# ==================================================================== # # 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% ") } #' @importFrom crayon blue bold red #' @importFrom dplyr %>% pull search_type_in_df <- function(x, type) { # try to find columns based on type found <- NULL colnames(x) <- trimws(colnames(x)) # -- mo if (type == "mo") { if ("mo" %in% lapply(x, class)) { found <- colnames(x)[lapply(x, class) == "mo"][1] } else if (any(colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$")) { found <- colnames(x)[colnames(x) %like% "^(mo|microorganism|organism|bacteria|bacterie)s?$"][1] } else if (any(colnames(x) %like% "^(microorganism|organism|bacteria|bacterie)")) { found <- colnames(x)[colnames(x) %like% "^(microorganism|organism|bacteria|bacterie)"][1] } else if (any(colnames(x) %like% "species")) { found <- colnames(x)[colnames(x) %like% "species"][1] } } # -- key antibiotics if (type == "keyantibiotics") { if (any(colnames(x) %like% "^key.*(ab|antibiotics)")) { found <- colnames(x)[colnames(x) %like% "^key.*(ab|antibiotics)"][1] } } # -- date if (type == "date") { if (any(colnames(x) %like% "^(specimen date|specimen_date|spec_date)")) { # WHONET support found <- colnames(x)[colnames(x) %like% "^(specimen date|specimen_date|spec_date)"][1] if (!any(class(x %>% 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 seq_len(ncol(x))) { if (any(class(x %>% pull(i)) %in% c("Date", "POSIXct"))) { found <- colnames(x)[i] break } } } } # -- patient id if (type == "patient_id") { if (any(colnames(x) %like% "^(identification |patient|patid)")) { found <- colnames(x)[colnames(x) %like% "^(identification |patient|patid)"][1] } } # -- specimen if (type == "specimen") { if (any(colnames(x) %like% "(specimen type|spec_type)")) { found <- colnames(x)[colnames(x) %like% "(specimen type|spec_type)"][1] } else if (any(colnames(x) %like% "^(specimen)")) { found <- colnames(x)[colnames(x) %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 } stopifnot_installed_package <- function(package) { # no "utils::installed.packages()" since it requires non-staged install since R 3.6.0 # https://developer.r-project.org/Blog/public/2019/02/14/staged-install/index.html get(".packageName", envir = asNamespace(package)) return(invisible()) } "%or%" <- function(x, y) { if (is.null(x) | is.null(y)) { if (is.null(x)) { return(y) } else { return(x) } } ifelse(!is.na(x), x, ifelse(!is.na(y), y, NA)) } class_integrity_check <- function(value, type, check_vector) { if (!all(value[!is.na(value)] %in% check_vector)) { warning(paste0("invalid ", type, ", NA generated"), call. = FALSE) value[!value %in% check_vector] <- NA } value }