R/juvenile_month_dynamic.R
In CVPIA-OSC/lateFallRunDSM: Structured Decision Fall Run Model for CVPIA
Defines functions
juvenile_month_dynamic
Documented in
juvenile_month_dynamic
#' Juvenile Month Dynamics
#' @param hypothesis
#' @param fish list object containing tracking matrices for juveniles, juveniles at chips, and adults in ocean
#' @param year
#' @param month
#' @param rearing_survival
#' @param migratory_survival
#' @param habitat
#' @param ..params
#' @examples
#' fish = list(juveniles = juveniles, north_delta_fish = north_delta_fish, south_delta_fish = south_delta_fish,
#' juveniles_at_chipps = juveniles_at_chipps,
#' adults_in_ocean = adults_in_ocean)
juvenile_month_dynamic <- function(hypothesis, fish, year, month, rearing_survival,
migratory_survival, habitat, ..params,
avg_ocean_transition_month, stochastic) {
juveniles <- fish$juveniles
lower_mid_sac_fish <- fish$lower_mid_sac_fish
lower_sac_fish <- fish$lower_sac_fish
upper_mid_sac_fish <- fish$upper_mid_sac_fish
sutter_fish <- fish$sutter_fish
yolo_fish <- fish$yolo_fish
san_joaquin_fish <- fish$san_joaquin_fish
north_delta_fish <- fish$north_delta_fish
south_delta_fish <- fish$south_delta_fish
juveniles_at_chipps <- fish$juveniles_at_chipps
adults_in_ocean <- fish$adults_in_ocean
if (hypothesis == 3) {
route <- lateFallRunDSM::route_alternative
route_regional <- lateFallRunDSM::route_regional_alternative
route_bypass <- lateFallRunDSM::route_bypass_alternative
}
migrants <- matrix(0, nrow = 31, ncol = 4,
dimnames = list(lateFallRunDSM::watershed_labels,
lateFallRunDSM::size_class_labels))
if (month == 11) {
# all remaining fish outmigrate
migrants <- juveniles
sutter_fish <- migrate(sutter_fish, migratory_survival$sutter, stochastic = stochastic)
upper_mid_sac_fish <- migrate(upper_mid_sac_fish + migrants[1:15, ], migratory_survival$uppermid_sac, stochastic = stochastic)
migrants[1:15, ] <- upper_mid_sac_fish + sutter_fish
lower_mid_sac_fish <- migrate(lower_mid_sac_fish + migrants[1:20, ], migratory_survival$lowermid_sac, stochastic = stochastic)
yolo_fish <- migrate(yolo_fish, migratory_survival$yolo, stochastic = stochastic)
migrants[1:20, ] <- lower_mid_sac_fish + yolo_fish
lower_sac_fish <- migrate(lower_sac_fish + migrants[1:27, ], migratory_survival$lower_sac, stochastic = stochastic)
san_joaquin_fish <- migrate(migrants[28:30, ] + san_joaquin_fish, migratory_survival$san_joaquin, stochastic = stochastic)
migrants[28:30, ] <- san_joaquin_fish
delta_fish <- route_and_rear_deltas(year = year, month = month,
migrants = round(migrants),
north_delta_fish = north_delta_fish,
south_delta_fish = south_delta_fish,
north_delta_habitat = habitat$north_delta,
south_delta_habitat = habitat$south_delta,
freeport_flows = ..params$freeport_flows,
cc_gates_days_closed = ..params$cc_gates_days_closed,
rearing_survival_delta = rearing_survival$delta,
migratory_survival_delta = migratory_survival$delta,
migratory_survival_bay_delta = migratory_survival$bay_delta,
juveniles_at_chipps = juveniles_at_chipps,
growth_rates = ..params$growth_rates,
territory_size = ..params$territory_size,
stochastic = stochastic)
juveniles_at_chipps <- delta_fish$juveniles_at_chipps
migrants_at_golden_gate <- delta_fish$migrants_at_golden_gate
} else {
if (hypothesis == 2 & month == 4) {
# send specified proportion of fry out of tributaries
leave_battle <- if (stochastic) {
rbinom(1, juveniles[3, ], ..params$prob_fry_leave)
} else {
round(juveniles[3, ] * ..params$prob_fry_leave)
}
leave_clear <- if (stochastic) {
rbinom(1, juveniles[7, ], ..params$prob_fry_leave)
} else {
round(juveniles[7, ] * ..params$prob_fry_leave)
}
juveniles[1, ] <- juveniles[1, ] + leave_battle + leave_clear
juveniles[3, ] <- juveniles[3, ] - leave_battle
juveniles[7, ] <- juveniles[7, ] - leave_clear
}
upper_sac_trib_fish <- route(year = year,
month = month,
juveniles = juveniles[1:15, ],
inchannel_habitat = habitat$inchannel[1:15],
floodplain_habitat = habitat$floodplain[1:15],
prop_pulse_flows = ..params$prop_pulse_flows[1:15, ],
.pulse_movement_intercept = ..params$.pulse_movement_intercept,
.pulse_movement_proportion_pulse = ..params$.pulse_movement_proportion_pulse,
.pulse_movement_medium = ..params$.pulse_movement_medium,
.pulse_movement_large = ..params$.pulse_movement_large,
.pulse_movement_vlarge = ..params$.pulse_movement_vlarge,
.pulse_movement_medium_pulse = ..params$.pulse_movement_medium_pulse,
.pulse_movement_large_pulse = ..params$.pulse_movement_large_pulse,
.pulse_movement_very_large_pulse = ..params$.pulse_movement_very_large_pulse,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[16, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
