R/GetInput.R
In eeholmes/VRAP: VRAP for RER and Viability Computations
Defines functions
GetInput
Documented in
GetInput
#' @title GetInput
#' @description Read in a .rav file and assign all the variables
#' @param InFile the name of the .rav file
#' @return Returns the list of all inputs
GetInput = function(InFile){
require(stringr)
#The rav file has , as end of input/separator
inputs = list()
inputs$InFile = InFile
readit = function(skip, n){
x = read.table(InFile,nrows=1,sep=",",stringsAsFactors=FALSE,skip=skip)[1,n]
if(is.character(x)) x = str_trim(x)
x
}
# GET TITLE FOR RUN
inputs$Title = readit(0,1) #line 1
# -------------------- RUN PARAMETERS SECTION ---------------------------------
# INPUT RANDOM NUMBER SEED, NUMBER OF CYCLES AND REPETITIONS,
# MINIMUM AND MAXIMUM AGE
inputs$RanSeed = readit(1,1) #line 2, RanSeed
inputs$NRuns = readit(2,1) #line 2, NRuns
inputs$NYears = readit(3,1) #line 3, NYears
inputs$MinAge = readit(4,1) #line 4, NYears
inputs$MaxAge = readit(4,2) #line 4, NYears
inputs$ConvergeCrit = readit(5,1) #line 5, ConvergeCrit
inputs$CenterCov = readit(6,1) #line 6, was debug Debugg
inputs$CenterCov = toupper(inputs$CenterCov)
if(!(inputs$CenterCov %in% c("YES", "NO"))) stop("Unknown covariate centering selection (yes/no only)")
if(inputs$CenterCov=="YES"){
inputs$logMSMu = readit(6,2) #line 6, the mean used for centering in DM: mean log MS
inputs$logFlowMu = readit(6,3) #line 6, the mean used for centering in DM: mean log Flow. Note flow is logged.
}
# ----- END OF RUN PARAMETERS SECTION ------------------------
# ----- STOCK-RECRUIT SECTION -------------------------------
# GET FORM OF SPAWNER RECRUIT FUNCTION AND PARAMETERS
# njs updated these explanations
# BSRa = productivity parameter
# BSRb = density dependent prarameter
# BSRc = marine survival paramater - M^c
# BSRd = freshwater survival parameter - exp(dF)(d should be entered as negative)
# HOC2 - Hockey stick R=Min(aS,b) a = producitvity b=MaxRecruits
# HOC3 - R = Min(aS,) exp(dF) (freshwater index - may be used to predict smolts)
# HOC4 - R= Min(aS,) M^c exp(dF)
# RIC2 - Ricker R=aS exp(-bS) a = productvity b=1/capacity
# RIC3 - R= aS exp(-bS+dF) (freshwater index - may be used to predict smolts)
# RIC4 - Ricker with marine survival and freshwater survival
# R=aS M^c exp(-bS+dF)
# BEV2 - Beverton-Holt R=1/(b+a/S) a = 1/productivity b=1/MaxRecruits
# BEV3 - R=1/(b+a/S) exp(dF)(freshwater index - may be used to predict smolts)
# BEV4 - BH with marine survival and freshwater survival
# R=1/(a+b/S)M^c exp(dF)
inputs$SRType = readit(7,1) #line 8, SRType
inputs$SRType = toupper(inputs$SRType)
SRType=inputs$SRType
allowedSRType = c("HOC2", "HOC3", "HOC4", "BEV2", "BEV3", "BEV4", "RIC2", "RIC3", "RIC4")
if(!(SRType %in% allowedSRType)) stop("Unknown stock recruit type")
if(SRType %in% c("HOC2", "RIC2", "BEV2")){
inputs$BSRa = readit(8,1) #line 4, NYears
inputs$BSRb = readit(8,2) #line 4, NYears
inputs$BSRc = 0;
inputs$BSRd = 0;
