R/17-downstreamMigration.R
In danStich/shadia: American shad dam passage performance standard model for R
Defines functions
downstreamMigration
Documented in
downstreamMigration
#' @title Downstream migration model
#'
#' @description Internal function used to apply a
#' series of list-based projection operations
#' to calculate the numbers of males, females, and juveniles
#' reaching each downstream production unit conditional on
#' starting production unit, migration route, and age.
#'
#' Not intended to be called directly, but visible for
#' model transparency.
#'
#' @return A list containing lists of the numbers of fish from
#' each cohort reaching consecutive production units, and the
#' number of fish from each cohort reaching the ocean.
#'
#' @export
#'
downstreamMigration <- function() {
if (river == "penobscot") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the Bay- including the
# adjustment for proportional passage through the Stillwater Branch that was
# described in Holbrook et al. (2011) and Stich et al. (2015).
# Piscataquis out-migrants that used the main-stem around Marsh Island
sPU_Pisc <- c()
sPU_Pisc[[1]] <- OpenD * (downstreamS^puRkm[[1]][1])
sPU_Pisc[[2]] <- (OpenD^2) * (downstreamS^puRkm[[1]][2])
sPU_Pisc[[3]] <- sPU_Pisc[[2]] *
(((1 - pStillwaterD) * MilfordD) + (pStillwaterD * StillwaterD * OronoD *
GilmanD)) *
(downstreamS^puRkm[[1]][3])
sPU_Pisc[[4]] <- sPU_Pisc[[3]] * HowlandD * (downstreamS^puRkm[[1]][4])
sPU_Pisc[[5]] <- sPU_Pisc[[4]] * BrownsMillD * (downstreamS^puRkm[[1]][5])
sPU_Pisc[[6]] <- sPU_Pisc[[5]] * MooseheadD * (downstreamS^puRkm[[1]][6])
sPU_Pisc[[7]] <- sPU_Pisc[[6]] * GuilfordD * (downstreamS^puRkm[[1]][7])
# Mainstem out-migrants that used the main-stem around Marsh Island
sPU_Main <- c()
sPU_Main[[1]] <- OpenD * (downstreamS^puRkm[[2]][1])
sPU_Main[[2]] <- (OpenD^2) * (downstreamS^puRkm[[2]][2])
sPU_Main[[3]] <- sPU_Pisc[[2]] * (((1 - pStillwaterD) * MilfordD) +
(pStillwaterD * StillwaterD * OronoD * GilmanD)) * (downstreamS^
puRkm[[2]][3])
sPU_Main[[4]] <- sPU_Main[[3]] * WestEnfieldD * (downstreamS^puRkm[[2]][4])
sPU_Main[[5]] <- sPU_Main[[4]] * MattaceunkD * (downstreamS^puRkm[[2]][5])
# Piscataquis out-migrants that used the Stillwater Branch around Marsh Island
sPU_PiscStill <- c()
sPU_PiscStill[[1]] <- OpenD * (downstreamS^puRkm[[3]][1])
sPU_PiscStill[[2]] <- (OpenD^2) * (downstreamS^puRkm[[3]][2])
sPU_PiscStill[[3]] <- sPU_PiscStill[[2]] *
(((1 - pStillwaterD) * MilfordD) + (pStillwaterD * StillwaterD * OronoD)) *
(downstreamS^puRkm[[3]][3])
sPU_PiscStill[[4]] <- sPU_PiscStill[[3]] * (((1 - pStillwaterD) * 1.00) +
(pStillwaterD * GilmanD)) * (downstreamS^puRkm[[3]][4])
sPU_PiscStill[[5]] <- sPU_PiscStill[[4]] * HowlandD *
(downstreamS^puRkm[[3]][5])
sPU_PiscStill[[6]] <- sPU_PiscStill[[5]] * BrownsMillD *
(downstreamS^puRkm[[3]][6])
sPU_PiscStill[[7]] <- sPU_PiscStill[[6]] * MooseheadD *
(downstreamS^puRkm[[3]][7])
sPU_PiscStill[[8]] <- sPU_PiscStill[[7]] * GuilfordD *
(downstreamS^puRkm[[3]][8])
# Mainstem out-migrants that used the Stillwater Branch around Marsh Island
sPU_MainStill <- c()
sPU_MainStill[[1]] <- OpenD * (downstreamS^puRkm[[4]][1])
sPU_MainStill[[2]] <- (OpenD^2) * (downstreamS^puRkm[[4]][2])
sPU_MainStill[[3]] <- sPU_MainStill[[2]] *
(((1 - pStillwaterD) * MilfordD) + (pStillwaterD * StillwaterD * OronoD)) *
(downstreamS^puRkm[[4]][3])
sPU_MainStill[[4]] <- sPU_MainStill[[3]] * (((1 - pStillwaterD) * 1.00) +
(pStillwaterD * GilmanD)) * (downstreamS^puRkm[[4]][4])
sPU_MainStill[[5]] <- sPU_MainStill[[4]] * WestEnfieldD *
(downstreamS^puRkm[[4]][5])
sPU_MainStill[[6]] <- sPU_MainStill[[5]] * MattaceunkD *
(downstreamS^puRkm[[4]][6])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the Bay- including the
# adjustment for proportional passage through the Stillwater Branch that was
# described in Holbrook et al. (2011) and Stich et al. (2015).
# Piscataquis out-migrants that used the main-stem around Marsh Island
sPUj_Pisc <- c()
sPUj_Pisc[[1]] <- OpenD * (downstreamS^puRkm[[1]][1])
sPUj_Pisc[[2]] <- (OpenD^2) * (downstreamS^puRkm[[1]][2])
sPUj_Pisc[[3]] <- sPUj_Pisc[[2]] *
(((1 - pStillwaterD) * MilfordDj) +
(pStillwaterD * StillwaterDj * OronoDj * GilmanDj)) * (downstreamS^
puRkm[[1]][3])
sPUj_Pisc[[4]] <- sPUj_Pisc[[3]] * HowlandDj * (downstreamS^puRkm[[1]][4])
sPUj_Pisc[[5]] <- sPUj_Pisc[[4]] * BrownsMillDj * (downstreamS^puRkm[[1]][5])
sPUj_Pisc[[6]] <- sPUj_Pisc[[5]] * MooseheadDj * (downstreamS^puRkm[[1]][6])
sPUj_Pisc[[7]] <- sPUj_Pisc[[6]] * GuilfordDj * (downstreamS^puRkm[[1]][7])
# Mainstem out-migrants that used the main-stem around Marsh Island
sPUj_Main <- c()
sPUj_Main[[1]] <- OpenD * (downstreamS^puRkm[[2]][1])
sPUj_Main[[2]] <- (OpenD^2) * (downstreamS^puRkm[[2]][2])
sPUj_Main[[3]] <- sPUj_Pisc[[2]] * (((1 - pStillwaterD) * MilfordDj) +
(pStillwaterD * StillwaterDj * OronoDj * GilmanDj)) * (downstreamS^
puRkm[[2]][3])
sPUj_Main[[4]] <- sPUj_Main[[3]] * WestEnfieldDj * (downstreamS^puRkm[[2]][4])
sPUj_Main[[5]] <- sPUj_Main[[4]] * MattaceunkDj * (downstreamS^puRkm[[2]][5])
# Piscataquis out-migrants that used the Stillwater Branch around Marsh Island
sPUj_PiscStill <- c()
sPUj_PiscStill[[1]] <- OpenD * (downstreamS^puRkm[[3]][1])
sPUj_PiscStill[[2]] <- (OpenD^2) * (downstreamS^puRkm[[3]][2])
sPUj_PiscStill[[3]] <- sPUj_PiscStill[[2]] *
(((1 - pStillwaterD) * MilfordDj) + (pStillwaterD * StillwaterDj * OronoDj)) *
(downstreamS^puRkm[[3]][3])
sPUj_PiscStill[[4]] <- sPUj_PiscStill[[3]] * (((1 - pStillwaterD) * 1.00) +
(pStillwaterD * GilmanDj)) * (downstreamS^puRkm[[3]][4])
sPUj_PiscStill[[5]] <- sPUj_PiscStill[[4]] * HowlandDj *
(downstreamS^puRkm[[3]][5])
sPUj_PiscStill[[6]] <- sPUj_PiscStill[[5]] * BrownsMillDj *
(downstreamS^puRkm[[3]][6])
sPUj_PiscStill[[7]] <- sPUj_PiscStill[[6]] * MooseheadDj *
(downstreamS^puRkm[[3]][7])
sPUj_PiscStill[[8]] <- sPUj_PiscStill[[7]] * GuilfordDj *
(downstreamS^puRkm[[3]][8])
# Mainstem out-migrants that used the Stillwater Branch around Marsh Island
sPUj_MainStill <- c()
sPUj_MainStill[[1]] <- OpenD * (downstreamS^puRkm[[4]][1])
sPUj_MainStill[[2]] <- (OpenD^2) * (downstreamS^puRkm[[4]][2])
sPUj_MainStill[[3]] <- sPUj_MainStill[[2]] *
(((1 - pStillwaterD) * MilfordDj) + (pStillwaterD * StillwaterDj * OronoDj)) *
(downstreamS^puRkm[[4]][3])
sPUj_MainStill[[4]] <- sPUj_MainStill[[3]] * (((1 - pStillwaterD) * 1.00) +
(pStillwaterD * GilmanDj)) * (downstreamS^puRkm[[4]][4])
sPUj_MainStill[[5]] <- sPUj_MainStill[[4]] * WestEnfieldDj *
(downstreamS^puRkm[[4]][5])
sPUj_MainStill[[6]] <- sPUj_MainStill[[5]] * MattaceunkDj *
(downstreamS^puRkm[[4]][6])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU from each upstream migration route
malesOut <- vector(mode = "list", length = length(males))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPU_Pisc)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU_Pisc)[, i]
}
# Mainstem-to-mainstem spawners
for (i in 1:length(sPU_Main)) {
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_Main)[, i]
}
# Stillwater-to-piscataquis spawners
for (i in 1:length(sPU_PiscStill)) {
malesOut[[3]][[i]] <- mapply("*", males[[3]], sPU_PiscStill)[, i]
}
# Stillwater-to-mainstem spawners
for (i in 1:length(sPU_MainStill)) {
malesOut[[4]][[i]] <- mapply("*", males[[4]], sPU_MainStill)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum) +
apply(data.frame(malesOut[[3]]), 1, sum) +
apply(data.frame(malesOut[[4]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU in each route
femalesOut <- vector(mode = "list", length = length(females))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPU_Pisc)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU_Pisc)[, i]
}
# Mainstem-to-mainstem spawners
for (i in 1:length(sPU_Main)) {
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_Main)[, i]
}
# Stillwater-to-piscataquis spawners
for (i in 1:length(sPU_PiscStill)) {
femalesOut[[3]][[i]] <- mapply("*", females[[3]], sPU_PiscStill)[, i]
}