upper_sac_trib_rear <- rear(juveniles = upper_sac_trib_fish$inchannel,
survival_rate = rearing_survival$inchannel[1:15, ],
growth = ..params$growth_rates,
floodplain_juveniles = upper_sac_trib_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[1:15, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = ..params$weeks_flooded[1:15, month, year],
stochastic = stochastic)
juveniles[1:15, ] <- upper_sac_trib_rear$inchannel + upper_sac_trib_rear$floodplain
# route migrant fish into Upper-mid Sac Region (fish from watersheds 1:15)
# regional fish stay and rear
# or migrate further downstream or in sutter bypass
upper_mid_sac_fish <- route_regional(month = month,
year = year,
migrants = upper_mid_sac_fish + upper_sac_trib_fish$migrants,
inchannel_habitat = habitat$inchannel[16],
floodplain_habitat = habitat$floodplain[16],
prop_pulse_flows = ..params$prop_pulse_flows[16, , drop = FALSE],
migration_survival_rate = migratory_survival$uppermid_sac,
proportion_flow_bypass = ..params$proportion_flow_bypass,
detour = "sutter",
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[21, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
sutter_fish <- route_bypass(bypass_fish = sutter_fish + upper_mid_sac_fish$detoured,
bypass_habitat = habitat$sutter,
migration_survival_rate = migratory_survival$sutter,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[21, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
migrants[1:15, ] <- upper_mid_sac_fish$migrants + sutter_fish$migrants
upper_mid_sac_fish <- rear(juveniles = upper_mid_sac_fish$inchannel,
survival_rate = rearing_survival$inchannel[16, ],
growth = ..params$growth_rates,
floodplain_juveniles = upper_mid_sac_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[16, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = rep(..params$weeks_flooded[16, month, year], nrow(upper_mid_sac_fish$inchannel)),
stochastic = stochastic)
upper_mid_sac_fish <- upper_mid_sac_fish$inchannel + upper_mid_sac_fish$floodplain
sutter_fish <- rear(juveniles = sutter_fish$inchannel,
survival_rate = matrix(rep(rearing_survival$sutter, nrow(sutter_fish$inchannel)), ncol = 4, byrow = TRUE),
growth = ..params$growth_rates,
stochastic = stochastic)
# route migrant fish into Lower-mid Sac Region (fish from watersheds 18:20, and migrants from Upper-mid Sac Region)
# regional fish stay and rear
# or migrate further downstream or in yolo bypass
lower_mid_sac_trib_fish <- route(year = year,
month = month,
juveniles = juveniles[18:20, ],
inchannel_habitat = habitat$inchannel[18:20],
floodplain_habitat = habitat$floodplain[18:20],
prop_pulse_flows = ..params$prop_pulse_flows[18:20, ],
.pulse_movement_intercept = ..params$.pulse_movement_intercept,
.pulse_movement_proportion_pulse = ..params$.pulse_movement_proportion_pulse,
.pulse_movement_medium = ..params$.pulse_movement_medium,
.pulse_movement_large = ..params$.pulse_movement_large,
.pulse_movement_vlarge = ..params$.pulse_movement_vlarge,
.pulse_movement_medium_pulse = ..params$.pulse_movement_medium_pulse,
.pulse_movement_large_pulse = ..params$.pulse_movement_large_pulse,
.pulse_movement_very_large_pulse = ..params$.pulse_movement_very_large_pulse,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[24, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
lower_mid_sac_trib_rear <- rear(juveniles = lower_mid_sac_trib_fish$inchannel,
survival_rate = rearing_survival$inchannel[18:20, ],
growth = ..params$growth_rates,
floodplain_juveniles = lower_mid_sac_trib_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[18:20, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = ..params$weeks_flooded[18:20, month, year],
stochastic = stochastic)
juveniles[18:20, ] <- lower_mid_sac_trib_rear$inchannel + lower_mid_sac_trib_rear$floodplain
migrants[18:20, ] <- lower_mid_sac_trib_fish$migrants
lower_mid_sac_fish <- route_regional(month = month,
year = year,
migrants = lower_mid_sac_fish + migrants[1:20, ],
inchannel_habitat = habitat$inchannel[21],
floodplain_habitat = habitat$floodplain[21],
prop_pulse_flows = ..params$prop_pulse_flows[21, , drop = FALSE],
migration_survival_rate = migratory_survival$lowermid_sac,
proportion_flow_bypass = ..params$proportion_flow_bypass,
detour = 'yolo',
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[24, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
yolo_fish <- route_bypass(bypass_fish = yolo_fish + lower_mid_sac_fish$detoured,
bypass_habitat = habitat$yolo,
migration_survival_rate = migratory_survival$yolo,
territory_size = ..params$territory_size,
temperature_downstream = 17, # hardcoded for <18C
