From 5e45fdcf2a98ba993d3e674ea88b6fb6b0057411 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Wed, 26 Aug 2020 11:33:54 +0200 Subject: [PATCH] (v1.3.0.9007) tibble printing --- DESCRIPTION | 4 +- NAMESPACE | 8 +++ NEWS.md | 8 ++- R/disk.R | 16 +++++ R/eucast_rules.R | 36 +++++++++--- R/mic.R | 16 +++++ R/mo.R | 49 ++++++++++++++-- R/mo_property.R | 7 ++- R/rsi.R | 18 ++++++ R/zzz.R | 55 ++++++++++++++++++ data-raw/antibiotics.dta | Bin 329492 -> 329492 bytes data-raw/antibiotics.sas | Bin 1880064 -> 1880064 bytes data-raw/antibiotics.sav | Bin 1406605 -> 1406605 bytes data-raw/antibiotics.xlsx | Bin 66082 -> 66082 bytes data-raw/antivirals.dta | Bin 68841 -> 68841 bytes data-raw/antivirals.sas | Bin 81920 -> 81920 bytes data-raw/antivirals.sav | Bin 69306 -> 69306 bytes data-raw/antivirals.xlsx | Bin 13934 -> 13934 bytes data-raw/intrinsic_resistant.dta | Bin 3909333 -> 3909333 bytes data-raw/intrinsic_resistant.sas | Bin 3985408 -> 3985408 bytes data-raw/intrinsic_resistant.sav | Bin 4353410 -> 4353410 bytes data-raw/intrinsic_resistant.xlsx | Bin 524509 -> 524509 bytes data-raw/microorganisms.dta | Bin 26468289 -> 26468289 bytes data-raw/microorganisms.old.dta | Bin 1896607 -> 1896607 bytes data-raw/microorganisms.old.sas | Bin 1941504 -> 1941504 bytes data-raw/microorganisms.old.sav | Bin 2034367 -> 2034367 bytes data-raw/microorganisms.old.xlsx | Bin 453023 -> 453023 bytes data-raw/microorganisms.sas | Bin 27521024 -> 27521024 bytes data-raw/microorganisms.sav | Bin 29548953 -> 29548953 bytes data-raw/microorganisms.xlsx | Bin 6401595 -> 6401595 bytes data-raw/rsi_translation.dta | Bin 3121505 -> 3121505 bytes data-raw/rsi_translation.sas | Bin 3334144 -> 3334144 bytes data-raw/rsi_translation.sav | Bin 3582161 -> 3582161 bytes data-raw/rsi_translation.xlsx | Bin 656226 -> 656225 bytes data/microorganisms.codes.rda | Bin 35612 -> 31336 bytes docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/datasets.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 54 +++++++++-------- docs/pkgdown.yml | 2 +- docs/reference/AMR.html | 2 +- docs/reference/WHONET.html | 2 +- docs/reference/ab_property.html | 2 +- .../reference/antibiotic_class_selectors.html | 2 +- docs/reference/antibiotics.html | 2 +- docs/reference/as.ab.html | 2 +- docs/reference/as.mo.html | 5 +- docs/reference/as.rsi.html | 2 +- docs/reference/eucast_rules.html | 2 +- docs/reference/example_isolates.html | 2 +- docs/reference/example_isolates_unclean.html | 2 +- docs/reference/index.html | 4 +- docs/reference/intrinsic_resistant.html | 2 +- docs/reference/microorganisms.codes.html | 10 ++-- docs/reference/microorganisms.html | 2 +- docs/reference/microorganisms.old.html | 2 +- docs/reference/mo_property.html | 2 +- docs/reference/rsi_translation.html | 2 +- docs/survey.html | 2 +- man/as.mo.Rd | 3 +- man/microorganisms.codes.Rd | 4 +- 64 files changed, 266 insertions(+), 77 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 58fe84c04..83141de83 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.3.0.9006 -Date: 2020-08-21 +Version: 1.3.0.9007 +Date: 2020-08-26 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NAMESPACE b/NAMESPACE index d189314fa..d66e8ebb3 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -40,6 +40,10 @@ S3method(format,bug_drug_combinations) S3method(kurtosis,data.frame) S3method(kurtosis,default) S3method(kurtosis,matrix) +S3method(pillar_shaft,disk) +S3method(pillar_shaft,mic) +S3method(pillar_shaft,mo) +S3method(pillar_shaft,rsi) S3method(plot,mic) S3method(plot,resistance_predict) S3method(plot,rsi) @@ -58,6 +62,10 @@ S3method(skewness,matrix) S3method(summary,mic) S3method(summary,mo) S3method(summary,rsi) +S3method(type_sum,disk) +S3method(type_sum,mic) +S3method(type_sum,mo) +S3method(type_sum,rsi) export("%like%") export("%like_case%") export(ab_atc) diff --git a/NEWS.md b/NEWS.md index c415c0ef8..41a517919 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.3.0.9006 -## Last updated: 21 August 2020 +# AMR 1.3.0.9007 +## Last updated: 26 August 2020 ### New * Data set `intrinsic_resistant`. This data set contains all bug-drug combinations where the 'bug' is intrinsic resistant to the 'drug' according to the latest