# Stillwater-to-mainstem spawners
for (i in 1:length(sPU_MainStill)) {
femalesOut[[4]][[i]] <- mapply("*", females[[4]], sPU_MainStill)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum) +
apply(data.frame(femalesOut[[3]]), 1, sum) +
apply(data.frame(femalesOut[[4]]), 1, sum)
# Calculate the number of recruits reaching the ocean
# DOES NOT INCLUDE ELEVATED MORTALITY FOR JUVENILES YET, ALTHOUGH I
# THINK THOSE DATA ARE AVAILABLE
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPUj_Pisc)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]][[i]], sPUj_Pisc[i])
}
# Mainstem-to-mainstem spawners
for (i in 1:length(sPUj_Main)) {
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]][[i]], sPUj_Main[i])
}
# Stillwater-to-piscataquis spawners
for (i in 1:length(sPUj_PiscStill)) {
recruitsOut[[3]][[i]] <- mapply("*", recruits[[3]][[i]], sPUj_PiscStill[i])
}
# Stillwater-to-mainstem spawners
for (i in 1:length(sPUj_MainStill)) {
recruitsOut[[4]][[i]] <- mapply("*", recruits[[4]][[i]], sPUj_MainStill[i])
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU_Pisc = sPU_Pisc,
sPU_Main = sPU_Main,
sPU_PiscStill = sPU_PiscStill,
sPU_MainStill = sPU_MainStill,
sPUj_Pisc = sPUj_Pisc,
sPUj_Main = sPUj_Main,
sPUj_PiscStill = sPUj_PiscStill,
sPUj_MainStill = sPUj_MainStill,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "merrimack") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem at Pawtucket
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * EssexD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * (((1 - pBypassD) * PawtucketD) + pBypassD * PawtucketBypassD) *
(downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * AmoskeagD * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * HooksetD * (downstreamS^puRkm[[1]][5])
# Bypass at Pawtucket
sPU_bp <- c()
sPU_bp[[1]] <- downstreamS^puRkm[[2]][1]
sPU_bp[[2]] <- sPU_bp[[1]] * EssexD * (downstreamS^puRkm[[2]][2])
sPU_bp[[3]] <- sPU_bp[[2]] * (((1 - pBypassD) * PawtucketD) + pBypassD * PawtucketBypassD) *
(downstreamS^puRkm[[1]][3])
sPU_bp[[4]] <- sPU_bp[[3]] * AmoskeagD * (downstreamS^puRkm[[2]][4])
sPU_bp[[5]] <- sPU_bp[[4]] * HooksetD * (downstreamS^puRkm[[2]][5])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem at Pawtucket
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * EssexDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * (((1 - pBypassD) * PawtucketDj) + pBypassD * PawtucketBypassDj) *
(downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * AmoskeagDj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * HooksetDj * (downstreamS^puRkm[[1]][5])
# Bypass at Pawtucket
sPU_bpj <- c()
sPU_bpj[[1]] <- downstreamS^puRkm[[2]][1]
sPU_bpj[[2]] <- sPU_bpj[[1]] * EssexDj * (downstreamS^puRkm[[2]][2])
sPU_bpj[[3]] <- sPU_bpj[[2]] * (((1 - pBypassD) * PawtucketDj) + pBypassD * PawtucketBypassDj) *
(downstreamS^puRkm[[1]][3])
sPU_bpj[[4]] <- sPU_bpj[[3]] * AmoskeagDj * (downstreamS^puRkm[[2]][4])
sPU_bpj[[5]] <- sPU_bpj[[4]] * HooksetDj * (downstreamS^puRkm[[2]][5])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_bp)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_bp)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPUj)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]][[i]], sPUj[i])
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]][[i]], sPU_bpj[i])
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "connecticut") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# In connecticut river, need to add loss for take at males[[1]][[4]]northfield mountain
# This occurs for adults and juveniles in the turners falls head pond
# and in the vernon dam head pond. We use independent rates for adults
# and for juveniles in each of the reaches.
# Juveniles - these are summed into a single route already
# for applying carrying capacity, so we just do that one:
recruits[[1]][[4]] <- recruits[[1]][[4]] * northfield$turnersJ
recruits[[1]][[5]] <- recruits[[1]][[5]] * northfield$vernonJ
# Males, both routes:
males[[1]][[4]] <- males[[1]][[4]] * northfield$turnersA
males[[1]][[5]] <- males[[1]][[5]] * northfield$vernonA
males[[2]][[4]] <- males[[2]][[4]] * northfield$turnersA
males[[2]][[5]] <- males[[2]][[5]] * northfield$vernonA
# Females, both routes:
females[[1]][[4]] <- females[[1]][[4]] * northfield$turnersA
females[[1]][[5]] <- females[[1]][[5]] * northfield$vernonA
females[[2]][[4]] <- females[[2]][[4]] * northfield$turnersA
females[[2]][[5]] <- females[[2]][[5]] * northfield$vernonA
# In the connecticut river, all downstream fish passage
# is designed to occur through gatehouse, so we can get
# away with one migration route here.
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * HolyokeD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * CabotD * (downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * GatehouseD * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * VernonD * (downstreamS^puRkm[[1]][5])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * HolyokeDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * CabotDj * (downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * GatehouseDj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * VernonDj * (downstreamS^puRkm[[1]][5])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPUj)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]][[i]], sPUj[i])
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "susquehanna") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
sPU_jun <- vector(mode = "list", length = nPU[1])
sPU_jun[[1]] <- downstreamS^puRkm[[1]][1]
sPU_jun[[2]] <- sPU_jun[[1]] * ConowingoD * (downstreamS^puRkm[[1]][2])
sPU_jun[[3]] <- sPU_jun[[2]] * HoltwoodD * (downstreamS^puRkm[[1]][3])
sPU_jun[[4]] <- sPU_jun[[3]] * SafeHarborD * (downstreamS^puRkm[[1]][4])
sPU_jun[[5]] <- sPU_jun[[4]] * YorkHavenD * (downstreamS^puRkm[[1]][5])
sPU_jun[[6]] <- sPU_jun[[5]] * junConfluenceD * (downstreamS^puRkm[[1]][6])
sPU_wes <- vector(mode = "list", length = nPU[2])
sPU_wes[[1]] <- downstreamS^puRkm[[1]][1]
sPU_wes[[2]] <- sPU_wes[[1]] * ConowingoD * (downstreamS^puRkm[[2]][2])
sPU_wes[[3]] <- sPU_wes[[2]] * HoltwoodD * (downstreamS^puRkm[[2]][3])
sPU_wes[[4]] <- sPU_wes[[3]] * SafeHarborD * (downstreamS^puRkm[[2]][4])
sPU_wes[[5]] <- sPU_wes[[4]] * YorkHavenD * (downstreamS^puRkm[[2]][5])
sPU_wes[[6]] <- sPU_wes[[5]] * SunburyD * (downstreamS^puRkm[[2]][6])
sPU_wes[[7]] <- sPU_wes[[6]] * WilliamsportD * (downstreamS^puRkm[[2]][7])
sPU_wes[[8]] <- sPU_wes[[7]] * LockHavenD * (downstreamS^puRkm[[2]][8])
sPU_che <- vector(mode = "list", length = nPU[3])
sPU_che[[1]] <- downstreamS^puRkm[[3]][1]
sPU_che[[2]] <- sPU_che[[1]] * ConowingoD * (downstreamS^puRkm[[3]][2])
sPU_che[[3]] <- sPU_che[[2]] * HoltwoodD * (downstreamS^puRkm[[3]][3])
sPU_che[[4]] <- sPU_che[[3]] * SafeHarborD * (downstreamS^puRkm[[3]][4])
sPU_che[[5]] <- sPU_che[[4]] * YorkHavenD * (downstreamS^puRkm[[3]][5])
sPU_che[[6]] <- sPU_che[[5]] * SunburyD * (downstreamS^puRkm[[3]][6])
sPU_che[[7]] <- sPU_che[[6]] * NyD * (downstreamS^puRkm[[3]][7])
sPU_che[[8]] <- sPU_che[[7]] * ChaseHibbardD * (downstreamS^puRkm[[3]][8])
sPU_nor <- vector(mode = "list", length = nPU[4])
sPU_nor[[1]] <- downstreamS^puRkm[[1]][1]
sPU_nor[[2]] <- sPU_nor[[1]] * ConowingoD * (downstreamS^puRkm[[4]][2])
sPU_nor[[3]] <- sPU_nor[[2]] * HoltwoodD * (downstreamS^puRkm[[4]][3])
sPU_nor[[4]] <- sPU_nor[[3]] * SafeHarborD * (downstreamS^puRkm[[4]][4])
sPU_nor[[5]] <- sPU_nor[[4]] * YorkHavenD * (downstreamS^puRkm[[4]][5])
sPU_nor[[6]] <- sPU_nor[[5]] * SunburyD * (downstreamS^puRkm[[4]][6])
sPU_nor[[7]] <- sPU_nor[[6]] * NyD * (downstreamS^puRkm[[4]][7])
sPU_nor[[8]] <- sPU_nor[[7]] * RockBottomD * (downstreamS^puRkm[[4]][8])
sPU_nor[[9]] <- sPU_nor[[8]] * UnadillaReachD * (downstreamS^puRkm[[4]][9])
sPU_nor[[10]] <- sPU_nor[[9]] * ColliersvilleD * (downstreamS^puRkm[[4]][10])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
sPU_junj <- vector(mode = "list", length = nPU[1])
sPU_junj[[1]] <- downstreamS^puRkm[[1]][1]