inputs$AveEnv = 1
}
# Skip the next 6 lines and jump to line 16
if(SRType %in% c("HOC3", "RIC3", "BEV3")){
inputs$BSRa = readit(8,1)
inputs$BSRb = readit(8,2)
inputs$BSRc = 0;
inputs$BSRd = readit(8,3)
# skip next 3 lines
inputs$FlowAve = readit(12,1)
inputs$FlowCV = readit(12,2)
inputs$TrndCycF = readit(13,1)
if(!(inputs$TrndCycF %in% c("Autoc", "Trend", "Cycle"))) stop("Unknown trend/cycle function for Flow")
inputs$TCF1 = readit(14,1)
inputs$TCF2 = readit(14,2)
inputs$TCF3 = readit(14,3)
inputs$BSRc = 0
inputs$FlowSD = inputs$FlowCV * inputs$FlowAve
if(inputs$FlowSD > 0){
inputs$GammaFlowA = inputs$FlowAve * inputs$FlowAve / (inputs$FlowSD * inputs$FlowSD)
inputs$GammaFlowB = (inputs$FlowSD * inputs$FlowSD) / inputs$FlowAve
}else{
inputs$GammaFlowA = 0
inputs$GammaFlowB = 0
}
inputs$AveEnv = exp(inputs$BSRd * inputs$FlowAve)
}
if(SRType %in% c("HOC4", "RIC4", "BEV4")){
inputs$BSRa = readit(8,1)
inputs$BSRb = readit(8,2)
inputs$BSRc = readit(8,3);
inputs$BSRd = readit(8,4)
inputs$MarAve = readit(9,1)
inputs$MarCV = readit(9,2)
inputs$TrndCycM = readit(10,1)
if(!(inputs$TrndCycM %in% c("Autoc", "Trend", "Cycle"))) stop("Unknown trend/cycle function for marine survival")
inputs$TCM1 = readit(11,1)
inputs$TCM2 = readit(11,2)
inputs$TCM3 = readit(11,3)
inputs$FlowAve = readit(12,1)
inputs$FlowCV = readit(12,2)
inputs$TrndCycF = readit(13,1)
if(!(inputs$TrndCycF %in% c("Autoc", "Trend", "Cycle"))) stop("Unknown trend/cycle function for Flow")
inputs$TCF1 = readit(14,1)
inputs$TCF2 = readit(14,2)
inputs$TCF3 = readit(14,3)
inputs$MarSD = inputs$MarCV * inputs$MarAve
if(inputs$MarSD > 0){
inputs$GammaMarA = inputs$MarAve * inputs$MarAve / (inputs$MarSD * inputs$MarSD)
inputs$GammaMarB = (inputs$MarSD * inputs$MarSD) / inputs$MarAve
}else{
inputs$GammaMarA = 0
inputs$GammaMarB = 0
}
inputs$FlowSD = inputs$FlowCV * inputs$FlowAve
if(inputs$FlowSD > 0){
inputs$GammaFlowA = inputs$FlowAve * inputs$FlowAve / (inputs$FlowSD * inputs$FlowSD)
inputs$GammaFlowB = (inputs$FlowSD * inputs$FlowSD) / inputs$FlowAve
}else{
inputs$GammaFlowA = 0
inputs$GammaFlowB = 0
}
inputs$AveEnv = inputs$MarAve^inputs$BSRc * exp(inputs$BSRd * inputs$FlowAve)
}
# depensation with DL1=depensation esc; DL2 = QET; DR % of predicted R realized at QET
inputs$depen = readit(15,1)
inputs$depen = toupper(inputs$depen)
if(!(inputs$depen %in% c("YES", "NO"))) stop("Unknown depensation selection (yes/no only)")
inputs$DL1 = readit(16,1)
inputs$DL2 = readit(16,2)
inputs$DR = readit(16,3)
if(!is.numeric(inputs$DL1)) stop("rav line 17: DL1 should be numeric.")
if(!is.numeric(inputs$DL2)) stop("rav line 17: QET should be numeric. Enter 0 if no quasi-extinction threshold (i.e. threshold = 0).")
if(!is.numeric(inputs$DR)) stop("rav line 17: DR (3rd param) should be numeric.")
if(inputs$depen=="NO"){
if(inputs$DL1 != 0) stop("rav line 17: if no depensation, DL1 should be 0.")
if(inputs$DR != 1) stop("rav line 17: if no depensation, DR (3rd param) should be 1.")
