_files/figure-html/plot 5-1.png b/docs/articles/AMR_files/figure-html/plot 5-1.png
index 95f86455..9ca46f79 100644
Binary files a/docs/articles/AMR_files/figure-html/plot 5-1.png and b/docs/articles/AMR_files/figure-html/plot 5-1.png differ
diff --git a/docs/articles/SPSS.html b/docs/articles/SPSS.html
index 30afa341..4ff4c81f 100644
--- a/docs/articles/SPSS.html
+++ b/docs/articles/SPSS.html
@@ -40,7 +40,7 @@
       
       
         AMR (for R)
-        0.6.0
+        0.6.1.9002
@@ -192,7 +192,7 @@

How to import data from SPSS / SAS / Stata

Matthijs S. Berends

-

27 March 2019

+

05 April 2019

diff --git a/docs/articles/benchmarks.html b/docs/articles/benchmarks.html index 08ac4c56..c8ea0422 100644 --- a/docs/articles/benchmarks.html +++ b/docs/articles/benchmarks.html @@ -40,7 +40,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002 @@ -192,7 +192,7 @@

Benchmarks

Matthijs S. Berends

-

27 March 2019

+

05 April 2019

@@ -218,13 +218,13 @@ print(S.aureus, unit = "ms", signif = 2) #> Unit: milliseconds #> expr min lq mean median uq max neval -#> as.mo("sau") 18.0 18.0 22 18.0 20.0 48 10 -#> as.mo("stau") 48.0 48.0 76 67.0 92.0 150 10 -#> as.mo("staaur") 18.0 18.0 24 19.0 22.0 62 10 -#> as.mo("STAAUR") 18.0 18.0 23 18.0 20.0 61 10 -#> as.mo("S. aureus") 29.0 29.0 35 29.0 30.0 76 10 -#> as.mo("S. aureus") 29.0 29.0 37 29.0 30.0 79 10 -#> as.mo("Staphylococcus aureus") 8.2 8.2 13 8.2 8.4 52 10 +#> as.mo("sau") 18.0 18.0 27 18.0 20.0 62 10 +#> as.mo("stau") 48.0 48.0 61 49.0 91.0 92 10 +#> as.mo("staaur") 18.0 18.0 18 18.0 18.0 19 10 +#> as.mo("STAAUR") 18.0 18.0 18 18.0 18.0 20 10 +#> as.mo("S. aureus") 29.0 29.0 29 29.0 29.0 29 10 +#> as.mo("S. aureus") 28.0 29.0 48 29.0 73.0 130 10 +#> as.mo("Staphylococcus aureus") 8.1 8.1 13 8.2 8.6 52 10

In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.

To achieve this speed, the as.mo function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of Thermus islandicus (B_THERMS_ISL), a bug probably never found before in humans:

T.islandicus <- microbenchmark(as.mo("theisl"),
@@ -236,12 +236,12 @@
 print(T.islandicus, unit = "ms", signif = 2)
 #> Unit: milliseconds
 #>                         expr min  lq mean median  uq max neval
-#>              as.mo("theisl") 460 460  500    510 510 560    10
-#>              as.mo("THEISL") 460 470  490    490 510 530    10
-#>       as.mo("T. islandicus")  74  74   84     75  78 120    10
-#>      as.mo("T.  islandicus")  74  75   88     75 120 120    10
-#>  as.mo("Thermus islandicus")  73  73   84     74  75 130    10
-

That takes 7.6 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like Thermus islandicus) are almost fast - these are the most probable input from most data sets.

+#> as.mo("theisl") 460 460 480 470 510 510 10 +#> as.mo("THEISL") 460 470 490 490 510 540 10 +#> as.mo("T. islandicus") 73 73 84 73 77 130 10 +#> as.mo("T. islandicus") 73 73 88 75 120 120 10 +#> as.mo("Thermus islandicus") 73 73 80 73 74 130 10 +

That takes 8 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like Thermus islandicus) are almost fast - these are the most probable input from most data sets.

In the figure below, we compare Escherichia coli (which is very common) with Prevotella brevis (which is moderately common) and with Thermus islandicus (which is very uncommon):

par(mar = c(5, 16, 4, 2)) # set more space for left margin text (16)
 
@@ -257,111 +257,110 @@
         main = "Benchmarks per prevalence")

In reality, the as.mo() functions learns from its own output to speed up determinations for next times. In above figure, this effect was disabled to show the difference with the boxplot below - when you would use as.mo() yourself:

-
#> File /home/uscloud/.Rhistory_mo removed.

-

The highest outliers are the first times. All next determinations were done in only thousands of seconds.

+

The highest outliers are the first times. All next determinations were done in only thousands of seconds. For now, learning only works per session. If R is closed or terminated, the algorithms reset. This will probably be resolved in a next version.

Still, uncommon microorganisms take a lot more time than common microorganisms, especially the first time. To relieve this pitfall and further improve performance, two important calculations take almost no time at all: repetitive results and already precalculated results.

Repetitive results

Repetitive results are unique values that are present more than once. Unique values will only be calculated once by as.mo(). We will use mo_fullname() for this test - a helper function that returns the full microbial name (genus, species and possibly subspecies) which uses as.mo() internally.

-
library(dplyr)
-# take all MO codes from the septic_patients data set
-x <- septic_patients$mo %>%
-  # keep only the unique ones
-  unique() %>%
-  # pick 50 of them at random
-  sample(50) %>%
-  # paste that 10,000 times
-  rep(10000) %>%
-  # scramble it
-  sample()
-  
-# got indeed 50 times 10,000 = half a million?
-length(x)
-#> [1] 500000
-
-# and how many unique values do we have?
-n_distinct(x)
-#> [1] 50
-
-# now let's see:
-run_it <- microbenchmark(mo_fullname(x),
-                         times = 10)
-print(run_it, unit = "ms", signif = 3)
-#> Unit: milliseconds
-#>            expr min  lq mean median  uq  max neval
-#>  mo_fullname(x) 825 845  887    867 903 1080    10
-

So transforming 500,000 values (!!) of 50 unique values only takes 0.87 seconds (867 ms). You only lose time on your unique input values.

+
library(dplyr)
+# take all MO codes from the septic_patients data set
+x <- septic_patients$mo %>%
+  # keep only the unique ones
+  unique() %>%
+  # pick 50 of them at random
+  sample(50) %>%
+  # paste that 10,000 times
+  rep(10000) %>%
+  # scramble it
+  sample()
+  
+# got indeed 50 times 10,000 = half a million?
+length(x)
+#> [1] 500000
+
+# and how many unique values do we have?
+n_distinct(x)
+#> [1] 50
+
+# now let's see:
+run_it <- microbenchmark(mo_fullname(x),
+                         times = 10)
+print(run_it, unit = "ms", signif = 3)
+#> Unit: milliseconds
+#>            expr min  lq mean median  uq max neval
+#>  mo_fullname(x) 689 730  762    752 778 938    10
+

So transforming 500,000 values (!!) of 50 unique values only takes 0.75 seconds (751 ms). You only lose time on your unique input values.

Precalculated results

What about precalculated results? If the input is an already precalculated result of a helper function like mo_fullname(), it almost doesn’t take any time at all (see ‘C’ below):

-
run_it <- microbenchmark(A = mo_fullname("B_STPHY_AUR"),
-                         B = mo_fullname("S. aureus"),
-                         C = mo_fullname("Staphylococcus aureus"),
-                         times = 10)
-print(run_it, unit = "ms", signif = 3)
-#> Unit: milliseconds
-#>  expr    min     lq   mean median     uq    max neval
-#>     A 12.400 12.700 13.100 13.000 13.400 13.700    10
-#>     B 26.300 26.600 27.900 28.400 28.700 29.000    10
-#>     C  0.486  0.502  0.727  0.821  0.849  0.982    10
+
run_it <- microbenchmark(A = mo_fullname("B_STPHY_AUR"),
+                         B = mo_fullname("S. aureus"),
+                         C = mo_fullname("Staphylococcus aureus"),
+                         times = 10)
+print(run_it, unit = "ms", signif = 3)
+#> Unit: milliseconds
+#>  expr    min     lq   mean median     uq   max neval
+#>     A 12.200 12.300 12.500 12.400 12.600 13.40    10
+#>     B 25.800 26.300 26.800 26.600 26.900 28.50    10
+#>     C  0.477  0.724  0.779  0.825  0.848  1.07    10

So going from mo_fullname("Staphylococcus aureus") to "Staphylococcus aureus" takes 0.0008 seconds - it doesn’t even start calculating if the result would be the same as the expected resulting value. That goes for all helper functions:

