R/WriteRapFile.R

In eeholmes/VRAPCpp: VRAP 2nd edition with C++ for RER and Viability Computations

#' @title Write Rap File from VRAP 2.0 inputs list
#' @description Takes the input list and writes a .rap file. 
#' @details Takes the inputs list and write a .rap file that can be input into 
#' VRAP 2.0 function \link[VRAPS]{ReadRapFile} or \link[VRAPS]{GetInput}.  Note that in VRAP 2.0,
#' the beginning and ending ER (or Pop) values are given in absolute values not as a fraction
#' of base level as in VRAP 1.0.
#' @param inputs A list of the necessary input values for \link{RunSims2R} and \link{RunSims2C}.
#' @param ravFileName Name of the .rav file that data will be written to.
#' @return Nothing. The data is written to FileName.

WriteRapFile <- function(inputs, FileName="tmp.rav"){
  # Error checking
  if(!(inputs$errorType %in% c("GAMMA","LOGNORMAL"))){
    stop("ERROR: WriteRapFile requires errorType = GAMMA or LOGNORMAL.")
  }
  if(inputs$depen != "NO") stop("ERROR: WriteRapFile requires depen = NO.")
  if(inputs$EscChoice != "YES") stop("ERROR: WriteRapFile requires EscChoice = YES.")
  if(!(toupper(inputs$SRType) %in% c("RIC2", "HOC2", "BEV2"))) stop("ERROR: WriteRapFile requires SRType be RIC2, HOC2 or BEV2.")
  
  fileText <- paste("Example, ",  ", Title
", inputs$RanSeed, ", Random seed; 0 gives random seed; numbers give fixed seed
", inputs$NRuns, ", Number of runs
", inputs$NYears, ", Number of years
2, 5, Minimum and maximum age (fixed; do not change)
", inputs$ConvergeCrit, ", Convergence criterion (% error) for target ER
NO, 0, -Inf, VRAP 2.0 has no covariates; Center covariate flag and log MS and log Flow mean
", inputs$SRType, ", Spawner Recruit function. Must be Ric2, Hoc2, Bev2
", inputs$prod,",",inputs$cap,", S/R a; b parameters
VRAP 2.0 has no covariates; Mean and CV for c
VRAP 2.0 has no covariates; Variability type for c
VRAP 2.0 has no covariates; Variability params for c
VRAP 2.0 has no covariates; Mean and CV for d
VRAP 2.0 has no covariates; Variability type for d
VRAP 2.0 has no covariates; Variability params for d
", inputs$depen, ", Depensation? (Must be NO for VRAP 2.0)
0, 0, 1, 1) Esc. level for depensation to start 2) QET quasi-extinction threshold, 3)% predicted return at QET (or for r/s=1 third parameter = 1)
", inputs$EscChoice, ", Determine recruits from adult spawners (Must be YES for VRAP 2.0)
", inputs$errorType, ", Stock-recruit variation type
", inputs$SRErrorA,",",inputs$SRErrorB,", 0, if gamma, shape and scale.  if lognormal, log sd and lag-1 autocor.  3rd param is unused but req for VRAP 1.0.
NO, VRAP 2.0 does not use; Smolt to adult survival w/variation
VRAP 2.0 ignores; was beta params for smolt to adult survival
0, VRAP 2.0 does not implement breakpoints; was Number of breakpoints
1, VRAP 2.0 does not implement breakpoints; was Level to use as base regime
0.67, Arbitrary. Must be between 0 and 1 and used by VRAP 1.0 to set step sizes
", ifelse(inputs$MgmtError,"YES","NO"), ", Include error (YES or NO) in ER management
", inputs$GammaMgmtA,",", inputs$GammaMgmtB, ", Gamma parameters for management error
", inputs$ECrit, ", Lower escapement threshold
", inputs$ERecovery, ",", inputs$EndAv, ", Upper escapement threshold (MSY);  # yrs to ave.
", inputs$StepFunc, ", Step ER (ER) or  Pop Capacity (Pop)?
", inputs$StepSize, ", Step size
", inputs$StepStart, ", ", inputs$StepEnd, ", Min & max ER or Pop for sims
", inputs$CohortStart[1],", Initial population size at Age  1 
", inputs$CohortStart[2],", Initial population size at Age  2 
", inputs$CohortStart[3],", Initial population size at Age  3 
", inputs$CohortStart[4],", Initial population size at Age  4 
", inputs$CohortStart[5],", Initial population size at Age  5 
", inputs$NatMort[1], ", Age 1 natural mortality
", inputs$NatMort[2], ", Age 2 natural mortality
", inputs$NatMort[3], ", Age 3 natural mortality
", inputs$NatMort[4], ", Age 4 natural mortality
", inputs$NatMort[5], ", Age 5 natural mortality
", inputs$MatRate[2], ", Age 2 average maturation rate
", inputs$MatRate[3], ", Age 3 average maturation rate
", inputs$MatRate[4], ", Age 4 average maturation rate
", inputs$MatRate[5], ", Age 5 average maturation rate
", inputs$PTU[2], ",", inputs$MatU[2],", Age 2 average mixed-maturity and mature fishery fishing rates
", inputs$PTU[3],",", inputs$MatU[3],", Age 3 average mixed-maturity and mature fishery fishing rates
", inputs$PTU[4],",", inputs$MatU[4],", Age 4 average mixed-maturity and mature fishery fishing rates
", inputs$PTU[5],",", inputs$MatU[5],", Age 5 average mixed-maturity and mature fishery fishing rates
endofinput, end of input indicator
",sep="")
  
  cat(fileText, file=FileName)
}