#' Androscoggin River Model
#'
#' Dam passage performance standard model for
#' Androscoggin River, Maine, USA
#'
#' @param nRuns The number of times that the
#' model will be run.
#'
#' @param species Species for which the model will be
#' run. Current options include American \code{'shad'} and
#' \code{'blueback'} herring.
#'
#' @param nYears The number of years for which
#' each run will last. The default is 40 years
#' to match default FERC license duration.
#'
#' @param n_adults Number of starting adults in
#' population.
#'
#' @param p_sabattus Probability of using the
#' Sabattus River for migration. Default is
#' based on proportional distribution of habitat
#' in each route.
#'
#' @param timing The amount of time required for
#' upstream passage by individual fish (in days),
#' where the default (1) indicates a 24-h dam
#' passage performance standard and the value is
#' specified as a proportion of 1 day.
#'
#' @param upstream A named list of upstream dam
#' passage efficiencies at each dam in the
#' Androscoggin River and its largest tributary, the
#' Sabattus River.
#'
#' Users may specify a single value of upstream
#' passage at each dam, or a vector of upstream
#' passage efficiencies at each dam. Note that
#' passage efficiences passed as vectors are
#' randomly sampled during each model run
#' (not each year). Therefore, multiple model runs
#' are necessary if more than one passage efficiency
#' is supplied for any dam. As a rough rule of thumb
#' we advise a minimum of 100 runs per combination of
#' management parameters (upstream timing and passage,
#' and downstream survival through dams).
#'
#' @param downstream A named list of downstream
#' dam passage efficiencies at each dam in the
#' Androscoggin river.
#'
#' @param downstream_juv A named list of downstream
#' dam passage efficiencies at each dam in the
#' Androscoggin River for juveniles.
#'
#' @param inRiverF Annual, recreational harvest in river.
#' Parameterized as an annual rate [0, 1].
#'
#' @param commercialF Commercial fishery mortality
#' in marine environment incurred through targeted
#' fisheries. Parameterized as an annual rate [0, 1].
#'
#' @param bycatchF Marine bycatch mortality of
#' species in non-target fisheries.
#' Parameterized as an annual rate [0, 1].
#'
#' @param indirect Indirect mortality incurred during
#' freshwater migration as a result of dam-related
#' impacts (e.g., injury, predation, etc.).
#'
#' @param latent Latent mortality incurred during estuary
#' passage as a result of dam-related impacts (e.g., injury,
#' delay, etc.).
#'
#' @param watershed A logical indicating whether or not
#' to use the same dam passage efficiencies at all dams
#' for upstream and downstream. If watershed = TRUE, then
#' the first element in lists `upstream`, `downstream`,
#' and `downstream_juv` are recycled for all subsequent dams.
#'
#' @param k_method Method used to impose carrying capacity. The
#' default, `cumulative`, assumes that carrying capacity is based on
#' all available habitat through the most upstream occupied production
#' units in a given migration route. The alternative, 'discrete' assumes
#' that carrying capacity is applied within discrete production units
#' based on the numbers, and was the method used in Stich et al. (2019).
#'
#' @param sensitivity Whether to return a dataframe for sensitivity
#' analysis. The default is set to FALSE for faster run time and smaller
#' memory load in parallel processing.
#'
#' @param spatially_explicit_output Whether to return population size in each production unit.
#'
#' @param output_years Whether to return all years (default = `NULL`) or only
#' final year of each simulation (`"last"`).
#'
#' @param output_p_repeat A logical indicating whether to return pRepeat by
#' age (in years) with the output. The default value is `FALSE` to
#' limit output size in physical memory.
#'
#' @return Returns a dataframe when sensitivity = FALSE (default).
#' Returns a list of two named dataframes when sensitivity = TRUE.
#' The first dataframe (\code{res}) contains user-defined
#' inputs and available model outputs depending on optional arguments.
#' The second dataframe (\code{sens}) contains input variables for
#' sensitivity analysis if desired. If run in parallel, returns a list of
#' lists of dataframes.
