R/summariseLGRtrapDaily.R

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

#' @title Summarise LGR Trap Database
#'
#' @description Summarise LGR trap database on dailiy time-step
#'
#' @author Kevin See
#'
#' @param trap_df data.frame as created by \code{readLGRtrapDB}.
#' @param spp species to summarise trap data for. Possible species are: \code{Chinook} and \code{Steelhead}.
#' @param incl_clip_sthd should clipped steelhead in the trap be included in this summary? Should match with the window counts. Default is \code{TRUE}.
#' @param sthd_B_run should numbers of B run steelhead be reported? These are defined as wild steelhead greater than 780mm in length. Default is \code{FALSE}.
#'
#' @import lubridate dplyr
#' @return NULL
#' @export
#' @examples #summariseLGRtrapDaily(readLGRtrapDB())

summariseLGRtrapDaily = function(trap_df,
                                 spp = c('Chinook', 'Steelhead'),
                                 incl_clip_sthd = TRUE,
                                 sthd_B_run = FALSE) {

  spp = match.arg(spp)

  # filter for selected species
  trap_df = trap_df %>%
    filter(Species == spp)

  # drop unclipped steelhead if only focusing on unclipped fish
  if(!incl_clip_sthd & spp == 'Steelhead') trap_df = trap_df %>%
    # use only unclipped steelhead (to match with windown counts)
    filter(LGDMarkAD == 'AI')

  # summarise by spawnyear, species and day
  lgr_trap_daily = trap_df %>%
    # mutate(SpawnYear = gsub('^SY', '', SpawnYear),
    #               SpawnYear = as.integer(SpawnYear),
    #               SpawnYear = ifelse(!is.na(SpawnYear), SpawnYear, ifelse(Species == 'Chinook', year(Date), ifelse(Species == 'Steelhead' & Date >= ymd(paste0(year(Date), '0701')), year(Date) + 1, year(Date))))) %>%
    group_by(Date) %>%
    summarize(trap_fish = length(MasterID),
              Wild.morph = sum(LGDRear=='W'),
              Hatch.morph = sum(LGDRear=='H'),
              NA.morph = sum(LGDRear %in% c('U', 'NI')),
              Wild.PBT = sum(grepl('W$', SRR)),
              HNC.PBT = sum(grepl('H$', SRR) & LGDMarkAD=='AI'),
              Hatch.PBT = sum(grepl('H$', SRR) & LGDMarkAD=='AD'),
              NA.PBT = sum(!(grepl('W$', SRR) | grepl('H$', SRR))),
              n_invalid = sum(LGDValid != 1)) %>%
    ungroup() %>%
    arrange(Date)

  if(sthd_B_run) lgr_trap_daily = lgr_trap_daily %>%
    left_join(trap_df %>%
                group_by(Date) %>%
                summarize(tot_B_run_sthd = sum(Species == 'Steelhead' & LGDFLmm >= 780 & grepl('W$', SRR))) %>%
                ungroup()) %>%
    select(Date:NA.PBT, tot_B_run_sthd, n_invalid)

  lgr_trap_daily = lgr_trap_daily %>%
    mutate(Date = ymd(Date))

  return(lgr_trap_daily)

}