R/accFunctions.R

In dcangst/fitr: Bacterial Growth Rate Estimation in R

#' transform OD values
#'
#' internal function to transform od values. -Inf, NaN values are replaced with NA.
#'
#' @param data data
#' @param od_colnr col with OD values
#' @param time_colnr col with times
#' @param trafo which trafo to use
#' @param logBase which logbase (default: 2)
#' @section Output:
#'    data.frame as input with new colum 'ODtrans'
#' @keywords fitr
.gcDataTrafo <- function(data, od_colnr, time_colnr, trafo, logBase = 2) {
  data <- data[with(data, order(data[, time_colnr])), ]

  if (trafo == "logNN0") {
    data$ODtrans <- log(data[, od_colnr] / data[1, od_colnr], logBase)
  } else if (trafo == "log") {
    data$ODtrans <- log(data[, od_colnr], logBase)
  } else if (trafo == "none") {
    data$ODtrans <- data[, od_colnr]
  } else {
    stop("invalid trafo argument!")
  }

  data$ODtrans[!is.finite(data$ODtrans)] <- NA

  return(data)
}
#' generate color gradient
#'
#' with colors from blue(low) to red(high)
#' NA get the same color as the lowest value.
#'
#' @param x a numeric vector
#' @section Output:
#'    character vector with colors
#' @keywords fitr
.rgbColorGradient <- function(x) {
  x <- x + abs(min(x, na.rm = TRUE))
  x[is.na(x)] <- 0

  color <- rgb(
    (x - min(x, na.rm = TRUE)) / (max(x, na.rm = TRUE) - min(x, na.rm = TRUE)),
    0,
    1 - (x - min(x, na.rm = TRUE)) / (max(x, na.rm = TRUE) - min(x, na.rm = TRUE)))
  return(color)
}

#' add attributes with error codes to data.frame
#'
#'
#' @param best a data.frame from \code{\link{"pickfit"}}
#' @section Output:
#'    data.frame with attribute \code{"error codes"}
#' @keywords fitr
.attrErrorCodes <- function(best, min_numP, RsqCutoff, growthCheck) {
  attr(best, "error codes") <- data.frame(
    code = c("a", "b", "c", "d"),
    description = c(
      "no valid fits",
      paste("no fits with", min_numP, "points"),
      paste("no fits with adj.r.sq >=", RsqCutoff),
      paste("no growth (growthCheck=", growthCheck, ")")
    )
  )
  return(best)
}