#' model bacteria generation from elk
#'
#' This function is the bacteria source-model deer The model
#' generates input for HSPF. The specific outputs from this source model
#' are loads from the beaver to land and directly to the stream
#' The load to the land is in the form of load/acre for forest
#' PLS in a sub-watershed that the source-model contributes to and
#' the hourly load to the stream in the form of a MUTSIN file. The
#' input for the model is from an ASCII text file. Use the text below
#' as a template for the input file. The symbol used for comments in
#' the input file is "***". The definitions for the symbols used in
#' the template are: YYYY is four-digit year, MM two-digit month,
#' DD is the two-digit day, ## is an integer, #.# is a floating point
#' number, and #.#E+## is a number in scientific notation
#' @param chr.file.input is the input file for the model
#' @export
wildlife.Elk <- function(chr.file.input) {
## read input files
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$parameter == "Watershed", "value"])
## land use information
lu.pasture.area.season.1 <- as.numeric(df.input$value[
df.input$parameter == "Season 1 Pasture Area in Watershed (ac)"])
lu.forest.area.season.1 <- as.numeric(df.input$value[
df.input$parameter == "Season 1 Forest Area in Watershed (ac)"])
lu.habitatarea.season.1 <- lu.pasture.area.season.1 + lu.forest.area.season.1
lu.pasture.area.season.2 <- as.numeric(df.input$value[
df.input$parameter == "Season 2 Pasture Area in Watershed (ac)"])
lu.forest.area.season.2 <- as.numeric(df.input$value[
df.input$parameter == "Season 2 Forest Area in Watershed (ac)"])
lu.habitatarea.season.2 <- lu.pasture.area.season.2 + lu.forest.area.season.2
### Percent of Landuse with Stream access
lu.pasture.percent.w.season.1 <- as.numeric(df.input$value[
df.input$parameter == "Season 1 Percent of Pasture with stream access"]) / 100
lu.forest.percent.w.season.1 <- as.numeric(df.input$value[
df.input$parameter == "Season 1 Percent of Forest with stream access"]) / 100
lu.pasture.percent.w.season.2 <- as.numeric(df.input$value[
df.input$parameter == "Season 2 Percent of Pasture with stream access"]) / 100
lu.forest.percent.w.season.2 <- as.numeric(df.input$value[
df.input$parameter == "Season 2 Percent of Forest with stream access"]) / 100
## animal information
## months for seasons
amn.months.season.1 <- as.numeric(strsplit(df.input$value[
df.input$parameter == "Season 1 Months (numbers)"], split = ",")[[1]])
amn.months.season.2 <- as.numeric(strsplit(df.input$value[
df.input$parameter == "Season 2 Months (numbers)"], split = ",")[[1]])
## Animal Densities
amn.animal.density.pasture.season.1 <- as.numeric(df.input$value[
df.input$parameter == "Season 1 Animal Density for Pasture in watershed (animal/ac)"])
amn.animal.density.forest.season.1 <- as.numeric(df.input$value[
df.input$parameter == "Season 1 Animal Density for Forest in watershed (animal/ac)"])
amn.animal.density.pasture.season.2 <- as.numeric(df.input$value[
df.input$parameter == "Season 2 Animal Density for Pasture in watershed (animal/ac)"])
amn.animal.density.forest.season.2 <- as.numeric(df.input$value[
df.input$parameter == "Season 2 Animal Density for Forest in watershed (animal/ac)"])
## Percent animals around streams
amn.percentstream.pasture.season.1 <- as.numeric(df.input$value[
df.input$parameter == "Season 1 Percent of animals on Pasture in and around streams"]) / 100
amn.percentstream.forest.season.1 <- as.numeric(df.input$value[
df.input$parameter == "Season 1 Percent of animals on Forest in and around streams"]) / 100
amn.percentstream.pasture.season.2 <- as.numeric(df.input$value[
df.input$parameter == "Season 2 Percent of animals on Pasture in and around streams"]) / 100
amn.percentstream.forest.season.2 <- as.numeric(df.input$value[
df.input$parameter == "Season 2 Percent of animals on Forest in and around streams"]) / 100
## bacteria production per animal
amn.bac.prod <- as.numeric(df.input$value[
df.input$parameter == "Bacteria Production of animal per day (orgs/day)"])
amn.SQLIM.factor <- as.numeric(df.input$value[
df.input$parameter == "SQOLIM multiplcation factor"])
