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 |

**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...

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? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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

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