EUCAST insights. It contains just two columns: `microorganism` and `antibiotic`. @@ -34,7 +34,11 @@ #> Class #> [1] 24 24 ``` +* Speed improvement for `eucast_rules()` * Overall speed improvement by tweaking joining functions +* Function `mo_shortname()` now return the genus for input where the species is unknown +* BORSA is now recognised as an abbreviation for a *Staphylococcus aureus*, meaning that e.g. `mo_genus("BORSA")` will return "Staphylococcus" +* Support for coloured `tibble` printing of classes `mo`, `rsi`, `mic` and `disk` # AMR 1.3.0 diff --git a/R/disk.R b/R/disk.R index 004f0f901..fadbabcea 100644 --- a/R/disk.R +++ b/R/disk.R @@ -114,6 +114,22 @@ is.disk <- function(x) { inherits(x, "disk") } +#' @method pillar_shaft disk +#' @export +pillar_shaft.disk <- function(x, ...) { + style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE) + new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE) + out <- trimws(format(x)) + out[is.na(x)] <- style_na(NA) + new_pillar_shaft_simple(out, align = "right", min_width = 3) +} + +#' @method type_sum disk +#' @export +type_sum.disk <- function(x, ...) { + "disk" +} + #' @method print disk #' @export #' @noRd diff --git a/R/eucast_rules.R b/R/eucast_rules.R index 08adceef7..acda0d52d 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -350,6 +350,9 @@ eucast_rules <- function(x, verbose = verbose, ...) + # data preparation ---- + message(font_blue("NOTE: Preparing data..."), appendLF = FALSE) + AMC <- cols_ab["AMC"] AMK <- cols_ab["AMK"] AMP <- cols_ab["AMP"] @@ -429,7 +432,7 @@ eucast_rules <- function(x, rule_name = character(0), stringsAsFactors = FALSE) - # helper function for editing the table + # helper function for editing the table ---- edit_rsi <- function(to, rule, rows, cols) { cols <- unique(cols[!is.na(cols) & !is.null(cols)]) if (length(rows) > 0 & length(cols) > 0) { @@ -508,10 +511,21 @@ eucast_rules <- function(x, changed = 0)) } - # save original table + + old_cols <- colnames(x) + old_attributes <- attributes(x) + x <- as.data.frame(x, stringsAsFactors = FALSE) # no tibbles, data.tables, etc. + # create unique row IDs - combination of the MO and all ABx columns (so they will only run once per unique combination) + x$`.rowid` <- sapply(as.list(as.data.frame(t(x[, c(col_mo, cols_ab), drop = FALSE]))), function(x) { + x[is.na(x)] <- "." + paste0(x, collapse = "") + }) + + # save original table, with the new .rowid column + x_original.bak <- x + # keep only unique rows for MO and ABx + x <- x %>% distinct(`.rowid`, .keep_all = TRUE) x_original <- x - x_original_attr <- attributes(x) - x_original <- as.data.frame(x_original, stringsAsFactors = FALSE) # no tibbles, data.tables, etc. # join to microorganisms data set x <- as.data.frame(x, stringsAsFactors = FALSE) @@ -520,6 +534,7 @@ eucast_rules <- function(x, left_join_microorganisms(by = col_mo, suffix = c("_oldcols", "")) x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL) x$genus_species <- paste(x$genus, x$species) + message(font_blue("OK.")) if (ab_missing(AMP) & !ab_missing(AMX)) { # ampicillin column is missing, but amoxicillin is available @@ -528,7 +543,7 @@ eucast_rules <- function(x, } # nolint start - # antibiotic classes + # antibiotic classes ---- aminoglycosides <- c(TOB, GEN, KAN, NEO, NET, SIS) tetracyclines <- c(DOX, MNO, TCY) # since EUCAST v3.1 tigecycline (TGC) is set apart polymyxins <- c(PLB, COL) @@ -544,7 +559,7 @@ eucast_rules <- function(x, fluoroquinolones <- c(OFX, CIP, NOR, LVX, MFX) # nolint end - # Help function to get available antibiotic column names ------------------ + # help function to get available antibiotic column names ------------------ get_antibiotic_columns <- function(x, df) { x <- trimws(unlist(strsplit(x, ",", fixed = TRUE))) y <- character(0) @@ -923,7 +938,12 @@ eucast_rules <- function(x, verbose_info } else { # reset original attributes - attributes(x_original) <- x_original_attr - x_original + x_original <- x_original[, c(col_mo, cols_ab, ".rowid"), drop = FALSE] + x_original.bak <- x_original.bak[, setdiff(colnames(x_original.bak), c(col_mo, cols_ab)), drop = FALSE] + x_original.bak <- x_original.bak %>% + left_join(x_original, by = ".rowid") + x_original.bak <- x_original.bak[, old_cols, drop = FALSE] + attributes(x_original.bak) <- old_attributes + x_original.bak } } diff --git a/R/mic.R b/R/mic.R index 1243e89c9..daa796354 100755 --- a/R/mic.R +++ b/R/mic.R @@ -171,6 +171,22 @@ droplevels.mic <- function(x, exclude = ifelse(anyNA(levels(x)), NULL, NA), ...) x } +#' @method pillar_shaft mic +#' @export +pillar_shaft.mic <- function(x, ...) { + style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE) + new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE) + out <- trimws(format(x)) + out[is.na(x)] <- style_na(NA) + new_pillar_shaft_simple(out, align = "right", min_width = 4) +} + +#' @method type_sum mic +#' @export +type_sum.mic <- function(x, ...) { + "mic" +} + #' @method print mic #' @export #' @noRd diff --git a/R/mo.R b/R/mo.R index e8e373610..0a0486548 100755 --- a/R/mo.R +++ b/R/mo.R @@ -159,7 +159,8 @@ #' select(microorganism_name) %>% #' as.mo() #' -#' # and can even contain 2 columns, which is convenient for genus/species combinations: +#' # and can even contain 2 columns, which is convenient +#' # for genus/species combinations: #' df$mo <- df %>% #' select(genus, species) %>% #' as.mo() @@ -459,13 +460,15 @@ exec_as.mo <- function(x, x <- gsub("(th|ht|t)+", "(th|ht|t)+", x) x <- gsub("a+", "a+", x) x <- gsub("u+", "u+", x) - # allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica and -a (needs perl for the negative backward lookup): + # allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica, -ia and -a (needs perl for the negative backward lookup): x <- gsub("(u\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+)(?![a-z])", "(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE) x <- gsub("(\\[iy\\]\\+\\(c\\|k\\|q\\|qu\\+\\|s\\|z\\|x\\|ks\\)\\+a\\+)(?![a-z])", "(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE) x <- gsub("(\\[iy\\]\\+u\\+m)(?![a-z])", "(u[s|m]|[iy][ck]?u[ms]|[iy]?[ck]?a)", x, perl = TRUE) + x <- gsub("(\\[iy\\]\\+a\\+)(?![a-z])", + "([iy]*a+|[iy]+a*)", x, perl = TRUE) x <- gsub("e+", "e+", x) x <- gsub("o+", "o+", x) x <- gsub("(.)\\1+", "\\1+", x) @@ -636,7 +639,7 @@ exec_as.mo <- function(x, } # translate known trivial abbreviations to genus + species ---- - if (toupper(x_backup_without_spp[i]) %in% c("MRSA", "MSSA", "VISA", "VRSA") + if (toupper(x_backup_without_spp[i]) %in% c("MRSA", "MSSA", "VISA", "VRSA", "BORSA") | x_backup_without_spp[i] %like_case% " (mrsa|mssa|visa|vrsa) ") { x[i] <- lookup(fullname == "Staphylococcus aureus") next @@ -1523,12 +1526,50 @@ format_uncertainty_as_df <- function(uncertainty_level, df } +#' @method pillar_shaft mo +#' @export +pillar_shaft.mo <- function(x, ...) { + # import from the pillar package, without being dependent on it! + style_na <- import_fn("style_na", "pillar", error_on_fail = FALSE) + style_subtle <- import_fn("style_subtle", "pillar", error_on_fail = FALSE) + new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE) + if (is.null(style_na) | is.null(style_subtle) | is.null(new_pillar_shaft_simple)) { + return(x) + } + + out <- format(x) + # grey out the kingdom (part until first "_") + out[!is.na(x)] <- gsub("^([A-Z]+_)(.*)", paste0(style_subtle("\\1"), "\\2"), out[!is.na(x)]) + # and grey out every _ + out[!is.na(x)] <- gsub("_", style_subtle("_"), out[!is.na(x)]) + + # markup NA and UNKNOWN + out[is.na(x)] <- style_na(" NA") + out[x == "UNKNOWN"] <- style_na(" UNKNOWN") + + # make it always fit exactly + new_pillar_shaft_simple(out, + align = "left", + width = max(nchar(x)) + ifelse(length(x[x %in% c(NA, "UNKNOWN")]) > 0, + 2, + 0)) +} + +#' @method type_sum mo +#' @export +type_sum.mo <- function(x, ...) { + "mo" +} + #' @method print mo #' @export #' @noRd -print.mo <- function(x, ...) { +print.mo <- function(x, print.shortnames = FALSE, ...) { cat("Class \n") x_names <- names(x) + if (is.null(x_names) & print.shortnames == TRUE) { + x_names <- tryCatch(mo_shortname(x, ...), error = function(e) NULL) + } x <- as.character(x) names(x) <- x_names print.default(x, quote = FALSE) diff --git a/R/mo_property.R b/R/mo_property.R index 5b079e595..bae87e835 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -161,13 +161,18 @@ mo_shortname <- function(x, language = get_locale(), ...) { } # get first char of genus and complete species in English - shortnames <- paste0(substr(mo_genus(x.mo, language = NULL), 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL))) + genera <- mo_genus(x.mo, language = NULL) + shortnames <- paste0(substr(genera, 1, 1), ". ", replace_empty(mo_species(x.mo, language = NULL))) + # exceptions for where no species is known + shortnames[shortnames %like% ".