#' @title Summarise PIT tag data
#'
#' @description Summarise night passage and re-ascension data from PIT tags at Lower Granite Dam on a daily time-step
#'
#' @author Kevin See
#'
#' @param pit_data data.frame containing PIT tag data to summarise, queried using \code{queryPITtagData}
#'
#' @import lubridate dplyr
#' @export
#' @return NULL
#' @examples summarisePITdataDaily(pit_all)
summarisePITdataDaily = function(pit_data) {
# clean up a few columns
pit_data = pit_data %>%
mutate(Period = factor(Period,
levels = c('D', 'N')),
ReAscent = if_else(!is.na(TagIdAscentCount) & TagIdAscentCount > 1,
T, F),
SpawnYear = if_else(Species %in% c('Chinook', 'Coho'),
Year,
if_else(Species == 'Steelhead' & Date >= ymd(paste0(Year, '0701')),
Year + 1,
Year)))
# summarise rates by day
lgr_night_reasc_daily = pit_data %>%
select(Species, SpawnYear, Date, TagId, RearType, Period, ReAscent) %>%
distinct() %>%
arrange(Species, SpawnYear, TagId, Date) %>%
group_by(Species, SpawnYear, Date) %>%
summarise(tot_tags = n_distinct(TagId),
day_tags = n_distinct(TagId[Period=='D']),
reascent_tags = n_distinct(TagId[ReAscent]),
tot_tags_W = n_distinct(TagId[RearType == 'W']),
day_tags_W = n_distinct(TagId[Period=='D' & RearType == 'W']),
reascent_tags_W = n_distinct(TagId[ReAscent & RearType == 'W']),
tot_tags_H = n_distinct(TagId[RearType == 'H']),
day_tags_H = n_distinct(TagId[Period=='D' & RearType == 'H']),
reascent_tags_H = n_distinct(TagId[ReAscent & RearType == 'H'])) %>%
ungroup()
return(lgr_night_reasc_daily)
}
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