sPU_junj[[2]] <- sPU_junj[[1]] * ConowingoDj * (downstreamS^puRkm[[1]][2])
sPU_junj[[3]] <- sPU_junj[[2]] * HoltwoodDj * (downstreamS^puRkm[[1]][3])
sPU_junj[[4]] <- sPU_junj[[3]] * SafeHarborDj * (downstreamS^puRkm[[1]][4])
sPU_junj[[5]] <- sPU_junj[[4]] * YorkHavenDj * (downstreamS^puRkm[[1]][5])
sPU_junj[[6]] <- sPU_junj[[5]] * junConfluenceDj * (downstreamS^puRkm[[1]][6])
sPU_wesj <- vector(mode = "list", length = nPU[2])
sPU_wesj[[1]] <- downstreamS^puRkm[[1]][1]
sPU_wesj[[2]] <- sPU_wesj[[1]] * ConowingoDj * (downstreamS^puRkm[[2]][2])
sPU_wesj[[3]] <- sPU_wesj[[2]] * HoltwoodDj * (downstreamS^puRkm[[2]][3])
sPU_wesj[[4]] <- sPU_wesj[[3]] * SafeHarborDj * (downstreamS^puRkm[[2]][4])
sPU_wesj[[5]] <- sPU_wesj[[4]] * YorkHavenDj * (downstreamS^puRkm[[2]][5])
sPU_wesj[[6]] <- sPU_wesj[[5]] * SunburyDj * (downstreamS^puRkm[[2]][6])
sPU_wesj[[7]] <- sPU_wesj[[6]] * WilliamsportDj * (downstreamS^puRkm[[2]][7])
sPU_wesj[[8]] <- sPU_wesj[[7]] * LockHavenDj * (downstreamS^puRkm[[2]][8])
sPU_chej <- vector(mode = "list", length = nPU[3])
sPU_chej[[1]] <- downstreamS^puRkm[[1]][1]
sPU_chej[[2]] <- sPU_chej[[1]] * ConowingoDj * (downstreamS^puRkm[[3]][2])
sPU_chej[[3]] <- sPU_chej[[2]] * HoltwoodDj * (downstreamS^puRkm[[3]][3])
sPU_chej[[4]] <- sPU_chej[[3]] * SafeHarborDj * (downstreamS^puRkm[[3]][4])
sPU_chej[[5]] <- sPU_chej[[4]] * YorkHavenDj * (downstreamS^puRkm[[3]][5])
sPU_chej[[6]] <- sPU_chej[[5]] * SunburyDj * (downstreamS^puRkm[[3]][6])
sPU_chej[[7]] <- sPU_chej[[6]] * NyDj * (downstreamS^puRkm[[3]][7])
sPU_chej[[8]] <- sPU_chej[[7]] * ChaseHibbardDj * (downstreamS^puRkm[[3]][8])
sPU_norj <- vector(mode = "list", length = nPU[4])
sPU_norj[[1]] <- downstreamS^puRkm[[1]][1]
sPU_norj[[2]] <- sPU_norj[[1]] * ConowingoDj * (downstreamS^puRkm[[4]][2])
sPU_norj[[3]] <- sPU_norj[[2]] * HoltwoodDj * (downstreamS^puRkm[[4]][3])
sPU_norj[[4]] <- sPU_norj[[3]] * SafeHarborDj * (downstreamS^puRkm[[4]][4])
sPU_norj[[5]] <- sPU_norj[[4]] * YorkHavenDj * (downstreamS^puRkm[[4]][5])
sPU_norj[[6]] <- sPU_norj[[5]] * SunburyDj * (downstreamS^puRkm[[4]][6])
sPU_norj[[7]] <- sPU_norj[[6]] * NyDj * (downstreamS^puRkm[[4]][7])
sPU_norj[[8]] <- sPU_norj[[7]] * RockBottomDj * (downstreamS^puRkm[[4]][8])
sPU_norj[[9]] <- sPU_norj[[8]] * UnadillaReachDj * (downstreamS^puRkm[[4]][9])
sPU_norj[[10]] <- sPU_norj[[9]] * ColliersvilleDj * (downstreamS^puRkm[[4]][10])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU from each upstream migration route
malesOut <- vector(mode = "list", length = length(males))
# Juniata
for (i in 1:length(sPU_jun)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU_jun)[, i]
}
# West Branch
for (i in 1:length(sPU_wes)) {
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_wes)[, i]
}
# Chemung
for (i in 1:length(sPU_che)) {
malesOut[[3]][[i]] <- mapply("*", males[[3]], sPU_che)[, i]
}
# North Branch
for (i in 1:length(sPU_nor)) {
malesOut[[4]][[i]] <- mapply("*", males[[4]], sPU_nor)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum) +
apply(data.frame(malesOut[[3]]), 1, sum) +
apply(data.frame(malesOut[[4]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
# Juniata
for (i in 1:length(sPU_jun)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU_jun)[, i]
}
# West Branch
for (i in 1:length(sPU_wes)) {
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_wes)[, i]
}
# Chemung
for (i in 1:length(sPU_che)) {
femalesOut[[3]][[i]] <- mapply("*", females[[3]], sPU_che)[, i]
}
# North Brance
for (i in 1:length(sPU_nor)) {
femalesOut[[4]][[i]] <- mapply("*", females[[4]], sPU_nor)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum) +
apply(data.frame(femalesOut[[3]]), 1, sum) +
apply(data.frame(femalesOut[[4]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Juniata
for (i in 1:length(sPU_junj)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]][[i]], sPU_junj[i])
}
# West Branch
for (i in 1:length(sPU_wesj)) {
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]][[i]], sPU_wesj[i])
}
# Chemung
for (i in 1:length(sPU_chej)) {
recruitsOut[[3]][[i]] <- mapply("*", recruits[[3]][[i]], sPU_chej[i])
}
# North Branch
for (i in 1:length(sPU_norj)) {
recruitsOut[[4]][[i]] <- mapply("*", recruits[[4]][[i]], sPU_norj[i])
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU_jun = sPU_jun,
sPU_wes = sPU_wes,
sPU_che = sPU_che,
sPU_nor = sPU_nor,
sPU_junj = sPU_junj,
sPU_wesj = sPU_wesj,
sPU_chej = sPU_chej,
sPU_norj = sPU_norj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "saco") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem at Pawtucket
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * cataractD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * springD * (downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * skeltonD * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * barmillsD * (downstreamS^puRkm[[1]][5])
sPU[[6]] <- sPU[[5]] * buxtonD * (downstreamS^puRkm[[1]][6])
sPU[[7]] <- sPU[[6]] * bonnyD * (downstreamS^puRkm[[1]][7])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem at Pawtucket
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * cataractDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * springDj * (downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * skeltonDj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * barmillsDj * (downstreamS^puRkm[[1]][5])
sPUj[[6]] <- sPUj[[5]] * buxtonDj * (downstreamS^puRkm[[1]][6])
sPUj[[7]] <- sPUj[[6]] * bonnyDj * (downstreamS^puRkm[[1]][7])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPUj)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]][[i]], sPUj[i])
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "kennebec") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * lockwoodD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * hydrokennD * (downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * shawmutD * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * westonD * (downstreamS^puRkm[[1]][5])
# Sebasticook
sPU_seb <- c()
sPU_seb[[1]] <- downstreamS^puRkm[[2]][1]
sPU_seb[[2]] <- sPU_seb[[1]] * bentonD * (downstreamS^puRkm[[2]][2])
sPU_seb[[3]] <- sPU_seb[[2]] * burnhamD * (downstreamS^puRkm[[2]][3])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * lockwoodDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * hydrokennDj * (downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * shawmutDj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * westonDj * (downstreamS^puRkm[[1]][5])
# Bypass at Pawtucket
sPU_sebj <- c()
sPU_sebj[[1]] <- downstreamS^puRkm[[2]][1]
sPU_sebj[[2]] <- sPU_sebj[[1]] * bentonDj * (downstreamS^puRkm[[2]][2])
sPU_sebj[[3]] <- sPU_sebj[[2]] * burnhamDj * (downstreamS^puRkm[[2]][3])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
}
for (i in 1:length(sPU_seb)) {
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_seb)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
}
for (i in 1:length(sPU_seb)) {
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_seb)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem
recruitsOut <- vector(mode = "list", length = length(recruits))
for (i in 1:length(sPU)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]], sPUj)
}
# Sebasticook
for (i in 1:length(sPU_seb)) {
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]], sPU_sebj)
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
sPU_seb = sPU_seb,
sPU_sebj = sPU_sebj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "hudson") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Upper Hudson
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * federalD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * C01D * (downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * C02D * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * C03D * (downstreamS^puRkm[[1]][5])
sPU[[6]] <- sPU[[5]] * C04D * (downstreamS^puRkm[[1]][6])
sPU[[7]] <- sPU[[6]] * C05D * (downstreamS^puRkm[[1]][7])
sPU[[8]] <- sPU[[7]] * C06D * (downstreamS^puRkm[[1]][8])
# Mohawk
sPU_moh <- c()
