make.dat: writes and sets up an input data set (setup file) for IRATE...
In IRATER: A R Interface for the Instantaneous RATEs (IRATE) Model

Description Usage Arguments Author(s) References See Also

View source: R/make.dat.r

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

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
         
)

`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`)

Robert K. Bauer

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

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.