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

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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.

Author
Eric Ward, Jim Thorson, NOAA, NWFSC, Seattle, USA
Date of publication
2014-08-11 05:17:29
Maintainer
Eric Ward - NOAA Federal <eric.ward@noaa.gov>
License
GPL-2
Version
1.0

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Man pages

cMx
Converts and object to a matrix
ComputeIndices
Computes indices from fitted delta-GLMM model
ComputeMleIndices
Computes maximum likelihood indices from fitted delta-GLMM...
ConvergencePlot
Makes plots related to MCMC convergence diagnostics
corFunction
Function to calculate the correlations from the precision...
doMCMCDiags
doMCMCDiags is the master diagnostic function
fitDeltaGLM
Fitting Delta-Generalized Linear Mixed Models
loadFn
loadFn
logDensity
logDensity
MapData
MapData is function that makes a map by latitude / depth
MCMCDiagnosticsPlot
McmcDiagnosticsPlot does Gelman-Rubin and optionally Geweke...
nwfscDeltaGLM-package
Package for conducting Bayesian estimation of CPUE index...
PlotData
PlotData is the function that makes plots of raw data before...
PlotOffset
PlotOffset plots the positive and presence absence offset
PosteriorPredictive
PosteriorPredictive is the function that converts the raw...
processData
processData is the function that converts the raw trawl data...
readIn
readIn...
SimSimple
SimSimple...
strata.fn
strata.fn...

Files in this package

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