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
migrants[1:20, ] <- lower_mid_sac_fish$migrants + yolo_fish$migrants
lower_mid_sac_fish <- rear(juveniles = lower_mid_sac_fish$inchannel,
survival_rate = rearing_survival$inchannel[21, ],
growth = ..params$growth_rates,
floodplain_juveniles = lower_mid_sac_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[21, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = rep(..params$weeks_flooded[21, month, year], nrow(lower_mid_sac_fish$inchannel)),
stochastic = stochastic)
lower_mid_sac_fish <- lower_mid_sac_fish$inchannel + lower_mid_sac_fish$floodplain
yolo_fish <- rear(juveniles = yolo_fish$inchannel,
survival_rate = matrix(rep(rearing_survival$yolo, nrow(yolo_fish$inchannel)), ncol = 4, byrow = TRUE),
growth = ..params$growth_rates,
stochastic = stochastic)
# route migrant fish into Lower Sac Region (fish from watershed 23, and migrants from Lower-mid Sac Region)
# regional fish stay and rear
# or migrate north delta
lower_sac_trib_fish <- route(year = year,
month = month,
juveniles = juveniles[23, , drop = FALSE],
inchannel_habitat = habitat$inchannel[23],
floodplain_habitat = habitat$floodplain[23],
prop_pulse_flows = ..params$prop_pulse_flows[23, , drop = FALSE],
.pulse_movement_intercept = ..params$.pulse_movement_intercept,
.pulse_movement_proportion_pulse = ..params$.pulse_movement_proportion_pulse,
.pulse_movement_medium = ..params$.pulse_movement_medium,
.pulse_movement_large = ..params$.pulse_movement_large,
.pulse_movement_vlarge = ..params$.pulse_movement_vlarge,
.pulse_movement_medium_pulse = ..params$.pulse_movement_medium_pulse,
.pulse_movement_large_pulse = ..params$.pulse_movement_large_pulse,
.pulse_movement_very_large_pulse = ..params$.pulse_movement_very_large_pulse,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp_delta[month, year, 1],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
lower_sac_trib_rear <- rear(juveniles = lower_sac_trib_fish$inchannel,
survival_rate = rearing_survival$inchannel[23, , drop = FALSE],
growth = ..params$growth_rates,
floodplain_juveniles = lower_sac_trib_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[23, , drop = FALSE],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = ..params$weeks_flooded[23, month, year],
stochastic = stochastic)
juveniles[23, ] <- lower_sac_trib_rear$inchannel + lower_sac_trib_rear$floodplain
migrants[23, ] <- lower_sac_trib_fish$migrants
lower_sac_fish <- route_regional(month = month,
year = year,
migrants = lower_sac_fish + migrants[1:27, ],
inchannel_habitat = habitat$inchannel[24],
floodplain_habitat = habitat$floodplain[24],
prop_pulse_flows = ..params$prop_pulse_flows[24, , drop = FALSE],
migration_survival_rate = migratory_survival$lower_sac,
territory_size = ..params$territory_size,
temperature_downstream = 17, #hardcoded <18C
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
migrants[1:27, ] <- lower_sac_fish$migrants
lower_sac_fish <- rear(juveniles = lower_sac_fish$inchannel,
survival_rate = rearing_survival$inchannel[24, ],
growth = ..params$growth_rates,
floodplain_juveniles = lower_sac_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[24, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = rep(..params$weeks_flooded[24, month, year], nrow(lower_sac_fish$inchannel)),
stochastic = stochastic)
lower_sac_fish <- lower_sac_fish$inchannel + lower_sac_fish$floodplain
# route southern natal fish stay and rear or migrate downstream ------
# route migrant fish into South Delta Region (fish from watersheds 25:27)
# regional fish stay and rear
# or migrate to south delta
south_delta_trib_fish <- route(year = year,
month = month,
juveniles = juveniles[25:27, ],
inchannel_habitat = habitat$inchannel[25:27],
floodplain_habitat = habitat$floodplain[25:27],
prop_pulse_flows = ..params$prop_pulse_flows[25:27, ],
.pulse_movement_intercept = ..params$.pulse_movement_intercept,
.pulse_movement_proportion_pulse = ..params$.pulse_movement_proportion_pulse,
.pulse_movement_medium = ..params$.pulse_movement_medium,
.pulse_movement_large = ..params$.pulse_movement_large,
.pulse_movement_vlarge = ..params$.pulse_movement_vlarge,
.pulse_movement_medium_pulse = ..params$.pulse_movement_medium_pulse,
.pulse_movement_large_pulse = ..params$.pulse_movement_large_pulse,
.pulse_movement_very_large_pulse = ..params$.pulse_movement_very_large_pulse,
territory_size = ..params$territory_size,
temperature_downstream = 17, #hardcoded <18C
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
south_delta_trib_rear <- rear(juveniles = south_delta_trib_fish$inchannel,
survival_rate = rearing_survival$inchannel[25:27, ],