}
inputs$EscChoice = readit(17,1)
inputs$EscChoice = toupper(inputs$EscChoice)
if(!(inputs$EscChoice %in% c("YES", "NO"))) stop("Unknown escapement choice selection (yes/no only)")
# GET PARAMETERS TO ADD VARIABILITY TO STOCK RECRUIT FUNCTION
# SRErrorA and B are used for Hoc2, Ric2 and Bev2, SRErrorA, SRErrorB and ResCorPar (optional)
# are used for Hoc3, Ric3, Bev3, Hoc4, Ric4, and Bev4
inputs$SurvScale = readit(18,1)
inputs$SurvScale = toupper(inputs$SurvScale)
if(!(inputs$SurvScale %in% c("YES", "NO"))) stop("Unknown SR variability selection (yes/no only)")
if(inputs$SurvScale == "YES"){
inputs$SRErrorA = readit(19,1)
inputs$SRErrorB = readit(19,2)
inputs$ResCorParameter = readit(19,3)
}
# GET PARAMETERS FOR SMOLT TO ADULT (MARINE) SURVIVAL IF STOCK RECRUIT FUNCTION
# IS FOR SMOLTS FROM SPAWNERS (FRESHWATER PRODUCTION)
inputs$MarSurv = readit(20,1)
inputs$MarSurv = toupper(inputs$MarSurv)
if(!(inputs$MarSurv %in% c("YES", "NO"))) stop("Unknown marine survival selection (yes/no only)")
if(inputs$MarSurv == "YES"){
inputs$BetaMarA = readit(21,1)
inputs$BetaMarB = readit(21,2)
inputs$CorrMS = readit(21,3)
}
# --------- END OF STOCK RECRUIT SECTION -----------------------------
# --------- FISHERY MANAGEMENT PARAMETERS ---------------------------
# INPUT THE NUMBER OF BREAKPOINTS AND DIMENSION ARRAYS
# EEH: Per comments from Norma, I am not allowing more than 1 breakpoint
# EEH: Norma indicated that this code was untested and examination of BufferInit.R
# EEH: makes me uncertain what it really does if there is more than one breakpoint.
inputs$NumBreakPoints = readit(22,1)
if(!(inputs$NumBreakPoints %in% c(0,1))) stop("Line 23 in rav file: only 0 or 1 breakpoints allowed for specification of the harvest regime.")
# IDENTIFY WHICH LEVEL IS THE BASE REGIME
inputs$BaseRegime = readit(23,1)
inputs$EscpmntBreakPoint = rep(NA,inputs$NumBreakPoints+1)
inputs$TargetU = rep(NA,inputs$NumBreakPoints+1)
# begin dynamically keeping track of line number
cline=24
# INPUT BREAKPOINTS AND TARGET EXPLOITATION RATES
for(BreakPoint in 1:(inputs$NumBreakPoints + 1)){
if(BreakPoint <= inputs$NumBreakPoints){
inputs$EscpmntBreakPoint[BreakPoint] = readit(cline,1)
inputs$TargetU[BreakPoint] = readit(cline,2)
cline=cline+1
}else{
inputs$TargetU[BreakPoint] = readit(cline,1)
cline=cline+1
}
}
# INPUT PARAMETERS FOR MANAGEMENT ERROR
inputs$MgmtError = readit(cline,1); cline=cline+1
inputs$MgmtError = toupper(inputs$MgmtError)
if(!(inputs$MgmtError %in% c("YES", "NO"))) stop("Unknown manag error selection (yes/no only)")
# Read in dummy values if management error is No
if(inputs$MgmtError == "YES"){
inputs$GammaMgmtA = readit(cline,1);
inputs$GammaMgmtB = readit(cline,2); cline=cline+1
}else{
inputs$GammaMgmtA = 0
inputs$GammaMgmtB = 0
cline=cline+1
}
# ------------------ END OF FISHERY MANAGMENT INPUTS --------------------
inputs$ECrit = readit(cline,1); cline=cline+1
inputs$ERecovery = readit(cline,1);