#'
#' The following named columns may be returned in \code{res}:
#'
#' \itemize{
#' \item \code{year} Year of simulation
#' \item \code{species} Species used for simulation
#' \item \code{p_sabattus} Probability of fish using the Sabattus River during upstream migration and spawning
#' \item \code{timing_brunswick...timing_paris} Passage timing input by user
#' \item \code{brunswick_us...fortier_us} User-specified upstream passage efficiencies
#' \item \code{brunswick_ds...fortier_ds} User-specified downstream passage efficiencies
#' \item \code{brunswick_dsj...fortier_dsj} User-specified juvenile downstream passage efficiencies
#' \item \code{F.inRiver} User-specified recreational fishing mortality
#' \item \code{F.commercial} User-specified recreational fishing mortality
#' \item \code{F.recreational} User-specified recreational fishing mortality
#' \item \code{indirectM} User-specified indirect mortality dams
#' \item \code{indirectM} User-specified latent mortality
#' \item \code{pRepeat_Age1...pRepeat_AgeN} Age-specific probability of repeat spawning
#' \item \code{N_IA...N_IB} Production unit-specific population size after in-river fishery mortality
#' \item \code{populationSize} Number of spawners returning to the river
#' }
#'
#' The following named columns are returned in \code{sens}:
#' \itemize{
#' \item \code{S.downstream} Downstream survival per kilometer
#' \item \code{S.marine} Marine survival as an annual rate
#' \item \code{popStart} Starting population size
#' \item \code{p.female} Probability of being female
#' \item \code{S.prespawnM} Prespawn survival rate for males
#' \item \code{S.postspawnM} Postspawn survival rate for males
#' \item \code{S.prespawnF} Postspawn survival rate for males
#' \item \code{S.postspawnF} Postspawn survival rate for males
#' \item \code{S.juvenile} Hatch to out-migrant survival rate
#' \item \code{b.Arr} Mean arrival date for males
#' \item \code{r.Arr} Mean arrival date for females
#' \item \code{ATUspawn1} Accumulated thermal units at initiation of spawn
#' \item \code{ATUspawn2} Accumulated thermal units at termination of spawn
#' \item \code{Dspawn1} Initial spawning date
#' \item \code{Dspawn2} Terminal spawning date
#' \item \code{linF} L-infinity parameter from the von Bertalanffy growth function for females
#' \item \code{kF} K parameter from the von Bertalanffy growth function for females
#' \item \code{t0F} t0 parameter from the von Bertalanffy growth function for females
#' \item \code{linM} L-infinity parameter from the von Bertalanffy growth function for males
#' \item \code{kM} K parameter from the von Bertalanffy growth function for males
#' \item \code{t0M} t0 parameter from the von Bertalanffy growth function for males
#' \item \code{b.length} Mean length of males
#' \item \code{r.length} Mean length of females
#' \item \code{spawnInt} Mean spawning interval
#' \item \code{batchSize} Mean batch size
#' \item \code{resTime} Mean residence time
#' \item \code{s.Optim} Mean optimal ground speed
#' \item \code{d.Max} Mean maximum daily movement rate
#' \item \code{tortuosity} Path tortuosity parameter
#' \item \code{motivation} Seasonal change in fish "motivation" for upstream movement
#' \item \code{daily.move} Mean realized daily movement rate
#' \item \code{habStoch} Habitat stochasticity
#' }
#'
#' @section
#' Schematic of production units coming soon
#'
# #' \if{html}{\figure{kennebec.png}{Kennebec River}}
# #' \if{latex}{\figure{kennebec.png}{options: width=0.5in}}
#'
#' @section
#' Warning about serial execution and memory limits:
#'
#' Currently, internal functions rely on \code{list2env()} to return
#' lists to a temporary environment created in the
#' \code{androscogginRiverModel()} function. Consequently, lists
#' that are exported must be limited in size. Therefore,
#' users currently need to limit the number of runs per
#' call (\code{nRuns} argument) to less than 10 or R will
#' hit memory limits quickly. In reality, serial
#' execution is prohibitively slow unless implemented
#' using manual parallel processing (e.g., bash scripting).
#'
#' In order to achieve a desired number of runs for a given
#' set of inputs, the recommended approach is to use
#' parallel execution as demonstrated using the \code{snowfall}
#' package in the example below.
#'
#' @example /inst/examples/sf-exampleANR.R
#'
#' @export
androscogginRiverModel <- function(
nRuns = 1,
species = "shad",
nYears = 40,
n_adults = 1e4,
timing = rep(1, 12),
p_sabattus = 0.05,
upstream = list(
brunswick = 1,
pejepscot = 1,
worumbo = 1,
lbarker = 1,
ubarker = 1,
littlefield = 1,
hackett = 1,
marcal = 1,
welchville = 1,
paris = 1,
farwell = 1,
fortier = 1
),
downstream = list(
brunswick = 1,
pejepscot = 1,
worumbo = 1,
lbarker = 1,
ubarker = 1,
littlefield = 1,
hackett = 1,
marcal = 1,
welchville = 1,
paris = 1,
farwell = 1,
fortier = 1
),
downstream_juv = list(
brunswick = 1,
pejepscot = 1,
worumbo = 1,
lbarker = 1,
ubarker = 1,
littlefield = 1,
hackett = 1,
marcal = 1,
welchville = 1,
paris = 1,
farwell = 1,
fortier = 1
),
inRiverF = 0,
commercialF = 0,
bycatchF = 0,
indirect = 1,
latent = 1,
watershed = FALSE,
k_method = "cumulative",
sensitivity = FALSE,
spatially_explicit_output = FALSE,
output_years = NULL,
output_p_repeat = FALSE) {
# Error message for passage efficiencies
if ((length(upstream) != 12) | (length(downstream) != 12)) {
stop("
`upstream` and `downstream` must each have 12 elements.")