sPU_moh[[1]] <- downstreamS^puRkm[[2]][1]
sPU_moh[[2]] <- sPU_moh[[1]] * federalD * (downstreamS^puRkm[[2]][2])
sPU_moh[[3]] <- sPU_moh[[2]] * E02D * (downstreamS^puRkm[[2]][3])
sPU_moh[[4]] <- sPU_moh[[3]] * E03D * (downstreamS^puRkm[[2]][4])
sPU_moh[[5]] <- sPU_moh[[4]] * E04D * (downstreamS^puRkm[[2]][5])
sPU_moh[[6]] <- sPU_moh[[5]] * E05D * (downstreamS^puRkm[[2]][6])
sPU_moh[[7]] <- sPU_moh[[6]] * E06D * (downstreamS^puRkm[[2]][7])
sPU_moh[[8]] <- sPU_moh[[7]] * E07D * (downstreamS^puRkm[[2]][8])
sPU_moh[[9]] <- sPU_moh[[8]] * E08D * (downstreamS^puRkm[[2]][9])
sPU_moh[[10]] <- sPU_moh[[9]] * E09D * (downstreamS^puRkm[[2]][10])
sPU_moh[[11]] <- sPU_moh[[10]] * E10D * (downstreamS^puRkm[[2]][11])
sPU_moh[[12]] <- sPU_moh[[11]] * E11D * (downstreamS^puRkm[[2]][12])
sPU_moh[[13]] <- sPU_moh[[12]] * E12D * (downstreamS^puRkm[[2]][13])
sPU_moh[[14]] <- sPU_moh[[13]] * E13D * (downstreamS^puRkm[[2]][14])
sPU_moh[[15]] <- sPU_moh[[14]] * E14D * (downstreamS^puRkm[[2]][15])
sPU_moh[[16]] <- sPU_moh[[15]] * E15D * (downstreamS^puRkm[[2]][16])
sPU_moh[[17]] <- sPU_moh[[16]] * E16D * (downstreamS^puRkm[[2]][17])
sPU_moh[[18]] <- sPU_moh[[17]] * E17D * (downstreamS^puRkm[[2]][18])
sPU_moh[[19]] <- sPU_moh[[18]] * E18D * (downstreamS^puRkm[[2]][19])
sPU_moh[[20]] <- sPU_moh[[19]] * E19D * (downstreamS^puRkm[[2]][20])
sPU_moh[[21]] <- sPU_moh[[20]] * E20D * (downstreamS^puRkm[[2]][21])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Upper Hudson
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * federalDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * C01Dj * (downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * C02Dj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * C03Dj * (downstreamS^puRkm[[1]][5])
sPUj[[6]] <- sPUj[[5]] * C04Dj * (downstreamS^puRkm[[1]][6])
sPUj[[7]] <- sPUj[[6]] * C05Dj * (downstreamS^puRkm[[1]][7])
sPUj[[8]] <- sPUj[[7]] * C06Dj * (downstreamS^puRkm[[1]][8])
# Bypass at Pawtucket
sPU_mohj <- c()
sPU_mohj[[1]] <- downstreamS^puRkm[[2]][1]
sPU_mohj[[2]] <- sPU_mohj[[1]] * federalDj * (downstreamS^puRkm[[2]][2])
sPU_mohj[[3]] <- sPU_mohj[[2]] * E02Dj * (downstreamS^puRkm[[2]][3])
sPU_mohj[[4]] <- sPU_mohj[[3]] * E03Dj * (downstreamS^puRkm[[2]][4])
sPU_mohj[[5]] <- sPU_mohj[[4]] * E04Dj * (downstreamS^puRkm[[2]][5])
sPU_mohj[[6]] <- sPU_mohj[[5]] * E05Dj * (downstreamS^puRkm[[2]][6])
sPU_mohj[[7]] <- sPU_mohj[[6]] * E06Dj * (downstreamS^puRkm[[2]][7])
sPU_mohj[[8]] <- sPU_mohj[[7]] * E07Dj * (downstreamS^puRkm[[2]][8])
sPU_mohj[[9]] <- sPU_mohj[[8]] * E08Dj * (downstreamS^puRkm[[2]][9])
sPU_mohj[[10]] <- sPU_mohj[[9]] * E09Dj * (downstreamS^puRkm[[2]][10])
sPU_mohj[[11]] <- sPU_mohj[[10]] * E10Dj * (downstreamS^puRkm[[2]][11])
sPU_mohj[[12]] <- sPU_mohj[[11]] * E11Dj * (downstreamS^puRkm[[2]][12])
sPU_mohj[[13]] <- sPU_mohj[[12]] * E12Dj * (downstreamS^puRkm[[2]][13])
sPU_mohj[[14]] <- sPU_mohj[[13]] * E13Dj * (downstreamS^puRkm[[2]][14])
sPU_mohj[[15]] <- sPU_mohj[[14]] * E14Dj * (downstreamS^puRkm[[2]][15])
sPU_mohj[[16]] <- sPU_mohj[[15]] * E15Dj * (downstreamS^puRkm[[2]][16])
sPU_mohj[[17]] <- sPU_mohj[[16]] * E16Dj * (downstreamS^puRkm[[2]][17])
sPU_mohj[[18]] <- sPU_mohj[[17]] * E17Dj * (downstreamS^puRkm[[2]][18])
sPU_mohj[[19]] <- sPU_mohj[[18]] * E18Dj * (downstreamS^puRkm[[2]][19])
sPU_mohj[[20]] <- sPU_mohj[[19]] * E19Dj * (downstreamS^puRkm[[2]][20])
sPU_mohj[[21]] <- sPU_mohj[[20]] * E20Dj * (downstreamS^puRkm[[2]][21])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
}
for (i in 1:length(sPU_moh)) {
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_moh)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
}
for (i in 1:length(sPU_moh)) {
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_moh)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Upper Hudson
recruitsOut <- vector(mode = "list", length = length(recruits))
for (i in 1:length(sPU)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]], sPUj)
}
# Mohawk River
for (i in 1:length(sPU_moh)) {
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]], sPU_mohj)
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
sPU_moh = sPU_moh,
sPU_mohj = sPU_mohj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "androscoggin") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * brunswickD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * pejepscotD * (downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * worumboD * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * lbarkerD * (downstreamS^puRkm[[1]][5])
sPU[[6]] <- sPU[[5]] * ubarkerD * (downstreamS^puRkm[[1]][6])
sPU[[7]] <- sPU[[6]] * littlefieldD * (downstreamS^puRkm[[1]][7])
sPU[[8]] <- sPU[[7]] * hackettD * (downstreamS^puRkm[[1]][8])
sPU[[9]] <- sPU[[8]] * marcalD * (downstreamS^puRkm[[1]][9])
sPU[[10]] <- sPU[[9]] * welchvilleD * (downstreamS^puRkm[[1]][10])
sPU[[11]] <- sPU[[10]] * parisD * (downstreamS^puRkm[[1]][11])
# Sabattus
sPU_sab <- c()
sPU_sab[[1]] <- downstreamS^puRkm[[2]][1]
sPU_sab[[2]] <- sPU_sab[[1]] * brunswickD * (downstreamS^puRkm[[2]][2])
sPU_sab[[3]] <- sPU_sab[[2]] * pejepscotD * (downstreamS^puRkm[[2]][3])
sPU_sab[[4]] <- sPU_sab[[3]] * worumboD * (downstreamS^puRkm[[2]][5])
sPU_sab[[5]] <- sPU_sab[[4]] * farwellD * (downstreamS^puRkm[[2]][5])
sPU_sab[[6]] <- sPU_sab[[5]] * fortierD * (downstreamS^puRkm[[2]][6])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * brunswickDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * pejepscotDj * (downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * worumboDj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * lbarkerDj * (downstreamS^puRkm[[1]][5])
sPUj[[6]] <- sPUj[[5]] * ubarkerDj * (downstreamS^puRkm[[1]][6])
sPUj[[7]] <- sPUj[[6]] * littlefieldDj * (downstreamS^puRkm[[1]][7])
sPUj[[8]] <- sPUj[[7]] * hackettDj * (downstreamS^puRkm[[1]][8])
sPUj[[9]] <- sPUj[[8]] * marcalDj * (downstreamS^puRkm[[1]][9])
sPUj[[10]] <- sPUj[[9]] * welchvilleDj * (downstreamS^puRkm[[1]][10])
sPUj[[11]] <- sPUj[[10]] * parisDj * (downstreamS^puRkm[[1]][11])
# Sabattus
sPU_sabj <- c()
sPU_sabj[[1]] <- downstreamS^puRkm[[2]][1]
sPU_sabj[[2]] <- sPU_sabj[[1]] * brunswickDj * (downstreamS^puRkm[[2]][2])
sPU_sabj[[3]] <- sPU_sabj[[2]] * pejepscotDj * (downstreamS^puRkm[[2]][3])
sPU_sabj[[4]] <- sPU_sabj[[3]] * worumboDj * (downstreamS^puRkm[[2]][5])
sPU_sabj[[5]] <- sPU_sabj[[4]] * farwellDj * (downstreamS^puRkm[[2]][5])
sPU_sabj[[6]] <- sPU_sabj[[5]] * fortierDj * (downstreamS^puRkm[[2]][6])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
}
for (i in 1:length(sPU_sab)) {
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_sab)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
}
for (i in 1:length(sPU_sab)) {
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_sab)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem
recruitsOut <- vector(mode = "list", length = length(recruits))
for (i in 1:length(sPU)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]], sPUj)
}
# Sabattus
for (i in 1:length(sPU_sab)) {
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]], sPU_sabj)
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
sPU_sab = sPU_sab,
sPU_sabj = sPU_sabj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
}
danStich/shadia documentation built on Nov. 2, 2023, 6:43 a.m.
R Package Documentation
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Defines functions downstreamMigration
Documented in downstreamMigration
#' @title Downstream migration model
#'
#' @description Internal function used to apply a
#' series of list-based projection operations
#' to calculate the numbers of males, females, and juveniles
#' reaching each downstream production unit conditional on
#' starting production unit, migration route, and age.
#'
#' Not intended to be called directly, but visible for
#' model transparency.
#'
#' @return A list containing lists of the numbers of fish from
#' each cohort reaching consecutive production units, and the
#' number of fish from each cohort reaching the ocean.