-
run_it <- microbenchmark(A = mo_species("aureus"),
-                         B = mo_genus("Staphylococcus"),
-                         C = mo_fullname("Staphylococcus aureus"),
-                         D = mo_family("Staphylococcaceae"),
-                         E = mo_order("Bacillales"),
-                         F = mo_class("Bacilli"),
-                         G = mo_phylum("Firmicutes"),
-                         H = mo_kingdom("Bacteria"),
-                         times = 10)
-print(run_it, unit = "ms", signif = 3)
-#> Unit: milliseconds
-#>  expr   min    lq  mean median    uq   max neval
-#>     A 0.371 0.432 0.463  0.471 0.500 0.525    10
-#>     B 0.479 0.531 0.557  0.553 0.566 0.631    10
-#>     C 0.511 0.676 0.834  0.904 0.959 1.090    10
-#>     D 0.422 0.444 0.483  0.494 0.501 0.559    10
-#>     E 0.383 0.458 0.502  0.477 0.507 0.778    10
-#>     F 0.362 0.376 0.476  0.426 0.473 0.947    10
-#>     G 0.361 0.368 0.451  0.452 0.500 0.610    10
-#>     H 0.359 0.383 0.431  0.437 0.458 0.505    10
+
run_it <- microbenchmark(A = mo_species("aureus"),
+                         B = mo_genus("Staphylococcus"),
+                         C = mo_fullname("Staphylococcus aureus"),
+                         D = mo_family("Staphylococcaceae"),
+                         E = mo_order("Bacillales"),
+                         F = mo_class("Bacilli"),
+                         G = mo_phylum("Firmicutes"),
+                         H = mo_kingdom("Bacteria"),
+                         times = 10)
+print(run_it, unit = "ms", signif = 3)
+#> Unit: milliseconds
+#>  expr   min    lq  mean median    uq   max neval
+#>     A 0.376 0.386 0.436  0.436 0.479 0.516    10
+#>     B 0.467 0.501 0.561  0.567 0.599 0.700    10
+#>     C 0.503 0.782 0.850  0.918 0.971 1.040    10
+#>     D 0.403 0.471 0.488  0.491 0.525 0.588    10
+#>     E 0.343 0.429 0.456  0.445 0.485 0.638    10
+#>     F 0.380 0.403 0.447  0.453 0.491 0.520    10
+#>     G 0.385 0.421 0.458  0.447 0.487 0.575    10
+#>     H 0.396 0.455 0.484  0.491 0.515 0.549    10

Of course, when running mo_phylum("Firmicutes") the function has zero knowledge about the actual microorganism, namely S. aureus. But since the result would be "Firmicutes" too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.

Results in other languages

When the system language is non-English and supported by this AMR package, some functions will have a translated result. This almost does’t take extra time:

-
mo_fullname("CoNS", language = "en") # or just mo_fullname("CoNS") on an English system
-#> [1] "Coagulase-negative Staphylococcus (CoNS)"
-
-mo_fullname("CoNS", language = "es") # or just mo_fullname("CoNS") on a Spanish system
-#> [1] "Staphylococcus coagulasa negativo (SCN)"
-
-mo_fullname("CoNS", language = "nl") # or just mo_fullname("CoNS") on a Dutch system
-#> [1] "Coagulase-negatieve Staphylococcus (CNS)"
-
-run_it <- microbenchmark(en = mo_fullname("CoNS", language = "en"),
-                         de = mo_fullname("CoNS", language = "de"),
-                         nl = mo_fullname("CoNS", language = "nl"),
-                         es = mo_fullname("CoNS", language = "es"),
-                         it = mo_fullname("CoNS", language = "it"),
-                         fr = mo_fullname("CoNS", language = "fr"),
-                         pt = mo_fullname("CoNS", language = "pt"),
-                         times = 10)
-print(run_it, unit = "ms", signif = 4)
-#> Unit: milliseconds
-#>  expr   min    lq  mean median    uq   max neval
-#>    en 18.83 19.19 24.20  19.53 20.67 63.66    10
-#>    de 31.53 32.10 36.79  32.22 33.81 75.80    10
-#>    nl 31.24 31.78 32.22  32.10 32.24 33.43    10
-#>    es 31.40 32.07 45.82  33.08 75.31 76.95    10
-#>    it 31.17 31.95 36.82  32.09 32.19 79.48    10
-#>    fr 31.48 31.64 31.89  31.96 32.07 32.33    10
-#>    pt 31.27 31.66 36.80  32.06 32.34 80.53    10
+
mo_fullname("CoNS", language = "en") # or just mo_fullname("CoNS") on an English system
+#> [1] "Coagulase-negative Staphylococcus (CoNS)"
+
+mo_fullname("CoNS", language = "es") # or just mo_fullname("CoNS") on a Spanish system
+#> [1] "Staphylococcus coagulasa negativo (SCN)"
+
+mo_fullname("CoNS", language = "nl") # or just mo_fullname("CoNS") on a Dutch system
+#> [1] "Coagulase-negatieve Staphylococcus (CNS)"
+
+run_it <- microbenchmark(en = mo_fullname("CoNS", language = "en"),
+                         de = mo_fullname("CoNS", language = "de"),
+                         nl = mo_fullname("CoNS", language = "nl"),
+                         es = mo_fullname("CoNS", language = "es"),
+                         it = mo_fullname("CoNS", language = "it"),
+                         fr = mo_fullname("CoNS", language = "fr"),
+                         pt = mo_fullname("CoNS", language = "pt"),
+                         times = 10)
+print(run_it, unit = "ms", signif = 4)
+#> Unit: milliseconds
+#>  expr   min    lq  mean median    uq   max neval
+#>    en 18.96 19.05 19.17  19.10 19.28 19.50    10
+#>    de 31.11 31.58 40.75  32.11 33.36 75.57    10
+#>    nl 31.18 31.55 39.10  31.77 32.52 75.92    10
+#>    es 30.76 31.46 40.46  31.62 33.07 75.85    10
+#>    it 31.02 31.41 36.06  31.67 31.95 76.19    10
+#>    fr 31.02 31.66 36.36  31.84 32.46 76.22    10
+#>    pt 31.13 31.58 31.78  31.65 31.74 33.00    10

Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.

diff --git a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-5-1.png index 882bc183..d84e92d1 100644 Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-5-1.png and b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png index d642d2bb..26f9f845 100644 Binary files a/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png and b/docs/articles/benchmarks_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/docs/articles/index.html b/docs/articles/index.html index ffcbca60..7043ed48 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002 diff --git a/docs/authors.html b/docs/authors.html index 63ac49f5..e2f3dc56 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002 diff --git a/docs/index.html b/docs/index.html index 1a6a6a25..01073730 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002 @@ -281,7 +281,7 @@

The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of Aspergillus, Candida, Cryptococcus, Histoplasma, Pneumocystis, Saccharomyces and Trichophyton).

  • All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like Strongyloides and Taenia)

    • -

  • All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed

    • +

  • All ~21,000 previously accepted names of included (sub)species that have been taxonomically renamed

  • The responsible author(s) and year of scientific publication

    • This data is updated annually - check the included version with catalogue_of_life_version().

    diff --git a/docs/news/index.html b/docs/news/index.html index 514f3081..bd2e78a3 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002 @@ -232,9 +232,40 @@ +
    +

    +AMR 0.6.1.9001 Unreleased +

    +

    Note: latest development version

    +
    +

    +Changed

    + +
    +
    +
    +

    +AMR 0.6.1 2019-03-29 +

    +
    +

    +Changed

    + +
    +

    -AMR 0.6.0 Unreleased +AMR 0.6.0 2019-03-27

    New website!

    We’ve got a new website: https://msberends.gitlab.io/AMR (built with the great pkgdown)

    @@ -328,9 +359,9 @@ These functions use as.atc()

  • New vignettes about how to conduct AMR analysis, predict antimicrobial resistance, use the G-test and more. These are also available (and even easier readable) on our website: https://msberends.gitlab.io/AMR.

    • -
    +

    -Changed

    +Changed
    -
    +

    -Changed

    +Changed
    • Functions MDRO, BRMO, MRGN and EUCAST_exceptional_phenotypes were renamed to mdro, brmo, mrgn and eucast_exceptional_phenotypes
      • @@ -667,9 +698,9 @@ Using as.mo(..., allow_uncertain = 3)

      Renamed septic_patients$sex to septic_patients$gender

    -
    +

    -Changed

    +Changed
    • Added three antimicrobial agents to the antibiotics data set: Terbinafine (D01BA02), Rifaximin (A07AA11) and Isoconazole (D01AC05)
    • @@ -804,9 +835,9 @@ Using as.mo(..., allow_uncertain = 3)
    -
    +

    -Changed

    +Changed
    • Improvements for forecasting with resistance_predict and added more examples
    • More antibiotics added as parameters for EUCAST rules
      • @@ -890,9 +921,9 @@ Using as.mo(..., allow_uncertain = 3)New print format for tibbles and data.tables
    -
    +

    -Changed

    +Changed
    • Fixed rsi class for vectors that contain only invalid antimicrobial interpretations
    • Renamed dataset ablist to antibiotics @@ -949,6 +980,8 @@ Using as.mo(..., allow_uncertain = 3)

      Contents

        +
      • 0.6.1.9001
        • +
      • 0.6.1
      • 0.6.0
      • 0.5.0
      • 0.4.0
        • diff --git a/docs/reference/AMR-deprecated.html b/docs/reference/AMR-deprecated.html index d68dfa96..29980260 100644 --- a/docs/reference/AMR-deprecated.html +++ b/docs/reference/AMR-deprecated.html @@ -80,7 +80,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002
    @@ -243,10 +243,6 @@ 
    ratio(x, ratio)
 
-guess_mo(...)
-
-guess_atc(...)
-
 ab_property(...)
 
 ab_atc(...)
diff --git a/docs/reference/as.mo.html b/docs/reference/as.mo.html
index 59321a8d..32ca1fcb 100644
--- a/docs/reference/as.mo.html
+++ b/docs/reference/as.mo.html
@@ -80,7 +80,7 @@
       
       
         AMR (for R)
-        0.6.0
+        0.6.1.9002
    @@ -311,7 +311,9 @@ A microbial ID from this package (class: mo) typically looks like t

    Use the mo_property_* functions to get properties based on the returned code, see Examples.

    The algorithm uses data from the Catalogue of Life (see below) and from one other source (see ?microorganisms).

