# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Analysis # # # # SOURCE # # https://gitlab.com/msberends/AMR # # # # LICENCE # # (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # # # 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.gitlab.io/AMR. # # ==================================================================== # # No export, no Rd addin_insert_in <- function() { rstudioapi::insertText(" %in% ") } # No export, no Rd addin_insert_like <- function() { rstudioapi::insertText(" %like% ") } # No export, no Rd # works exactly like round(), but rounds `round(44.55, 1)` as 44.6 instead of 44.5 # and adds decimal zeroes until `digits` is reached when force_zero = TRUE round2 <- function(x, digits = 0, force_zero = TRUE) { # https://stackoverflow.com/a/12688836/4575331 val <- (trunc((abs(x) * 10 ^ digits) + 0.5) / 10 ^ digits) * sign(x) if (digits > 0 & force_zero == TRUE) { val[val != as.integer(val)] <- paste0(val[val != as.integer(val)], strrep("0", max(0, digits - nchar(gsub(".*[.](.*)$", "\\1", val[val != as.integer(val)]))))) } val } # Coefficient of variation (CV) cv <- function(x, na.rm = TRUE) { stats::sd(x, na.rm = na.rm) / base::abs(base::mean(x, na.rm = na.rm)) } # Coefficient of dispersion, or coefficient of quartile variation (CQV). # (Bonett et al., 2006: Confidence interval for a coefficient of quartile variation). cqv <- function(x, na.rm = TRUE) { fives <- stats::fivenum(x, na.rm = na.rm) (fives[4] - fives[2]) / (fives[4] + fives[2]) } # show bytes as kB/MB/GB # size_humanreadable(123456) # 121 kB # size_humanreadable(12345678) # 11.8 MB size_humanreadable <- function(bytes, decimals = 1) { bytes <- bytes %>% as.double() # Adapted from: # http://jeffreysambells.com/2012/10/25/human-readable-filesize-php size <- c('B','kB','MB','GB','TB','PB','EB','ZB','YB') factor <- floor((nchar(bytes) - 1) / 3) # added slight improvement; no decimals for B and kB: decimals <- rep(decimals, length(bytes)) decimals[size[factor + 1] %in% c('B', 'kB')] <- 0 out <- paste(sprintf(paste0("%.", decimals, "f"), bytes / (1024 ^ factor)), size[factor + 1]) out } percent_scales <- scales::percent # No export, no Rd # based on scales::percent percent <- function(x, round = 1, force_zero = FALSE, decimal.mark = getOption("OutDec"), ...) { x <- percent_scales(x = as.double(x), accuracy = 1 / 10 ^ round, decimal.mark = decimal.mark, ...) if (force_zero == FALSE) { x <- gsub("([.]%|%%)", "%", paste0(gsub("0+%$", "", x), "%")) } x } #' @importFrom crayon blue bold red #' @importFrom dplyr %>% pull search_type_in_df <- function(tbl, type) { # try to find columns based on type found <- NULL colnames(tbl) <- trimws(colnames(tbl)) # -- mo if (type == "mo") { if ("mo" %in% lapply(tbl, class)) { found <- colnames(tbl)[lapply(tbl, class) == "mo"][1] } else if (any(colnames(tbl) %like% "^(mo|microorganism|organism|bacteria)")) { found <- colnames(tbl)[colnames(tbl) %like% "^(mo|microorganism|organism|bacteria)"][1] } else if (any(colnames(tbl) %like% "species")) { found <- colnames(tbl)[colnames(tbl) %like% "species"][1] } } # -- key antibiotics if (type == "keyantibiotics") { if (any(colnames(tbl) %like% "^key.*(ab|antibiotics)")) { found <- colnames(tbl)[colnames(tbl) %like% "^key.