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compileGRAdata.R
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compileGRAdata.R
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#' @title STADEM Data Summary
#'
#' @description Query and summarise data for STADEM
#'
#' @author Kevin See
#'
#' @inheritParams getWindowCounts
#' @param yr spawn year.
#' @param damPIT the dam code for the dam you wish to query for PIT tag data.
#' Currently only available for Lower Granite Dam (\code{GRA}).
#' @param strata_beg 3 letter code for the day of the week each weekly strata
#' should begin on. Default value is \code{'Mon'}.
#' @param last_strata_min minimum length (in days) for the final strata. Default
#' value is 3.
#' @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}.
#' @param trap_dbase data frame object containing the GRA trapping data with
#' identical data types as in tblLGDMasterCombineExportJodyW; required fields
#' include MasterID, LGDNumPIT, CollectionDate, SRR, LGDSpecies, LGDRear,
#' LGDLifeStage, LGDMarkAD, LGDValid, LGDFlmm, PTAGISSxCGRAObse.
#' @param useDARTrate should the DART query for the trap rate be used? Default
#' is \code{FALSE}, which implies the trap rate is estimated by PIT tags.
#' @param trap_rate_cv constant coefficient of variation (CV) that should be
#' applied to estimates of trap rate queried by DART. Default value is
#' \code{0}.
#' @param trap_rate_dist distributional form for trap rate prior. \code{beta}
#' returns alpha and beta parameters for beta distribution. \code{logit}
#' returns mean and standard deviation in logit space.
#'
#' @import lubridate dplyr boot
#' @export
#' @return NULL
#' @examples compileGRAdata(2012)
compileGRAdata = function(yr,
spp = c('Chinook', 'Steelhead'),
dam = c('LWG', 'WFF', 'BON', 'TDA', 'JDA', 'MCN', 'IHR', 'LMN', 'LGS', 'PRO', 'ROZ', 'PRD', 'WAN', 'RIS', 'TUM', 'RRH', 'WEL', 'ZOS'),
# dam = c('LWG'),
start_date = NULL,
end_date = NULL,
incl_jacks = NULL,
sthd_type = c('all', 'unclipped'),
damPIT = c('GRA', 'PRA'),
strata_beg = 'Mon',
last_strata_min = 3,
sthd_B_run = FALSE,
trap_dbase = NULL,
incl_trapRate = T,
useDARTrate = F,
trap_rate_cv = 0,
trap_rate_dist = c('beta', 'logit')) {
# need a start date
stopifnot(!is.null(start_date))
# if not provided, set a few defaults
spp = match.arg(spp)
dam = match.arg(dam)
damPIT = match.arg(damPIT)
# if(dam != 'LWG') {
# stop('Currently only works for Lower Granite (code LWG)')
# }
sthd_type = match.arg(sthd_type)
trap_rate_dist = match.arg(trap_rate_dist)
if(is.null(trap_dbase)) {
stop('Trapping data is not supplied.')
}
if(is.null(incl_jacks)) {
incl_jacks = ifelse(spp == 'Chinook', T, F)
}
# currently pit tag query only works for Lower Granite
try( if(!damPIT %in% c('GRA', 'PRA')) stop('PIT tag queries currently only work for Lower Granite (code GRA) and Priest Rapids (PRA)') )
cat(paste0('Compiling data for ', spp, ' spawn year ', lubridate::year(lubridate::ymd(end_date)),'\n'))
#---------------------------------------------
# query window counts
cat('Querying window counts\n')
win_cnts = getWindowCounts(dam = dam,
spp = spp,
start_date = start_date,
end_date = end_date,
incl_jacks = incl_jacks,
sthd_type = sthd_type)
#--------------------------------------------------------
# query PIT tag data from previously tagged fish
cat('Querying night passage & reascension PIT tags\n')
pit_df = queryPITtagData(damPIT = 'GRA',
spp = spp,
start_date = start_date,
end_date = end_date)
#--------------------------------------------------------
# determine weekly strata
cat('Dividing into strata\n')
week_strata = weeklyStrata(start_date = start_date,
end_date = end_date,
strata_beg = strata_beg,
last_strata_min = last_strata_min)
# read in data for Chinook and steelhead
cat('Getting LGR trap data\n')
trap_yr = trap_dbase %>%
rename(Tag.ID = LGDNumPIT) %>%
mutate(Date = lubridate::floor_date(CollectionDate, unit = 'day'),
SppCode = LGDSpecies,
Tag.ID = as.character(Tag.ID),
Tag.ID = ifelse(nchar(Tag.ID) < 3, NA, Tag.ID),
Species = ifelse(SppCode == 1, 'Chinook', ifelse(SppCode == 3, 'Steelhead', NA))) %>%
filter(Species %in% c('Chinook', 'Steelhead'), # drop data from other species, and other runs of Chinook
Date >= lubridate::ymd(lubridate::int_start(week_strata[1])), # filter out records outside dates of interest
Date < lubridate::ymd(lubridate::int_end(week_strata[length(week_strata)]) + lubridate::dseconds(1)),
LGDLifeStage == 'RF', # filter out juveniles, keep only adults
(PTAgisSxCGRAObs != 'Yes' | is.na(PTAgisSxCGRAObs) ) ) # drop sort-by-code fish
# summarise by date for particular species
trap_df = summariseLGRtrapDaily(trap_df = trap_yr,
spp = spp,
sthd_B_run = sthd_B_run)
# add week number to trap data
trap_yr$week_num = NA
for(i in 1:length(week_strata)) {
trap_yr$week_num[with(trap_yr, which(Date %within% week_strata[i]))] = i
}
#--------------------------------------------------------
if(incl_trapRate) {
# Query trap rate from DART
cat('Estimating trap rate\n')
# estimate trap rate from PIT tags
if(!useDARTrate) {
trap_rate = tagTrapRate(trap_dataframe = trap_yr,
week_strata = week_strata) %>%
# mutate(trap_open = ifelse(n_trap > 0, T, F)) %>%
left_join(tibble(Start_Date = lubridate::int_start(week_strata),
week_num = 1:length(week_strata)), by = 'week_num') %>%
mutate(Start_Date = lubridate::ymd(Start_Date)) %>%
rename(n_trap_tags = n_trap,
n_poss_tags = n_tot, # include the tag counts going into trap rate calc.