inputs$EndAv = readit(cline,2); cline=cline+1
# INPUT STEP SIZE AND RANGE FOR TARGET EXPLOITATION RATES OR STARTING ESCAPEMENT
# This program outputs information for a range of either exploitation rates or
# starting escapement levels.
# The BUFFER levels input below represent percentages of the base target
# exploitation rate or the starting escapement level.
# (e.g., a Buffer of .05 means that the ER will be 5% of the base target rate.)
# You may enter a number greater than 1.0, which means that the ER will be
# greater than the base target rate. Under normal runs with 0 breakpoints,
# the base target rate is not used other than to determine start, end, and step
# levels.
inputs$StepFunc = readit(cline,1); cline=cline+1
inputs$StepFunc = toupper(inputs$StepFunc)
if(!(inputs$StepFunc %in% c("POP", "ER"))) stop("Unknown step selection")
inputs$BufferStep = readit(cline,1); cline=cline+1
inputs$BufferStart = readit(cline,1);
inputs$BufferEnd = readit(cline,2); cline=cline+1
#integer of the number of steps of ER or Pop Capacity to do # is 1:BufMax
inputs$BufMax = round((inputs$BufferEnd - inputs$BufferStart) / inputs$BufferStep + 1)
# INPUT LOWER AND UPPER ESCAPEMENT TEST LEVELS
# The LOWER ESCAPEMENT LEVEL (ECrit) is the escapement level used by the
# program to test how often the observed escapements fall below this level.
# It may represent a "critical" level below which the spawner-recruit function
# destabilizes, and the stock increases risk of extinction, or it could be any
# level one just wanted to monitor frequency of achieving less than or equal
# to that level.
# The UPPER ECSAPEMENT LEVEL (ERecovery) is the escapement level used to compare
# against the geometric mean of the last n (EndAv) years of the run. It may be a
# management escapement goal, an interim recovery level, or some other target level.
# ----------------------- BASE STOCK DATA SECTION -----------------------------
#
# INPUT INITIAL POPULATION SIZE BY AGE
# The initial population size by age, for all ages, is used to seed the model.
# In year 1, the management actions are applied to this population, and a portion of
# each size class escapes. By running the program over a range of starting population
# sizes, one can determine what minimum population size (or escapement) is needed
# to guarentee a probability of population viability.
# NJS Although the input allows for different MaxAge% from 5, the internal workings of the
# are fixed to 5 in many places.
inputs$CohortStart = rep(0,inputs$MaxAge)
for(Age in (inputs$MinAge - 1):inputs$MaxAge){
inputs$CohortStart[Age] = readit(cline,1); cline=cline+1
}
# INPUT NATURAL MORTALITY RATES
inputs$NatMort = rep(0,inputs$MaxAge)
for(Age in (inputs$MinAge - 1):inputs$MaxAge){
inputs$NatMort[Age] = readit(cline,1); cline=cline+1
}
# INPUT MATURATION RATES BY AGE (AEQ will be calculated)
inputs$MatRate = rep(0,inputs$MaxAge)
for(Age in inputs$MinAge:inputs$MaxAge){
inputs$MatRate[Age] = readit(cline,1); cline=cline+1
}
# INPUT PRETERMINAL AND MATURE EXPLOITATION RATES BY AGE
# These will be used to proportion target ER by age and fishery
# by def, PTU and MatU are 0 before MinAge
inputs$PTU = rep(0,inputs$MaxAge)
inputs$MatU = rep(0,inputs$MaxAge)
for(Age in inputs$MinAge:inputs$MaxAge){
inputs$PTU[Age] = readit(cline,1);
inputs$MatU[Age] = readit(cline,2); cline=cline+1
}
return(inputs)
}
eeholmes/VRAP documentation built on May 28, 2019, 8:24 a.m.