    Self-learning algoritm
    -The as.mo() function gains experience from previously determined microbial IDs and learns from it. This drastically improves both speed and reliability. Use clean_mo_history() to reset the algorithms. Only experience from your current AMR package version is used. This is done because in the future the taxonomic tree (which is included in this package) may change for any organism and it consequently has to rebuild its knowledge. Usually, any guess after the first try runs 80-95% faster than the first try. The algorithm saves its previous findings to ~/.Rhistory_mo.

    +The as.mo() function gains experience from previously determined microbial IDs and learns from it. This drastically improves both speed and reliability. Use clean_mo_history() to reset the algorithms. Only experience from your current AMR package version is used. This is done because in the future the taxonomic tree (which is included in this package) may change for any organism and it consequently has to rebuild its knowledge.

    +

    Usually, any guess after the first try runs 80-95% faster than the first try.

    +

    For now, learning only works per session. If R is closed or terminated, the algorithms reset. This will probably be resolved in a next version.

    Intelligent rules
    This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:

    • Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations

      • diff --git a/docs/reference/catalogue_of_life.html b/docs/reference/catalogue_of_life.html index c01c24fe..61469b73 100644 --- a/docs/reference/catalogue_of_life.html +++ b/docs/reference/catalogue_of_life.html @@ -80,7 +80,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002
    @@ -256,7 +256,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (

  • All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa

  • All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of Aspergillus, Candida, Cryptococcus, Histplasma, Pneumocystis, Saccharomyces and Trichophyton).

  • All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like Strongyloides and Taenia)

    • -

  • All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed

    • +

  • All ~21,000 previously accepted names of included (sub)species that have been taxonomically renamed

  • The complete taxonomic tree of all included (sub)species: from kingdom to subspecies

  • The responsible author(s) and year of scientific publication

    • diff --git a/docs/reference/count.html b/docs/reference/count.html index fb466f12..8b318dee 100644 --- a/docs/reference/count.html +++ b/docs/reference/count.html @@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_ AMR (for R) - 0.6.0 + 0.6.1.9002
    @@ -345,15 +345,15 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_ # Count co-resistance between amoxicillin/clav acid and gentamicin, # so we can see that combination therapy does a lot more than mono therapy. # Please mind that `portion_S` calculates percentages right away instead. -count_S(septic_patients$amcl) # S = 1057 (67.1%) -count_all(septic_patients$amcl) # n = 1576 +count_S(septic_patients$amcl) # S = 1342 (71.4%) +count_all(septic_patients$amcl) # n = 1879 count_S(septic_patients$gent) # S = 1372 (74.0%) count_all(septic_patients$gent) # n = 1855 with(septic_patients, - count_S(amcl, gent)) # S = 1396 (92.0%) -with(septic_patients, # n = 1517 + count_S(amcl, gent)) # S = 1660 (92.3%) +with(septic_patients, # n = 1798 n_rsi(amcl, gent)) # Get portions S/I/R immediately of all rsi columns diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index 2575dd2c..ca495fa5 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -80,7 +80,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002
    @@ -241,51 +241,48 @@
    - 
    eucast_rules(tbl, col_mo = NULL, info = TRUE,
-  rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE,
-  amcl = guess_ab_col(), amik = guess_ab_col(),
-  amox = guess_ab_col(), ampi = guess_ab_col(),
-  azit = guess_ab_col(), azlo = guess_ab_col(),
-  aztr = guess_ab_col(), cefa = guess_ab_col(),
-  cfep = guess_ab_col(), cfot = guess_ab_col(),
-  cfox = guess_ab_col(), cfra = guess_ab_col(),
-  cfta = guess_ab_col(), cftr = guess_ab_col(),
-  cfur = guess_ab_col(), chlo = guess_ab_col(),
-  cipr = guess_ab_col(), clar = guess_ab_col(),
-  clin = guess_ab_col(), clox = guess_ab_col(),
-  coli = guess_ab_col(), czol = guess_ab_col(),
-  dapt = guess_ab_col(), doxy = guess_ab_col(),
-  erta = guess_ab_col(), eryt = guess_ab_col(),
-  fosf = guess_ab_col(), fusi = guess_ab_col(),
-  gent = guess_ab_col(), imip = guess_ab_col(),
-  kana = guess_ab_col(), levo = guess_ab_col(),
-  linc = guess_ab_col(), line = guess_ab_col(),
-  mero = guess_ab_col(), mezl = guess_ab_col(),
-  mino = guess_ab_col(), moxi = guess_ab_col(),
-  nali = guess_ab_col(), neom = guess_ab_col(),
-  neti = guess_ab_col(), nitr = guess_ab_col(),
-  norf = guess_ab_col(), novo = guess_ab_col(),
-  oflo = guess_ab_col(), oxac = guess_ab_col(),
-  peni = guess_ab_col(), pipe = guess_ab_col(),
-  pita = guess_ab_col(), poly = guess_ab_col(),
-  pris = guess_ab_col(), qida = guess_ab_col(),
-  rifa = guess_ab_col(), roxi = guess_ab_col(),
-  siso = guess_ab_col(), teic = guess_ab_col(),
-  tetr = guess_ab_col(), tica = guess_ab_col(),
-  tige = guess_ab_col(), tobr = guess_ab_col(),
-  trim = guess_ab_col(), trsu = guess_ab_col(),
-  vanc = guess_ab_col())
+    
    eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints",
+  "expert", "other", "all"), verbose = FALSE, amcl = guess_ab_col(),
+  amik = guess_ab_col(), amox = guess_ab_col(),
+  ampi = guess_ab_col(), azit = guess_ab_col(),
+  azlo = guess_ab_col(), aztr = guess_ab_col(),
+  cefa = guess_ab_col(), cfep = guess_ab_col(),
+  cfot = guess_ab_col(), cfox = guess_ab_col(),
+  cfra = guess_ab_col(), cfta = guess_ab_col(),
+  cftr = guess_ab_col(), cfur = guess_ab_col(),
+  chlo = guess_ab_col(), cipr = guess_ab_col(),
+  clar = guess_ab_col(), clin = guess_ab_col(),
+  clox = guess_ab_col(), coli = guess_ab_col(),
+  czol = guess_ab_col(), dapt = guess_ab_col(),
+  doxy = guess_ab_col(), erta = guess_ab_col(),
+  eryt = guess_ab_col(), fosf = guess_ab_col(),
+  fusi = guess_ab_col(), gent = guess_ab_col(),
+  imip = guess_ab_col(), kana = guess_ab_col(),
+  levo = guess_ab_col(), linc = guess_ab_col(),
+  line = guess_ab_col(), mero = guess_ab_col(),
+  mezl = guess_ab_col(), mino = guess_ab_col(),
+  moxi = guess_ab_col(), nali = guess_ab_col(),
+  neom = guess_ab_col(), neti = guess_ab_col(),
+  nitr = guess_ab_col(), norf = guess_ab_col(),
+  novo = guess_ab_col(), oflo = guess_ab_col(),
+  oxac = guess_ab_col(), peni = guess_ab_col(),
+  pipe = guess_ab_col(), pita = guess_ab_col(),
+  poly = guess_ab_col(), pris = guess_ab_col(),
+  qida = guess_ab_col(), rifa = guess_ab_col(),
+  roxi = guess_ab_col(), siso = guess_ab_col(),
+  teic = guess_ab_col(), tetr = guess_ab_col(),
+  tica = guess_ab_col(), tige = guess_ab_col(),
+  tobr = guess_ab_col(), trim = guess_ab_col(),
+  trsu = guess_ab_col(), vanc = guess_ab_col(), ...)
 
-EUCAST_rules(...)
-
-interpretive_reading(...)
    
+eucast_rules_file()

    Arguments

    - - + + @@ -324,10 +321,18 @@

  • EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019.
    http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx

    • +

    For editing the reference file (which is available with eucast_rules_file), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like amcl. They can be separated by comma: "amcl, fluoroquinolones". The mo_property can be any column name from the microorganisms data set, or genus_species or gramstain. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180).

    Value

    -

    The input of tbl, possibly with edited values of antibiotics. Or, if verbose = TRUE, a data.frame with all original and new values of the affected bug-drug combinations.

    +

    The input of tbl_, possibly with edited values of antibiotics. Or, if verbose = TRUE, a data.frame with all original and new values of the affected bug-drug combinations.

    + +

    Details

    + +

    The file used for applying all EUCAST rules can be retrieved with eucast_rules_file(). It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by this function can be found when running this command:
    +AMR::EUCAST_RULES_FILE_LOCATION (without brackets).

    +

    In the source code it is located under ./inst/eucast/eucast_rules.tsv.

    +

    Note: When ampicillin (J01CA01) is not available but amoxicillin (J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance.

    Antibiotics

    @@ -456,6 +461,8 @@
  • Value
    • +
  • Details
    • +
  • Antibiotics
  • Read more on our website!
    • diff --git a/docs/reference/index.html b/docs/reference/index.html index 71a86a3a..e818a76c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002 @@ -311,7 +311,7 @@ @@ -549,7 +549,7 @@ diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 245c5734..f29bd10e 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -80,7 +80,7 @@ AMR (for R) - 0.6.0 + 0.6.1.9002 @@ -245,16 +245,16 @@

    Format

    -

    A data.frame with 16,911 observations and 4 variables:

    -
    col_id

    Catalogue of Life ID

    -
    tsn_new

    New Catalogue of Life ID

    -
    fullname

    Old taxonomic name of the microorganism

    +

    A data.frame with 21,342 observations and 4 variables:

    +
    col_id

    Catalogue of Life ID that was originally given

    +
    col_id_new

    New Catalogue of Life ID that responds to an entry in the microorganisms data set

    +
    fullname

    Old full taxonomic name of the microorganism

    ref

    Author(s) and year of concerning scientific publication

    Source

    -

    [3] Catalogue of Life: Annual Checklist (public online database), www.catalogueoflife.org.

