Files in stevencarlislewalker/lme4ord
Generalized Linear Mixed Models with Flexible (Co)Variance Structures
.Rbuildignore
DESCRIPTION
NAMESPACE
R/devianceFunctionConstruction.R
R/formulaParsing.R
R/laplace.R
R/lme4ord.R
R/nodeModel.R
R/optimization.R
R/outputAndInference.R
R/randomEffectsStructures.R
R/structuredGLMM.R
R/structuredSparseMatrices.R
R/utilities.R
R/zzz.R
README.md
inst/README/Makefile
inst/README/README.R
inst/README/README.Rmd
inst/README/figure/plot Zt-1.png
inst/README/figure/plot full cov-1.png
inst/README/figure/plot lambda-1.png
inst/README/figure/plot lambda-2.png
inst/README/figure/plot phylogeny-1.png
inst/README/figure/plot phylogeny-2.png
inst/README/figure/plot sim data-1.png
inst/README/figure/unnamed-chunk-1-1.png
inst/README/figure/unnamed-chunk-1-2.png
inst/README/figure/unnamed-chunk-4-1.png
inst/README/figure/unnamed-chunk-5-1.png
inst/README/figure/unnamed-chunk-6-1.png
inst/README/futureREADME.R
inst/README/oldREADME.Rmd
inst/extraData/loon.csv
inst/githubIssues/confInt/Makefile
inst/githubIssues/confInt/confInt.Rmd
inst/githubIssues/confInt/confInt.md
inst/githubIssues/confInt/figure/unnamed-chunk-4-1.png
inst/misc/customKronecker.R
inst/misc/edgeModel/edgeModel.R
inst/misc/fish.R
inst/misc/gblmer.R
inst/misc/generalDevfuns/Makefile
inst/misc/generalDevfuns/generalDevfuns.R
inst/misc/generalDevfuns/generalDevfuns.Rnw
inst/misc/generalDevfuns/generalDevfuns.pdf
inst/misc/generalDevfuns/generalDevfuns.tex
inst/misc/glmerf.R
inst/misc/matchingWithTony.R
inst/misc/mkGeneralGlmerDevfun.R
inst/misc/mkPenaltyFunction.R
inst/misc/modelDescription/Makefile
inst/misc/modelDescription/modelDescription.pdf
inst/misc/modelDescription/modelDescription.tex
inst/misc/modelSpecificationTools.R
inst/misc/notesOnGlmerDevfuns/Makefile
inst/misc/notesOnGlmerDevfuns/notesOnGlmerDevfuns.Rmd
inst/misc/notesOnGlmerDevfuns/notesOnGlmerDevfuns.md
inst/misc/old.R
inst/misc/pglmer.R
inst/misc/pglmm.R
inst/modelTypes/expDecay/expDecay.Rnw
inst/modelTypes/expDecay/expDecay.pdf
inst/modelTypes/factAnal/factAnal.Rnw
inst/modelTypes/factAnal/factAnal.pdf
inst/skeletons/setReTrm.R
inst/testdata/mkSimDat.R
man-roxygen/setReTrm.R
man/Ops.strucMatrix.Rd
man/as.strucMatrix.Rd
man/assignWith.Rd
man/bind.Rd
man/changeSparseFormat.Rd
man/chol.Rd
man/compressStrucGlmer.Rd
man/count.Rd
man/covExpDecay.Rd
man/denseInds.Rd
man/edgeTipIndicator.Rd
man/factors.Rd
man/family.strucGlmer.Rd
man/familySimFun.Rd
man/figures/modularizationDiagram.png
man/flattenIntVec.Rd
man/getInit.Rd
man/getModMatAndGrpFac.Rd
man/getReTrm.Rd
man/getRepPattern.Rd
man/kron.Rd
man/langOps.Rd
man/laplace.Rd
man/listOfSubscriptingCallsWithListOfIndices.Rd
man/listTranspose.Rd
man/lme4ord.Rd
man/mkGeneralGlmerDevfun.Rd
man/mkParInds.Rd
man/mkPenaltyFun.Rd
man/mkReTrmStructs.Rd
man/mkSparseTrans.Rd
man/mkTrans.Rd
man/nChoose2Inv.Rd
man/orthProcrustesRotMat.Rd
man/packReTrm.Rd
man/parLength.Rd
man/pars.Rd
man/printReTrm.Rd
man/rStrucMatrix.Rd
man/resetTransConst.Rd
man/scalarMult.Rd
man/setLowerUpperDefault.Rd
man/setReTrm.Rd
man/setReTrm.cooccur.Rd
man/setReTrm.expDecay.Rd
man/setReTrm.factAnal.Rd
man/setReTrm.flexvar.Rd
man/setReTrm.identity.Rd
man/setReTrm.lme4.Rd
man/setReTrm.nlmeCorStruct.Rd
man/setReTrm.obslev.Rd
man/setReTrm.phyloEdge.Rd
man/setReTrm.sem.Rd
man/setReTrm.varExp.Rd
man/setReTrm.varIdent.Rd
man/showSkeleton.Rd
man/simAddArgs.Rd
man/simReTrm.Rd
man/simStrucParsedForm.Rd
man/simplifyFacList.Rd
man/simplifyStrucMatrix.Rd
man/sort.strucMatrix.Rd
man/sortedBind.Rd
man/splitForm.Rd
man/stanCov.Rd
man/strucGlmer-class.Rd
man/strucGlmer.Rd
man/strucMatrix-class.Rd
man/strucMatrix.Rd
man/strucMatrixBlank.Rd
man/strucMatrixCol.Rd
man/strucMatrixCompSymm.Rd
man/strucMatrixConstVarChol.Rd
man/strucMatrixCorFactor.Rd
man/strucMatrixCorMatChol.Rd
man/strucMatrixDiag.Rd
man/strucMatrixExpChol.Rd
man/strucMatrixFull.Rd
man/strucMatrixGenFullTri.Rd
man/strucMatrixIdent.Rd
man/strucMatrixInd.Rd
man/strucMatrixOneOffDiag.Rd
man/strucMatrixOnes.Rd
man/strucMatrixSymm.Rd
man/strucMatrixTri.Rd
man/strucMatrixVarWithCovariate.Rd
man/strucMkDevfun.Rd
man/strucOpt.Rd
man/strucParseFormula.Rd
man/subset.Rd
man/tipNodeRelationship.Rd
man/triInds.Rd
man/update.reTrmStruct.Rd
tests/factAnal.R
tests/familySimFun.R
tests/gaussianFamily.R
tests/generalGlmer.R
tests/loon.R
tests/nChoose2Inv.R
tests/nlmeCorStructCorBrownian.R
tests/nlmeCorStructExpVar.R
tests/phyloEdge.R
tests/splitForm.R
tests/strucMatrix.R
tests/update.R
