R/Cow_Calf_Sub_Model.R

In kbrannan/bacteriaSourceModels: Models for estimation of bacteria loads from several sources

#' model bacteria generation from cow-calf agricultural operation
#'
#' This function is the bacteria source-model cow-calf systems
#' and generates input for HSPF. The specific outputs from
#' this source model are loads from the cow-calf system to the land
#' and directly to the stream. The load to the land is in the form
#' of load/acre for each PLS in a sub-watershed that the source-model
#' contributes to and the daily load to the stream.
#' The input for the model is from an ASCII text file. For the input
#' file. The symbol used for comments in the input file is "***".
#' ":" is used to seperate parameter names or descriptions from values.
#' The function returns a data.frame with populations for different
#' locations in the sub-watershed along with the associated bacteria loads.
#' @param chr.file.input is the input file for the model
#' @export

cow.calf <- function(chr.file.input) {

  ## read input file
  df.input <- utils::read.delim(chr.file.input,
                         sep=":", comment.char="*", stringsAsFactors=FALSE,
                         header=FALSE)
  names(df.input) <- c("parameter","value")


## set values for variables

## get sub watershed number
  chr.sub <- gsub("([^0-9]){1, }", "" , df.input[df.input$parameter == "Watershed", "value"])


## land use information
  ## pasture area
  lu.pasture.area  <- as.numeric(df.input$value[
    df.input$parameter == "Pasture Area in Watershed (ac)"])
  ## forest area
  lu.forest.area  <- as.numeric(df.input$value[
    df.input$parameter == "Forest Area in Watershed (ac)"])
  ## % pasture with stream access
  lu.pasture.w    <- as.numeric(df.input$value[
    df.input$parameter == "Percent of pasture with stream access"]) / 100
  ## % forest with stream access
  lu.forest.w     <- as.numeric(df.input$value[
    df.input$parameter == "Percent of forest with stream access"]) / 100

## animal management information
  ## cow-calf pair stocking density ac/pair
  amng.sd <-
    as.numeric(df.input$value[
      df.input$parameter ==
        "Average Stocking Density for Pasture in watershed (ac/Cow-Calf pair)"])
  ## adjustment in cow size to account for calf growth in cow-calf pair
  amng.adj.size   <- as.numeric(strsplit(df.input$value[
    df.input$parameter == "Adjusted animal size"],",")[[1]])
  ## stocking schedule for pasture
  amng.in.pasture <- as.numeric(strsplit(df.input$value[
    df.input$parameter == "Pasture"],",")[[1]])
  ## stocking schedule for confinement
  amng.in.confine <- as.numeric(strsplit(df.input$value[
    df.input$parameter == "Confinement"],",")[[1]])
  ## stocking schedule for forest
  amng.in.forest  <- as.numeric(strsplit(df.input$value[
    df.input$parameter == "Forest"],",")[[1]])

## animal information
  ## bacteria production by cow #/(day-cow)
  ainfo.bac.prod <- as.numeric(
    df.input$value[df.input$parameter ==
                     "Fecal Coliform production by animal (org/(day-animal))"])
  ## SQOLIM factor > 1
  ainfo.sqolim.fac <- as.numeric(
    df.input$value[df.input$parameter ==
                     "SQOLIM multiplcation factor"])
  ## % of time cow-calf pair are in our around stream when on pasture
  ainfo.pasture.in.strm <- as.numeric(
    df.input$value[
      df.input$parameter ==
        "Percent of animals on pasture in and around streams"]) / 100
  ## % of time cow-calf pair are in our around stream when in forest
  ainfo.forest.in.strm  <- as.numeric(df.input$value[
    df.input$parameter ==
      "Percent of animals on forest in and around streams"]) / 100

## calculations
  ## pairs
  am.pairs     <- lu.pasture.area / amng.sd
  am.pairs.adj <- am.pairs * amng.adj.size

  ## pair location
  loc.pasture <- amng.in.pasture * am.pairs.adj
  loc.confine <- amng.in.confine * am.pairs.adj
  loc.forest  <- amng.in.forest * am.pairs.adj

