nwfscDeltaGLM: Bayesian delta-GLM package for constructing indices of CPUE data

The nwfscDeltaGLM package provides a Bayesian framework for constructing CPUE indices out of stratified survey (or commercial) fisheries landings data. The model can also be applied to similarly stratified bycatch data. The model is very flexible, optionally allowing the incorporation of strata, year, and vessel effects, strata x year and vessel x year interactions, and fixed covariates. Several parameterization for including offsets (effort) are also included. Each of these can be included in the presence-absence (occupancy) model or the positive component of the delta-GLM model.

AuthorEric Ward, Jim Thorson, NOAA, NWFSC, Seattle, USA
Date of publication2014-08-11 05:17:29
MaintainerEric Ward - NOAA Federal <eric.ward@noaa.gov>
LicenseGPL-2
Version1.0

View on R-Forge

Functions

cMx Man page
ComputeIndices Man page
ComputeMleIndices Man page
ConvergencePlot Man page
corFunction Man page
doMCMCDiags Man page
fitDeltaGLM Man page
loadFn Man page
logDensity Man page
MapData Man page
McmcDiagnosticsPlot Man page
nwfscDeltaGLM Man page
nwfscDeltaGLM-package Man page
PlotData Man page
PlotOffset Man page
PosteriorPredictive Man page
processData Man page
readIn Man page
SimSimple Man page
strata.fn Man page

Files

nwfscDeltaGLM/DESCRIPTION
nwfscDeltaGLM/NAMESPACE
nwfscDeltaGLM/R
nwfscDeltaGLM/R/ComputeIndices.R nwfscDeltaGLM/R/ComputeMleIndices.R
nwfscDeltaGLM/R/ConvergencePlot.r
nwfscDeltaGLM/R/LoadFn.r
nwfscDeltaGLM/R/MCMCDiagnosticsPlot.R
nwfscDeltaGLM/R/MapData.r
nwfscDeltaGLM/R/PlotData.R
nwfscDeltaGLM/R/PlotOffset.r
nwfscDeltaGLM/R/PosteriorPredictive.r
nwfscDeltaGLM/R/SimSimple.R nwfscDeltaGLM/R/cMx.R
nwfscDeltaGLM/R/corFunction.r
nwfscDeltaGLM/R/doMCMCDiags.r
nwfscDeltaGLM/R/fitDeltaGLM.R nwfscDeltaGLM/R/logDensity.R nwfscDeltaGLM/R/onLoad.R
nwfscDeltaGLM/R/processData.r
nwfscDeltaGLM/R/readIn.R
nwfscDeltaGLM/R/strata.fn.r
nwfscDeltaGLM/R/updateDeltaGLMcode.R
nwfscDeltaGLM/data
nwfscDeltaGLM/data/AFSCforeign_hauls.txt.gz
nwfscDeltaGLM/data/Example_Species.txt.gz
nwfscDeltaGLM/data/SA3.txt.gz
nwfscDeltaGLM/examples
nwfscDeltaGLM/examples/Example_Species.csv
nwfscDeltaGLM/examples/Example_delta-GLMM.R
nwfscDeltaGLM/examples/Example_delta-GLMM_simulation.R
nwfscDeltaGLM/examples/INPFCandStateLatitudeBounds.txt
nwfscDeltaGLM/examples/Testing_delta-GLMM_calibration.R
nwfscDeltaGLM/examples/bayesGLM_Writeup_2.15.docx
nwfscDeltaGLM/examples/defaultLimits.csv
nwfscDeltaGLM/man
nwfscDeltaGLM/man/ComputeIndices.Rd nwfscDeltaGLM/man/ComputeMleIndices.Rd nwfscDeltaGLM/man/ConvergencePlot.Rd nwfscDeltaGLM/man/MCMCDiagnosticsPlot.Rd nwfscDeltaGLM/man/MapData.Rd nwfscDeltaGLM/man/PlotData.Rd nwfscDeltaGLM/man/PlotOffset.Rd nwfscDeltaGLM/man/PosteriorPredictive.Rd nwfscDeltaGLM/man/SimSimple.Rd nwfscDeltaGLM/man/cMx.Rd nwfscDeltaGLM/man/corFunction.Rd nwfscDeltaGLM/man/doMCMCDiags.Rd nwfscDeltaGLM/man/fitDeltaGLM.Rd nwfscDeltaGLM/man/loadFn.Rd nwfscDeltaGLM/man/logDensity.Rd nwfscDeltaGLM/man/nwfscDeltaGLM-package.Rd nwfscDeltaGLM/man/processData.Rd nwfscDeltaGLM/man/readIn.Rd nwfscDeltaGLM/man/strata.fn.Rd
nwfscDeltaGLM/nwfscDeltaGLM.Rproj

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.