growth = ..params$growth_rates,
floodplain_juveniles = south_delta_trib_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[25:27, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = ..params$weeks_flooded[25:27, month, year],
stochastic = stochastic)
juveniles[25:27, ] <- south_delta_trib_rear$inchannel + south_delta_trib_rear$floodplain
migrants[25:27, ] <- south_delta_trib_fish$migrants
# route migrant fish into San Joquin River (fish from watersheds 28:30)
# regional fish stay and rear
# or migrate to south delta
san_joaquin_trib_fish <- route(year = year,
month = month,
juveniles = juveniles[28:30, ],
inchannel_habitat = habitat$inchannel[28:30],
floodplain_habitat = habitat$floodplain[28:30],
prop_pulse_flows = ..params$prop_pulse_flows[28:30, ],
.pulse_movement_intercept = ..params$.pulse_movement_intercept,
.pulse_movement_proportion_pulse = ..params$.pulse_movement_proportion_pulse,
.pulse_movement_medium = ..params$.pulse_movement_medium,
.pulse_movement_large = ..params$.pulse_movement_large,
.pulse_movement_vlarge = ..params$.pulse_movement_vlarge,
.pulse_movement_medium_pulse = ..params$.pulse_movement_medium_pulse,
.pulse_movement_large_pulse = ..params$.pulse_movement_large_pulse,
.pulse_movement_very_large_pulse = ..params$.pulse_movement_very_large_pulse,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[31, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
san_joaquin_trib_rear <- rear(juveniles = san_joaquin_trib_fish$inchannel,
survival_rate = rearing_survival$inchannel[28:30, ],
growth = ..params$growth_rates,
floodplain_juveniles = san_joaquin_trib_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[28:30, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = ..params$weeks_flooded[28:30, month, year],
stochastic = stochastic)
juveniles[28:30, ] <- san_joaquin_trib_rear$inchannel + san_joaquin_trib_rear$floodplain
san_joaquin_fish <- route_regional(month = month,
year = year,
migrants = san_joaquin_fish + san_joaquin_trib_fish$migrants,
inchannel_habitat = habitat$inchannel[31],
floodplain_habitat = habitat$floodplain[31],
prop_pulse_flows = ..params$prop_pulse_flows[31, , drop = FALSE],
migration_survival_rate = migratory_survival$san_joaquin,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[31, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
migrants[28:30, ] <- san_joaquin_fish$migrants
san_joaquin_fish <- rear(juveniles = san_joaquin_fish$inchannel,
survival_rate = rearing_survival$inchannel[31, ],
growth = ..params$growth_rates,
floodplain_juveniles = san_joaquin_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[31, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = rep(..params$weeks_flooded[31, month, year], nrow(san_joaquin_fish$inchannel)),
stochastic = stochastic)
san_joaquin_fish <- san_joaquin_fish$inchannel + san_joaquin_fish$floodplain
delta_fish <- route_and_rear_deltas(year = year, month = month,
migrants = round(migrants),
north_delta_fish = north_delta_fish,
south_delta_fish = south_delta_fish,
north_delta_habitat = habitat$north_delta,
south_delta_habitat = habitat$south_delta,
freeport_flows = ..params$freeport_flows,
cc_gates_days_closed = ..params$cc_gates_days_closed,
rearing_survival_delta = rearing_survival$delta,
migratory_survival_delta = migratory_survival$delta,
migratory_survival_bay_delta = migratory_survival$bay_delta,
juveniles_at_chipps = juveniles_at_chipps,
growth_rates = ..params$growth_rates,
territory_size = ..params$territory_size,
stochastic = stochastic)
migrants_at_golden_gate <- delta_fish$migrants_at_golden_gate
north_delta_fish <- delta_fish$north_delta_fish
south_delta_fish <- delta_fish$south_delta_fish
juveniles_at_chipps <- delta_fish$juveniles_at_chipps
}
adults_in_ocean <- adults_in_ocean + ocean_entry_success(migrants = migrants_at_golden_gate,
month = month,
avg_ocean_transition_month = avg_ocean_transition_month,
.ocean_entry_success_length = ..params$.ocean_entry_success_length,
..ocean_entry_success_int = ..params$..ocean_entry_success_int,
.ocean_entry_success_months = ..params$.ocean_entry_success_months,
stochastic = stochastic)
return(list(juveniles = juveniles,
lower_mid_sac_fish = lower_mid_sac_fish,
lower_sac_fish = lower_sac_fish,
upper_mid_sac_fish = upper_mid_sac_fish,
sutter_fish = sutter_fish,
yolo_fish = yolo_fish,
san_joaquin_fish = san_joaquin_fish,
north_delta_fish = north_delta_fish,
south_delta_fish = south_delta_fish,
juveniles_at_chipps = juveniles_at_chipps,
adults_in_ocean = adults_in_ocean)
)
}
CVPIA-OSC/lateFallRunDSM documentation built on June 30, 2022, 10:04 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions juvenile_month_dynamic