[.] spp[.]"] <- genera[shortnames %like% ".[.] spp[.]"] # exceptions for Staphylococci shortnames[shortnames == "S. coagulase-negative"] <- "CoNS" shortnames[shortnames == "S. coagulase-positive"] <- "CoPS" # exceptions for Streptococci: Streptococcus Group A -> GAS shortnames[shortnames %like% "S. group [ABCDFGHK]"] <- paste0("G", gsub("S. group ([ABCDFGHK])", "\\1", shortnames[shortnames %like% "S. group [ABCDFGHK]"]), "S") + # unknown species etc. + shortnames[shortnames %like% "unknown"] <- paste0("(", trimws(gsub("[^a-zA-Z -]", "", shortnames[shortnames %like% "unknown"])), ")") load_mo_failures_uncertainties_renamed(metadata) translate_AMR(shortnames, language = language, only_unknown = FALSE) diff --git a/R/rsi.R b/R/rsi.R index f8bf46f76..5af30b38f 100755 --- a/R/rsi.R +++ b/R/rsi.R @@ -670,6 +670,24 @@ exec_as.rsi <- function(method, class = c("rsi", "ordered", "factor")) } +#' @method pillar_shaft rsi +#' @export +pillar_shaft.rsi <- function(x, ...) { + out <- trimws(format(x)) + out[is.na(x)] <- font_grey(" NA") + out[x == "S"] <- font_green_bg(font_white(" S ")) + out[x == "I"] <- font_yellow_bg(font_black(" I ")) + out[x == "R"] <- font_red_bg(font_white(" R ")) + new_pillar_shaft_simple <- import_fn("new_pillar_shaft_simple", "pillar", error_on_fail = FALSE) + new_pillar_shaft_simple(out, align = "left", width = 3) +} + +#' @method type_sum rsi +#' @export +type_sum.rsi <- function(x, ...) { + "rsi" +} + #' @method print rsi #' @export #' @noRd diff --git a/R/zzz.R b/R/zzz.R index 053213b1b..574f5bb44 100755 --- a/R/zzz.R +++ b/R/zzz.R @@ -27,7 +27,19 @@ assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR")) + + # support for tibble headers (type_sum) and tibble columns content (pillar_shaft) + s3_register("pillar::pillar_shaft", "mo") + s3_register("tibble::type_sum", "mo") + s3_register("pillar::pillar_shaft", "rsi") + s3_register("tibble::type_sum", "rsi") + s3_register("pillar::pillar_shaft", "mic") + s3_register("tibble::type_sum", "mic") + s3_register("pillar::pillar_shaft", "disk") + s3_register("tibble::type_sum", "disk") } +pillar_shaft <- import_fn("pillar_shaft", "pillar", error_on_fail = FALSE) +type_sum <- import_fn("type_sum", "tibble", error_on_fail = FALSE) .onAttach <- function(...) { if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(Sys.getenv("AMR_silentstart", FALSE)))) { @@ -73,3 +85,46 @@ create_MO.old_lookup <- function() { # so arrange data on prevalence first, then full name MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ] } + +# copied from vctrs::s3_register +s3_register <- function (generic, class, method = NULL) { + stopifnot(is.character(generic), length(generic) == 1) + stopifnot(is.character(class), length(class) == 1) + pieces <- strsplit(generic, "::")[[1]] + stopifnot(length(pieces) == 2) + package <- pieces[[1]] + generic <- pieces[[2]] + caller <- parent.frame() + get_method_env <- function() { + top <- topenv(caller) + if (isNamespace(top)) { + asNamespace(environmentName(top)) + } + else { + caller + } + } + get_method <- function(method, env) { + if (is.null(method)) { + get(paste0(generic, ".", class), envir = get_method_env()) + } + else { + method + } + } + method_fn <- get_method(method) + stopifnot(is.function(method_fn)) + setHook(packageEvent(package, "onLoad"), function(...) { + ns <- asNamespace(package) + method_fn <- get_method(method) + registerS3method(generic, class, method_fn, envir = ns) + }) + if (!isNamespaceLoaded(package)) { + return(invisible()) + } + envir <- asNamespace(package) + if (exists(generic, envir)) { + registerS3method(generic, class, method_fn, envir = envir) + } + invisible() +} diff --git a/data-raw/antibiotics.dta b/data-raw/antibiotics.dta index 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-