}
# Error message for maximum number of years
if (as.numeric(substr(Sys.time(), start = 1, stop = 4)) + nYears > 2099) {
stop("
Error:
The current year plus `nYears` must not
exceed 2099 because the models rely on
climate predictions that are limited to
that time period.")
}
# Message for using watershed == TRUE
if (watershed) {
cat("WARNING: when watershed is set to TRUE,
upstream and downstream passage rate(s) for
Brunswick Dam will be used at all dams in the
watershed.", "\n", "\n")
}
# Create hidden workspace
.shadia <- new.env()
# Assign species
.shadia$species <- species
# Assign River
.shadia$river <- "androscoggin"
.shadia$region <- "Northern Iteroparous"
# Choose climate scenario
# Right now, these are set as 'current' in all
# models except Connecticut River. Hidden from
# user because we lack projections from other
# systems.
.shadia$climate <- "current"
# Assign sensitivity option
.shadia$sensitivity <- sensitivity
# Assign k_method option
.shadia$k_method <- k_method
# Passage variable assignment -----
# Upstream and downstream passage
### DSS: would like to re-write this all
pDraws <- upstream
dDraws <- downstream
djDraws <- downstream_juv
# For watershed applications of
# the model, all values need to
# match
# Adult upstream
sampU <- sample(pDraws[[1]], 1)
pDraws <- lapply(
pDraws,
function(x) {
if (watershed) {
x <- sampU
}
else {
x <- x
}
}
)
.shadia$up <- as.vector(mapply(sample, pDraws, 1))
# Adult downstream
sampD <- sample(dDraws[[1]], 1)
dDraws <- lapply(
dDraws,
function(x) {
if (watershed) {
x <- sampD
}
else {
x <- x
}
}
)
.shadia$d <- as.vector(mapply(sample, dDraws, 1))
# Juvenile downstream
sampDj <- sample(djDraws[[1]], 1)
djDraws <- lapply(
djDraws,
function(x) {
if (watershed) {
x <- sampDj
}
else {
x <- x
}
}
)
.shadia$dj <- as.vector(mapply(sample, djDraws, 1))
# Probability of using sabattaus
.shadia$p_sabattus <- p_sabattus
# Upstream timing
timely <- timing
# Survival reduction due to delay in project head ponds
delay <- 1
# Data load and memory pre-allocation -----
# Pre-allocate output vectors
environment(defineOutputVectors) <- .shadia
list2env(defineOutputVectors(), envir = .shadia)
# Time-invariant system-specific data ----
# Maximum age
if (.shadia$species == "shad") {
.shadia$maxAge <- getMaxAge(region = .shadia$region)
}
if (.shadia$species == "blueback") {
.shadia$maxAge <- 7
}
# Define probability of recruitment to spawn
# using regional estimates from ASMFC (2020)
if (.shadia$species == "shad") {
.shadia$spawnRecruit <- getMaturity(region = .shadia$region)
}
if (.shadia$species == "blueback") {
.shadia$spawnRecruit <- c(0, 0.01, 0.48, 0.90, 1, 1, 1)
}
### NEED TO REPLACE WITH UPDATED ESTIMATES
# Initial probabilities of repeat spawning -
# will be derived in annual loop after this
if (.shadia$species == "shad") {
.shadia$pRepeat <- c(0, 0, 0, 0.03, 0.11, 0.38, 0.87, 1, 1, 1, 1, 1, 1)
}
if (.shadia$species == "blueback") {
.shadia$pRepeat <- c(0, 0, 0.004, 0.28, 0.83, 1, 1)
}
# Length-weight regression parameters by region
# and separated by sex
### Not used for shad, and not implemented for BBH
.shadia$m_lw_params <- length_weight %>% subset(region == "NI" & sex == "M")
.shadia$f_lw_params <- length_weight %>% subset(region == "NI" & sex == "F")
# Fishing mortality
.shadia$commercialF <- rep(commercialF, .shadia$maxAge)
.shadia$bycatchF <- rep(bycatchF, .shadia$maxAge)