## Calculations
## land use
## without stream access
lu.land.wo.stream.access.pasture.season.1 <- (1 - lu.pasture.percent.w.season.1) * lu.pasture.area.season.1
lu.land.wo.stream.access.forest.season.1 <- (1 - lu.forest.percent.w.season.1) * lu.forest.area.season.1
lu.land.wo.stream.access.total.season.1 <- lu.land.wo.stream.access.pasture.season.1 + lu.land.wo.stream.access.forest.season.1
lu.land.wo.stream.access.pasture.season.2 <- (1 - lu.pasture.percent.w.season.2) * lu.pasture.area.season.2
lu.land.wo.stream.access.forest.season.2 <- (1 - lu.forest.percent.w.season.2) * lu.forest.area.season.2
lu.land.wo.stream.access.total.season.2 <- lu.land.wo.stream.access.pasture.season.2 + lu.land.wo.stream.access.forest.season.2
## with stream access
lu.land.w.stream.access.pasture.season.1 <- lu.pasture.percent.w.season.1 * lu.pasture.area.season.1
lu.land.w.stream.access.forest.season.1 <- lu.forest.percent.w.season.1 * lu.forest.area.season.1
lu.land.w.stream.access.total.season.1 <- lu.land.w.stream.access.pasture.season.1 + lu.land.w.stream.access.forest.season.1
lu.land.w.stream.access.pasture.season.2 <- lu.pasture.percent.w.season.2 * lu.pasture.area.season.2
lu.land.w.stream.access.forest.season.2 <- lu.forest.percent.w.season.2 * lu.forest.area.season.2
lu.land.w.stream.access.total.season.2 <- lu.land.w.stream.access.pasture.season.2 + lu.land.w.stream.access.forest.season.2
## populations
## overall locations
pop.pasture.season.1 <- lu.pasture.area.season.1 * amn.animal.density.pasture.season.1
pop.forest.season.1 <- lu.forest.area.season.1 * amn.animal.density.forest.season.1
pop.total.season.1 <- pop.pasture.season.1 + pop.forest.season.1
pop.pasture.season.2 <- lu.pasture.area.season.2 * amn.animal.density.pasture.season.2
pop.forest.season.2 <- lu.forest.area.season.2 * amn.animal.density.forest.season.2
pop.total.season.2 <- pop.pasture.season.2 + pop.forest.season.2
## on-land without stream access
pop.pasture.on.land.wo.season.1 <- amn.animal.density.pasture.season.1 * lu.land.wo.stream.access.pasture.season.1
pop.forest.on.land.wo.season.1 <- amn.animal.density.pasture.season.1 * lu.land.wo.stream.access.forest.season.1
pop.total.on.land.wo.season.1 <- pop.pasture.on.land.wo.season.1 + pop.forest.on.land.wo.season.1
pop.pasture.on.land.wo.season.2 <- amn.animal.density.pasture.season.2 * lu.land.wo.stream.access.pasture.season.2
pop.forest.on.land.wo.season.2 <- amn.animal.density.pasture.season.2 * lu.land.wo.stream.access.forest.season.2
pop.total.on.land.wo.season.2 <- pop.pasture.on.land.wo.season.2 + pop.forest.on.land.wo.season.2
## with stream access
pop.pasture.w.season.1 <- amn.animal.density.pasture.season.1 * lu.land.w.stream.access.pasture.season.1
pop.forest.w.season.1 <- amn.animal.density.pasture.season.1 * lu.land.w.stream.access.forest.season.1
pop.pasture.w.season.2 <- amn.animal.density.pasture.season.2 * lu.land.w.stream.access.pasture.season.2
pop.forest.w.season.2 <- amn.animal.density.pasture.season.2 * lu.land.w.stream.access.forest.season.2
## on-land with stream access
pop.pasture.on.land.w.season.1 <- (1 - amn.percentstream.pasture.season.1) * pop.pasture.w.season.1
pop.forest.on.land.w.season.1 <- (1 - amn.percentstream.forest.season.1) * pop.forest.w.season.1
pop.total.on.land.w.season.1 <- pop.pasture.on.land.w.season.1 + pop.forest.on.land.w.season.1
pop.pasture.on.land.w.season.2 <- (1 - amn.percentstream.pasture.season.2) * pop.pasture.w.season.2
pop.forest.on.land.w.season.2 <- (1 - amn.percentstream.forest.season.2) * pop.forest.w.season.2
pop.total.on.land.w.season.2 <- pop.pasture.on.land.w.season.2 + pop.forest.on.land.w.season.2
## in stream
pop.pasture.in.stream.season.1 <- amn.percentstream.pasture.season.1 * pop.pasture.w.season.1
pop.forest.in.stream.season.1 <- amn.percentstream.forest.season.1 * pop.forest.w.season.1
pop.total.in.stream.season.1 <- pop.pasture.in.stream.season.1 + pop.forest.in.stream.season.1
pop.pasture.in.stream.season.2 <- amn.percentstream.pasture.season.2 * pop.pasture.w.season.2
pop.forest.in.stream.season.2 <- amn.percentstream.forest.season.2 * pop.forest.w.season.2
pop.total.in.stream.season.2 <- pop.pasture.in.stream.season.2 + pop.forest.in.stream.season.2
## on-land
pop.pasture.on.land.season.1 <- pop.pasture.on.land.wo.season.1 + pop.pasture.on.land.w.season.1