#'
#' @export
#'
downstreamMigration <- function() {
if (river == "penobscot") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the Bay- including the
# adjustment for proportional passage through the Stillwater Branch that was
# described in Holbrook et al. (2011) and Stich et al. (2015).
# Piscataquis out-migrants that used the main-stem around Marsh Island
sPU_Pisc <- c()
sPU_Pisc[[1]] <- OpenD * (downstreamS^puRkm[[1]][1])
sPU_Pisc[[2]] <- (OpenD^2) * (downstreamS^puRkm[[1]][2])
sPU_Pisc[[3]] <- sPU_Pisc[[2]] *
(((1 - pStillwaterD) * MilfordD) + (pStillwaterD * StillwaterD * OronoD *
GilmanD)) *
(downstreamS^puRkm[[1]][3])
sPU_Pisc[[4]] <- sPU_Pisc[[3]] * HowlandD * (downstreamS^puRkm[[1]][4])
sPU_Pisc[[5]] <- sPU_Pisc[[4]] * BrownsMillD * (downstreamS^puRkm[[1]][5])
sPU_Pisc[[6]] <- sPU_Pisc[[5]] * MooseheadD * (downstreamS^puRkm[[1]][6])
sPU_Pisc[[7]] <- sPU_Pisc[[6]] * GuilfordD * (downstreamS^puRkm[[1]][7])
# Mainstem out-migrants that used the main-stem around Marsh Island
sPU_Main <- c()
sPU_Main[[1]] <- OpenD * (downstreamS^puRkm[[2]][1])
sPU_Main[[2]] <- (OpenD^2) * (downstreamS^puRkm[[2]][2])
sPU_Main[[3]] <- sPU_Pisc[[2]] * (((1 - pStillwaterD) * MilfordD) +
(pStillwaterD * StillwaterD * OronoD * GilmanD)) * (downstreamS^
puRkm[[2]][3])
sPU_Main[[4]] <- sPU_Main[[3]] * WestEnfieldD * (downstreamS^puRkm[[2]][4])
sPU_Main[[5]] <- sPU_Main[[4]] * MattaceunkD * (downstreamS^puRkm[[2]][5])
# Piscataquis out-migrants that used the Stillwater Branch around Marsh Island
sPU_PiscStill <- c()
sPU_PiscStill[[1]] <- OpenD * (downstreamS^puRkm[[3]][1])
sPU_PiscStill[[2]] <- (OpenD^2) * (downstreamS^puRkm[[3]][2])
sPU_PiscStill[[3]] <- sPU_PiscStill[[2]] *
(((1 - pStillwaterD) * MilfordD) + (pStillwaterD * StillwaterD * OronoD)) *
(downstreamS^puRkm[[3]][3])
sPU_PiscStill[[4]] <- sPU_PiscStill[[3]] * (((1 - pStillwaterD) * 1.00) +
(pStillwaterD * GilmanD)) * (downstreamS^puRkm[[3]][4])
sPU_PiscStill[[5]] <- sPU_PiscStill[[4]] * HowlandD *
(downstreamS^puRkm[[3]][5])
sPU_PiscStill[[6]] <- sPU_PiscStill[[5]] * BrownsMillD *
(downstreamS^puRkm[[3]][6])
sPU_PiscStill[[7]] <- sPU_PiscStill[[6]] * MooseheadD *
(downstreamS^puRkm[[3]][7])
sPU_PiscStill[[8]] <- sPU_PiscStill[[7]] * GuilfordD *
(downstreamS^puRkm[[3]][8])
# Mainstem out-migrants that used the Stillwater Branch around Marsh Island
sPU_MainStill <- c()
sPU_MainStill[[1]] <- OpenD * (downstreamS^puRkm[[4]][1])
sPU_MainStill[[2]] <- (OpenD^2) * (downstreamS^puRkm[[4]][2])
sPU_MainStill[[3]] <- sPU_MainStill[[2]] *
(((1 - pStillwaterD) * MilfordD) + (pStillwaterD * StillwaterD * OronoD)) *
(downstreamS^puRkm[[4]][3])
sPU_MainStill[[4]] <- sPU_MainStill[[3]] * (((1 - pStillwaterD) * 1.00) +
(pStillwaterD * GilmanD)) * (downstreamS^puRkm[[4]][4])
sPU_MainStill[[5]] <- sPU_MainStill[[4]] * WestEnfieldD *
(downstreamS^puRkm[[4]][5])
sPU_MainStill[[6]] <- sPU_MainStill[[5]] * MattaceunkD *
(downstreamS^puRkm[[4]][6])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the Bay- including the
# adjustment for proportional passage through the Stillwater Branch that was
# described in Holbrook et al. (2011) and Stich et al. (2015).
# Piscataquis out-migrants that used the main-stem around Marsh Island
sPUj_Pisc <- c()
sPUj_Pisc[[1]] <- OpenD * (downstreamS^puRkm[[1]][1])
sPUj_Pisc[[2]] <- (OpenD^2) * (downstreamS^puRkm[[1]][2])
sPUj_Pisc[[3]] <- sPUj_Pisc[[2]] *
(((1 - pStillwaterD) * MilfordDj) +
(pStillwaterD * StillwaterDj * OronoDj * GilmanDj)) * (downstreamS^
puRkm[[1]][3])
sPUj_Pisc[[4]] <- sPUj_Pisc[[3]] * HowlandDj * (downstreamS^puRkm[[1]][4])
sPUj_Pisc[[5]] <- sPUj_Pisc[[4]] * BrownsMillDj * (downstreamS^puRkm[[1]][5])
sPUj_Pisc[[6]] <- sPUj_Pisc[[5]] * MooseheadDj * (downstreamS^puRkm[[1]][6])
sPUj_Pisc[[7]] <- sPUj_Pisc[[6]] * GuilfordDj * (downstreamS^puRkm[[1]][7])
# Mainstem out-migrants that used the main-stem around Marsh Island
sPUj_Main <- c()
sPUj_Main[[1]] <- OpenD * (downstreamS^puRkm[[2]][1])
sPUj_Main[[2]] <- (OpenD^2) * (downstreamS^puRkm[[2]][2])
sPUj_Main[[3]] <- sPUj_Pisc[[2]] * (((1 - pStillwaterD) * MilfordDj) +
(pStillwaterD * StillwaterDj * OronoDj * GilmanDj)) * (downstreamS^
puRkm[[2]][3])
sPUj_Main[[4]] <- sPUj_Main[[3]] * WestEnfieldDj * (downstreamS^puRkm[[2]][4])
sPUj_Main[[5]] <- sPUj_Main[[4]] * MattaceunkDj * (downstreamS^puRkm[[2]][5])
# Piscataquis out-migrants that used the Stillwater Branch around Marsh Island
sPUj_PiscStill <- c()
sPUj_PiscStill[[1]] <- OpenD * (downstreamS^puRkm[[3]][1])
sPUj_PiscStill[[2]] <- (OpenD^2) * (downstreamS^puRkm[[3]][2])
sPUj_PiscStill[[3]] <- sPUj_PiscStill[[2]] *
(((1 - pStillwaterD) * MilfordDj) + (pStillwaterD * StillwaterDj * OronoDj)) *
(downstreamS^puRkm[[3]][3])
sPUj_PiscStill[[4]] <- sPUj_PiscStill[[3]] * (((1 - pStillwaterD) * 1.00) +
(pStillwaterD * GilmanDj)) * (downstreamS^puRkm[[3]][4])
sPUj_PiscStill[[5]] <- sPUj_PiscStill[[4]] * HowlandDj *
(downstreamS^puRkm[[3]][5])
sPUj_PiscStill[[6]] <- sPUj_PiscStill[[5]] * BrownsMillDj *
(downstreamS^puRkm[[3]][6])
sPUj_PiscStill[[7]] <- sPUj_PiscStill[[6]] * MooseheadDj *
(downstreamS^puRkm[[3]][7])
sPUj_PiscStill[[8]] <- sPUj_PiscStill[[7]] * GuilfordDj *
(downstreamS^puRkm[[3]][8])
# Mainstem out-migrants that used the Stillwater Branch around Marsh Island
sPUj_MainStill <- c()
sPUj_MainStill[[1]] <- OpenD * (downstreamS^puRkm[[4]][1])
sPUj_MainStill[[2]] <- (OpenD^2) * (downstreamS^puRkm[[4]][2])
sPUj_MainStill[[3]] <- sPUj_MainStill[[2]] *
(((1 - pStillwaterD) * MilfordDj) + (pStillwaterD * StillwaterDj * OronoDj)) *
(downstreamS^puRkm[[4]][3])
sPUj_MainStill[[4]] <- sPUj_MainStill[[3]] * (((1 - pStillwaterD) * 1.00) +
(pStillwaterD * GilmanDj)) * (downstreamS^puRkm[[4]][4])
sPUj_MainStill[[5]] <- sPUj_MainStill[[4]] * WestEnfieldDj *
(downstreamS^puRkm[[4]][5])
sPUj_MainStill[[6]] <- sPUj_MainStill[[5]] * MattaceunkDj *
(downstreamS^puRkm[[4]][6])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU from each upstream migration route
malesOut <- vector(mode = "list", length = length(males))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPU_Pisc)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU_Pisc)[, i]
}
# Mainstem-to-mainstem spawners
for (i in 1:length(sPU_Main)) {
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_Main)[, i]
}
# Stillwater-to-piscataquis spawners
for (i in 1:length(sPU_PiscStill)) {
malesOut[[3]][[i]] <- mapply("*", males[[3]], sPU_PiscStill)[, i]
}
# Stillwater-to-mainstem spawners
for (i in 1:length(sPU_MainStill)) {
malesOut[[4]][[i]] <- mapply("*", males[[4]], sPU_MainStill)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum) +
apply(data.frame(malesOut[[3]]), 1, sum) +
apply(data.frame(malesOut[[4]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU in each route
femalesOut <- vector(mode = "list", length = length(females))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPU_Pisc)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU_Pisc)[, i]
}
# Mainstem-to-mainstem spawners
for (i in 1:length(sPU_Main)) {
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_Main)[, i]
}
# Stillwater-to-piscataquis spawners
for (i in 1:length(sPU_PiscStill)) {
femalesOut[[3]][[i]] <- mapply("*", females[[3]], sPU_PiscStill)[, i]
}
# Stillwater-to-mainstem spawners
for (i in 1:length(sPU_MainStill)) {
femalesOut[[4]][[i]] <- mapply("*", females[[4]], sPU_MainStill)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum) +
apply(data.frame(femalesOut[[3]]), 1, sum) +
apply(data.frame(femalesOut[[4]]), 1, sum)
# Calculate the number of recruits reaching the ocean
# DOES NOT INCLUDE ELEVATED MORTALITY FOR JUVENILES YET, ALTHOUGH I
# THINK THOSE DATA ARE AVAILABLE
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPUj_Pisc)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]][[i]], sPUj_Pisc[i])
}
# Mainstem-to-mainstem spawners
for (i in 1:length(sPUj_Main)) {
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]][[i]], sPUj_Main[i])
}
# Stillwater-to-piscataquis spawners
for (i in 1:length(sPUj_PiscStill)) {