.shadia$inRiverF <- inRiverF
# Survival rates for various life-history stages
# Define ocean survival for each age (1-M from Hoenig 1983 in ASMFC 2007
# stock assessment). This is now used only to seed the population. All
# models now use climate-informed mortality estimates for VBGF parameters
# derived as part of the 2020 ASMFC stock assessment.
.shadia$downstreamS <- 1 # Survival per km (natural)
.shadia$oceanSurvival <- rep(rbeta(1, 320, 400), .shadia$maxAge)
# Hydro system configuration
environment(defineHydroSystem) <- .shadia
.shadia$hydro_out <- defineHydroSystem(river = .shadia$river)
.shadia$nRoutes <- .shadia$hydro_out$nRoutes
.shadia$nDams <- .shadia$hydro_out$nDams
.shadia$maxrkm <- .shadia$hydro_out$maxrkm
.shadia$damRkms <- .shadia$hydro_out$damRkms
.shadia$nPU <- .shadia$hydro_out$nPU
# Habitat numbers and configuration
.shadia$habitat <- defineHabitat(
river = .shadia$river,
nRoutes = .shadia$nRoutes,
species = .shadia$species,
k_method = .shadia$k_method,
p_up = .shadia$p_sabattus
)
# Temperature data (daily averages by year)
environment(setUpTemperatureData) <- .shadia
.shadia$mu <- setUpTemperatureData(river = .shadia$river)
### Can the outer loop be eliminated?
# Outer loop for number of simulations (nRuns) ----
# this is how many runs it will do for each nYears
for (k in 1:nRuns) {
.shadia$k <- k
### NONE OF THIS RELIES ON LOOPING ANYMORE
# Dam passage efficiencies
environment(definePassageRates) <- .shadia
list2env(definePassageRates(.shadia$river), envir = .shadia)
### WILL THROW GLOBAL BINDING NOTES ON CHECK
# Upstream passage efficiencies and migration route
environment(annualUpstream) <- .shadia
.shadia$ann_up <- annualUpstream(.shadia$river, .shadia$damRkms)
.shadia$times <- .shadia$ann_up$times
.shadia$upEffs <- .shadia$ann_up$upEffs
# Define in-river fishing mortality for
# each PU in each of the four
# possible migration routes
environment(fwFishingMort) <- .shadia
.shadia$inriv <- fwFishingMort(.shadia$inRiverF,
river = .shadia$river,
nRoutes = .shadia$nRoutes
)
# Starting population structure -----
# Define starting population structure for each simulation
environment(simStartingPop) <- .shadia
.shadia$starting_pop <- simStartingPop(
adults = n_adults,
.shadia$maxAge,
.shadia$oceanSurvival,
.shadia$spawnRecruit
)
.shadia$pop <- .shadia$starting_pop$pop
.shadia$spawningPool <- .shadia$starting_pop$spawningPool
.shadia$recruitmentPool <- .shadia$starting_pop$recruitmentPool
### THIS STAYS IN AS A LOOP UNLESS CHANGED INTERNALLY
# Inner loop -----
# Run sim for nYears
for (n in 1:nYears) {
# Assign iterator to a var so it
# can be accessed in functions called
.shadia$n <- n
# Reset the scalar based on population size
.shadia$scalar <- setScalar(.shadia$spawningPool)
# Scale the population
scaled_pop <- scalePop(
.shadia$pop,
.shadia$spawningPool,
.shadia$recruitmentPool,
.shadia$scalar
)
.shadia$pop <- scaled_pop[[1]]
.shadia$spawningPool <- scaled_pop[[2]]
.shadia$recruitmentPool <- scaled_pop[[3]]
# Perform innerLoopSampling
environment(innerLoopSampling) <- .shadia
list2env(innerLoopSampling(.shadia$habitat), envir = .shadia)
# Process fish and eggs
# Make matrices to hold fish
environment(populationMatrices) <- .shadia
list2env(populationMatrices(), envir = .shadia)
# Fill them in and change them into cohorts
environment(processCohorts) <- .shadia
list2env(processCohorts(), envir = .shadia)
# Downstream migration
# Post-spawning mortality
environment(postSpawnMortality) <- .shadia
list2env(postSpawnMortality(), envir = .shadia)
# Define downstream migration survival rate matrices
# and then apply them to calculate the number of adult
# and juvenile fish surviving to the ocean.
environment(downstreamMigration) <- .shadia
list2env(downstreamMigration(), envir = .shadia)
# . The next generation -----
# next year (after applying ocean survival)
environment(nextGeneration) <- .shadia
list2env(nextGeneration(), envir = .shadia)
# . Store output in pre-allocated vectors -----
environment(fillOutputVectors) <- .shadia
list2env(fillOutputVectors(), envir = .shadia)
} # Year loop
} # Simulation loop
# Write the simulation results to an object
# that can be returned to workspace
environment(writeData) <- .shadia
writeData()
}
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