Last chance! 50% off unlimited learning
Sale ends in
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
).dat) to be created.
data.frame with release dates (rel.date in "Date"-format) as well as the age (numeric) of released individuals (if age dependent).
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).
TRUE).
TRUE).
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: 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: 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.
FALSE)
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: 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.
FALSE)
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: 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: 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.
TRUE)
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: 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: 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,
TRUE)