AMR/R/misc.R

# ==================================================================== #
# 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.gitab.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
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
}

# No export, no Rd
percent <- function(x, round = 1, force_zero = FALSE, decimal.mark = getOption("OutDec"), ...) {

  decimal.mark.options <- getOption("OutDec")
  options(OutDec = ".")

  val <- round2(x, round + 2, force_zero = FALSE) # round up 0.5
  val <- round(x = val * 100, digits = round) # remove floating point error

  if (force_zero == TRUE) {
    if (any(val == as.integer(val) & !is.na(val))) {
      # add zeroes to all integers
      val[val == as.integer(as.character(val))] <- paste0(val[val == as.integer(val)], ".", strrep(0, round))
    }
    # add extra zeroes if needed
    val_decimals <- nchar(gsub(".*[.](.*)", "\\1", as.character(val)))
    val[val_decimals < round] <- paste0(val[val_decimals < round], strrep(0, max(0, round - val_decimals)))
  }
  pct <- base::paste0(val, "%")
  pct[pct %in% c("NA%", "NaN%")] <- NA_character_
  if (decimal.mark != ".") {
    pct <- gsub(".", decimal.mark, pct, fixed = TRUE)
  }
  options(OutDec = decimal.mark.options)
  pct
}

check_available_columns <- function(tbl, col.list, info = TRUE) {
  # check columns
  col.list <- col.list[!is.na(col.list) & !is.null(col.list)]
  names(col.list) <- col.list
  col.list.bak <- col.list
  # are they available as upper case or lower case then?
  for (i in 1:length(col.list)) {
    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
    }
  }
  if (!all(col.list %in% colnames(tbl))) {
    if (info == TRUE) {
      warning('These 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,
              call. = FALSE)
    }
  }
  col.list
}

# 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
}

#' @importFrom crayon blue bold
#' @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") {
    for (i in 1:ncol(tbl)) {
      if (any(colnames(tbl) %like% "^(Specimen date)")) {
        # WHONET support
        found <- colnames(tbl)[colnames(tbl) %like% "^(Specimen date)"][1]
      } else if ("Date" %in% class(tbl %>% pull(i)) | "POSIXct" %in% class(tbl %>% pull(i))) {
        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)")) {
      found <- colnames(tbl)[colnames(tbl) %like% "(specimen 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
}