  ## pair location with or without stream
  loc.pasture.w  <- lu.pasture.w * loc.pasture
  loc.pasture.wo <- (1 - lu.pasture.w) * loc.pasture
  loc.forest.w   <- lu.forest.w * loc.forest
  loc.forest.wo  <- (1 - lu.forest.w) * loc.forest

  ## pair location in stream or not
  loc.pasture.w.strm <- loc.pasture.w * ainfo.pasture.in.strm
  loc.pasture.w.lnd  <- loc.pasture.w * (1 - ainfo.pasture.in.strm)
  loc.forest.w.strm   <- loc.forest.w * ainfo.forest.in.strm
  loc.forest.w.lnd    <- loc.forest.w * (1 - ainfo.forest.in.strm)

  ##
  ## bacteria load calculations
  bac.total.adj   <- am.pairs.adj * ainfo.bac.prod
  bac.total <- sum(bac.total.adj)
  bac.confine <- loc.confine * ainfo.bac.prod
  bac.pasture <- loc.pasture * ainfo.bac.prod
  bac.forest  <- loc.forest * ainfo.bac.prod
  bac.pasture.w.lnd  <- loc.pasture.w.lnd * ainfo.bac.prod
  bac.pasture.wo <- loc.pasture.wo * ainfo.bac.prod
  bac.pasture.w.strm  <- loc.pasture.w.strm * ainfo.bac.prod
  bac.forest.w.lnd   <- loc.forest.w.lnd * ainfo.bac.prod
  bac.forest.wo  <- loc.forest.wo * ainfo.bac.prod
  bac.forest.w.strm  <- loc.forest.w.strm * ainfo.bac.prod

  ##
  ## bacteria loads to end points (besides confinement)
  bac.pasture.lnd <- bac.pasture.wo + bac.pasture.w.lnd
  bac.forest.lnd  <- bac.forest.wo + bac.forest.w.lnd
  bac.strm <- bac.pasture.w.strm + bac.forest.w.strm

  ##
  ## accum calc to accomadate zero land areas
  accum.pasture <- 0
  if(lu.pasture.area > 0) {
    accum.pasture <- bac.pasture.lnd / lu.pasture.area
  }
  accum.forest <- 0
  if(lu.forest.area > 0) {
    accum.forest <- bac.forest.lnd / lu.forest.area
  }

  ##
  ## SubModelOutput => df.output
  df.output <- data.frame(
    sub = chr.sub,
    Month = format(as.POSIXct(paste0("1967-",1:12,"-01")), format = "%b"),
    num.of.pairs = am.pairs * rep(1,12),
    au = am.pairs.adj,
    pairs.on.pasture.on.land = loc.pasture.wo + loc.pasture.w.lnd,
    pairs.on.pasture.in.stream = loc.pasture.w.strm,
    pairs.in.confinement = loc.confine,
    pairs.in.forest.on.land = loc.forest.wo + loc.forest.w.lnd,
    pairs.in.forest.in.stream = loc.forest.w.strm,
    Bacteria.on.pasture.on.land = bac.pasture.wo + bac.pasture.w.lnd,
    Bacteria.on.pasture.to.stream = bac.pasture.w.strm,
    Bacteria.in.confinement = bac.confine,
    Bacteria.in.forest.on.land = bac.forest.wo + bac.forest.w.lnd,
    Bacteria.in.forest.to.stream  = bac.forest.w.strm,
    Bacteria.direct.to.stream = bac.strm,
    Accum.pasture = accum.pasture,
    Accum.forest = accum.forest,
    Lim.pasture = ainfo.sqolim.fac * bac.pasture.lnd / lu.pasture.area,
    Lim.forest = ainfo.sqolim.fac * bac.forest.lnd / lu.forest.area,
    stringsAsFactors = FALSE)

  ##
  ### return results
  return(df.output)
}