recruitsOut[[3]][[i]] <- mapply("*", recruits[[3]][[i]], sPUj_PiscStill[i])
}
# Stillwater-to-mainstem spawners
for (i in 1:length(sPUj_MainStill)) {
recruitsOut[[4]][[i]] <- mapply("*", recruits[[4]][[i]], sPUj_MainStill[i])
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU_Pisc = sPU_Pisc,
sPU_Main = sPU_Main,
sPU_PiscStill = sPU_PiscStill,
sPU_MainStill = sPU_MainStill,
sPUj_Pisc = sPUj_Pisc,
sPUj_Main = sPUj_Main,
sPUj_PiscStill = sPUj_PiscStill,
sPUj_MainStill = sPUj_MainStill,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "merrimack") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem at Pawtucket
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * EssexD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * (((1 - pBypassD) * PawtucketD) + pBypassD * PawtucketBypassD) *
(downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * AmoskeagD * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * HooksetD * (downstreamS^puRkm[[1]][5])
# Bypass at Pawtucket
sPU_bp <- c()
sPU_bp[[1]] <- downstreamS^puRkm[[2]][1]
sPU_bp[[2]] <- sPU_bp[[1]] * EssexD * (downstreamS^puRkm[[2]][2])
sPU_bp[[3]] <- sPU_bp[[2]] * (((1 - pBypassD) * PawtucketD) + pBypassD * PawtucketBypassD) *
(downstreamS^puRkm[[1]][3])
sPU_bp[[4]] <- sPU_bp[[3]] * AmoskeagD * (downstreamS^puRkm[[2]][4])
sPU_bp[[5]] <- sPU_bp[[4]] * HooksetD * (downstreamS^puRkm[[2]][5])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem at Pawtucket
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * EssexDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * (((1 - pBypassD) * PawtucketDj) + pBypassD * PawtucketBypassDj) *
(downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * AmoskeagDj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * HooksetDj * (downstreamS^puRkm[[1]][5])
# Bypass at Pawtucket
sPU_bpj <- c()
sPU_bpj[[1]] <- downstreamS^puRkm[[2]][1]
sPU_bpj[[2]] <- sPU_bpj[[1]] * EssexDj * (downstreamS^puRkm[[2]][2])
sPU_bpj[[3]] <- sPU_bpj[[2]] * (((1 - pBypassD) * PawtucketDj) + pBypassD * PawtucketBypassDj) *
(downstreamS^puRkm[[1]][3])
sPU_bpj[[4]] <- sPU_bpj[[3]] * AmoskeagDj * (downstreamS^puRkm[[2]][4])
sPU_bpj[[5]] <- sPU_bpj[[4]] * HooksetDj * (downstreamS^puRkm[[2]][5])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_bp)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_bp)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPUj)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]][[i]], sPUj[i])
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]][[i]], sPU_bpj[i])
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "connecticut") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# In connecticut river, need to add loss for take at males[[1]][[4]]northfield mountain
# This occurs for adults and juveniles in the turners falls head pond
# and in the vernon dam head pond. We use independent rates for adults
# and for juveniles in each of the reaches.
# Juveniles - these are summed into a single route already
# for applying carrying capacity, so we just do that one:
recruits[[1]][[4]] <- recruits[[1]][[4]] * northfield$turnersJ
recruits[[1]][[5]] <- recruits[[1]][[5]] * northfield$vernonJ
# Males, both routes:
males[[1]][[4]] <- males[[1]][[4]] * northfield$turnersA
males[[1]][[5]] <- males[[1]][[5]] * northfield$vernonA
males[[2]][[4]] <- males[[2]][[4]] * northfield$turnersA
males[[2]][[5]] <- males[[2]][[5]] * northfield$vernonA
# Females, both routes:
females[[1]][[4]] <- females[[1]][[4]] * northfield$turnersA
females[[1]][[5]] <- females[[1]][[5]] * northfield$vernonA
females[[2]][[4]] <- females[[2]][[4]] * northfield$turnersA
females[[2]][[5]] <- females[[2]][[5]] * northfield$vernonA
# In the connecticut river, all downstream fish passage
# is designed to occur through gatehouse, so we can get
# away with one migration route here.
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * HolyokeD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * CabotD * (downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * GatehouseD * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * VernonD * (downstreamS^puRkm[[1]][5])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * HolyokeDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * CabotDj * (downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * GatehouseDj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * VernonDj * (downstreamS^puRkm[[1]][5])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPUj)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]][[i]], sPUj[i])
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "susquehanna") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
sPU_jun <- vector(mode = "list", length = nPU[1])
sPU_jun[[1]] <- downstreamS^puRkm[[1]][1]
sPU_jun[[2]] <- sPU_jun[[1]] * ConowingoD * (downstreamS^puRkm[[1]][2])
sPU_jun[[3]] <- sPU_jun[[2]] * HoltwoodD * (downstreamS^puRkm[[1]][3])
sPU_jun[[4]] <- sPU_jun[[3]] * SafeHarborD * (downstreamS^puRkm[[1]][4])
sPU_jun[[5]] <- sPU_jun[[4]] * YorkHavenD * (downstreamS^puRkm[[1]][5])
sPU_jun[[6]] <- sPU_jun[[5]] * junConfluenceD * (downstreamS^puRkm[[1]][6])
sPU_wes <- vector(mode = "list", length = nPU[2])
sPU_wes[[1]] <- downstreamS^puRkm[[1]][1]
sPU_wes[[2]] <- sPU_wes[[1]] * ConowingoD * (downstreamS^puRkm[[2]][2])
sPU_wes[[3]] <- sPU_wes[[2]] * HoltwoodD * (downstreamS^puRkm[[2]][3])
sPU_wes[[4]] <- sPU_wes[[3]] * SafeHarborD * (downstreamS^puRkm[[2]][4])
sPU_wes[[5]] <- sPU_wes[[4]] * YorkHavenD * (downstreamS^puRkm[[2]][5])
sPU_wes[[6]] <- sPU_wes[[5]] * SunburyD * (downstreamS^puRkm[[2]][6])
sPU_wes[[7]] <- sPU_wes[[6]] * WilliamsportD * (downstreamS^puRkm[[2]][7])
sPU_wes[[8]] <- sPU_wes[[7]] * LockHavenD * (downstreamS^puRkm[[2]][8])
sPU_che <- vector(mode = "list", length = nPU[3])
sPU_che[[1]] <- downstreamS^puRkm[[3]][1]
sPU_che[[2]] <- sPU_che[[1]] * ConowingoD * (downstreamS^puRkm[[3]][2])
sPU_che[[3]] <- sPU_che[[2]] * HoltwoodD * (downstreamS^puRkm[[3]][3])
sPU_che[[4]] <- sPU_che[[3]] * SafeHarborD * (downstreamS^puRkm[[3]][4])
sPU_che[[5]] <- sPU_che[[4]] * YorkHavenD * (downstreamS^puRkm[[3]][5])
sPU_che[[6]] <- sPU_che[[5]] * SunburyD * (downstreamS^puRkm[[3]][6])
sPU_che[[7]] <- sPU_che[[6]] * NyD * (downstreamS^puRkm[[3]][7])
sPU_che[[8]] <- sPU_che[[7]] * ChaseHibbardD * (downstreamS^puRkm[[3]][8])
sPU_nor <- vector(mode = "list", length = nPU[4])
sPU_nor[[1]] <- downstreamS^puRkm[[1]][1]
sPU_nor[[2]] <- sPU_nor[[1]] * ConowingoD * (downstreamS^puRkm[[4]][2])
sPU_nor[[3]] <- sPU_nor[[2]] * HoltwoodD * (downstreamS^puRkm[[4]][3])
sPU_nor[[4]] <- sPU_nor[[3]] * SafeHarborD * (downstreamS^puRkm[[4]][4])
sPU_nor[[5]] <- sPU_nor[[4]] * YorkHavenD * (downstreamS^puRkm[[4]][5])
sPU_nor[[6]] <- sPU_nor[[5]] * SunburyD * (downstreamS^puRkm[[4]][6])
sPU_nor[[7]] <- sPU_nor[[6]] * NyD * (downstreamS^puRkm[[4]][7])
sPU_nor[[8]] <- sPU_nor[[7]] * RockBottomD * (downstreamS^puRkm[[4]][8])
sPU_nor[[9]] <- sPU_nor[[8]] * UnadillaReachD * (downstreamS^puRkm[[4]][9])
sPU_nor[[10]] <- sPU_nor[[9]] * ColliersvilleD * (downstreamS^puRkm[[4]][10])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
sPU_junj <- vector(mode = "list", length = nPU[1])
sPU_junj[[1]] <- downstreamS^puRkm[[1]][1]
sPU_junj[[2]] <- sPU_junj[[1]] * ConowingoDj * (downstreamS^puRkm[[1]][2])
sPU_junj[[3]] <- sPU_junj[[2]] * HoltwoodDj * (downstreamS^puRkm[[1]][3])
sPU_junj[[4]] <- sPU_junj[[3]] * SafeHarborDj * (downstreamS^puRkm[[1]][4])
sPU_junj[[5]] <- sPU_junj[[4]] * YorkHavenDj * (downstreamS^puRkm[[1]][5])
sPU_junj[[6]] <- sPU_junj[[5]] * junConfluenceDj * (downstreamS^puRkm[[1]][6])
sPU_wesj <- vector(mode = "list", length = nPU[2])
sPU_wesj[[1]] <- downstreamS^puRkm[[1]][1]
sPU_wesj[[2]] <- sPU_wesj[[1]] * ConowingoDj * (downstreamS^puRkm[[2]][2])
sPU_wesj[[3]] <- sPU_wesj[[2]] * HoltwoodDj * (downstreamS^puRkm[[2]][3])
sPU_wesj[[4]] <- sPU_wesj[[3]] * SafeHarborDj * (downstreamS^puRkm[[2]][4])
sPU_wesj[[5]] <- sPU_wesj[[4]] * YorkHavenDj * (downstreamS^puRkm[[2]][5])