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Defines functions GetInput
Documented in GetInput
#' @title GetInput
#' @description Read in a .rav file and assign all the variables
#' @param InFile the name of the .rav file
#' @return Returns the list of all inputs
GetInput = function(InFile){
require(stringr)
#The rav file has , as end of input/separator
inputs = list()
inputs$InFile = InFile
readit = function(skip, n){
x = read.table(InFile,nrows=1,sep=",",stringsAsFactors=FALSE,skip=skip)[1,n]
if(is.character(x)) x = str_trim(x)
x
}
# GET TITLE FOR RUN
inputs$Title = readit(0,1) #line 1
# -------------------- RUN PARAMETERS SECTION ---------------------------------
# INPUT RANDOM NUMBER SEED, NUMBER OF CYCLES AND REPETITIONS,
# MINIMUM AND MAXIMUM AGE
inputs$RanSeed = readit(1,1) #line 2, RanSeed
inputs$NRuns = readit(2,1) #line 2, NRuns
inputs$NYears = readit(3,1) #line 3, NYears
inputs$MinAge = readit(4,1) #line 4, NYears
inputs$MaxAge = readit(4,2) #line 4, NYears
inputs$ConvergeCrit = readit(5,1) #line 5, ConvergeCrit
inputs$CenterCov = readit(6,1) #line 6, was debug Debugg
inputs$CenterCov = toupper(inputs$CenterCov)
if(!(inputs$CenterCov %in% c("YES", "NO"))) stop("Unknown covariate centering selection (yes/no only)")
if(inputs$CenterCov=="YES"){
inputs$logMSMu = readit(6,2) #line 6, the mean used for centering in DM: mean log MS
inputs$logFlowMu = readit(6,3) #line 6, the mean used for centering in DM: mean log Flow. Note flow is logged.
}
# ----- END OF RUN PARAMETERS SECTION ------------------------
# ----- STOCK-RECRUIT SECTION -------------------------------
# GET FORM OF SPAWNER RECRUIT FUNCTION AND PARAMETERS
# njs updated these explanations
# BSRa = productivity parameter
# BSRb = density dependent prarameter
# BSRc = marine survival paramater - M^c
# BSRd = freshwater survival parameter - exp(dF)(d should be entered as negative)
# HOC2 - Hockey stick R=Min(aS,b) a = producitvity b=MaxRecruits
# HOC3 - R = Min(aS,) exp(dF) (freshwater index - may be used to predict smolts)
# HOC4 - R= Min(aS,) M^c exp(dF)
# RIC2 - Ricker R=aS exp(-bS) a = productvity b=1/capacity
# RIC3 - R= aS exp(-bS+dF) (freshwater index - may be used to predict smolts)
# RIC4 - Ricker with marine survival and freshwater survival
# R=aS M^c exp(-bS+dF)
# BEV2 - Beverton-Holt R=1/(b+a/S) a = 1/productivity b=1/MaxRecruits
# BEV3 - R=1/(b+a/S) exp(dF)(freshwater index - may be used to predict smolts)
# BEV4 - BH with marine survival and freshwater survival
# R=1/(a+b/S)M^c exp(dF)
inputs$SRType = readit(7,1) #line 8, SRType
inputs$SRType = toupper(inputs$SRType)
SRType=inputs$SRType
allowedSRType = c("HOC2", "HOC3", "HOC4", "BEV2", "BEV3", "BEV4", "RIC2", "RIC3", "RIC4")
if(!(SRType %in% allowedSRType)) stop("Unknown stock recruit type")
if(SRType %in% c("HOC2", "RIC2", "BEV2")){
inputs$BSRa = readit(8,1) #line 4, NYears
inputs$BSRb = readit(8,2) #line 4, NYears
inputs$BSRc = 0;
inputs$BSRd = 0;
inputs$AveEnv = 1