Translation table with 5,582 common microorganism codes

+

Translation table with 5,583 common microorganism codes

Source: R/data.R
@@ -247,7 +247,7 @@

Format

-

A data.frame with 5,582 observations and 2 variables:

    +

    A data.frame with 5,583 observations and 2 variables:

    • code
      Commonly used code of a microorganism

    • mo
      ID of the microorganism in the microorganisms data set

    diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index 7068a1712..5bc2e2ae5 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -82,7 +82,7 @@ AMR (for R) - 1.3.0.9006 + 1.3.0.9007
diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 07cb42bb3..e7d09bd52 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -82,7 +82,7 @@ AMR (for R) - 1.3.0.9006 + 1.3.0.9007
diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 40b490136..8b9b175f4 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.3.0.9006 + 1.3.0.9007 diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html index 87de2770f..f73ed4bfa 100644 --- a/docs/reference/rsi_translation.html +++ b/docs/reference/rsi_translation.html @@ -82,7 +82,7 @@ AMR (for R) - 1.3.0.9006 + 1.3.0.9007 diff --git a/docs/survey.html b/docs/survey.html index 910af8440..b04f90ffe 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.3.0.9006 + 1.3.0.9007 diff --git a/man/as.mo.Rd b/man/as.mo.Rd index 694911c07..c39ce545f 100644 --- a/man/as.mo.Rd +++ b/man/as.mo.Rd @@ -203,7 +203,8 @@ df$mo <- df \%>\% select(microorganism_name) \%>\% as.mo() -# and can even contain 2 columns, which is convenient for genus/species combinations: +# and can even contain 2 columns, which is convenient +# for genus/species combinations: df$mo <- df \%>\% select(genus, species) \%>\% as.mo() diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd index d0c5314cb..5a23c10a5 100644 --- a/man/microorganisms.codes.Rd +++ b/man/microorganisms.codes.Rd @@ -3,9 +3,9 @@ \docType{data} \name{microorganisms.codes} \alias{microorganisms.codes} -\title{Translation table with 5,582 common microorganism codes} +\title{Translation table with 5,583 common microorganism codes} \format{ -A \code{\link{data.frame}} with 5,582 observations and 2 variables: +A \code{\link{data.frame}} with 5,583 observations and 2 variables: \itemize{ \item \code{code}\cr Commonly used code of a microorganism \item \code{mo}\cr ID of the microorganism in the \link{microorganisms} data set