Documented in juvenile_month_dynamic
#' Juvenile Month Dynamics
#' @param hypothesis
#' @param fish list object containing tracking matrices for juveniles, juveniles at chips, and adults in ocean
#' @param year
#' @param month
#' @param rearing_survival
#' @param migratory_survival
#' @param habitat
#' @param ..params
#' @examples
#' fish = list(juveniles = juveniles, north_delta_fish = north_delta_fish, south_delta_fish = south_delta_fish,
#' juveniles_at_chipps = juveniles_at_chipps,
#' adults_in_ocean = adults_in_ocean)
juvenile_month_dynamic <- function(hypothesis, fish, year, month, rearing_survival,
migratory_survival, habitat, ..params,
avg_ocean_transition_month, stochastic) {
juveniles <- fish$juveniles
lower_mid_sac_fish <- fish$lower_mid_sac_fish
lower_sac_fish <- fish$lower_sac_fish
upper_mid_sac_fish <- fish$upper_mid_sac_fish
sutter_fish <- fish$sutter_fish
yolo_fish <- fish$yolo_fish
san_joaquin_fish <- fish$san_joaquin_fish
north_delta_fish <- fish$north_delta_fish
south_delta_fish <- fish$south_delta_fish
juveniles_at_chipps <- fish$juveniles_at_chipps
adults_in_ocean <- fish$adults_in_ocean
if (hypothesis == 3) {
route <- lateFallRunDSM::route_alternative
route_regional <- lateFallRunDSM::route_regional_alternative
route_bypass <- lateFallRunDSM::route_bypass_alternative
}
migrants <- matrix(0, nrow = 31, ncol = 4,
dimnames = list(lateFallRunDSM::watershed_labels,
lateFallRunDSM::size_class_labels))
if (month == 11) {
# all remaining fish outmigrate
migrants <- juveniles
sutter_fish <- migrate(sutter_fish, migratory_survival$sutter, stochastic = stochastic)
upper_mid_sac_fish <- migrate(upper_mid_sac_fish + migrants[1:15, ], migratory_survival$uppermid_sac, stochastic = stochastic)
migrants[1:15, ] <- upper_mid_sac_fish + sutter_fish
lower_mid_sac_fish <- migrate(lower_mid_sac_fish + migrants[1:20, ], migratory_survival$lowermid_sac, stochastic = stochastic)
yolo_fish <- migrate(yolo_fish, migratory_survival$yolo, stochastic = stochastic)
migrants[1:20, ] <- lower_mid_sac_fish + yolo_fish
lower_sac_fish <- migrate(lower_sac_fish + migrants[1:27, ], migratory_survival$lower_sac, stochastic = stochastic)
san_joaquin_fish <- migrate(migrants[28:30, ] + san_joaquin_fish, migratory_survival$san_joaquin, stochastic = stochastic)
migrants[28:30, ] <- san_joaquin_fish
delta_fish <- route_and_rear_deltas(year = year, month = month,
migrants = round(migrants),
north_delta_fish = north_delta_fish,
south_delta_fish = south_delta_fish,
north_delta_habitat = habitat$north_delta,
south_delta_habitat = habitat$south_delta,
freeport_flows = ..params$freeport_flows,
cc_gates_days_closed = ..params$cc_gates_days_closed,
rearing_survival_delta = rearing_survival$delta,
migratory_survival_delta = migratory_survival$delta,
migratory_survival_bay_delta = migratory_survival$bay_delta,
juveniles_at_chipps = juveniles_at_chipps,
growth_rates = ..params$growth_rates,
territory_size = ..params$territory_size,
stochastic = stochastic)
juveniles_at_chipps <- delta_fish$juveniles_at_chipps
migrants_at_golden_gate <- delta_fish$migrants_at_golden_gate
} else {
if (hypothesis == 2 & month == 4) {
# send specified proportion of fry out of tributaries
leave_battle <- if (stochastic) {
rbinom(1, juveniles[3, ], ..params$prob_fry_leave)
} else {
round(juveniles[3, ] * ..params$prob_fry_leave)
}
leave_clear <- if (stochastic) {
rbinom(1, juveniles[7, ], ..params$prob_fry_leave)
} else {
round(juveniles[7, ] * ..params$prob_fry_leave)
}
juveniles[1, ] <- juveniles[1, ] + leave_battle + leave_clear
juveniles[3, ] <- juveniles[3, ] - leave_battle
juveniles[7, ] <- juveniles[7, ] - leave_clear
}
upper_sac_trib_fish <- route(year = year,
month = month,
juveniles = juveniles[1:15, ],
inchannel_habitat = habitat$inchannel[1:15],
floodplain_habitat = habitat$floodplain[1:15],
prop_pulse_flows = ..params$prop_pulse_flows[1:15, ],
.pulse_movement_intercept = ..params$.pulse_movement_intercept,
.pulse_movement_proportion_pulse = ..params$.pulse_movement_proportion_pulse,
.pulse_movement_medium = ..params$.pulse_movement_medium,
.pulse_movement_large = ..params$.pulse_movement_large,
.pulse_movement_vlarge = ..params$.pulse_movement_vlarge,
.pulse_movement_medium_pulse = ..params$.pulse_movement_medium_pulse,
.pulse_movement_large_pulse = ..params$.pulse_movement_large_pulse,
.pulse_movement_very_large_pulse = ..params$.pulse_movement_very_large_pulse,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[16, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
upper_sac_trib_rear <- rear(juveniles = upper_sac_trib_fish$inchannel,
