remake.dat: load and reparameterize an existing IRATE-model setup file

Description Usage Arguments Details Author(s) See Also Examples

View source: R/remake.dat.r

Description

loads an existing IRATE-model setup file (incl. tag release and recapture data) and allows to reparameterize and save it as a new setup file for IRATE model runs. Note that reparameterization will depend on the tagging dataset inlcuded in the old setup. (e.g. a "harvest and catch-&-release"-serup is not feasable with a former harvest-only data set.)

Usage

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remake.dat(old.setup.name, new.setup.name, age.dependent=T,
           only.harvested=T,...)

Arguments

old.setup.name

character string defining the name of the existing IRATE-model setup file (.dat) to be loaded.

new.setup.name

character string defining the name of the IRATE-model setup file (.dat) to be created.

age.dependent

whether setup file should be created for an age dependent model (default = TRUE).

only.harvested

optional, whether actual releases of recaptures should be treated as harvested or a release-recapture model should be defined. (default = TRUE).

...

Additional arguments, see Details

Details

HM
hooking-mortality value for each recapture year (default = 0.09), only required for release-recapture model, otherwise being ignored.

eM,pM,sM,Mb
eM: whether to estimate natural mortality (default = TRUE),
if set TRUE:
pM: beginning years of different natural mortality periods,
sM: starting values of different natural mortality periods,
Mb: natural mortality lower and upper boundary values for model runs.

eF,pF,sF,Fb
eF: whether to estimate fishing mortality (default = TRUE),
if set TRUE:
pF: beginning years of different fishing mortality periods,
sF: starting values of different fishing mortality periods,
Fb: fishing mortality lower and upper boundary values for model runs.

eT=T,pT,sT,Tb
eT: whether to estimate tagging mortality (default = TRUE),
if set TRUE:
pT: beginning years of different tagging mortality periods,
sT: starting values of different tagging mortality periods,
Tb: tagging mortality lower and upper boundary values for model runs.

combine.Hrr_and_Rrr whether to combine Harvest & Release reporting rates (default = FALSE)

eHrr=F,pHrr,sHrr,Hrrb
eHrr: whether to estimate harvest reporting rates (default = FALSE),
if set TRUE:
pHrr: beginning years of different harvest reporting periods,
sHrr: starting values of different harvest reporting periods,
Hrrb: harvest reporting lower and upper boundary values for model runs.

eRrr=F,pRrr,sRrr,Rrrb
eRrr: whether to estimate release reporting rates (default = FALSE),
if set TRUE:
pRrr: beginning years of different release reporting periods,
sRrr: starting values of different release reporting periods,
Rrrb: release reporting lower and upper boundary values for model runs.

combine.HRS_and_RRS whether to combine Harvest & Release Retention Survival (default = FALSE)

eHRS=F,pHRS,sHRS,HRSb
eHRS: whether to estimate harvest-retention survival rates (default = FALSE),
if set TRUE:
pHRS: beginning years of harvest-retention survival periods,
sHRS: starting values of different-harvest retention survival periods,
HRSb: lower and upper boundary values of harvest-retention survival rates for model runs.

eRRS=F,pRRS,sRRS,RRSb
eRRS: whether to estimate release-retention survival rates (default = FALSE),
if set TRUE:
pRRS: beginning years of release-retention survival periods,
sRRS: starting values of different release-retention survival periods,
RRSb: lower and upper boundary values of release-retention survival rates for model runs.

incomplete.mix=F,pNonMix,sNonMix,NonMixb
incomplete.mix: whether to assume incomplete mixing of tagged and wild population (default = FALSE),
if set TRUE:
pNonMix: beginning years of incomplete mixing periods,
sNonMix: starting values of incomplete mixing periods,
NonMixb: of release-retention survival rates lower and upper boundary values for model runs.

combine.HS_and_RS whether to combine Harvest & Release Selectivity (default = TRUE)

eHS=F,pHS,sHS,HSb
eHS: whether to estimate age-depdendent harvest selectivity rates (default = FALSE),
if set TRUE:
pHS: beginning years of age-depdendent harvest selectivity periods,
sHS: starting values of age-depdendent harvest selectivity periods,
HSb: lower and upper boundary values of age-depdendent harvest selectivity rates for model runs.

eRS=F,pRS,sRS,RSb
eRS: whether to estimate age-depdendent release selectivity rates (default = FALSE),
if set TRUE:
pRS: beginning years of age-depdendent release selectivity periods,
sRS: starting values of age-depdendent release selectivity periods,
RSb: lower and upper boundary values of age-depdendent release selectivity rates for model runs.

eMS=F,aMS,sMS
eMS: whether to estimate age-depdendent natural mortality rates (default = TRUE; only considered if age.dependent is set TRUE),
if set TRUE:
aMS: beginning age classes of age-dependent natural mortality rates (age classes are counted from 1 onwards irrespective of their age-values),
sMS: starting values of (grouped) age-depdendent natural mortality rates,

use.L.const whether to set likelihood function constant (default = TRUE)

Author(s)

Robert K. Bauer

See Also

IRATE.examples, make.dat, read.dat

Examples

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# old.setup <- "JiangADCR" # select old IRATE setup to reparameterize 
# old.setup.path <- system.file(paste0("IRATE.examples/",old.setup,".dat"), package = "IRATER")

# new.setup <- new.setup.path <- "JiangAICR_manual"
# system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
# system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder

# setwd(new.setup.path)
# remake.dat(old.setup,new.setup,age.dependent = F) # reparameterize old setup
# run.IRATE(setup.new) # run new setup

IRATER documentation built on May 1, 2019, 7:32 p.m.