}
# Skip the next 6 lines and jump to line 16
if(SRType %in% c("HOC3", "RIC3", "BEV3")){
inputs$BSRa = readit(8,1)
inputs$BSRb = readit(8,2)
inputs$BSRc = 0;
inputs$BSRd = readit(8,3)
# skip next 3 lines
inputs$FlowAve = readit(12,1)
inputs$FlowCV = readit(12,2)
inputs$TrndCycF = readit(13,1)
if(!(inputs$TrndCycF %in% c("Autoc", "Trend", "Cycle"))) stop("Unknown trend/cycle function for Flow")
inputs$TCF1 = readit(14,1)
inputs$TCF2 = readit(14,2)
inputs$TCF3 = readit(14,3)
inputs$BSRc = 0
inputs$FlowSD = inputs$FlowCV * inputs$FlowAve
if(inputs$FlowSD > 0){
inputs$GammaFlowA = inputs$FlowAve * inputs$FlowAve / (inputs$FlowSD * inputs$FlowSD)
inputs$GammaFlowB = (inputs$FlowSD * inputs$FlowSD) / inputs$FlowAve
}else{
inputs$GammaFlowA = 0
inputs$GammaFlowB = 0
}
inputs$AveEnv = exp(inputs$BSRd * inputs$FlowAve)
}
if(SRType %in% c("HOC4", "RIC4", "BEV4")){
inputs$BSRa = readit(8,1)
inputs$BSRb = readit(8,2)
inputs$BSRc = readit(8,3);
inputs$BSRd = readit(8,4)
inputs$MarAve = readit(9,1)
inputs$MarCV = readit(9,2)
inputs$TrndCycM = readit(10,1)
if(!(inputs$TrndCycM %in% c("Autoc", "Trend", "Cycle"))) stop("Unknown trend/cycle function for marine survival")
inputs$TCM1 = readit(11,1)
inputs$TCM2 = readit(11,2)
inputs$TCM3 = readit(11,3)
inputs$FlowAve = readit(12,1)
inputs$FlowCV = readit(12,2)
inputs$TrndCycF = readit(13,1)
if(!(inputs$TrndCycF %in% c("Autoc", "Trend", "Cycle"))) stop("Unknown trend/cycle function for Flow")
inputs$TCF1 = readit(14,1)
inputs$TCF2 = readit(14,2)
inputs$TCF3 = readit(14,3)
inputs$MarSD = inputs$MarCV * inputs$MarAve
if(inputs$MarSD > 0){
inputs$GammaMarA = inputs$MarAve * inputs$MarAve / (inputs$MarSD * inputs$MarSD)
inputs$GammaMarB = (inputs$MarSD * inputs$MarSD) / inputs$MarAve
}else{
inputs$GammaMarA = 0
inputs$GammaMarB = 0
}
inputs$FlowSD = inputs$FlowCV * inputs$FlowAve
if(inputs$FlowSD > 0){
inputs$GammaFlowA = inputs$FlowAve * inputs$FlowAve / (inputs$FlowSD * inputs$FlowSD)
inputs$GammaFlowB = (inputs$FlowSD * inputs$FlowSD) / inputs$FlowAve
}else{
inputs$GammaFlowA = 0
inputs$GammaFlowB = 0
}
inputs$AveEnv = inputs$MarAve^inputs$BSRc * exp(inputs$BSRd * inputs$FlowAve)
}
# depensation with DL1=depensation esc; DL2 = QET; DR % of predicted R realized at QET
inputs$depen = readit(15,1)
inputs$depen = toupper(inputs$depen)
if(!(inputs$depen %in% c("YES", "NO"))) stop("Unknown depensation selection (yes/no only)")
inputs$DL1 = readit(16,1)
inputs$DL2 = readit(16,2)
inputs$DR = readit(16,3)
if(!is.numeric(inputs$DL1)) stop("rav line 17: DL1 should be numeric.")
if(!is.numeric(inputs$DL2)) stop("rav line 17: QET should be numeric. Enter 0 if no quasi-extinction threshold (i.e. threshold = 0).")
if(!is.numeric(inputs$DR)) stop("rav line 17: DR (3rd param) should be numeric.")
if(inputs$depen=="NO"){
if(inputs$DL1 != 0) stop("rav line 17: if no depensation, DL1 should be 0.")
if(inputs$DR != 1) stop("rav line 17: if no depensation, DR (3rd param) should be 1.")