    +

    Catalogue of Life: Annual Checklist (public online taxonomic database), www.catalogueoflife.org (check included annual version with catalogue_of_life_version()).

    Catalogue of Life

    diff --git a/docs/reference/portion.html b/docs/reference/portion.html index ba6a9ffa..43621143 100644 --- a/docs/reference/portion.html +++ b/docs/reference/portion.html @@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port AMR (for R) - 0.6.0 + 0.6.1.9002 @@ -368,14 +368,14 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port # Calculate co-resistance between amoxicillin/clav acid and gentamicin, # so we can see that combination therapy does a lot more than mono therapy: -septic_patients %>% portion_S(amcl) # S = 67.1% -septic_patients %>% count_all(amcl) # n = 1576 +septic_patients %>% portion_S(amcl) # S = 71.4% +septic_patients %>% count_all(amcl) # n = 1879 septic_patients %>% portion_S(gent) # S = 74.0% septic_patients %>% count_all(gent) # n = 1855 -septic_patients %>% portion_S(amcl, gent) # S = 92.0% -septic_patients %>% count_all(amcl, gent) # n = 1517 +septic_patients %>% portion_S(amcl, gent) # S = 92.3% +septic_patients %>% count_all(amcl, gent) # n = 1798 septic_patients %>% diff --git a/index.md b/index.md index 00bb6ca2..7677cd2a 100644 --- a/index.md +++ b/index.md @@ -98,7 +98,7 @@ Included are: * All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like *Strongyloides* and *Taenia*) -* All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed +* All ~21,000 previously accepted names of included (sub)species that have been taxonomically renamed * The responsible author(s) and year of scientific publication diff --git a/inst/eucast/eucast_rules.tsv b/inst/eucast/eucast_rules.tsv new file mode 100644 index 00000000..651c3e5c --- /dev/null +++ b/inst/eucast/eucast_rules.tsv @@ -0,0 +1,182 @@ +if_mo_property like_is_one_of this_value and_these_antibiotics have_these_values then_change_these_antibiotics to_value reference.rule reference.rule_group +order is Enterobacteriales ampi S amox S Enterobacteriales (Order) Breakpoints +order is Enterobacteriales ampi I amox I Enterobacteriales (Order) Breakpoints +order is Enterobacteriales ampi R amox R Enterobacteriales (Order) Breakpoints +genus is Staphylococcus peni, cfox S ampi, amox, pipe, tica S Staphylococcus Breakpoints +genus is Staphylococcus peni, cfox R, S oxac, clox S Staphylococcus Breakpoints +genus is Staphylococcus cfox R all_betalactams R Staphylococcus Breakpoints +genus_species is Staphylococcus saprophyticus ampi S amox, amcl, pipe, pita S Staphylococcus Breakpoints +genus is Staphylococcus cfox S carbapenems, cephalosporins_without_cfta S Staphylococcus Breakpoints +genus is Staphylococcus cfox I carbapenems, cephalosporins_without_cfta I Staphylococcus Breakpoints +genus is Staphylococcus cfox R carbapenems, cephalosporins_without_cfta R Staphylococcus Breakpoints +genus is Staphylococcus norf S cipr, levo, moxi, oflo S Staphylococcus Breakpoints +genus is Staphylococcus eryt S azit, clar, roxi S Staphylococcus Breakpoints +genus is Staphylococcus eryt I azit, clar, roxi I Staphylococcus Breakpoints +genus is Staphylococcus eryt R azit, clar, roxi R Staphylococcus Breakpoints +genus is Staphylococcus tetr S doxy, mino S Staphylococcus Breakpoints +genus_species is Enterococcus faecium ampi R all_betalactams R Enterococcus Breakpoints +genus is Enterococcus ampi S amox, amcl, pipe, pita S Enterococcus Breakpoints +genus is Enterococcus ampi I amox, amcl, pipe, pita I Enterococcus Breakpoints +genus is Enterococcus ampi R amox, amcl, pipe, pita R Enterococcus Breakpoints +genus is Enterococcus norf S cipr, levo S Enterococcus Breakpoints +genus is Enterococcus norf I cipr, levo I Enterococcus Breakpoints +genus is Enterococcus norf R cipr, levo R Enterococcus Breakpoints +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ peni S aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl S Streptococcus groups A, B, C, G Breakpoints +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ peni I aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl I Streptococcus groups A, B, C, G Breakpoints +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ peni R aminopenicillins, ureidopenicillins, cephalosporins, carbapenems, clox, amcl R Streptococcus groups A, B, C, G Breakpoints +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ norf S levo, moxi S Streptococcus groups A, B, C, G Breakpoints +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ eryt S azit, clar, roxi S Streptococcus groups A, B, C, G Breakpoints +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ eryt I azit, clar, roxi I Streptococcus groups A, B, C, G Breakpoints +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ eryt R azit, clar, roxi R Streptococcus groups A, B, C, G Breakpoints +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G)$ tetr S doxy, mino S Streptococcus groups A, B, C, G Breakpoints +genus_species is Streptococcus pneumoniae peni S ampi, amox, amcl, pipe, pita S Streptococcus pneumoniae Breakpoints +genus_species is Streptococcus pneumoniae ampi S amox, amcl, pipe, pita S Streptococcus pneumoniae Breakpoints +genus_species is Streptococcus pneumoniae ampi I amox, amcl, pipe, pita I Streptococcus pneumoniae Breakpoints +genus_species is Streptococcus pneumoniae ampi R amox, amcl, pipe, pita R Streptococcus pneumoniae Breakpoints +genus_species is Streptococcus pneumoniae norf S levo, moxi S Streptococcus pneumoniae Breakpoints +genus_species is Streptococcus pneumoniae eryt S azit, clar, roxi S Streptococcus pneumoniae Breakpoints +genus_species is Streptococcus pneumoniae eryt I azit, clar, roxi I Streptococcus pneumoniae Breakpoints +genus_species is Streptococcus pneumoniae eryt R azit, clar, roxi R Streptococcus pneumoniae Breakpoints +genus_species is Streptococcus pneumoniae tetr S doxy, mino S Streptococcus pneumoniae Breakpoints +genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ peni S ampi, amox, amcl, pipe, pita S Viridans group streptococci Breakpoints +genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ ampi S amox, amcl, pipe, pita S Viridans group streptococci Breakpoints +genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ ampi I amox, amcl, pipe, pita I Viridans group streptococci Breakpoints +genus_species like ^Streptococcus (australis|bovis|constellatus|cristatus|gallolyticus|gordonii|infantarius|infantis|mitis|mutans|oligofermentans|oralis|peroris|pseudopneumoniae|salivarius|sinensis|sobrinus|thermophilus|vestibularis|anginosus|equinus|intermedius|parasanguinis|sanguinis)$ ampi R amox, amcl, pipe, pita R Viridans group streptococci Breakpoints +genus_species is Haemophilus influenzae ampi S amox, pipe S Haemophilus influenzae Breakpoints +genus_species is ^Haemophilus influenzae ampi I amox, pipe I Haemophilus influenzae Breakpoints +genus_species is Haemophilus influenzae ampi R amox, pipe R Haemophilus influenzae Breakpoints +genus_species is Haemophilus influenzae peni S ampi, amox, amcl, pipe, pita S Haemophilus influenzae Breakpoints +genus_species is Haemophilus influenzae amcl S pita S Haemophilus influenzae Breakpoints +genus_species is Haemophilus influenzae amcl I pita I Haemophilus influenzae Breakpoints +genus_species is Haemophilus influenzae amcl R pita R Haemophilus influenzae Breakpoints +genus_species is Haemophilus influenzae nali S cipr, levo, moxi, oflo S Haemophilus influenzae Breakpoints +genus_species is Haemophilus influenzae tetr S doxy, mino S Haemophilus influenzae Breakpoints +genus_species is Moraxella catarrhalis amcl S pita S Moraxella catarrhalis Breakpoints +genus_species is Moraxella catarrhalis amcl I pita I Moraxella catarrhalis Breakpoints +genus_species is Moraxella catarrhalis amcl R pita R Moraxella catarrhalis Breakpoints +genus_species is Moraxella catarrhalis nali S cipr, levo, moxi, oflo S Moraxella catarrhalis Breakpoints +genus_species is Moraxella catarrhalis eryt S azit, clar, roxi S Moraxella catarrhalis Breakpoints +genus_species is Moraxella catarrhalis eryt I azit, clar, roxi I Moraxella catarrhalis Breakpoints +genus_species is Moraxella catarrhalis eryt R azit, clar, roxi R Moraxella catarrhalis Breakpoints +genus_species is Moraxella catarrhalis tetr S doxy, mino S Moraxella catarrhalis Breakpoints +genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus , Propionibacterium peni S ampi, amox, pipe, pita, tica S Anaerobic Gram positives Breakpoints +genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus , Propionibacterium peni I ampi, amox, pipe, pita, tica I Anaerobic Gram positives Breakpoints +genus one_of Actinomyces, Bifidobacterium, Clostridium, Cutibacterium, Eggerthella, Eubacterium, Lactobacillus , Propionibacterium peni R ampi, amox, pipe, pita, tica R Anaerobic Gram positives Breakpoints +genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella peni S ampi, amox, pipe, pita, tica S Anaerobic Gram negatives Breakpoints +genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella peni I ampi, amox, pipe, pita, tica I Anaerobic Gram negatives Breakpoints +genus one_of Bacteroides, Bilophila , Fusobacterium, Mobiluncus, Porphyromonas, Prevotella peni R ampi, amox, pipe, pita, tica R Anaerobic Gram negatives Breakpoints +genus_species is Pasteurella multocida peni S ampi, amox S Pasteurella multocida Breakpoints +genus_species is Pasteurella multocida peni I ampi, amox I Pasteurella multocida Breakpoints +genus_species is Pasteurella multocida peni R ampi, amox R