survival_rate = rearing_survival$inchannel[1:15, ],
growth = ..params$growth_rates,
floodplain_juveniles = upper_sac_trib_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[1:15, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = ..params$weeks_flooded[1:15, month, year],
stochastic = stochastic)
juveniles[1:15, ] <- upper_sac_trib_rear$inchannel + upper_sac_trib_rear$floodplain
# route migrant fish into Upper-mid Sac Region (fish from watersheds 1:15)
# regional fish stay and rear
# or migrate further downstream or in sutter bypass
upper_mid_sac_fish <- route_regional(month = month,
year = year,
migrants = upper_mid_sac_fish + upper_sac_trib_fish$migrants,
inchannel_habitat = habitat$inchannel[16],
floodplain_habitat = habitat$floodplain[16],
prop_pulse_flows = ..params$prop_pulse_flows[16, , drop = FALSE],
migration_survival_rate = migratory_survival$uppermid_sac,
proportion_flow_bypass = ..params$proportion_flow_bypass,
detour = "sutter",
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[21, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
sutter_fish <- route_bypass(bypass_fish = sutter_fish + upper_mid_sac_fish$detoured,
bypass_habitat = habitat$sutter,
migration_survival_rate = migratory_survival$sutter,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[21, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
migrants[1:15, ] <- upper_mid_sac_fish$migrants + sutter_fish$migrants
upper_mid_sac_fish <- rear(juveniles = upper_mid_sac_fish$inchannel,
survival_rate = rearing_survival$inchannel[16, ],
growth = ..params$growth_rates,
floodplain_juveniles = upper_mid_sac_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[16, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = rep(..params$weeks_flooded[16, month, year], nrow(upper_mid_sac_fish$inchannel)),
stochastic = stochastic)
upper_mid_sac_fish <- upper_mid_sac_fish$inchannel + upper_mid_sac_fish$floodplain
sutter_fish <- rear(juveniles = sutter_fish$inchannel,
survival_rate = matrix(rep(rearing_survival$sutter, nrow(sutter_fish$inchannel)), ncol = 4, byrow = TRUE),
growth = ..params$growth_rates,
stochastic = stochastic)
# route migrant fish into Lower-mid Sac Region (fish from watersheds 18:20, and migrants from Upper-mid Sac Region)
# regional fish stay and rear
# or migrate further downstream or in yolo bypass
lower_mid_sac_trib_fish <- route(year = year,
month = month,
juveniles = juveniles[18:20, ],
inchannel_habitat = habitat$inchannel[18:20],
floodplain_habitat = habitat$floodplain[18:20],
prop_pulse_flows = ..params$prop_pulse_flows[18:20, ],
.pulse_movement_intercept = ..params$.pulse_movement_intercept,
.pulse_movement_proportion_pulse = ..params$.pulse_movement_proportion_pulse,
.pulse_movement_medium = ..params$.pulse_movement_medium,
.pulse_movement_large = ..params$.pulse_movement_large,
.pulse_movement_vlarge = ..params$.pulse_movement_vlarge,
.pulse_movement_medium_pulse = ..params$.pulse_movement_medium_pulse,
.pulse_movement_large_pulse = ..params$.pulse_movement_large_pulse,
.pulse_movement_very_large_pulse = ..params$.pulse_movement_very_large_pulse,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[24, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
lower_mid_sac_trib_rear <- rear(juveniles = lower_mid_sac_trib_fish$inchannel,
survival_rate = rearing_survival$inchannel[18:20, ],
growth = ..params$growth_rates,
floodplain_juveniles = lower_mid_sac_trib_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[18:20, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = ..params$weeks_flooded[18:20, month, year],
stochastic = stochastic)
juveniles[18:20, ] <- lower_mid_sac_trib_rear$inchannel + lower_mid_sac_trib_rear$floodplain
migrants[18:20, ] <- lower_mid_sac_trib_fish$migrants
lower_mid_sac_fish <- route_regional(month = month,
year = year,
migrants = lower_mid_sac_fish + migrants[1:20, ],
inchannel_habitat = habitat$inchannel[21],
floodplain_habitat = habitat$floodplain[21],
prop_pulse_flows = ..params$prop_pulse_flows[21, , drop = FALSE],
migration_survival_rate = migratory_survival$lowermid_sac,
proportion_flow_bypass = ..params$proportion_flow_bypass,
detour = 'yolo',
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[24, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
yolo_fish <- route_bypass(bypass_fish = yolo_fish + lower_mid_sac_fish$detoured,
bypass_habitat = habitat$yolo,
migration_survival_rate = migratory_survival$yolo,
territory_size = ..params$territory_size,
temperature_downstream = 17, # hardcoded for <18C
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