*(ab|antibiotics)"][1] } } # -- date if (type == "date") { if (any(colnames(tbl) %like% "^(specimen date|specimen_date|spec_date)")) { # WHONET support found <- colnames(tbl)[colnames(tbl) %like% "^(specimen date|specimen_date|spec_date)"][1] if (!any(class(tbl %>% pull(found)) %in% c("Date", "POSIXct"))) { stop(red(paste0("ERROR: Found column `", bold(found), "` to be used as input for `col_", type, "`, but this column contains no valid dates. Transform its values to valid dates first.")), call. = FALSE) } } else { for (i in 1:ncol(tbl)) { if (any(class(tbl %>% pull(i)) %in% c("Date", "POSIXct"))) { found <- colnames(tbl)[i] break } } } } # -- patient id if (type == "patient_id") { if (any(colnames(tbl) %like% "^(identification |patient|patid)")) { found <- colnames(tbl)[colnames(tbl) %like% "^(identification |patient|patid)"][1] } } # -- specimen if (type == "specimen") { if (any(colnames(tbl) %like% "(specimen type|spec_type)")) { found <- colnames(tbl)[colnames(tbl) %like% "(specimen type|spec_type)"][1] } else if (any(colnames(tbl) %like% "^(specimen)")) { found <- colnames(tbl)[colnames(tbl) %like% "^(specimen)"][1] } } if (!is.null(found)) { msg <- paste0("NOTE: Using column `", bold(found), "` as input for `col_", type, "`.") if (type %in% c("keyantibiotics", "specimen")) { msg <- paste(msg, "Use", bold(paste0("col_", type), " = FALSE"), "to prevent this.") } message(blue(msg)) } found } get_ab_col <- function(columns, ab) { columns[names(columns) == ab] } get_column_abx <- function(tbl, soft_dependencies = NULL, hard_dependencies = NULL, verbose = FALSE, AMC = guess_ab_col(), AMK = guess_ab_col(), AMX = guess_ab_col(), AMP = guess_ab_col(), AZM = guess_ab_col(), AZL = guess_ab_col(), ATM = guess_ab_col(), RID = guess_ab_col(), FEP = guess_ab_col(), CTX = guess_ab_col(), FOX = guess_ab_col(), CED = guess_ab_col(), CAZ = guess_ab_col(), CRO = guess_ab_col(), CXM = guess_ab_col(), CHL = guess_ab_col(), CIP = guess_ab_col(), CLR = guess_ab_col(), CLI = guess_ab_col(), FLC = guess_ab_col(), COL = guess_ab_col(), CZO = guess_ab_col(), DAP = guess_ab_col(), DOX = guess_ab_col(), ETP = guess_ab_col(), ERY = guess_ab_col(), FOS = guess_ab_col(), FUS = guess_ab_col(), GEN = guess_ab_col(), IPM = guess_ab_col(), KAN = guess_ab_col(), LVX = guess_ab_col(), LIN = guess_ab_col(), LNZ = guess_ab_col(), MEM = guess_ab_col(), MTR = guess_ab_col(), MEZ = guess_ab_col(), MNO = guess_ab_col(), MFX = guess_ab_col(), NAL = guess_ab_col(), NEO = guess_ab_col(), NET = guess_ab_col(), NIT = guess_ab_col(), NOR = guess_ab_col(), NOV = guess_ab_col(), OFX = guess_ab_col(), OXA = guess_ab_col(), PEN = guess_ab_col(), PIP = guess_ab_col(), TZP = guess_ab_col(), PLB = guess_ab_col(), PRI = guess_ab_col(), QDA = guess_ab_col(), RIF = guess_ab_col(), RXT = guess_ab_col(), SIS = guess_ab_col(), TEC = guess_ab_col(), TCY = guess_ab_col(), TIC = guess_ab_col(), TGC = guess_ab_col(), TOB = guess_ab_col(), TMP = guess_ab_col(), SXT = guess_ab_col(), VAN = guess_ab_col()) { # check columns if (identical(AMC, as.name("guess_ab_col"))) AMC <- guess_ab_col(tbl, "AMC", verbose = verbose) if (identical(AMK, as.name("guess_ab_col"))) AMK <- guess_ab_col(tbl, "AMK", verbose = verbose) if (identical(AMX, as.name("guess_ab_col"))) AMX <- guess_ab_col(tbl, "AMX", verbose = verbose) if (identical(AMP, as.name("guess_ab_col"))) AMP <- guess_ab_col(tbl, "AMP", verbose = verbose) if (identical(AZM, as.name("guess_ab_col"))) AZM <- guess_ab_col(tbl, "AZM", verbose = verbose) if (identical(AZL, as.name("guess_ab_col"))) AZL <- guess_ab_col(tbl, "AZL", verbose = verbose) if (identical(ATM, as.name("guess_ab_col"))) ATM <- guess_ab_col(tbl, "ATM", verbose = verbose) if (identical(RID, as.name("guess_ab_col"))) RID <- guess_ab_col(tbl, "RID", verbose = verbose) if (identical(FEP, as.name("guess_ab_col"))) FEP <- guess_ab_col(tbl, "FEP", verbose = verbose) if (identical(CTX, as.name("guess_ab_col"))) CTX <- guess_ab_col(tbl, "CTX", verbose = verbose) if (identical(FOX, as.name("guess_ab_col"))) FOX <- guess_ab_col(tbl, "FOX", verbose = verbose) if (identical(CED, as.name("guess_ab_col"))) CED <- guess_ab_col(tbl, "CED", verbose = verbose) if (identical(CAZ, as.name("guess_ab_col"))) CAZ <- guess_ab_col(tbl, "CAZ", verbose = verbose) if (identical(CRO, as.name("guess_ab_col"))) CRO <- guess_ab_col(tbl, "CRO", verbose = verbose) if (identical(CXM, as.name("guess_ab_col"))) CXM <- guess_ab_col(tbl, "CXM", verbose = verbose) if (identical(CHL, as.name("guess_ab_col"))) CHL <- guess_ab_col(tbl, "CHL", verbose = verbose) if (identical(CIP, as.name("guess_ab_col"))) CIP <- guess_ab_col(tbl, "CIP", verbose = verbose) if (identical(CLR, as.name("guess_ab_col"))) CLR <- guess_ab_col(tbl, "CLR", verbose = verbose) if (identical(CLI, as.name("guess_ab_col"))) CLI <- guess_ab_col(tbl, "CLI", verbose = verbose) if (identical(FLC, as.name("guess_ab_col"))) FLC <- guess_ab_col(tbl, "FLC", verbose = verbose) if (identical(COL, as.name("guess_ab_col"))) COL <- guess_ab_col(tbl, "COL", verbose = verbose) if (identical(CZO, as.name("guess_ab_col"))) CZO <- guess_ab_col(tbl, "CZO", verbose = verbose) if (identical(DAP, as.name("guess_ab_col"))) DAP <- guess_ab_col(tbl, "DAP", verbose = verbose) if (identical(DOX, as.name("guess_ab_col"))) DOX <- guess_ab_col(tbl, "DOX", verbose = verbose) if (identical(ETP, as.name("guess_ab_col"))) ETP <- guess_ab_col(tbl, "ETP", verbose = verbose) if (identical(ERY, as.name("guess_ab_col"))) ERY <- guess_ab_col(tbl, "ERY", verbose = verbose) if (identical(FOS, as.name("guess_ab_col"))) FOS <- guess_ab_col(tbl, "FOS", verbose = verbose) if (identical(FUS, as.name("guess_ab_col"))) FUS <- guess_ab_col(tbl, "FUS", verbose = verbose) if (identical(GEN, as.name("guess_ab_col"))) GEN <- guess_ab_col(tbl, "GEN", verbose = verbose) if (identical(IPM, as.name("guess_ab_col"))) IPM <- guess_ab_col(tbl, "IPM", verbose = verbose) if (identical(KAN, as.name("guess_ab_col"))) KAN <- guess_ab_col(tbl, "KAN", verbose = verbose) if (identical(LVX, as.name("guess_ab_col"))) LVX <- guess_ab_col(tbl, "LVX", verbose = verbose) if (identical(LIN, as.name("guess_ab_col"))) LIN <- guess_ab_col(tbl, "LIN", verbose = verbose) if (identical(LNZ, as.name("guess_ab_col"))) LNZ <- guess_ab_col(tbl, "LNZ", verbose = verbose) if (identical(MEM, as.name("guess_ab_col"))) MEM <- guess_ab_col(tbl, "MEM", verbose = verbose) if (identical(MTR, as.name("guess_ab_col"))) MTR <- guess_ab_col(tbl, "MTR", verbose = verbose) if (identical(MEZ, as.name("guess_ab_col"))) MEZ <- guess_ab_col(tbl, "MEZ", verbose = verbose) if (identical(MNO, as.name("guess_ab_col"))) MNO <- guess_ab_col(tbl, "MNO", verbose = verbose) if (identical(MFX, as.name("guess_ab_col"))) MFX <- guess_ab_col(tbl, "MFX", verbose = verbose) if (identical(NAL, as.name("guess_ab_col"))) NAL <- guess_ab_col(tbl, "NAL", verbose = verbose) if (identical(NEO, as.name("guess_ab_col"))) NEO <- guess_ab_col(tbl, "NEO", verbose = verbose) if (identical(NET, as.name("guess_ab_col"))) NET <- guess_ab_col(tbl, "NET", verbose = verbose) if (identical(NIT, as.name("guess_ab_col"))) NIT <- guess_ab_col(tbl, "NIT", verbose = verbose) if (identical(NOR, as.name("guess_ab_col"))) NOR <- guess_ab_col(tbl, "NOR", verbose = verbose) if (identical(NOV, as.name("guess_ab_col"))) NOV <- guess_ab_col(tbl, "NOV", verbose = verbose) if (identical(OFX, as.name("guess_ab_col"))) OFX <- guess_ab_col(tbl, "OFX", verbose = verbose) if (identical(OXA, as.name("guess_ab_col"))) OXA <- guess_ab_col(tbl, "OXA", verbose = verbose) if (identical(PEN, as.name("guess_ab_col"))) PEN <- guess_ab_col(tbl, "PEN", verbose = verbose) if (identical(PIP, as.name("guess_ab_col"))) PIP <- guess_ab_col(tbl, "PIP", verbose = verbose) if (identical(TZP, as.name("guess_ab_col"))) TZP <- guess_ab_col(tbl, "TZP", verbose = verbose) if (identical(PLB, as.name("guess_ab_col"))) PLB <- guess_ab_col(tbl, "PLB", verbose = verbose) if (identical(PRI, as.name("guess_ab_col"))) PRI <- guess_ab_col(tbl, "PRI", verbose = verbose) if (identical(QDA, as.name("guess_ab_col"))) QDA <- guess_ab_col(tbl, "QDA", verbose = verbose) if (identical(RIF, as.name("guess_ab_col"))) RIF <- guess_ab_col(tbl, "RIF", verbose = verbose) if (identical(RXT, as.name("guess_ab_col"))) RXT <- guess_ab_col(tbl, "RXT", verbose = verbose) if (identical(SIS, as.name("guess_ab_col"))) SIS <- guess_ab_col(tbl, "SIS", verbose = verbose) if (identical(TEC, as.name("guess_ab_col"))) TEC <- guess_ab_col(tbl, "TEC", verbose = verbose) if (identical(TCY, as.name("guess_ab_col"))) TCY <- guess_ab_col(tbl, "TCY", verbose = verbose) if (identical(TIC, as.name("guess_ab_col"))) TIC <- guess_ab_col(tbl, "TIC", verbose = verbose) if (identical(TGC, as.name("guess_ab_col"))) TGC <- guess_ab_col(tbl, "TGC", verbose = verbose) if (identical(TOB, as.name("guess_ab_col"))) TOB <- guess_ab_col(tbl, "TOB", verbose = verbose) if (identical(TMP, as.name("guess_ab_col"))) TMP <- guess_ab_col(tbl, "TMP", verbose = verbose) if (identical(SXT, as.name("guess_ab_col"))) SXT <- guess_ab_col(tbl, "SXT", verbose = verbose) if (identical(VAN, as.name("guess_ab_col"))) VAN <- guess_ab_col(tbl, "VAN", verbose = verbose) columns_available <- c(AMC = AMC, AMK = AMK, AMX = AMX, AMP = AMP, AZM = AZM, AZL = AZL, ATM = ATM, RID = RID, FEP = FEP, CTX = CTX, FOX = FOX, CED = CED, CAZ = CAZ, CRO = CRO, CXM = CXM, CHL = CHL, CIP = CIP, CLR = CLR, CLI = CLI, FLC = FLC, COL = COL, CZO = CZO, DAP = DAP, DOX = DOX, ETP = ETP, ERY = ERY, FOS = FOS, FUS = FUS, GEN = GEN, IPM = IPM, KAN = KAN, LVX = LVX, LIN = LIN, LNZ = LNZ, MEM = MEM, MTR = MTR, MEZ = MEZ, MNO = MNO, MFX = MFX, NAL = NAL, NEO = NEO, NET = NET, NIT = NIT, NOR = NOR, NOV = NOV, OFX = OFX, OXA = OXA, PEN = PEN, PIP = PIP, TZP = TZP, PLB = PLB, PRI = PRI, QDA = QDA, RIF = RIF, RXT = RXT, SIS = SIS, TEC = TEC, TCY = TCY, TIC = TIC, TGC = TGC, TOB = TOB, TMP = TMP, SXT = SXT, VAN = VAN) if (!is.null(hard_dependencies)) { if (!all(hard_dependencies %in% names(columns_available[!is.na(columns_available)]))) { # missing