Pasteurella multocida Breakpoints +genus_species is Campylobacter coli eryt S azit, clar S Campylobacter coli Breakpoints +genus_species is Campylobacter coli eryt I azit, clar I Campylobacter coli Breakpoints +genus_species is Campylobacter coli eryt R azit, clar R Campylobacter coli Breakpoints +genus_species is Campylobacter coli tetr S doxy S Campylobacter coli Breakpoints +genus_species is Campylobacter coli tetr I doxy I Campylobacter coli Breakpoints +genus_species is Campylobacter coli tetr R doxy R Campylobacter coli Breakpoints +genus_species is Campylobacter jejuni eryt S azit, clar S Campylobacter jejuni Breakpoints +genus_species is Campylobacter jejuni eryt I azit, clar I Campylobacter jejuni Breakpoints +genus_species is Campylobacter jejuni eryt R azit, clar R Campylobacter jejuni Breakpoints +genus_species is Campylobacter jejuni tetr S doxy S Campylobacter jejuni Breakpoints +genus_species is Campylobacter jejuni tetr I doxy I Campylobacter jejuni Breakpoints +genus_species is Campylobacter jejuni tetr R doxy R Campylobacter jejuni Breakpoints +genus_species is Aerococcus sanguinicola norf S fluoroquinolones S Aerococcus sanguinicola Breakpoints +genus_species is Aerococcus sanguinicola norf I fluoroquinolones I Aerococcus sanguinicola Breakpoints +genus_species is Aerococcus sanguinicola norf R fluoroquinolones R Aerococcus sanguinicola Breakpoints +genus_species is Aerococcus sanguinicola cipr S levo S Aerococcus sanguinicola Breakpoints +genus_species is Aerococcus sanguinicola cipr I levo I Aerococcus sanguinicola Breakpoints +genus_species is Aerococcus sanguinicola cipr R levo R Aerococcus urinae Breakpoints +genus_species is Aerococcus urinae norf S fluoroquinolones S Aerococcus urinae Breakpoints +genus_species is Aerococcus urinae norf I fluoroquinolones I Aerococcus urinae Breakpoints +genus_species is Aerococcus urinae norf R fluoroquinolones R Aerococcus urinae Breakpoints +genus_species is Aerococcus urinae cipr S levo S Aerococcus urinae Breakpoints +genus_species is Aerococcus urinae cipr I levo I Aerococcus urinae Breakpoints +genus_species is Aerococcus urinae cipr R levo R Aerococcus urinae Breakpoints +genus_species is Kingella kingae peni S ampi, amox S Kingella kingae Breakpoints +genus_species is Kingella kingae peni I ampi, amox I Kingella kingae Breakpoints +genus_species is Kingella kingae peni R ampi, amox R Kingella kingae Breakpoints +genus_species is Kingella kingae eryt S azit, clar S Kingella kingae Breakpoints +genus_species is Kingella kingae eryt I azit, clar I Kingella kingae Breakpoints +genus_species is Kingella kingae eryt R azit, clar R Kingella kingae Breakpoints +genus_species is Kingella kingae tetr S doxy S Kingella kingae Breakpoints +family is Enterobacteriaceae peni, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +fullname like ^Citrobacter (koseri|amalonaticus|sedlakii|farmeri|rodentium) aminopenicillins, tica R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +fullname like ^Citrobacter (freundii|braakii|murliniae|werkmanii|youngae) aminopenicillins, amcl, czol, cfox R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Enterobacter cloacae aminopenicillins, amcl, czol, cfox R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Enterobacter aerogenes aminopenicillins, amcl, czol, cfox R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Escherichia hermanni aminopenicillins, tica R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Hafnia alvei aminopenicillins, amcl, czol, cfox R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus is Klebsiella aminopenicillins, tica R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Morganella morganii aminopenicillins, amcl, czol, tetracyclines, polymyxins, nitr R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Proteus mirabilis tetracyclines, tige, polymyxins, nitr R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Proteus penneri aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Proteus vulgaris aminopenicillins, czol, cfur, tetracyclines, tige, polymyxins, nitr R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Providencia rettgeri aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Providencia stuartii aminopenicillins, amcl, czol, cfur, tetracyclines, tige, polymyxins, nitr R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus is Raoultella aminopenicillins, tica R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Serratia marcescens aminopenicillins, amcl, czol, cfox, cfur, tetracyclines[tetracyclines != na.rm(mino)], polymyxins, nitr R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Yersinia enterocolitica aminopenicillins, amcl, tica, czol, cfox R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus_species is Yersinia pseudotuberculosis poly, coli R Table 01: Intrinsic resistance in Enterobacteriaceae Expert Rules +genus one_of Achromobacter, Acinetobacter, Alcaligenes, Bordatella, Burkholderia, Elizabethkingia, Flavobacterium, Ochrobactrum, Pseudomonas, Stenotrophomonas peni, cfox, cfur, glycopeptides, fusi, macrolides, linc, streptogramins, rifa, dapt, line R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +genus_species is Acinetobacter baumannii aminopenicillins, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, doxy, tetr R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +genus_species is Acinetobacter pittii aminopenicillins, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, doxy, tetr R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +genus_species is Acinetobacter nosocomialis aminopenicillins, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, doxy, tetr R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +genus_species is Acinetobacter calcoaceticus aminopenicillins, amcl, czol, cfot, cftr, aztr, erta, trim, fosf, doxy, tetr R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +genus_species is Achromobacter xylosoxidans aminopenicillins, czol, cfot, cftr, erta R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +fullname like ^Burkholderia (cepacia|multivorans|cenocepacia|stabilis|vietnamiensis|dolosa|ambifaria|anthina|pyrrocinia|ubonensis) aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, aztr, erta, cipr, chlo, aminoglycosides, trim, fosf, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +genus_species is Elizabethkingia meningoseptica aminopenicillins, amcl, tica, czol, cfot, cftr, cfta, cfep, aztr, erta, imip, mero, polymyxins R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +genus_species is Ochrobactrum anthropi aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, cfta, cfep, aztr, erta R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +genus_species is Pseudomonas aeruginosa aminopenicillins, amcl, czol, cfot, cftr, erta, chlo, kana, neom, trim, trsu, tetracyclines, tige R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +genus_species is Stenotrophomonas maltophilia aminopenicillins, amcl, tica, pipe, pita, czol, cfot, cftr, cfta, aztr, erta, imip, mero, aminoglycosides, trim, fosf, tetr R Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria Expert Rules +genus one_of Haemophilus, Moraxella, Neisseria, Campylobacter glycopeptides, linc, dapt, line R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules +genus_species is Haemophilus influenzae fusi, streptogramins R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules +genus_species is Moraxella catarrhalis trim R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules +genus is Neisseria trim R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules +genus_species is Campylobacter fetus fusi, streptogramins, trim, nali R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules +genus_species is Campylobacter jejuni fusi, streptogramins, trim R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules +genus_species is Campylobacter coli fusi, streptogramins, trim R Table 03: Intrinsic resistance in other Gram-negative bacteria Expert Rules +gramstain is Gram positive aztr, polymyxins, nali R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus saprophyticus fusi, cfta, fosf, novo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus cohnii cfta, novo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus xylosus cfta, novo R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus capitis cfta, fosf R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus aureus cfta R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus epidermidis cfta R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus coagulase-negative cfta R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus hominis cfta R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus haemolyticus cfta R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus intermedius cfta R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Staphylococcus pseudintermedius cfta R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus is Streptococcus fusi, aminoglycosides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Enterococcus faecalis fusi, cfta, cephalosporins_without_cfta, aminoglycosides, macrolides, clin, qida, trim, trsu R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Enterococcus gallinarum fusi, cfta, cephalosporins_without_cfta, aminoglycosides, macrolides, clin, qida, vanc, trim, trsu R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Enterococcus casseliflavus fusi, cfta, cephalosporins_without_cfta, aminoglycosides, macrolides, clin, qida, vanc, trim, trsu R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Enterococcus faecium fusi, cfta, cephalosporins_without_cfta, aminoglycosides, macrolides, trim, trsu R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus is Corynebacterium fosf R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Listeria monocytogenes cephalosporins R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus is Leuconostoc, Pediococcus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus is Lactobacillus glycopeptides R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Clostridium ramosum vanc R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species is Clostridium innocuum vanc R Table 04: Intrinsic resistance in Gram-positive bacteria Expert Rules +genus_species like ^Streptococcus (pyogenes|agalactiae|dysgalactiae|group A|group B|group C|group G) peni S aminopenicillins, cephalosporins, carbapenems S Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules +genus is Enterococcus ampi R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules +genus is Enterococcus amox R ureidopenicillins, carbapenems R Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci Expert Rules +family is Enterobacteriaceae tica, pipe R, S pipe R Table 09: Interpretive rules for B-lactam agents and Gram-negative rods Expert Rules +genus is .