migrants[1:20, ] <- lower_mid_sac_fish$migrants + yolo_fish$migrants
lower_mid_sac_fish <- rear(juveniles = lower_mid_sac_fish$inchannel,
survival_rate = rearing_survival$inchannel[21, ],
growth = ..params$growth_rates,
floodplain_juveniles = lower_mid_sac_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[21, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = rep(..params$weeks_flooded[21, month, year], nrow(lower_mid_sac_fish$inchannel)),
stochastic = stochastic)
lower_mid_sac_fish <- lower_mid_sac_fish$inchannel + lower_mid_sac_fish$floodplain
yolo_fish <- rear(juveniles = yolo_fish$inchannel,
survival_rate = matrix(rep(rearing_survival$yolo, nrow(yolo_fish$inchannel)), ncol = 4, byrow = TRUE),
growth = ..params$growth_rates,
stochastic = stochastic)
# route migrant fish into Lower Sac Region (fish from watershed 23, and migrants from Lower-mid Sac Region)
# regional fish stay and rear
# or migrate north delta
lower_sac_trib_fish <- route(year = year,
month = month,
juveniles = juveniles[23, , drop = FALSE],
inchannel_habitat = habitat$inchannel[23],
floodplain_habitat = habitat$floodplain[23],
prop_pulse_flows = ..params$prop_pulse_flows[23, , drop = FALSE],
.pulse_movement_intercept = ..params$.pulse_movement_intercept,
.pulse_movement_proportion_pulse = ..params$.pulse_movement_proportion_pulse,
.pulse_movement_medium = ..params$.pulse_movement_medium,
.pulse_movement_large = ..params$.pulse_movement_large,
.pulse_movement_vlarge = ..params$.pulse_movement_vlarge,
.pulse_movement_medium_pulse = ..params$.pulse_movement_medium_pulse,
.pulse_movement_large_pulse = ..params$.pulse_movement_large_pulse,
.pulse_movement_very_large_pulse = ..params$.pulse_movement_very_large_pulse,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp_delta[month, year, 1],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
lower_sac_trib_rear <- rear(juveniles = lower_sac_trib_fish$inchannel,
survival_rate = rearing_survival$inchannel[23, , drop = FALSE],
growth = ..params$growth_rates,
floodplain_juveniles = lower_sac_trib_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[23, , drop = FALSE],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = ..params$weeks_flooded[23, month, year],
stochastic = stochastic)
juveniles[23, ] <- lower_sac_trib_rear$inchannel + lower_sac_trib_rear$floodplain
migrants[23, ] <- lower_sac_trib_fish$migrants
lower_sac_fish <- route_regional(month = month,
year = year,
migrants = lower_sac_fish + migrants[1:27, ],
inchannel_habitat = habitat$inchannel[24],
floodplain_habitat = habitat$floodplain[24],
prop_pulse_flows = ..params$prop_pulse_flows[24, , drop = FALSE],
migration_survival_rate = migratory_survival$lower_sac,
territory_size = ..params$territory_size,
temperature_downstream = 17, #hardcoded <18C
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
migrants[1:27, ] <- lower_sac_fish$migrants
lower_sac_fish <- rear(juveniles = lower_sac_fish$inchannel,
survival_rate = rearing_survival$inchannel[24, ],
growth = ..params$growth_rates,
floodplain_juveniles = lower_sac_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[24, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = rep(..params$weeks_flooded[24, month, year], nrow(lower_sac_fish$inchannel)),
stochastic = stochastic)
lower_sac_fish <- lower_sac_fish$inchannel + lower_sac_fish$floodplain
# route southern natal fish stay and rear or migrate downstream ------
# route migrant fish into South Delta Region (fish from watersheds 25:27)
# regional fish stay and rear
# or migrate to south delta
south_delta_trib_fish <- route(year = year,
month = month,
juveniles = juveniles[25:27, ],
inchannel_habitat = habitat$inchannel[25:27],
floodplain_habitat = habitat$floodplain[25:27],
prop_pulse_flows = ..params$prop_pulse_flows[25:27, ],
.pulse_movement_intercept = ..params$.pulse_movement_intercept,
.pulse_movement_proportion_pulse = ..params$.pulse_movement_proportion_pulse,
.pulse_movement_medium = ..params$.pulse_movement_medium,
.pulse_movement_large = ..params$.pulse_movement_large,
.pulse_movement_vlarge = ..params$.pulse_movement_vlarge,
.pulse_movement_medium_pulse = ..params$.pulse_movement_medium_pulse,
.pulse_movement_large_pulse = ..params$.pulse_movement_large_pulse,
.pulse_movement_very_large_pulse = ..params$.pulse_movement_very_large_pulse,
territory_size = ..params$territory_size,
temperature_downstream = 17, #hardcoded <18C
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
south_delta_trib_rear <- rear(juveniles = south_delta_trib_fish$inchannel,
survival_rate = rearing_survival$inchannel[25:27, ],
growth = ..params$growth_rates,