a hard dependency will return NA and consequently the data will not be analysed missing <- hard_dependencies[!hard_dependencies %in% names(columns_available[!is.na(columns_available)])] generate_warning_abs_missing(missing, any = FALSE) return(NA) } } if (!is.null(soft_dependencies)) { if (!all(soft_dependencies %in% names(columns_available[!is.na(columns_available)]))) { # missing a soft dependency may lower the reliability missing <- soft_dependencies[!soft_dependencies %in% names(columns_available[!is.na(columns_available)])] missing <- paste0("`", missing, "` (", ab_name(missing, tolower = TRUE), ")") warning('Reliability might be improved if these antimicrobial results would be available too: ', paste(missing, collapse = ", "), immediate. = TRUE, call. = FALSE) } } #deps <- c(soft_dependencies, hard_dependencies) #if (length(deps) > 0) { # columns_available[names(columns_available) %in% deps] #} else { columns_available #} } generate_warning_abs_missing <- function(missing, any = FALSE) { missing <- paste0("`", missing, "` (", ab_name(missing, tolower = TRUE), ")") if (any == TRUE) { any_txt <- c(" any of", "is") } else { any_txt <- c("", "are") } warning(paste0("Introducing NAs since", any_txt[1], " these antimicrobials ", any_txt[2], " required: ", paste(missing, collapse = ", ")), immediate. = TRUE, call. = FALSE) } stopifnot_installed_package <- function(package) { if (!package %in% base::rownames(utils::installed.packages())) { stop("this function requires the ", package, " package.", call. = FALSE) } } # translate strings based on inst/translations.tsv #' @importFrom dplyr %>% filter t <- function(from, language = get_locale()) { # if (getOption("AMR_locale", "en") != language) { # language <- getOption("AMR_locale", "en") # } if (is.null(language)) { return(from) } if (language %in% c("en", "")) { return(from) } df_trans <- utils::read.table(file = system.file("translations.tsv", package = "AMR"), sep = "\t", stringsAsFactors = FALSE, header = TRUE, blank.lines.skip = TRUE, fill = TRUE, strip.white = TRUE, encoding = "UTF-8", fileEncoding = "UTF-8", na.strings = c(NA, "", NULL)) if (!language %in% df_trans$lang) { stop("Unsupported language: '", language, "' - use one of: ", paste0("'", sort(unique(df_trans$lang)), "'", collapse = ", "), call. = FALSE) } df_trans <- df_trans %>% filter(lang == language) # default case sensitive if value if 'ignore.case' is missing: df_trans$ignore.case[is.na(df_trans$ignore.case)] <- FALSE # default not using regular expressions (fixed = TRUE) if 'fixed' is missing: df_trans$fixed[is.na(df_trans$fixed)] <- TRUE # check if text to look for is in one of the patterns any_form_in_patterns <- tryCatch(any(from %like% paste0("(", paste(df_trans$pattern, collapse = "|"), ")")), error = function(e) { warning("Translation not possible. Please open an issue on GitLab (https://gitlab.com/msberends/AMR/issues) or GitHub (https://github.com/msberends/AMR/issues).", call. = FALSE) return(FALSE) }) if (NROW(df_trans) == 0 | !any_form_in_patterns) { return(from) } for (i in 1:nrow(df_trans)) { from <- gsub(x = from, pattern = df_trans$pattern[i], replacement = df_trans$replacement[i], fixed = df_trans$fixed[i], ignore.case = df_trans$ignore.case[i]) } # force UTF-8 for diacritics base::enc2utf8(from) }