* eryt S azit, clar S Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules +genus is .* eryt I azit, clar I Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules +genus is .* eryt R azit, clar R Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins Expert Rules +genus is Staphylococcus tobr R kana, amik R Table 12: Interpretive rules for aminoglycosides Expert Rules +genus is Staphylococcus gent R aminoglycosides R Table 12: Interpretive rules for aminoglycosides Expert Rules +family is Enterobacteriaceae gent, tobr I, S gent R Table 12: Interpretive rules for aminoglycosides Expert Rules +family is Enterobacteriaceae gent, tobr R, I tobr R Table 12: Interpretive rules for aminoglycosides Expert Rules +genus is Staphylococcus moxi R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules +genus_species is Streptococcus pneumoniae moxi R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules +family is Enterobacteriaceae cipr R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules +genus_species is Neisseria gonorrhoeae cipr R fluoroquinolones R Table 13: Interpretive rules for quinolones Expert Rules +genus is .* amcl R ampi, amox R Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R Other rules +genus is .* pita R pipe R Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R Other rules +genus is .* trsu R trim R Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R Other rules +genus is .* ampi S amcl S Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S Other rules +genus is .* amox S amcl S Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S Other rules +genus is .* pipe S pita S Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S Other rules +genus is .* trim S trsu S Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S Other rules diff --git a/inst/rstudio/addins.dcf b/inst/rstudio/addins.dcf index 609d2607..a87253d2 100644 --- a/inst/rstudio/addins.dcf +++ b/inst/rstudio/addins.dcf @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # Name: Insert %in% diff --git a/man/AMR-deprecated.Rd b/man/AMR-deprecated.Rd index 5aa113d4..743f9547 100644 --- a/man/AMR-deprecated.Rd +++ b/man/AMR-deprecated.Rd @@ -3,8 +3,6 @@ \name{AMR-deprecated} \alias{AMR-deprecated} \alias{ratio} -\alias{guess_mo} -\alias{guess_atc} \alias{ab_property} \alias{ab_atc} \alias{ab_official} @@ -19,10 +17,6 @@ \usage{ ratio(x, ratio) -guess_mo(...) - -guess_atc(...) - ab_property(...) ab_atc(...) diff --git a/man/catalogue_of_life.Rd b/man/catalogue_of_life.Rd index d28f5139..7daee1ac 100644 --- a/man/catalogue_of_life.Rd +++ b/man/catalogue_of_life.Rd @@ -21,7 +21,7 @@ Included are: \item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa} \item{All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales. The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).} \item{All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like \emph{Strongyloides} and \emph{Taenia})} - \item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed} + \item{All ~21,000 previously accepted names of included (sub)species that have been taxonomically renamed} \item{The complete taxonomic tree of all included (sub)species: from kingdom to subspecies} \item{The responsible author(s) and year of scientific publication} } diff --git a/man/count.Rd b/man/count.Rd index adebc5b3..d0bd3b1d 100644 --- a/man/count.Rd +++ b/man/count.Rd @@ -98,15 +98,15 @@ septic_patients \%>\% # Count co-resistance between amoxicillin/clav acid and gentamicin, # so we can see that combination therapy does a lot more than mono therapy. # Please mind that `portion_S` calculates percentages right away instead. -count_S(septic_patients$amcl) # S = 1057 (67.1\%) -count_all(septic_patients$amcl) # n = 1576 +count_S(septic_patients$amcl) # S = 1342 (71.4\%) +count_all(septic_patients$amcl) # n = 1879 count_S(septic_patients$gent) # S = 1372 (74.0\%) count_all(septic_patients$gent) # n = 1855 with(septic_patients, - count_S(amcl, gent)) # S = 1396 (92.0\%) -with(septic_patients, # n = 1517 + count_S(amcl, gent)) # S = 1660 (92.3\%) +with(septic_patients, # n = 1798 n_rsi(amcl, gent)) # Get portions S/I/R immediately of all rsi columns diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index 4ed10b16..17e785c4 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -2,8 +2,7 @@ % Please edit documentation in R/eucast_rules.R \name{eucast_rules} \alias{eucast_rules} -\alias{EUCAST_rules} -\alias{interpretive_reading} +\alias{eucast_rules_file} \title{EUCAST rules} \source{ \itemize{ @@ -21,49 +20,48 @@ \url{http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx} } } + + For editing the reference file (which is available with \code{\link{eucast_rules_file}}), these values can all be used for target antibiotics: aminoglycosides, tetracyclines, polymyxins, macrolides, glycopeptides, streptogramins, cephalosporins, cephalosporins_without_cfta, carbapenems, aminopenicillins, ureidopenicillins, fluoroquinolones, all_betalactams, and all separate four letter codes like amcl. They can be separated by comma: \code{"amcl, fluoroquinolones"}. The mo_property can be any column name from the \code{\link{microorganisms}} data set, or \code{genus_species} or \code{gramstain}. This file contains references to the 'Burkholderia cepacia complex'. The species in this group can be found in: LiPuma JJ, 2015 (PMID 16217180). } \usage{ -eucast_rules(tbl, col_mo = NULL, info = TRUE, - rules = c("breakpoints", "expert", "other", "all"), verbose = FALSE, - amcl = guess_ab_col(), amik = guess_ab_col(), - amox = guess_ab_col(), ampi = guess_ab_col(), - azit = guess_ab_col(), azlo = guess_ab_col(), - aztr = guess_ab_col(), cefa = guess_ab_col(), - cfep = guess_ab_col(), cfot = guess_ab_col(), - cfox = guess_ab_col(), cfra = guess_ab_col(), - cfta = guess_ab_col(), cftr = guess_ab_col(), - cfur = guess_ab_col(), chlo = guess_ab_col(), - cipr = guess_ab_col(), clar = guess_ab_col(), - clin = guess_ab_col(), clox = guess_ab_col(), - coli = guess_ab_col(), czol = guess_ab_col(), - dapt = guess_ab_col(), doxy = guess_ab_col(), - erta = guess_ab_col(), eryt = guess_ab_col(), - fosf = guess_ab_col(), fusi = guess_ab_col(), - gent = guess_ab_col(), imip = guess_ab_col(), - kana = guess_ab_col(), levo = guess_ab_col(), - linc = guess_ab_col(), line = guess_ab_col(), - mero = guess_ab_col(), mezl = guess_ab_col(), - mino = guess_ab_col(), moxi = guess_ab_col(), - nali = guess_ab_col(), neom = guess_ab_col(), - neti = guess_ab_col(), nitr = guess_ab_col(), - norf = guess_ab_col(), novo = guess_ab_col(), - oflo = guess_ab_col(), oxac = guess_ab_col(), - peni = guess_ab_col(), pipe = guess_ab_col(), - pita = guess_ab_col(), poly = guess_ab_col(), - pris = guess_ab_col(), qida = guess_ab_col(), - rifa = guess_ab_col(), roxi = guess_ab_col(), - siso = guess_ab_col(), teic = guess_ab_col(), - tetr = guess_ab_col(), tica = guess_ab_col(), - tige = guess_ab_col(), tobr = guess_ab_col(), - trim = guess_ab_col(), trsu = guess_ab_col(), - vanc = guess_ab_col()) +eucast_rules(x, col_mo = NULL, info = TRUE, rules = c("breakpoints", + "expert", "other", "all"), verbose = FALSE, amcl = guess_ab_col(), + amik = guess_ab_col(), amox = guess_ab_col(), + ampi = guess_ab_col(), azit = guess_ab_col(), + azlo = guess_ab_col(), aztr = guess_ab_col(), + cefa = guess_ab_col(), cfep = guess_ab_col(), + cfot = guess_ab_col(), cfox = guess_ab_col(), + cfra = guess_ab_col(), cfta = guess_ab_col(), + cftr = guess_ab_col(), cfur = guess_ab_col(), + chlo = guess_ab_col(), cipr = guess_ab_col(), + clar = guess_ab_col(), clin = guess_ab_col(), + clox = guess_ab_col(), coli = guess_ab_col(), + czol = guess_ab_col(), dapt = guess_ab_col(), + doxy = guess_ab_col(), erta = guess_ab_col(), + eryt = guess_ab_col(), fosf = guess_ab_col(), + fusi = guess_ab_col(), gent = guess_ab_col(), + imip = guess_ab_col(), kana = guess_ab_col(), + levo = guess_ab_col(), linc = guess_ab_col(), + line = guess_ab_col(), mero = guess_ab_col(), + mezl = guess_ab_col(), mino = guess_ab_col(), + moxi = guess_ab_col(), nali = guess_ab_col(), + neom = guess_ab_col(), neti = guess_ab_col(), + nitr = guess_ab_col(), norf = guess_ab_col(), + novo = guess_ab_col(), oflo = guess_ab_col(), + oxac = guess_ab_col(), peni = guess_ab_col(), + pipe = guess_ab_col(), pita = guess_ab_col(), + poly = guess_ab_col(), pris = guess_ab_col(), + qida = guess_ab_col(), rifa = guess_ab_col(), + roxi = guess_ab_col(), siso = guess_ab_col(), + teic = guess_ab_col(), tetr = guess_ab_col(), + tica = guess_ab_col(), tige = guess_ab_col(), + tobr = guess_ab_col(), trim = guess_ab_col(), + trsu = guess_ab_col(), vanc = guess_ab_col(), ...) -EUCAST_rules(...) - -interpretive_reading(...) +eucast_rules_file() } \arguments{ -\item{tbl}{table with antibiotic columns, like e.g. \code{amox} and \code{amcl}} +\item{x}{data with antibiotic columns, like e.g. \code{amox} and \code{amcl}} \item{col_mo}{column name of the unique IDs of the microorganisms (see \code{\link{mo}}), defaults to the first column of class \code{mo}. Values will be coerced using \code{\link{as.mo}}.