pop.forest.on.land.season.1 <- pop.forest.on.land.wo.season.1 + pop.forest.on.land.w.season.1
pop.total.on.land.season.1 <- pop.pasture.on.land.season.1 + pop.forest.on.land.season.1
pop.pasture.on.land.season.2 <- pop.pasture.on.land.wo.season.2 + pop.pasture.on.land.w.season.2
pop.forest.on.land.season.2 <- pop.forest.on.land.wo.season.2 + pop.forest.on.land.w.season.2
pop.total.on.land.season.2 <- pop.pasture.on.land.season.2 + pop.forest.on.land.season.2
## bacteria loads
## overall locations
bac.total.season.1 <- amn.bac.prod * pop.total.season.1
bac.pasture.season.1 <- amn.bac.prod * pop.pasture.season.1
bac.forest.season.1 <- amn.bac.prod * pop.forest.season.1
bac.total.season.2 <- amn.bac.prod * pop.total.season.2
bac.pasture.season.2 <- amn.bac.prod * pop.pasture.season.2
bac.forest.season.2 <- amn.bac.prod * pop.forest.season.2
## on land
bac.total.on.land.season.1 <- pop.total.on.land.season.1 * amn.bac.prod
bac.pasture.on.land.season.1 <- pop.pasture.on.land.season.1 * amn.bac.prod
bac.forest.on.land.season.1 <- pop.forest.on.land.season.1 * amn.bac.prod
bac.total.on.land.season.2 <- pop.total.on.land.season.2 * amn.bac.prod
bac.pasture.on.land.season.2 <- pop.pasture.on.land.season.2 * amn.bac.prod
bac.forest.on.land.season.2 <- pop.forest.on.land.season.2 * amn.bac.prod
## in stream
bac.total.in.stream.season.1 <- pop.total.in.stream.season.1 * amn.bac.prod
bac.pasture.in.stream.season.1 <- pop.pasture.in.stream.season.1 * amn.bac.prod
bac.forest.in.stream.season.1 <- pop.forest.in.stream.season.1 * amn.bac.prod
bac.total.in.stream.season.2 <- pop.total.in.stream.season.2 * amn.bac.prod
bac.pasture.in.stream.season.2 <- pop.pasture.in.stream.season.2 * amn.bac.prod
bac.forest.in.stream.season.2 <- pop.forest.in.stream.season.2 * amn.bac.prod
## accum values
accum.pasture.season.1 <- 0
accum.forest.season.1 <- 0
accum.pasture.season.2 <- 0
accum.forest.season.2 <- 0
if(lu.pasture.area.season.1 > 0) {
accum.pasture.season.1 <- bac.pasture.on.land.season.1 /
lu.pasture.area.season.1
}
if(lu.forest.area.season.1 > 0) {
accum.forest.season.1 <- bac.forest.on.land.season.1 /
lu.forest.area.season.1
}
if(lu.pasture.area.season.2 > 0) {
accum.pasture.season.2 <- bac.pasture.on.land.season.2 /
lu.pasture.area.season.2
}
if(lu.forest.area.season.2 > 0) {
accum.forest.season.2 <- bac.forest.on.land.season.2 /
lu.forest.area.season.2
}
## Assemble output data frame
## season 1
df.output.season.1 <- data.frame(
Month=format(as.POSIXct(paste0("1967-",amn.months.season.1,"-01")), format = "%b"),
pop.total=pop.total.season.1,
pop.on.land=pop.total.on.land.season.1,
pop.in.stream=pop.total.in.stream.season.1,
Bacteria.total=bac.total.season.1,
Bacteria.on.land=bac.total.on.land.season.1,
Bacteria.direct.to.stream=bac.total.in.stream.season.1,
Accum.pasture=accum.pasture.season.1,
Accum.forest=accum.forest.season.1,
Lim.pasture=amn.SQLIM.factor * accum.pasture.season.1,
Lim.forest=amn.SQLIM.factor * accum.forest.season.1,
month.order=amn.months.season.1,
stringsAsFactors=FALSE)
## season 1
df.output.season.2 <- data.frame(
Month=format(as.POSIXct(paste0("1967-",amn.months.season.2,"-01")), format = "%b"),
pop.total=pop.total.season.2,
pop.on.land=pop.total.on.land.season.2,
pop.in.stream=pop.total.in.stream.season.2,
Bacteria.total=bac.total.season.2,
Bacteria.on.land=bac.total.on.land.season.2,
Bacteria.direct.to.stream=bac.total.in.stream.season.2,
Accum.pasture=accum.pasture.season.2,
Accum.forest=accum.forest.season.2,
Lim.pasture=amn.SQLIM.factor * accum.pasture.season.2,
Lim.forest=amn.SQLIM.factor * accum.forest.season.2,
month.order=amn.months.season.2,
stringsAsFactors=FALSE)
## combine, re-order for months and drop month.order column
df.output <- rbind(df.output.season.1, df.output.season.2)
df.output <- df.output[order(df.output$month.order), ]
df.output <- df.output[, -1 * grep("month.order", names(df.output))]
## may get NaN in accum becuase of zero areas for habitat. replace these
## these NaN with 0
df.nan <- df.output[, -1]
df.nan[is.na(df.nan)] <- 0
df.output <- cbind(sub = chr.sub, Month=df.output[, "Month"], df.nan)
##
## return results
return(df.output)
}
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