make.dat: writes and sets up an input data set (setup file) for IRATE...

Description Usage Arguments Author(s) References See Also

View source: R/make.dat.r

Description

writes and sets up an input data set (setup file) for IRATE model runs. Obligatory arguments are: setup.file.name, releases and recapture

Usage

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make.dat(setup.file.name, releases, recaptures, age.dependent=F,only.harvested=F,HM
         ,eM=T,pM,sM,Mb # natural mortality settings
         ,eF=T,pF,sF,Fb # fishing mortality settings
         ,eT=T,pT,sT,Tb # tagging mortality settings
         ,combine.Hrr_and_Rrr=F # combine Harvest & Release reporting rates
         ,eHrr=F,pHrr,sHrr,Hrrb # Harvest reporting rates
         ,eRrr=F,pRrr,sRrr,Rrrb # Release reporting rates
         ,combine.HRS_and_RRS=F # combine Harvest & Release Retention Survival
         ,eHRS=F,pHRS,sHRS,HRSb #  Harvest Retention Survival
         ,eRRS=F,pRRS,sRRS,RRSb #  Release Retention Survival
         ,incomplete.mix=F,pNonMix,sNonMix,NonMixb #  Non-Mixing
         ,combine.HS_and_RS=T # combine Harvest & Release Selectivity
         ,eHS=T,sHS,HSb # age-depdendent Harvest Selectivity
         ,eRS=F,sRS,RSb # age-depdendent Release Selectivity
         ,eMS=T,aMS,sMS # age-depdendent M Selectivity
         ,use.L.const=T # Likelihood Constant
         
)

Arguments

setup.file.name

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

releases

raw data.frame with release dates (rel.date in "Date"-format) as well as the age (numeric) of released individuals (if age dependent).

recaptures

raw data.frame with release & recpature dates (rel.date, rec.date in "Date"-format) as well as the age (numeric) of recaptured individuals and a vector harvested to indicate whether recaptured individuals were harvested or released (if age dependent).

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).

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,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,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,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,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,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,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,sHS,HSb

eHS: whether to estimate age-depdendent harvest selectivity rates (default = FALSE), if set TRUE:
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,sRS,RSb

eRS: whether to estimate age-depdendent release selectivity rates (default = FALSE), if set TRUE:
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,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

References

http://nft.nefsc.noaa.gov/IRATE.html

See Also

To check model setup files in detail see: read.dat.
To alter existent model setup files see: remake.dat.
To read model run results see: read.rep and read.par.
For preinstalled example runs and setup data see: run.IRATE.example.
To delete run files see: clean.IRATE.
For more information on admb model compiliation and run prodcudres see: compile_admb and run_admb from the R2admb-package


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