library(tidyverse)
library(devtools)
library(lubridate)
rst_prop_length <- read_csv('data-raw/rst_prop_length.csv')
get_habitats <- function(df, species, watershed, rst_prop_length) {
flows <- df$mean_flow_cfs
dates <- df$date
# scaling habitat area to above the screw trap
spawn_scale <- rst_prop_length %>%
filter(river == watershed, habitat == 'spawning') %>%
pull(prop_length)
rear_scale <- rst_prop_length %>%
filter(river == watershed, habitat == 'rearing') %>%
pull(prop_length)
spawn <- cvpiaHabitat::set_spawning_habitat(watershed,
species = species,
flow = flows) * spawn_scale
fry <- cvpiaHabitat::set_instream_habitat(watershed,
species = species,
life_stage = 'fry',
flow = flows) * rear_scale
juv <- cvpiaHabitat::set_instream_habitat(watershed,
species = species,
life_stage = 'juv',
flow = flows) * rear_scale
fp <- cvpiaHabitat::set_floodplain_habitat(watershed, species, flows) * rear_scale
habitat <- data.frame(date = dates,
spawn = spawn,
fry = fry,
juv = juv,
fp = fp,
screw_trap = watershed, stringsAsFactors = FALSE)
return(habitat)
}
get_all_habitats <- function(species) {
# RBDD 1999 2016
# rbdd_habitat <- get_rbdd_habitat(species)
# Feather 1998 2016
feather_habitat <- get_habitats(cvpiaCalibration::feather_flow, species, 'Feather River', rst_prop_length)
# Tuolumne 2007 2017
# tuolumne_habitat <- get_habitats(cvpiaCalibration::tuol_flow, species, 'Tuolumne River')
# American 2013 2016
american_habitat <- get_habitats(cvpiaCalibration::amer_flow, species, 'American River', rst_prop_length)
# Battle 1998 2016
# battle_habitat <- get_habitats(cvpiaCalibration::battle_flow, species, 'Battle Creek')
# Clear 1998 2016
clear_habitat <- get_habitats(cvpiaCalibration::clear_flow, species, 'Clear Creek', rst_prop_length)
# Mok 1999 2015
mokelumne_habitat <- get_habitats(cvpiaCalibration::moke_flow, species, 'Mokelumne River', rst_prop_length)
# Stan 1998 2016
stanislaus_habitat <- get_habitats(cvpiaCalibration::stan_flow, species, 'Stanislaus River', rst_prop_length)
# Deer 1992 2010
# deer_habitat <- get_habitats(cvpiaCalibration::deer_flow, species, 'Deer Creek')
all_habitats <- bind_rows(clear_habitat, american_habitat, feather_habitat,
mokelumne_habitat, stanislaus_habitat)
return(all_habitats)
}
fall_habitats <- get_all_habitats('fr')
use_data(fall_habitats, overwrite = TRUE)
# confirm that dates align and flow record is complete
fall_habitats %>%
group_by(screw_trap) %>%
summarise(start = min(date), end = max(date), n(), months = (year(end) - year(start) + 1) * 12)
spring_habitats <- get_all_habitats('sr')
use_data(spring_habitats, overwrite = TRUE)
steelhead_habitats <- get_all_habitats('st')
use_data(steelhead_habitats, overwrite = TRUE)
# No longer needed-------------------
get_rbdd_habitat <- function(species) {
mnths <- month(cvpiaCalibration::rbdd_flow$date)
flws <- cvpiaCalibration::rbdd_flow$mean_flow_cfs
rbdd_spawn <- purrr::map2_dbl(mnths, flws, function(month, flow) {
cvpiaHabitat::set_spawning_habitat('Upper Sacramento River',
species = species,
flow = flow, month = month)
})
rbdd_instream_fry <- purrr::map_dbl(flws, function(flow) {
cvpiaHabitat::set_instream_habitat('Upper Sacramento River',
species = species,
life_stage = 'fry',
flow = flow)
})
rbdd_instream_juv <- purrr::map_dbl(flws, function(flow) {
cvpiaHabitat::set_instream_habitat('Upper Sacramento River',
species = species,
life_stage = 'juv',
flow = flow)
})
rbdd_floodplain <- cvpiaHabitat::acres_to_square_meters(
cvpiaHabitat::set_floodplain_habitat('Upper Sacramento River', species, flws))
rbdd_habitat <- data.frame(date = cvpiaCalibration::rbdd_flow$date,
spawn = rbdd_spawn,
fry = rbdd_instream_fry,
juv = rbdd_instream_juv,
fp = rbdd_floodplain,
screw_trap = 'RBDD', stringsAsFactors = FALSE)
return(rbdd_habitat)
}
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