nwfscDeltaGLM: Bayesian delta-GLM package for constructing indices of CPUE data
Version 1.0

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
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("nwfscDeltaGLM", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

ComputeIndices: Computes indices from fitted delta-GLMM model
ComputeMleIndices: Computes maximum likelihood indices from fitted delta-GLMM...
doMCMCDiags: doMCMCDiags is the master diagnostic function
fitDeltaGLM: Fitting Delta-Generalized Linear Mixed Models
MCMCDiagnosticsPlot: McmcDiagnosticsPlot does Gelman-Rubin and optionally Geweke...
nwfscDeltaGLM-package: Package for conducting Bayesian estimation of CPUE index...
SimSimple: SimSimple...
See all...

All man pages Function index File listing

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...

Functions

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

Files

DESCRIPTION
NAMESPACE
R
R/ComputeIndices.R
R/ComputeMleIndices.R
R/ConvergencePlot.r
R/LoadFn.r
R/MCMCDiagnosticsPlot.R
R/MapData.r
R/PlotData.R
R/PlotOffset.r
R/PosteriorPredictive.r
R/SimSimple.R
R/cMx.R
R/corFunction.r
R/doMCMCDiags.r
R/fitDeltaGLM.R
R/logDensity.R
R/onLoad.R
R/processData.r
R/readIn.R
R/strata.fn.r
R/updateDeltaGLMcode.R
data
data/AFSCforeign_hauls.txt.gz
data/Example_Species.txt.gz
data/SA3.txt.gz
examples
examples/Example_Species.csv
examples/Example_delta-GLMM.R
examples/Example_delta-GLMM_simulation.R
examples/INPFCandStateLatitudeBounds.txt
examples/Testing_delta-GLMM_calibration.R
examples/bayesGLM_Writeup_2.15.docx
examples/defaultLimits.csv
man
man/ComputeIndices.Rd
man/ComputeMleIndices.Rd
man/ConvergencePlot.Rd
man/MCMCDiagnosticsPlot.Rd
man/MapData.Rd
man/PlotData.Rd
man/PlotOffset.Rd
man/PosteriorPredictive.Rd
man/SimSimple.Rd
man/cMx.Rd
man/corFunction.Rd
man/doMCMCDiags.Rd
man/fitDeltaGLM.Rd
man/loadFn.Rd
man/logDensity.Rd
man/nwfscDeltaGLM-package.Rd
man/processData.Rd
man/readIn.Rd
man/strata.fn.Rd
nwfscDeltaGLM.Rproj
nwfscDeltaGLM documentation built on May 21, 2017, 3:55 a.m.

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