}
inputs$EscChoice = readit(17,1)
inputs$EscChoice = toupper(inputs$EscChoice)
if(!(inputs$EscChoice %in% c("YES", "NO"))) stop("Unknown escapement choice selection (yes/no only)")
# GET PARAMETERS TO ADD VARIABILITY TO STOCK RECRUIT FUNCTION
# SRErrorA and B are used for Hoc2, Ric2 and Bev2, SRErrorA, SRErrorB and ResCorPar (optional)
# are used for Hoc3, Ric3, Bev3, Hoc4, Ric4, and Bev4
inputs$SurvScale = readit(18,1)
inputs$SurvScale = toupper(inputs$SurvScale)
if(!(inputs$SurvScale %in% c("YES", "NO"))) stop("Unknown SR variability selection (yes/no only)")
if(inputs$SurvScale == "YES"){
inputs$SRErrorA = readit(19,1)
inputs$SRErrorB = readit(19,2)
inputs$ResCorParameter = readit(19,3)
}
# GET PARAMETERS FOR SMOLT TO ADULT (MARINE) SURVIVAL IF STOCK RECRUIT FUNCTION
# IS FOR SMOLTS FROM SPAWNERS (FRESHWATER PRODUCTION)
inputs$MarSurv = readit(20,1)
inputs$MarSurv = toupper(inputs$MarSurv)
if(!(inputs$MarSurv %in% c("YES", "NO"))) stop("Unknown marine survival selection (yes/no only)")
if(inputs$MarSurv == "YES"){
inputs$BetaMarA = readit(21,1)
inputs$BetaMarB = readit(21,2)
inputs$CorrMS = readit(21,3)
}
# --------- END OF STOCK RECRUIT SECTION -----------------------------
# --------- FISHERY MANAGEMENT PARAMETERS ---------------------------
# INPUT THE NUMBER OF BREAKPOINTS AND DIMENSION ARRAYS
# EEH: Per comments from Norma, I am not allowing more than 1 breakpoint
# EEH: Norma indicated that this code was untested and examination of BufferInit.R
# EEH: makes me uncertain what it really does if there is more than one breakpoint.
inputs$NumBreakPoints = readit(22,1)
if(!(inputs$NumBreakPoints %in% c(0,1))) stop("Line 23 in rav file: only 0 or 1 breakpoints allowed for specification of the harvest regime.")
# IDENTIFY WHICH LEVEL IS THE BASE REGIME
inputs$BaseRegime = readit(23,1)
inputs$EscpmntBreakPoint = rep(NA,inputs$NumBreakPoints+1)
inputs$TargetU = rep(NA,inputs$NumBreakPoints+1)
# begin dynamically keeping track of line number
cline=24
# INPUT BREAKPOINTS AND TARGET EXPLOITATION RATES
for(BreakPoint in 1:(inputs$NumBreakPoints + 1)){
if(BreakPoint <= inputs$NumBreakPoints){
inputs$EscpmntBreakPoint[BreakPoint] = readit(cline,1)
inputs$TargetU[BreakPoint] = readit(cline,2)
cline=cline+1
}else{
inputs$TargetU[BreakPoint] = readit(cline,1)
cline=cline+1
}
}
# INPUT PARAMETERS FOR MANAGEMENT ERROR
inputs$MgmtError = readit(cline,1); cline=cline+1
inputs$MgmtError = toupper(inputs$MgmtError)
if(!(inputs$MgmtError %in% c("YES", "NO"))) stop("Unknown manag error selection (yes/no only)")
# Read in dummy values if management error is No
if(inputs$MgmtError == "YES"){
inputs$GammaMgmtA = readit(cline,1);
inputs$GammaMgmtB = readit(cline,2); cline=cline+1
}else{
inputs$GammaMgmtA = 0
inputs$GammaMgmtB = 0
cline=cline+1
}
# ------------------ END OF FISHERY MANAGMENT INPUTS --------------------
inputs$ECrit = readit(cline,1); cline=cline+1
inputs$ERecovery = readit(cline,1);