} @@ -78,11 +76,19 @@ interpretive_reading(...) \item{...}{parameters that are passed on to \code{eucast_rules}} } \value{ -The input of \code{tbl}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations. +The input of \code{tbl_}, possibly with edited values of antibiotics. Or, if \code{verbose = TRUE}, a \code{data.frame} with all original and new values of the affected bug-drug combinations. } \description{ Apply susceptibility rules as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, \url{http://eucast.org}), see \emph{Source}. This includes (1) expert rules, (2) intrinsic resistance and (3) inferred resistance as defined in their breakpoint tables. } +\details{ +The file used for applying all EUCAST rules can be retrieved with \code{\link{eucast_rules_file}()}. It returns an easily readable data set containing all rules. The original TSV file (tab separated file) that is being read by this function can be found when running this command: \cr +\code{AMR::EUCAST_RULES_FILE_LOCATION} (without brackets). + +In the source code it is located under \href{https://gitlab.com/msberends/AMR/blob/master/inst/eucast/eucast_rules.tsv}{\code{./inst/eucast/eucast_rules.tsv}}. + +\strong{Note:} When ampicillin (J01CA01) is not available but amoxicillin (J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. +} \section{Antibiotics}{ To define antibiotics column names, leave as it is to determine it automatically with \code{\link{guess_ab_col}} or input a text (case-insensitive) or use \code{NULL} to skip a column (e.g. \code{tica = NULL}). Non-existing columns will anyway be skipped with a warning. diff --git a/man/microorganisms.old.Rd b/man/microorganisms.old.Rd index e93f81c3..f8e470b8 100644 --- a/man/microorganisms.old.Rd +++ b/man/microorganisms.old.Rd @@ -4,15 +4,15 @@ \name{microorganisms.old} \alias{microorganisms.old} \title{Data set with previously accepted taxonomic names} -\format{A \code{\link{data.frame}} with 16,911 observations and 4 variables: +\format{A \code{\link{data.frame}} with 21,342 observations and 4 variables: \describe{ - \item{\code{col_id}}{Catalogue of Life ID} - \item{\code{tsn_new}}{New Catalogue of Life ID} - \item{\code{fullname}}{Old taxonomic name of the microorganism} + \item{\code{col_id}}{Catalogue of Life ID that was originally given} + \item{\code{col_id_new}}{New Catalogue of Life ID that responds to an entry in the \code{\link{microorganisms}} data set} + \item{\code{fullname}}{Old full taxonomic name of the microorganism} \item{\code{ref}}{Author(s) and year of concerning scientific publication} }} \source{ -[3] Catalogue of Life: Annual Checklist (public online database), \url{www.catalogueoflife.org}. +Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}). } \usage{ microorganisms.old diff --git a/man/portion.Rd b/man/portion.Rd index ee3f044e..705acf03 100644 --- a/man/portion.Rd +++ b/man/portion.Rd @@ -119,14 +119,14 @@ septic_patients \%>\% # Calculate co-resistance between amoxicillin/clav acid and gentamicin, # so we can see that combination therapy does a lot more than mono therapy: -septic_patients \%>\% portion_S(amcl) # S = 67.1\% -septic_patients \%>\% count_all(amcl) # n = 1576 +septic_patients \%>\% portion_S(amcl) # S = 71.4\% +septic_patients \%>\% count_all(amcl) # n = 1879 septic_patients \%>\% portion_S(gent) # S = 74.0\% septic_patients \%>\% count_all(gent) # n = 1855 -septic_patients \%>\% portion_S(amcl, gent) # S = 92.0\% -septic_patients \%>\% count_all(amcl, gent) # n = 1517 +septic_patients \%>\% portion_S(amcl, gent) # S = 92.3\% +septic_patients \%>\% count_all(amcl, gent) # n = 1798 septic_patients \%>\% diff --git a/reproduction_of_microorganisms.R b/reproduction_of_microorganisms.R index f8652a38..6b139e23 100644 --- a/reproduction_of_microorganisms.R +++ b/reproduction_of_microorganisms.R @@ -94,8 +94,8 @@ rm(ref_taxonomy) MOs <- data_total %>% filter( ( - # we only want all microorganisms and viruses - !kingdom %in% c("Animalia", "Plantae") + # we only want all MICROorganisms and no viruses + !kingdom %in% c("Animalia", "Plantae", "Viruses") # and no entries above genus level - all species already have a taxonomic tree & !rank %in% c("kingdom", "phylum", "superfamily", "class", "order", "family") # and not all fungi: Aspergillus, Candida, Trichphyton and Pneumocystis are the most important, @@ -115,7 +115,15 @@ MOs <- data_total %>% "Salinococcus", "Sanguibacteroides", "Schistosoma", "Scopulariopsis", "Scytalidium", "Sporobolomyces", "Stomatococcus", "Strongyloides", "Syncephalastraceae", "Taenia", "Torulopsis", "Trichinella", "Trichobilharzia", "Trichomonas", "Trichosporon", "Trichuris", "Trypanosoma", "Wuchereria") - ) %>% + # or the taxonomic entry is old - the species was renamed + | !is.na(col_id_new) + ) + +# filter old taxonomic names so only the ones with an existing reference will be kept +MOs <- MOs %>% + filter(is.na(col_id_new) | (!is.na(col_id_new) & col_id_new %in% MOs$col_id)) + +MOs <- MOs %>% # remove text if it contains 'Not assigned' like phylum in viruses mutate_all(~gsub("Not assigned", "", .)) @@ -176,7 +184,8 @@ MOs.old <- MOs %>% stringr::str_replace( string = fullname, pattern = stringr::fixed(authors2), - replacement = ""))), + replacement = "")) %>% + gsub(" (var|f|subsp)[.]", "", .)), ref) %>% filter(!is.na(fullname)) %>% distinct(fullname, .keep_all = TRUE) %>% @@ -185,9 +194,7 @@ MOs.old <- MOs %>% MOs <- MOs %>% filter(is.na(col_id_new) | source == "DSMZ") %>% transmute(col_id, - fullname = trimws(ifelse(kingdom == "Viruses", - gsub(":", "", ifelse(trimws(paste(species, subspecies)) == "", genus, paste(species, subspecies))), - paste(genus, species, subspecies))), + fullname = trimws(paste(genus, species, subspecies)), kingdom, phylum, class, @@ -203,9 +210,6 @@ MOs <- MOs %>% #distinct(fullname, .keep_all = TRUE) %>% filter(!grepl("unassigned", fullname, ignore.case = TRUE)) -# Keep only old names of species that are in MOs: -MOs.old <- MOs.old %>% filter(col_id_new %in% MOs$col_id) - # Filter out the DSMZ records that were renamed and are now in MOs.old MOs <- MOs %>% filter(!(source == "DSMZ" & fullname %in% MOs.old$fullname), diff --git a/tests/testthat.R b/tests/testthat.R index 35010329..778d4770 100755 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # library(testthat) diff --git a/tests/testthat/test-abname.R b/tests/testthat/test-abname.R index 39b0f4a3..a54d192f 100644 --- a/tests/testthat/test-abname.R +++ b/tests/testthat/test-abname.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("abname.R") diff --git a/tests/testthat/test-age.R b/tests/testthat/test-age.R index 0bf18745..2bd7e183 100644 --- a/tests/testthat/test-age.R +++ b/tests/testthat/test-age.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("age.R") diff --git a/tests/testthat/test-atc.R b/tests/testthat/test-atc.R index 34587335..5877ccf7 100755 --- a/tests/testthat/test-atc.R +++ b/tests/testthat/test-atc.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("atc.R") diff --git a/tests/testthat/test-atc_property.R b/tests/testthat/test-atc_property.R index 68abf8ce..bc3cae89 100644 --- a/tests/testthat/test-atc_property.R +++ b/tests/testthat/test-atc_property.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("atc_property.R") diff --git a/tests/testthat/test-availability.R b/tests/testthat/test-availability.R index cbc3f6b6..e4b52556 100644 --- a/tests/testthat/test-availability.R +++ b/tests/testthat/test-availability.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("availability.R") diff --git a/tests/testthat/test-count.R b/tests/testthat/test-count.R index 1dcdd956..ad9507cc 100644 --- a/tests/testthat/test-count.R +++ b/tests/testthat/test-count.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("count.R") diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R index 5e229011..a74aa11d 100644 --- a/tests/testthat/test-data.R +++ b/tests/testthat/test-data.