R/getWindowCounts.R

In KevinSee/STADEM: Estimate escapement past a dam with a window and trap facility

#' @title Compile Window Counts
#'
#' @description Query and compile window count results using the \code{queryWindowCnts} function.
#'
#' @author Kevin See
#'
#' @inheritParams queryWindowCnts
#' @param incl_jacks should jacks be included in the window count totals? \code{T / F}
#' @param sthd_type should window counts of steelhead be for all steelhead, or only unclipped (i.e. wild) fish? Default is \code{all}.
#'
#' @import dplyr tidyr
#' @export
#' @return NULL
#' @examples getWindowCounts(start_date = '20150301', end_date = '20150817')

getWindowCounts = function(dam = c('LWG', 'WFF', 'BON', 'TDA', 'JDA', 'MCN', 'IHR', 'LMN', 'LGS', 'PRO', 'ROZ', 'PRD', 'WAN', 'RIS', 'TUM', 'RRH', 'WEL', 'ZOS'),
                           spp = c('Chinook', 'Coho', 'Sockeye', 'Steelhead', 'Wild_Steelhead', 'Shad', 'Jack_Chinook', 'Jack_Coho', 'Jack_Sockeye', 'Jack_Steelhead', 'Lamprey', 'Bull_Trout'),
                           start_date = NULL,
                           end_date = NULL,
                           incl_jacks = F,
                           sthd_type = c('all', 'unclipped')) {

  # need a start date
  stopifnot(!is.null(start_date))

  # pull out default dam
  dam = match.arg(dam)

  # default species?
  spp = match.arg(spp)

  # include clipped steelhead in counts, or unclipped only?
  sthd_type = match.arg(sthd_type)

  if(spp == 'Steelhead' & sthd_type == 'unclipped') spp = 'Wild_Steelhead'

  # match up species code with species name
  spp_code_df = tibble(Species = c('Chinook', 'Coho', 'Sockeye', 'Steelhead', 'Wild_Steelhead', 'Shad', 'Jack_Chinook', 'Jack_Coho', 'Jack_Sockeye', 'Jack_Steelhead', 'Lamprey', 'Bull_Trout'),
                       code = c('fc', 'fk', 'fb', 'fs', 'fsw', 'fa', 'fcj', 'fkj', 'fbj', 'fsj', 'fl', 'ft'),
                       num_code = c(1,2,4,3, rep(NA, 8)))


  spp_code = spp_code_df$code[spp_code_df$Species == spp]

  win_cnts = queryWindowCnts(dam,
                             spp_code,
                             start_date,
                             end_date)

  if(!incl_jacks) win_cnts = win_cnts %>%
    tidyr::gather(Species, win_cnt, -(Year:Date)) %>%
    select(Species, everything())

  if(incl_jacks) {
    jack_code = spp_code_df$code[spp_code_df$Species == paste('Jack', spp, sep = '_')]
    jack_cnts = try(queryWindowCnts(dam,
                                    jack_code,
                                    start_date,
                                    end_date))
    stopifnot(class(jack_cnts) != 'try-error')

    adult_cnts = win_cnts
    names(adult_cnts)[match(spp, names(adult_cnts))] = 'adults'
    names(jack_cnts)[grepl(spp, names(jack_cnts))] = 'jacks'

    win_cnts = adult_cnts %>%
      full_join(jack_cnts, by = c('Year', 'Date')) %>%
      mutate_at(vars(adults, jacks),
                list(~ifelse(is.na(.), 0, .))) %>%
      mutate(win_cnt = adults + jacks) %>%
      mutate(Species = spp) %>%
      select(Species, Year, Date, win_cnt)
  }

  return(win_cnts)
}