R/units.R

In bcgov/wqbc: Tidy Water Quality Data and Calculate Thresholds for British Columbia

# Copyright 2015 Province of British Columbia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and limitations under the License.

get_unit_multiplier <- function(x) {
  units <- c(
    "ng/L" = 10^-9, "ug/L" = 10^-6, "mg/L" = 10^-3,
    "g/L" = 1, "kg/L" = 10^3,
    "pH" = 1,
    "degC" = 1, "C" = 1, "NTU" = 1,
    "Col.unit" = 1, "Rel" = 1,
    "CFU/dL" = 1, "CFU/100mL" = 1, "CFU/mL" = 0.01, "MPN/dL" = 1,
    "MPN/100mL" = 1, "MPN/mL" = 0.01, "CFU/g" = 0.01, "MPN/g" = 0.01,
    "m" = 1,
    "uS/cm" = 1
  )
  x <- units[x]
  names(x) <- NULL
  x
}

get_unit_type <- function(x) {
  type <- list(
    "concentration" = c("ng/L", "ug/L", "mg/L", "g/L", "kg/L"),
    "pH" = "pH",
    "Colour" = c("Col.unit", "Rel"),
    "Temperature" = c("degC", "C"),
    "Turbidity" = "NTU",
    "Coli" = c("CFU/dL", "CFU/100mL", "CFU/mL", "MPN/dL", "MPN/100mL", "MPN/mL", "CFU/g", "MPN/g"),
    "Distance" = "m",
    "Conductivity" = "uS/cm"
  )

  type <- unlist(type)
  names <- sub("\\d$", "", names(type))
  values <- type
  type <- names
  names(type) <- values

  x <- type[x]
  names(x) <- NULL
  x
}

#' Convert values to different units
#'
#' @param x a numeric vector of values to convert
#' @param from units to convert from
#' @param to units to convert to
#' @param messages should messages be printed when
#'
#' @details Currently supported units for \code{from} and \code{to} are:
#' c("ng/L", "ug/L", "mg/L", "g/L", "kg/L", "pH", "degC", "C", "CFU/dL", "MPN/dL", "CFU/100mL", "MPN/100mL", "CFU/g", "MPN/g", "CFU/mL", "MPN/mL", "Col.unit", "Rel", "NTU", "m", "uS/cm")
#'
#' @return a numeric vector of the converted values
#' @export
#'
#' @examples
#'
#' convert_values(1, "ug/L", "mg/L", messages = FALSE)
#'
#' df <- data.frame(
#'   value = c(1.256, 5400000, 12300, .00098),
#'   units = c("mg/L", "ng/L", "ug/L", "g/L"),
#'   stringsAsFactors = FALSE
#' )
#' df
#'
#' df$units_mg_L <- convert_values(df$value, from = df$units, to = "mg/L", messages = FALSE)
#' df
convert_values <- function(x, from, to, messages) {
  from <- substitute_units(from, messages = messages)
  to <- substitute_units(to, messages = messages)

  x <- x * get_unit_multiplier(from) / get_unit_multiplier(to)

  bol <- from != to & get_unit_type(from) != get_unit_type(to)
  bol <- is.na(bol) | bol

  if (any(bol)) {
    warning(sum(bol), " values have inconvertible units")
    is.na(x[bol]) <- TRUE
  }
  x
}