inputs$EndAv = readit(cline,2); cline=cline+1
# INPUT STEP SIZE AND RANGE FOR TARGET EXPLOITATION RATES OR STARTING ESCAPEMENT
# This program outputs information for a range of either exploitation rates or
# starting escapement levels.
# The BUFFER levels input below represent percentages of the base target
# exploitation rate or the starting escapement level.
# (e.g., a Buffer of .05 means that the ER will be 5% of the base target rate.)
# You may enter a number greater than 1.0, which means that the ER will be
# greater than the base target rate. Under normal runs with 0 breakpoints,
# the base target rate is not used other than to determine start, end, and step
# levels.
inputs$StepFunc = readit(cline,1); cline=cline+1
inputs$StepFunc = toupper(inputs$StepFunc)
if(!(inputs$StepFunc %in% c("POP", "ER"))) stop("Unknown step selection")
inputs$BufferStep = readit(cline,1); cline=cline+1
inputs$BufferStart = readit(cline,1);
inputs$BufferEnd = readit(cline,2); cline=cline+1
#integer of the number of steps of ER or Pop Capacity to do # is 1:BufMax
inputs$BufMax = round((inputs$BufferEnd - inputs$BufferStart) / inputs$BufferStep + 1)
# INPUT LOWER AND UPPER ESCAPEMENT TEST LEVELS
# The LOWER ESCAPEMENT LEVEL (ECrit) is the escapement level used by the
# program to test how often the observed escapements fall below this level.
# It may represent a "critical" level below which the spawner-recruit function
# destabilizes, and the stock increases risk of extinction, or it could be any
# level one just wanted to monitor frequency of achieving less than or equal
# to that level.
# The UPPER ECSAPEMENT LEVEL (ERecovery) is the escapement level used to compare
# against the geometric mean of the last n (EndAv) years of the run. It may be a
# management escapement goal, an interim recovery level, or some other target level.
# ----------------------- BASE STOCK DATA SECTION -----------------------------
#
# INPUT INITIAL POPULATION SIZE BY AGE
# The initial population size by age, for all ages, is used to seed the model.
# In year 1, the management actions are applied to this population, and a portion of
# each size class escapes. By running the program over a range of starting population
# sizes, one can determine what minimum population size (or escapement) is needed
# to guarentee a probability of population viability.
# NJS Although the input allows for different MaxAge% from 5, the internal workings of the
# are fixed to 5 in many places.
inputs$CohortStart = rep(0,inputs$MaxAge)
for(Age in (inputs$MinAge - 1):inputs$MaxAge){
inputs$CohortStart[Age] = readit(cline,1); cline=cline+1
}
# INPUT NATURAL MORTALITY RATES
inputs$NatMort = rep(0,inputs$MaxAge)
for(Age in (inputs$MinAge - 1):inputs$MaxAge){
inputs$NatMort[Age] = readit(cline,1); cline=cline+1
}
# INPUT MATURATION RATES BY AGE (AEQ will be calculated)
inputs$MatRate = rep(0,inputs$MaxAge)
for(Age in inputs$MinAge:inputs$MaxAge){
inputs$MatRate[Age] = readit(cline,1); cline=cline+1
}
# INPUT PRETERMINAL AND MATURE EXPLOITATION RATES BY AGE
# These will be used to proportion target ER by age and fishery
# by def, PTU and MatU are 0 before MinAge
inputs$PTU = rep(0,inputs$MaxAge)
inputs$MatU = rep(0,inputs$MaxAge)
for(Age in inputs$MinAge:inputs$MaxAge){
inputs$PTU[Age] = readit(cline,1);
inputs$MatU[Age] = readit(cline,2); cline=cline+1
}
return(inputs)
}
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