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