fcs2WriteModel: Write BUGS Model File

In aquaMetrics/fcs2: Fisheries Classification Scheme 2 For SNIFFER

Description

Creates a BUGS model file that describes the structure of the full FCS2 statistical model. This can be used by WinBUGS or OpenBUGS to fit the model.

Usage

fcs2WriteModel(
  filename = "model.bug",
  muLinearVars = c(),
  muRWVars = c(),
  muSpatialVar = NULL,
  rhoLinearVars = c(),
  rhoRWVars = c(),
  rhoSpatialVar = NULL,
  multiRun = FALSE,
  catchTotal = TRUE,
  catchRange = FALSE,
  qUnif = FALSE
)

Arguments

filename	the name or the BUGS model file to create.
muLinearVars	a character vector of linear terms in the abundance regression
muRWVars	a character vector of variables with first or second-order random walk terms in the abundance regression.
muSpatialVar	the name of the abundance spatial variable, if present.
rhoLinearVars	a character vector of linear terms in the abundance regression
rhoRWVars	a character vector of variables with first or second-order random walk terms in the prevalence regression.
rhoSpatialVar	the name of the prevalence spatial variable, if present.
multiRun	whether the multiple-run extension to the FCS2 model is required.
catchTotal	whether catch total data are present in the model.
catchRange	whether catch total range data are present in the model.
qUnif	whether to use a uniform prior for the catch probability q rather than the default beta prior. Although the uniform is a special case of the beta, this option may help BUGS fit the model.

Note

The user would not usually call this function directly as it is called if required by fcs2FitModel. However, it may be useful for creating a BUGS model file to be run by WinBUGS or OpenBUGS extenally.

See Also

fcs2FitModel

aquaMetrics/fcs2 documentation built on Aug. 21, 2021, 12:55 p.m.