Nothing
SS_makedatlist <-
function(styr=1971,
endyr=2001,
nseas=1,
months_per_seas=12,
spawn_seas=1,
Nfleet=1,
Nsurveys=1,
N_areas=1,
fleetnames=c("fishery1","survey1"),
surveytiming=0.5,
areas=1,
units_of_catch=1,
se_log_catch=0.01,
Ngenders=2,
Nages=40,
init_equil=0,
catch=NULL,
CPUE=NULL,
N_discard_fleets=0,
discard_data=NULL,
meanbodywt=NULL,
DF_for_meanbodywt=30,
lbin_method=2,
binwidth=2,
minimum_size=2,
maximum_size=90,
comp_tail_compression= -0.0001,
add_to_comp=0.0001,
max_combined_lbin=0,
lbin_vector=seq(22, 90, 2),
lencomp=NULL,
agebin_vector=1:25,
ageerror=data.frame(rbind(0:40+.5,.001,0:40+.5,seq(0.525,2.525,0.05))),
agecomp=NULL,
Lbin_method=3,
max_combined_age=1,
MeanSize_at_Age_obs=NULL,
N_environ_variables=0,
N_environ_obs=0,
N_sizefreq_methods=0,
do_tags=0,
morphcomp_data=0
){
SSversion <- "SSv3.24B"
N_lbins <- length(lbin_vector)
N_agebins <- length(agebin_vector)
N_catch <- ifelse(is.null(catch), 0, nrow(catch))
N_cpue <- ifelse(is.null(CPUE), 0, nrow(CPUE))
CPUEinfo <- data.frame(Fleet=1:(Nfleet+Nsurveys),Units=1,Errtype=0)
N_discard <- ifelse(is.null(discard_data), 0, nrow(discard_data))
N_meanbodywt <- ifelse(is.null(meanbodywt), 0, nrow(meanbodywt))
N_lencomp <- ifelse(is.null(lencomp), 0, nrow(lencomp))
N_ageerror_definitions <- ifelse(is.null(ageerror), 0, nrow(ageerror)/2)
N_agecomp <- ifelse(is.null(agecomp), 0, nrow(agecomp))
N_MeanSize_at_Age_obs <- ifelse(is.null(MeanSize_at_Age_obs), 0, nrow(MeanSize_at_Age_obs))
fleetinfo1 <- data.frame(rbind(rep(surveytiming,Nfleet+Nsurveys),
rep(areas,Nfleet+Nsurveys)))
names(fleetinfo1) <- fleetnames
names(fleetinfo1)[1] <- paste("#",names(fleetinfo1)[1],sep="")
fleetinfo1$input <- c("#_surveytiming","#_areas")
fleetinfo2 <- data.frame(rbind(rep(units_of_catch,Nfleet),
rep(se_log_catch,Nfleet)))
names(fleetinfo2) <- fleetnames[1:Nfleet]
names(fleetinfo2)[1] <- paste("#",names(fleetinfo2)[1],sep="")
fleetinfo2$input <- c("#_units_of_catch","#_se_log_catch")
names(ageerror) <- c("#_age0",paste("age",1:Nages,sep=""))
datlist <- list(SSversion = SSversion,
type = "Stock_Synthesis_data_file",
styr = styr,
endyr = endyr,
nseas = nseas,
months_per_seas = months_per_seas,
spawn_seas = spawn_seas,
Nfleet = Nfleet,
Nsurveys = Nsurveys,
N_areas = N_areas,
fleetnames = fleetnames,
surveytiming = surveytiming,
areas = areas,
units_of_catch = units_of_catch,
se_log_catch = se_log_catch,
fleetinfo1 = fleetinfo1,
fleetinfo2 = fleetinfo2,
Ngenders = Ngenders,
Nages = Nages,
init_equil = init_equil,
N_catch = N_catch,
catch = catch,
N_cpue = N_cpue,
CPUEinfo = CPUEinfo,
CPUE = CPUE,
N_discard_fleets = N_discard_fleets,
N_discard = N_discard,
discard_data = discard_data,
N_meanbodywt = N_meanbodywt,
meanbodywt = meanbodywt,
DF_for_meanbodywt=DF_for_meanbodywt,
lbin_method = lbin_method,
binwidth = binwidth,
minimum_size = minimum_size,
maximum_size = maximum_size,
comp_tail_compression = comp_tail_compression,
add_to_comp = add_to_comp,
max_combined_lbin = max_combined_lbin,
N_lbins = N_lbins,
lbin_vector = lbin_vector,
N_lencomp = N_lencomp,
lencomp = lencomp,
N_agebins = N_agebins,
agebin_vector = agebin_vector,
N_ageerror_definitions = N_ageerror_definitions,
ageerror = ageerror,
N_agecomp = N_agecomp,
agecomp = agecomp,
Lbin_method = Lbin_method,
max_combined_age = max_combined_age,
N_MeanSize_at_Age_obs = N_MeanSize_at_Age_obs,
MeanSize_at_Age_obs = MeanSize_at_Age_obs,
N_environ_variables = N_environ_variables,
N_environ_obs = N_environ_obs,
N_sizefreq_methods = N_sizefreq_methods,
do_tags = do_tags,
morphcomp_data = morphcomp_data
)
return(datlist)
}
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