sPU_wesj[[6]] <- sPU_wesj[[5]] * SunburyDj * (downstreamS^puRkm[[2]][6])
sPU_wesj[[7]] <- sPU_wesj[[6]] * WilliamsportDj * (downstreamS^puRkm[[2]][7])
sPU_wesj[[8]] <- sPU_wesj[[7]] * LockHavenDj * (downstreamS^puRkm[[2]][8])
sPU_chej <- vector(mode = "list", length = nPU[3])
sPU_chej[[1]] <- downstreamS^puRkm[[1]][1]
sPU_chej[[2]] <- sPU_chej[[1]] * ConowingoDj * (downstreamS^puRkm[[3]][2])
sPU_chej[[3]] <- sPU_chej[[2]] * HoltwoodDj * (downstreamS^puRkm[[3]][3])
sPU_chej[[4]] <- sPU_chej[[3]] * SafeHarborDj * (downstreamS^puRkm[[3]][4])
sPU_chej[[5]] <- sPU_chej[[4]] * YorkHavenDj * (downstreamS^puRkm[[3]][5])
sPU_chej[[6]] <- sPU_chej[[5]] * SunburyDj * (downstreamS^puRkm[[3]][6])
sPU_chej[[7]] <- sPU_chej[[6]] * NyDj * (downstreamS^puRkm[[3]][7])
sPU_chej[[8]] <- sPU_chej[[7]] * ChaseHibbardDj * (downstreamS^puRkm[[3]][8])
sPU_norj <- vector(mode = "list", length = nPU[4])
sPU_norj[[1]] <- downstreamS^puRkm[[1]][1]
sPU_norj[[2]] <- sPU_norj[[1]] * ConowingoDj * (downstreamS^puRkm[[4]][2])
sPU_norj[[3]] <- sPU_norj[[2]] * HoltwoodDj * (downstreamS^puRkm[[4]][3])
sPU_norj[[4]] <- sPU_norj[[3]] * SafeHarborDj * (downstreamS^puRkm[[4]][4])
sPU_norj[[5]] <- sPU_norj[[4]] * YorkHavenDj * (downstreamS^puRkm[[4]][5])
sPU_norj[[6]] <- sPU_norj[[5]] * SunburyDj * (downstreamS^puRkm[[4]][6])
sPU_norj[[7]] <- sPU_norj[[6]] * NyDj * (downstreamS^puRkm[[4]][7])
sPU_norj[[8]] <- sPU_norj[[7]] * RockBottomDj * (downstreamS^puRkm[[4]][8])
sPU_norj[[9]] <- sPU_norj[[8]] * UnadillaReachDj * (downstreamS^puRkm[[4]][9])
sPU_norj[[10]] <- sPU_norj[[9]] * ColliersvilleDj * (downstreamS^puRkm[[4]][10])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU from each upstream migration route
malesOut <- vector(mode = "list", length = length(males))
# Juniata
for (i in 1:length(sPU_jun)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU_jun)[, i]
}
# West Branch
for (i in 1:length(sPU_wes)) {
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_wes)[, i]
}
# Chemung
for (i in 1:length(sPU_che)) {
malesOut[[3]][[i]] <- mapply("*", males[[3]], sPU_che)[, i]
}
# North Branch
for (i in 1:length(sPU_nor)) {
malesOut[[4]][[i]] <- mapply("*", males[[4]], sPU_nor)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum) +
apply(data.frame(malesOut[[3]]), 1, sum) +
apply(data.frame(malesOut[[4]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
# Juniata
for (i in 1:length(sPU_jun)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU_jun)[, i]
}
# West Branch
for (i in 1:length(sPU_wes)) {
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_wes)[, i]
}
# Chemung
for (i in 1:length(sPU_che)) {
femalesOut[[3]][[i]] <- mapply("*", females[[3]], sPU_che)[, i]
}
# North Brance
for (i in 1:length(sPU_nor)) {
femalesOut[[4]][[i]] <- mapply("*", females[[4]], sPU_nor)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum) +
apply(data.frame(femalesOut[[3]]), 1, sum) +
apply(data.frame(femalesOut[[4]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Juniata
for (i in 1:length(sPU_junj)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]][[i]], sPU_junj[i])
}
# West Branch
for (i in 1:length(sPU_wesj)) {
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]][[i]], sPU_wesj[i])
}
# Chemung
for (i in 1:length(sPU_chej)) {
recruitsOut[[3]][[i]] <- mapply("*", recruits[[3]][[i]], sPU_chej[i])
}
# North Branch
for (i in 1:length(sPU_norj)) {
recruitsOut[[4]][[i]] <- mapply("*", recruits[[4]][[i]], sPU_norj[i])
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU_jun = sPU_jun,
sPU_wes = sPU_wes,
sPU_che = sPU_che,
sPU_nor = sPU_nor,
sPU_junj = sPU_junj,
sPU_wesj = sPU_wesj,
sPU_chej = sPU_chej,
sPU_norj = sPU_norj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "saco") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem at Pawtucket
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * cataractD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * springD * (downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * skeltonD * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * barmillsD * (downstreamS^puRkm[[1]][5])
sPU[[6]] <- sPU[[5]] * buxtonD * (downstreamS^puRkm[[1]][6])
sPU[[7]] <- sPU[[6]] * bonnyD * (downstreamS^puRkm[[1]][7])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem at Pawtucket
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * cataractDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * springDj * (downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * skeltonDj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * barmillsDj * (downstreamS^puRkm[[1]][5])
sPUj[[6]] <- sPUj[[5]] * buxtonDj * (downstreamS^puRkm[[1]][6])
sPUj[[7]] <- sPUj[[6]] * bonnyDj * (downstreamS^puRkm[[1]][7])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem-to-piscataquis spawners
for (i in 1:length(sPUj)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]][[i]], sPUj[i])
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "kennebec") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * lockwoodD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * hydrokennD * (downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * shawmutD * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * westonD * (downstreamS^puRkm[[1]][5])
# Sebasticook
sPU_seb <- c()
sPU_seb[[1]] <- downstreamS^puRkm[[2]][1]
sPU_seb[[2]] <- sPU_seb[[1]] * bentonD * (downstreamS^puRkm[[2]][2])
sPU_seb[[3]] <- sPU_seb[[2]] * burnhamD * (downstreamS^puRkm[[2]][3])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * lockwoodDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * hydrokennDj * (downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * shawmutDj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * westonDj * (downstreamS^puRkm[[1]][5])
# Bypass at Pawtucket
sPU_sebj <- c()
sPU_sebj[[1]] <- downstreamS^puRkm[[2]][1]
sPU_sebj[[2]] <- sPU_sebj[[1]] * bentonDj * (downstreamS^puRkm[[2]][2])
sPU_sebj[[3]] <- sPU_sebj[[2]] * burnhamDj * (downstreamS^puRkm[[2]][3])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
}
for (i in 1:length(sPU_seb)) {
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_seb)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
}
for (i in 1:length(sPU_seb)) {
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_seb)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem
recruitsOut <- vector(mode = "list", length = length(recruits))
for (i in 1:length(sPU)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]], sPUj)
}
# Sebasticook
for (i in 1:length(sPU_seb)) {
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]], sPU_sebj)
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
sPU_seb = sPU_seb,
sPU_sebj = sPU_sebj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "hudson") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Upper Hudson
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * federalD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * C01D * (downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * C02D * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * C03D * (downstreamS^puRkm[[1]][5])
sPU[[6]] <- sPU[[5]] * C04D * (downstreamS^puRkm[[1]][6])
sPU[[7]] <- sPU[[6]] * C05D * (downstreamS^puRkm[[1]][7])
sPU[[8]] <- sPU[[7]] * C06D * (downstreamS^puRkm[[1]][8])
# Mohawk
sPU_moh <- c()
sPU_moh[[1]] <- downstreamS^puRkm[[2]][1]
sPU_moh[[2]] <- sPU_moh[[1]] * federalD * (downstreamS^puRkm[[2]][2])
sPU_moh[[3]] <- sPU_moh[[2]] * E02D * (downstreamS^puRkm[[2]][3])
sPU_moh[[4]] <- sPU_moh[[3]] * E03D * (downstreamS^puRkm[[2]][4])
sPU_moh[[5]] <- sPU_moh[[4]] * E04D * (downstreamS^puRkm[[2]][5])
sPU_moh[[6]] <- sPU_moh[[5]] * E05D * (downstreamS^puRkm[[2]][6])
sPU_moh[[7]] <- sPU_moh[[6]] * E06D * (downstreamS^puRkm[[2]][7])
sPU_moh[[8]] <- sPU_moh[[7]] * E07D * (downstreamS^puRkm[[2]][8])
sPU_moh[[9]] <- sPU_moh[[8]] * E08D * (downstreamS^puRkm[[2]][9])
sPU_moh[[10]] <- sPU_moh[[9]] * E09D * (downstreamS^puRkm[[2]][10])
sPU_moh[[11]] <- sPU_moh[[10]] * E10D * (downstreamS^puRkm[[2]][11])