floodplain_juveniles = south_delta_trib_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[25:27, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = ..params$weeks_flooded[25:27, month, year],
stochastic = stochastic)
juveniles[25:27, ] <- south_delta_trib_rear$inchannel + south_delta_trib_rear$floodplain
migrants[25:27, ] <- south_delta_trib_fish$migrants
# route migrant fish into San Joquin River (fish from watersheds 28:30)
# regional fish stay and rear
# or migrate to south delta
san_joaquin_trib_fish <- route(year = year,
month = month,
juveniles = juveniles[28:30, ],
inchannel_habitat = habitat$inchannel[28:30],
floodplain_habitat = habitat$floodplain[28:30],
prop_pulse_flows = ..params$prop_pulse_flows[28:30, ],
.pulse_movement_intercept = ..params$.pulse_movement_intercept,
.pulse_movement_proportion_pulse = ..params$.pulse_movement_proportion_pulse,
.pulse_movement_medium = ..params$.pulse_movement_medium,
.pulse_movement_large = ..params$.pulse_movement_large,
.pulse_movement_vlarge = ..params$.pulse_movement_vlarge,
.pulse_movement_medium_pulse = ..params$.pulse_movement_medium_pulse,
.pulse_movement_large_pulse = ..params$.pulse_movement_large_pulse,
.pulse_movement_very_large_pulse = ..params$.pulse_movement_very_large_pulse,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[31, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
san_joaquin_trib_rear <- rear(juveniles = san_joaquin_trib_fish$inchannel,
survival_rate = rearing_survival$inchannel[28:30, ],
growth = ..params$growth_rates,
floodplain_juveniles = san_joaquin_trib_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[28:30, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = ..params$weeks_flooded[28:30, month, year],
stochastic = stochastic)
juveniles[28:30, ] <- san_joaquin_trib_rear$inchannel + san_joaquin_trib_rear$floodplain
san_joaquin_fish <- route_regional(month = month,
year = year,
migrants = san_joaquin_fish + san_joaquin_trib_fish$migrants,
inchannel_habitat = habitat$inchannel[31],
floodplain_habitat = habitat$floodplain[31],
prop_pulse_flows = ..params$prop_pulse_flows[31, , drop = FALSE],
migration_survival_rate = migratory_survival$san_joaquin,
territory_size = ..params$territory_size,
temperature_downstream = ..params$avg_temp[31, month, year],
density_dependent_survival = ..params$density_dependent_survival,
stochastic = stochastic)
migrants[28:30, ] <- san_joaquin_fish$migrants
san_joaquin_fish <- rear(juveniles = san_joaquin_fish$inchannel,
survival_rate = rearing_survival$inchannel[31, ],
growth = ..params$growth_rates,
floodplain_juveniles = san_joaquin_fish$floodplain,
floodplain_survival_rate = rearing_survival$floodplain[31, ],
floodplain_growth = ..params$growth_rates_floodplain,
weeks_flooded = rep(..params$weeks_flooded[31, month, year], nrow(san_joaquin_fish$inchannel)),
stochastic = stochastic)
san_joaquin_fish <- san_joaquin_fish$inchannel + san_joaquin_fish$floodplain
delta_fish <- route_and_rear_deltas(year = year, month = month,
migrants = round(migrants),
north_delta_fish = north_delta_fish,
south_delta_fish = south_delta_fish,
north_delta_habitat = habitat$north_delta,
south_delta_habitat = habitat$south_delta,
freeport_flows = ..params$freeport_flows,
cc_gates_days_closed = ..params$cc_gates_days_closed,
rearing_survival_delta = rearing_survival$delta,
migratory_survival_delta = migratory_survival$delta,
migratory_survival_bay_delta = migratory_survival$bay_delta,
juveniles_at_chipps = juveniles_at_chipps,
growth_rates = ..params$growth_rates,
territory_size = ..params$territory_size,
stochastic = stochastic)
migrants_at_golden_gate <- delta_fish$migrants_at_golden_gate
north_delta_fish <- delta_fish$north_delta_fish
south_delta_fish <- delta_fish$south_delta_fish
juveniles_at_chipps <- delta_fish$juveniles_at_chipps
}
adults_in_ocean <- adults_in_ocean + ocean_entry_success(migrants = migrants_at_golden_gate,
month = month,
avg_ocean_transition_month = avg_ocean_transition_month,
.ocean_entry_success_length = ..params$.ocean_entry_success_length,
..ocean_entry_success_int = ..params$..ocean_entry_success_int,
.ocean_entry_success_months = ..params$.ocean_entry_success_months,
stochastic = stochastic)
return(list(juveniles = juveniles,
lower_mid_sac_fish = lower_mid_sac_fish,
lower_sac_fish = lower_sac_fish,
upper_mid_sac_fish = upper_mid_sac_fish,
sutter_fish = sutter_fish,
yolo_fish = yolo_fish,
san_joaquin_fish = san_joaquin_fish,
north_delta_fish = north_delta_fish,
south_delta_fish = south_delta_fish,
juveniles_at_chipps = juveniles_at_chipps,
adults_in_ocean = adults_in_ocean)
)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.