gjam: Generalized Joint Attribute Modeling
Version 2.1.4

Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling.

Browse man pages Browse package API and functions Browse package files

AuthorJames S. Clark, Daniel Taylor-Rodriquez
Date of publication2017-05-11 15:59:03 UTC
MaintainerJames S. Clark <jimclark@duke.edu>
LicenseGPL (>= 2)
Version2.1.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("gjam")

Man pages

gjam: Gibbs sampler for gjam data
gjamCensorY: Censor gjam response data
gjamDeZero: Compress (de-zero) gjam data
gjamIIE: Indirect effects and interactions for gjam data
gjamIIEplot: Plots indirect effects and interactions for gjam data
gjamOrdination: Ordinate gjam data
gjam-package: Generalized Joint Attribute Modeling
gjamPlot: Plot gjam analysis
gjamPoints2Grid: Incidence point pattern to grid counts
gjamPredict: Predict gjam data
gjamPriorTemplate: Prior coefficients for gjam analysis
gjamReZero: Expand (re-zero) gjam data
gjamSimData: Simulated data for gjam analysis
gjamSpec2Trait: Ecological traits for gjam analysis
gjamTrimY: Trim gjam response data

Functions

GJAM Man page
add2matrix Source code
alphaPrior Source code
any_naCpp Source code
appendMatrix Source code
betaPrior Source code
betaWrapper Source code
between Source code
bins4data Source code
blockDiag Source code
boxplotQuant Source code
buildEffort Source code
buildYdata Source code
byGJAM Source code
byIndex Source code
byProdRcpp Source code
byRcpp Source code
capFirstLetter Source code
censorValues Source code
chains2density Source code
checkDesign Source code
checkYfactor Source code
cleanNames Source code
clusterPlot Source code
clusterWithGrid Source code
colorLegend Source code
colorSequence Source code
combineFacLevels Source code
condMVNRcpp Source code
conditionalMVN Source code
contrastCoeff Source code
cor2Cov Source code
corPlot Source code
cov2Cor Source code
cov2Dist Source code Source code
dMVN Source code
directIndirectCoeffs Source code
distanceMatrix Source code
expandSigma Source code
expandSigmaChains Source code
factorCoeffs2Zero Source code
figure1 Source code
fillMissingTimes Source code
fitText2Fig Source code
fnZRcpp Source code
getColor Source code
getContrasts Source code
getHoldLoHi Source code
getPars Source code
getPattern Source code
getPlotLayout Source code
getPmatKRcpp Source code
getScoreNorm Source code
getSigTable Source code
getStandX Source code
getTimeIndex Source code
getURowCol Source code
getUnstandX Source code
gjam Man page Source code Source code
gjam-package Man page
gjamBaselineHist Source code
gjamCensorSetup Source code
gjamCensorY Man page Source code
gjamCompW2Y Source code
gjamCuts2theta Source code
gjamDeZero Man page Source code
gjamGetCuts Source code
gjamGetTypes Source code
gjamHoldoutSetup Source code
gjamIIE Man page Source code
gjamIIEplot Man page Source code
gjamMissingValues Source code
gjamOrd Source code
gjamOrdination Man page Source code
gjamPlot Man page Source code Source code
gjamPlotPars Source code
gjamPoints2Grid Man page Source code
gjamPredict Man page Source code
gjamPredictTraits Source code
gjamPrediction Source code
gjamPriorTemplate Man page Source code
gjamReZero Man page Source code
gjamSetup Source code
gjamSimData Man page Source code
gjamSpec2Trait Man page Source code
gjamTrimY Man page Source code
gjamTrueVest Source code
gjamWLoop Source code
gjamWLoopTypes Source code
gjamWcatLoop Source code
gjamWcatLoop2 Source code
gjamXY Source code
invWbyRcpp Source code
lambdaPrior Source code
lowerFirstLetter Source code
mapSetup Source code
modalValuesInArray Source code
mputX_MVN Source code
multivarChainNames Source code
myBoxPlot Source code
ncidence2Grid Source code
nitW Source code
nteractionsFromGibbs Source code
nterp Source code
nterpRows Source code
nvMatZero Source code
nvertCondKronecker Source code
nvertSigma Source code
omitChainCol Source code
ordTraitsFromWts Source code
outFile Source code
paramWrapper Source code
pasteCols Source code
plotLabel Source code
plotObsPred Source code
plotXbyY Source code
predVsObs Source code
predictY2X_linear Source code
predictY2X_nonLinear Source code
print.gjam Man page Source code
processPars Source code
rMVN Source code
replaceString Source code
riwish Source code
rmatrixnormRcpp Source code
rmvnormArma2 Source code
rmvnormRcpp Source code
rwish Source code
sameByColumn Source code
sampleP Source code
setContrasts Source code
setLoHi Source code
setUpSim Source code
setupFactors Source code
setupReduct Source code
simData Source code
solveRcpp Source code
spec2Trait Source code
splitNames Source code
sqrtRootMatrix Source code
stackedBoxPlot Source code
summary.gjam Man page Source code
summaryWords Source code
tnorm Source code
tnormMVNmatrix Source code
tnormRcpp Source code
tnorm_cpp Source code
trMVNmatrixRcpp Source code
traitLabel Source code
traitTables Source code
updateBetaMet Source code
updateBetaTime Source code
updateTheta Source code
updateWishartNoPrior Source code
wWrapper Source code
wWrapperTime Source code
whichFactor Source code
xpredSetup Source code
yaxisHorizLabs Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/gjamVignette.Rmd
inst/doc/gjamVignette.R
inst/doc/gjamVignette.html
src
src/Makevars
src/Makevars.win
src/init.c
src/RcppExports.cpp
src/cppFns.cpp
NAMESPACE
R
R/gjamPlot.r
R/gjamPredict.r
R/gjamPoints2Grid.R
R/gjamReZero.r
R/gjamHfunctions.R
R/gjamPriorTemplate.r
R/RcppExports.R
R/gjamDeZero.r
R/gjamOrdination.R
R/gjamSpec2Trait.r
R/gjamTrimY.r
R/gjamIIEplot.r
R/gjamSimData.r
R/gjamCensorY.r
R/gjam.r
R/gjamIIE.r
vignettes
vignettes/gjamVignette.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/gjamPoints2Grid.Rd
man/gjamSpec2Trait.Rd
man/gjamPriorTemplate.Rd
man/gjamPlot.Rd
man/gjamSimData.Rd
man/gjamCensorY.Rd
man/gjamPredict.Rd
man/gjam-package.Rd
man/gjamOrdination.Rd
man/gjamReZero.Rd
man/gjamDeZero.Rd
man/gjamTrimY.Rd
man/gjam.Rd
man/gjamIIE.Rd
man/gjamIIEplot.Rd
gjam documentation built on May 19, 2017, 10:43 p.m.