sPU_moh[[12]] <- sPU_moh[[11]] * E11D * (downstreamS^puRkm[[2]][12])
sPU_moh[[13]] <- sPU_moh[[12]] * E12D * (downstreamS^puRkm[[2]][13])
sPU_moh[[14]] <- sPU_moh[[13]] * E13D * (downstreamS^puRkm[[2]][14])
sPU_moh[[15]] <- sPU_moh[[14]] * E14D * (downstreamS^puRkm[[2]][15])
sPU_moh[[16]] <- sPU_moh[[15]] * E15D * (downstreamS^puRkm[[2]][16])
sPU_moh[[17]] <- sPU_moh[[16]] * E16D * (downstreamS^puRkm[[2]][17])
sPU_moh[[18]] <- sPU_moh[[17]] * E17D * (downstreamS^puRkm[[2]][18])
sPU_moh[[19]] <- sPU_moh[[18]] * E18D * (downstreamS^puRkm[[2]][19])
sPU_moh[[20]] <- sPU_moh[[19]] * E19D * (downstreamS^puRkm[[2]][20])
sPU_moh[[21]] <- sPU_moh[[20]] * E20D * (downstreamS^puRkm[[2]][21])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Upper Hudson
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * federalDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * C01Dj * (downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * C02Dj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * C03Dj * (downstreamS^puRkm[[1]][5])
sPUj[[6]] <- sPUj[[5]] * C04Dj * (downstreamS^puRkm[[1]][6])
sPUj[[7]] <- sPUj[[6]] * C05Dj * (downstreamS^puRkm[[1]][7])
sPUj[[8]] <- sPUj[[7]] * C06Dj * (downstreamS^puRkm[[1]][8])
# Bypass at Pawtucket
sPU_mohj <- c()
sPU_mohj[[1]] <- downstreamS^puRkm[[2]][1]
sPU_mohj[[2]] <- sPU_mohj[[1]] * federalDj * (downstreamS^puRkm[[2]][2])
sPU_mohj[[3]] <- sPU_mohj[[2]] * E02Dj * (downstreamS^puRkm[[2]][3])
sPU_mohj[[4]] <- sPU_mohj[[3]] * E03Dj * (downstreamS^puRkm[[2]][4])
sPU_mohj[[5]] <- sPU_mohj[[4]] * E04Dj * (downstreamS^puRkm[[2]][5])
sPU_mohj[[6]] <- sPU_mohj[[5]] * E05Dj * (downstreamS^puRkm[[2]][6])
sPU_mohj[[7]] <- sPU_mohj[[6]] * E06Dj * (downstreamS^puRkm[[2]][7])
sPU_mohj[[8]] <- sPU_mohj[[7]] * E07Dj * (downstreamS^puRkm[[2]][8])
sPU_mohj[[9]] <- sPU_mohj[[8]] * E08Dj * (downstreamS^puRkm[[2]][9])
sPU_mohj[[10]] <- sPU_mohj[[9]] * E09Dj * (downstreamS^puRkm[[2]][10])
sPU_mohj[[11]] <- sPU_mohj[[10]] * E10Dj * (downstreamS^puRkm[[2]][11])
sPU_mohj[[12]] <- sPU_mohj[[11]] * E11Dj * (downstreamS^puRkm[[2]][12])
sPU_mohj[[13]] <- sPU_mohj[[12]] * E12Dj * (downstreamS^puRkm[[2]][13])
sPU_mohj[[14]] <- sPU_mohj[[13]] * E13Dj * (downstreamS^puRkm[[2]][14])
sPU_mohj[[15]] <- sPU_mohj[[14]] * E14Dj * (downstreamS^puRkm[[2]][15])
sPU_mohj[[16]] <- sPU_mohj[[15]] * E15Dj * (downstreamS^puRkm[[2]][16])
sPU_mohj[[17]] <- sPU_mohj[[16]] * E16Dj * (downstreamS^puRkm[[2]][17])
sPU_mohj[[18]] <- sPU_mohj[[17]] * E17Dj * (downstreamS^puRkm[[2]][18])
sPU_mohj[[19]] <- sPU_mohj[[18]] * E18Dj * (downstreamS^puRkm[[2]][19])
sPU_mohj[[20]] <- sPU_mohj[[19]] * E19Dj * (downstreamS^puRkm[[2]][20])
sPU_mohj[[21]] <- sPU_mohj[[20]] * E20Dj * (downstreamS^puRkm[[2]][21])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
}
for (i in 1:length(sPU_moh)) {
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_moh)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
}
for (i in 1:length(sPU_moh)) {
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_moh)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Upper Hudson
recruitsOut <- vector(mode = "list", length = length(recruits))
for (i in 1:length(sPU)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]], sPUj)
}
# Mohawk River
for (i in 1:length(sPU_moh)) {
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]], sPU_mohj)
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
sPU_moh = sPU_moh,
sPU_mohj = sPU_mohj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
if (river == "androscoggin") {
# Derive downstream passage efficiencies for each group of spawners in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem
sPU <- c()
sPU[[1]] <- downstreamS^puRkm[[1]][1]
sPU[[2]] <- sPU[[1]] * brunswickD * (downstreamS^puRkm[[1]][2])
sPU[[3]] <- sPU[[2]] * pejepscotD * (downstreamS^puRkm[[1]][3])
sPU[[4]] <- sPU[[3]] * worumboD * (downstreamS^puRkm[[1]][4])
sPU[[5]] <- sPU[[4]] * lbarkerD * (downstreamS^puRkm[[1]][5])
sPU[[6]] <- sPU[[5]] * ubarkerD * (downstreamS^puRkm[[1]][6])
sPU[[7]] <- sPU[[6]] * littlefieldD * (downstreamS^puRkm[[1]][7])
sPU[[8]] <- sPU[[7]] * hackettD * (downstreamS^puRkm[[1]][8])
sPU[[9]] <- sPU[[8]] * marcalD * (downstreamS^puRkm[[1]][9])
sPU[[10]] <- sPU[[9]] * welchvilleD * (downstreamS^puRkm[[1]][10])
sPU[[11]] <- sPU[[10]] * parisD * (downstreamS^puRkm[[1]][11])
# Sabattus
sPU_sab <- c()
sPU_sab[[1]] <- downstreamS^puRkm[[2]][1]
sPU_sab[[2]] <- sPU_sab[[1]] * brunswickD * (downstreamS^puRkm[[2]][2])
sPU_sab[[3]] <- sPU_sab[[2]] * pejepscotD * (downstreamS^puRkm[[2]][3])
sPU_sab[[4]] <- sPU_sab[[3]] * worumboD * (downstreamS^puRkm[[2]][5])
sPU_sab[[5]] <- sPU_sab[[4]] * farwellD * (downstreamS^puRkm[[2]][5])
sPU_sab[[6]] <- sPU_sab[[5]] * fortierD * (downstreamS^puRkm[[2]][6])
# Derive downstream passage efficiencies for each group of juveniles in each PU.
# This uses the starting position of the fish, and then incorporates cumulative
# dam passage efficiencies from the starting PU to the ocean.
# Mainstem
sPUj <- c()
sPUj[[1]] <- downstreamS^puRkm[[1]][1]
sPUj[[2]] <- sPUj[[1]] * brunswickDj * (downstreamS^puRkm[[1]][2])
sPUj[[3]] <- sPUj[[2]] * pejepscotDj * (downstreamS^puRkm[[1]][3])
sPUj[[4]] <- sPUj[[3]] * worumboDj * (downstreamS^puRkm[[1]][4])
sPUj[[5]] <- sPUj[[4]] * lbarkerDj * (downstreamS^puRkm[[1]][5])
sPUj[[6]] <- sPUj[[5]] * ubarkerDj * (downstreamS^puRkm[[1]][6])
sPUj[[7]] <- sPUj[[6]] * littlefieldDj * (downstreamS^puRkm[[1]][7])
sPUj[[8]] <- sPUj[[7]] * hackettDj * (downstreamS^puRkm[[1]][8])
sPUj[[9]] <- sPUj[[8]] * marcalDj * (downstreamS^puRkm[[1]][9])
sPUj[[10]] <- sPUj[[9]] * welchvilleDj * (downstreamS^puRkm[[1]][10])
sPUj[[11]] <- sPUj[[10]] * parisDj * (downstreamS^puRkm[[1]][11])
# Sabattus
sPU_sabj <- c()
sPU_sabj[[1]] <- downstreamS^puRkm[[2]][1]
sPU_sabj[[2]] <- sPU_sabj[[1]] * brunswickDj * (downstreamS^puRkm[[2]][2])
sPU_sabj[[3]] <- sPU_sabj[[2]] * pejepscotDj * (downstreamS^puRkm[[2]][3])
sPU_sabj[[4]] <- sPU_sabj[[3]] * worumboDj * (downstreamS^puRkm[[2]][5])
sPU_sabj[[5]] <- sPU_sabj[[4]] * farwellDj * (downstreamS^puRkm[[2]][5])
sPU_sabj[[6]] <- sPU_sabj[[5]] * fortierDj * (downstreamS^puRkm[[2]][6])
# Calculate number of males reaching the mouth of the river after spawn from
# each PU
malesOut <- vector(mode = "list", length = length(males))
for (i in 1:length(sPU)) {
malesOut[[1]][[i]] <- mapply("*", males[[1]], sPU)[, i]
}
for (i in 1:length(sPU_sab)) {
malesOut[[2]][[i]] <- mapply("*", males[[2]], sPU_sab)[, i]
}
# Sum number of males in each age from all PUs reaching river mouth
malesOut <- apply(data.frame(malesOut[[1]]), 1, sum) +
apply(data.frame(malesOut[[2]]), 1, sum)
# Calculate number of females reaching the mouth of the river after spawn from
# each PU
femalesOut <- vector(mode = "list", length = length(females))
for (i in 1:length(sPU)) {
femalesOut[[1]][[i]] <- mapply("*", females[[1]], sPU)[, i]
}
for (i in 1:length(sPU_sab)) {
femalesOut[[2]][[i]] <- mapply("*", females[[2]], sPU_sab)[, i]
}
# Sum number of females in each age from all PUs reaching river mouth
femalesOut <- apply(data.frame(femalesOut[[1]]), 1, sum) +
apply(data.frame(femalesOut[[2]]), 1, sum)
# Calculate the number of recruits reaching the ocean
recruitsOut <- vector(mode = "list", length = length(recruits))
# Mainstem
recruitsOut <- vector(mode = "list", length = length(recruits))
for (i in 1:length(sPU)) {
recruitsOut[[1]][[i]] <- mapply("*", recruits[[1]], sPUj)
}
# Sabattus
for (i in 1:length(sPU_sab)) {
recruitsOut[[2]][[i]] <- mapply("*", recruits[[2]], sPU_sabj)
}
# Sum number of recruits in each age from all PUs reaching river mouth
recruitsOut <- sum(unlist(recruitsOut))
# Sum total number of out migrants
outMigrants <- femalesOut + malesOut
return(
list(
sPU = sPU,
sPj = sPUj,
sPU_sab = sPU_sab,
sPU_sabj = sPU_sabj,
malesOut = malesOut,
femalesOut = femalesOut,
recruitsOut = recruitsOut,
outMigrants = outMigrants
)
)
}
}
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