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("data.R") @@ -27,36 +27,13 @@ test_that("data sets are valid", { expect_identical(nrow(microorganisms), length(unique(microorganisms$mo))) # there should be no diacritics (i.e. non ASCII) characters in the datasets - library(dplyr) - # check only character variables: - test_microorganisms <- microorganisms %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE) - test_microorganisms.old <- microorganisms.old %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE) - test_antibiotics <- antibiotics %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE) - test_septic_patients <- septic_patients %>% select_if(is.character) %>% as.data.frame(stringsAsFactors = FALSE) - # and compare them with their transformed version: - expect_identical(test_microorganisms, - test_microorganisms %>% - lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>% - as.data.frame(stringsAsFactors = FALSE)) - - expect_identical(test_microorganisms.old, - test_microorganisms.old %>% - lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>% - as.data.frame(stringsAsFactors = FALSE)) - - expect_identical(test_antibiotics, - test_antibiotics %>% - lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>% - as.data.frame(stringsAsFactors = FALSE)) - - expect_identical(test_septic_patients, - test_septic_patients %>% - lapply(iconv, from = "UTF-8", to = "ASCII//TRANSLIT") %>% - as.data.frame(stringsAsFactors = FALSE)) - + datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"] + for (i in 1:length(datasets)) { + dataset <- get(datasets[i], envir = asNamespace("AMR")) + expect_identical(dataset_UTF8_to_ASCII(dataset), dataset) + } }) - test_that("creation of data sets is valid", { df <- make() expect_lt(nrow(df[which(df$prevalence == 1), ]), nrow(df[which(df$prevalence == 2), ])) diff --git a/tests/testthat/test-deprecated.R b/tests/testthat/test-deprecated.R index d6a9fa32..387205d7 100644 --- a/tests/testthat/test-deprecated.R +++ b/tests/testthat/test-deprecated.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("deprecated.R") @@ -30,8 +30,6 @@ test_that("deprecated functions work", { expect_identical(suppressWarnings(ratio(c(772, 1611, 737), ratio = "1:2:1")), c(780, 1560, 780)) expect_identical(suppressWarnings(ratio(c(1752, 1895), ratio = c(1, 1))), c(1823.5, 1823.5)) - expect_warning(guess_mo("esco")) - expect_warning(guess_atc("amox")) expect_warning(ab_property("amox")) expect_warning(ab_atc("amox")) expect_warning(ab_official("amox")) diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-eucast_rules.R index 7e005fe4..1a85f501 100755 --- a/tests/testthat/test-eucast_rules.R +++ b/tests/testthat/test-eucast_rules.R @@ -16,13 +16,22 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("eucast_rules.R") test_that("EUCAST rules work", { + # thoroughly check input table + expect_true(file.exists(EUCAST_RULES_FILE_LOCATION)) + eucast_input_file <- eucast_rules_file() + expect_equal(colnames(eucast_input_file), + c("if_mo_property", "like_is_one_of", "this_value", + "and_these_antibiotics", "have_these_values", + "then_change_these_antibiotics", "to_value", + "reference.rule", "reference.rule_group")) + expect_error(suppressWarnings(eucast_rules(septic_patients, col_mo = "Non-existing"))) expect_identical(colnames(septic_patients), @@ -40,7 +49,6 @@ test_that("EUCAST rules work", { stringsAsFactors = FALSE) expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b) expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b) - expect_identical(suppressWarnings(interpretive_reading(a, "mo", info = TRUE)), b) a <- data.frame(mo = c("Staphylococcus aureus", "Streptococcus group A"), diff --git a/tests/testthat/test-filter_ab_class.R b/tests/testthat/test-filter_ab_class.R index 5bf8b842..029c80e2 100644 --- a/tests/testthat/test-filter_ab_class.R +++ b/tests/testthat/test-filter_ab_class.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("filter_ab_class.R") diff --git a/tests/testthat/test-first_isolate.R b/tests/testthat/test-first_isolate.R index 2fd92574..868b252a 100755 --- a/tests/testthat/test-first_isolate.R +++ b/tests/testthat/test-first_isolate.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("first_isolate.R") diff --git a/tests/testthat/test-freq.R b/tests/testthat/test-freq.R index ae45f75e..3bbdbe8e 100755 --- a/tests/testthat/test-freq.R +++ b/tests/testthat/test-freq.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("freq.R") diff --git a/tests/testthat/test-g.test.R b/tests/testthat/test-g.test.R index 080aa69b..1f3e6185 100644 --- a/tests/testthat/test-g.test.R +++ b/tests/testthat/test-g.test.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("g.test.R") diff --git a/tests/testthat/test-get_locale.R b/tests/testthat/test-get_locale.R index d4631dd3..1daee661 100644 --- a/tests/testthat/test-get_locale.R +++ b/tests/testthat/test-get_locale.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("get_locale.R") diff --git a/tests/testthat/test-ggplot_rsi.R b/tests/testthat/test-ggplot_rsi.R index 34d8c3de..b55b5741 100644 --- a/tests/testthat/test-ggplot_rsi.R +++ b/tests/testthat/test-ggplot_rsi.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("ggplot_rsi.R") diff --git a/tests/testthat/test-guess_ab_col.R b/tests/testthat/test-guess_ab_col.R index 5353d3e4..7ead1fa0 100644 --- a/tests/testthat/test-guess_ab_col.R +++ b/tests/testthat/test-guess_ab_col.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("guess_ab_col.R") diff --git a/tests/testthat/test-join_microorganisms.R b/tests/testthat/test-join_microorganisms.R index 833cfb5e..1f2bbaca 100755 --- a/tests/testthat/test-join_microorganisms.R +++ b/tests/testthat/test-join_microorganisms.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("join_microorganisms.R") diff --git a/tests/testthat/test-key_antibiotics.R b/tests/testthat/test-key_antibiotics.R index 212c5db1..83e97f5f 100644 --- a/tests/testthat/test-key_antibiotics.R +++ b/tests/testthat/test-key_antibiotics.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("key_antibiotics.R") diff --git a/tests/testthat/test-kurtosis.R b/tests/testthat/test-kurtosis.R index 1f40ba42..11287a3e 100644 --- a/tests/testthat/test-kurtosis.R +++ b/tests/testthat/test-kurtosis.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("kurtosis.R") diff --git a/tests/testthat/test-like.R b/tests/testthat/test-like.R index 6a0ee3d2..cdd35510 100644 --- a/tests/testthat/test-like.R +++ b/tests/testthat/test-like.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("like.R") diff --git a/tests/testthat/test-mdro.R b/tests/testthat/test-mdro.R index 1606f590..83078eff 100755 --- a/tests/testthat/test-mdro.R +++ b/tests/testthat/test-mdro.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("mdro.R") diff --git a/tests/testthat/test-mic.R b/tests/testthat/test-mic.R index e945752d..db158b3b 100755 --- a/tests/testthat/test-mic.R +++ b/tests/testthat/test-mic.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("mic.R") diff --git a/tests/testthat/test-misc.R b/tests/testthat/test-misc.R index f1a48d4e..2c7f24c2 100755 --- a/tests/testthat/test-misc.R +++ b/tests/testthat/test-misc.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("misc.R") diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R index d5d53b72..c92ef1dd 100644 --- a/tests/testthat/test-mo.R +++ b/tests/testthat/test-mo.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("mo.R") diff --git a/tests/testthat/test-mo_history.R b/tests/testthat/test-mo_history.R index 876823d0..04d83ed5 100644 --- a/tests/testthat/test-mo_history.R +++ b/tests/testthat/test-mo_history.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # # context("mo_history.R") diff --git a/tests/testthat/test-mo_property.R b/tests/testthat/test-mo_property.R index ba63aedc..68307088 100644 --- a/tests/testthat/test-mo_property.R +++ b/tests/testthat/test-mo_property.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("mo_property.R") diff --git a/tests/testthat/test-p.symbol.R b/tests/testthat/test-p.symbol.R index 3af4d7c3..57b0bbf5 100644 --- a/tests/testthat/test-p.symbol.R +++ b/tests/testthat/test-p.symbol.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("p.symbol.R") diff --git a/tests/testthat/test-portion.R b/tests/testthat/test-portion.R index c96a92a2..95907770 100755 --- a/tests/testthat/test-portion.R +++ b/tests/testthat/test-portion.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("portion.R") diff --git a/tests/testthat/test-read.4d.R b/tests/testthat/test-read.4d.R index 6a99b3ec..a52def16 100644 --- a/tests/testthat/test-read.4d.R +++ b/tests/testthat/test-read.4d.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("read.4d.R") diff --git a/tests/testthat/test-resistance_predict.R b/tests/testthat/test-resistance_predict.R index 21afff06..cb511b1a 100644 --- a/tests/testthat/test-resistance_predict.R +++ b/tests/testthat/test-resistance_predict.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("portion.R") diff --git a/tests/testthat/test-rsi.R b/tests/testthat/test-rsi.R index d75b5df4..422ea462 100644 --- a/tests/testthat/test-rsi.R +++ b/tests/testthat/test-rsi.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("rsi.R") diff --git a/tests/testthat/test-skewness.R b/tests/testthat/test-skewness.R index 35c8c9bd..7fc816f3 100644 --- a/tests/testthat/test-skewness.R +++ b/tests/testthat/test-skewness.R @@ -16,7 +16,7 @@ # This R package was created for academic research and was publicly # # released in the hope that it will be useful, but it comes WITHOUT # # ANY WARRANTY OR LIABILITY. # -# Visit our website for more info: https://msberends.gitab.io/AMR. # +# Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # context("skewness.R")
    tbl

    table with antibiotic columns, like e.g. amox and amcl

    		x

    data with antibiotic columns, like e.g. amox and amcl
    col_mo
    -

    eucast_rules() EUCAST_rules() interpretive_reading()

    +

    eucast_rules() eucast_rules_file()

    EUCAST rules
    -

    ratio() guess_mo() guess_atc() ab_property() ab_atc() ab_official() ab_name() ab_trivial_nl() ab_certe() ab_umcg() ab_tradenames() atc_ddd() atc_groups()

    +

    ratio() ab_property() ab_atc() ab_official() ab_name() ab_trivial_nl() ab_certe() ab_umcg() ab_tradenames() atc_ddd() atc_groups()

    Deprecated functions