trap_rate = rate,
trap_rate_se = rate_se) %>%
mutate(trap_open = if_else(n_trap_tags > 0, T, F)) %>%
select(Start_Date,
week_num,
trap_open,
everything())
}
# to use DART trap rate instead
# impose constant CV on trap rate estimates
if(useDARTrate) {
trap_rate = queryTrapRate(week_strata,
# spp = spp,
return_weekly = T) %>%
mutate(trap_rate = ActualRateInclusiveTime,
# add some error
trap_rate_se = trap_rate * trap_rate_cv) %>%
mutate(trap_open = if_else(trap_rate > 0, T, F)) %>%
select(Start_Date,
week_num,
trap_open,
everything())
}
trap_rate = trap_rate %>%
left_join(trap_yr %>%
group_by(week_num) %>%
summarise(trap_fish = n()),
by = 'week_num') %>%
mutate(trap_open = if_else(!trap_open & trap_fish > 0,
T, trap_open),
trap_open = if_else(is.na(trap_open), F, trap_open)) %>%
select(-trap_fish)
}
# if(trap_rate_dist == 'beta') {
# trap_rate = trap_rate %>%
# # set up parameters describing trap rate as a beta distribution
# mutate(trap_alpha = ((1 - trap_rate) / trap_rate_se^2 - 1 / trap_rate) * trap_rate^2,
# trap_alpha = ifelse(trap_alpha < 0, 0.01, trap_alpha),
# trap_beta = trap_alpha * (1 / trap_rate - 1),
# trap_alpha = ifelse(trap_open, trap_alpha, 1e-12),
# trap_beta = ifelse(trap_open, trap_beta, 1)) %>%
# select(Start_Date, week_num, n_trap_tags, n_poss_tags, matches('^trap')) %>% # include the tag observations
# distinct()
# }
#
# if(trap_rate_dist == 'logit') {
# trap_rate = trap_rate %>%
# # set up parameters describing trap rate as a logit distribution
# mutate(trap_mu = ifelse(trap_open, boot::logit(trap_rate), 1e-12),
# trap_sd = ifelse(trap_open, (1 / n_trap_tags) + (1 / (n_poss_tags - n_trap_tags)), 0)) %>%
# # trap_sd = ifelse(trap_open, boot::logit(trap_rate_se), 0)) %>%
# select(Start_Date, week_num, matches('^trap')) %>%
# distinct()
# }
#--------------------------------------------------------
# comnbine window counts, PIT tag data and trap summary on daily time-step
cat('Combining daily data\n')
dam_daily = win_cnts %>%
select(-Year) %>%
full_join(summarisePITdataDaily(pit_df) %>%
select(-SpawnYear),
by = c('Species', 'Date')) %>%
mutate_at(vars(tot_tags:reascent_tags_H),
list(~ifelse(is.na(.), 0, .))) %>%
left_join(trap_df,
by = 'Date')
#------------------------------------------
# get week strata for each date
cat('Summarising by week\n')
dam_daily$week_num = NA
for(i in 1:length(week_strata)) {
dam_daily$week_num[with(dam_daily, which(Date %within% week_strata[i]))] = i
}
#------------------------------------------
# summarise by week and add trap rate
dam_weekly = dam_daily %>%
group_by(week_num) %>%
summarise(Species = unique(Species),
Start_Date = min(Date)) %>%
ungroup() %>%
left_join(dam_daily %>%
group_by(week_num) %>%
summarise_at(vars(win_cnt:n_invalid),
list(sum),
na.rm = T) %>%
ungroup() %>%
mutate_at(vars(win_cnt:n_invalid),
list(~ifelse(is.na(.), 0, .))), by = 'week_num') %>%
mutate(window_open = ifelse(win_cnt > 0, T, F)) %>%
select(Species, Start_Date, week_num, everything())
if(incl_trapRate) {
dam_weekly = addTrapRate(dam_weekly,
trap_rate,
trap_rate_dist)
}
return(list('weekStrata' = week_strata,
'trapData' = trap_yr,
'dailyData' = dam_daily,
'weeklyData' = dam_weekly))
}