assignWith | Assign to an environment the value of an expression evaluated... |
as.strucMatrix | Coerce to and from structured sparse matrices |
bind | Row, column, and block-diagonal binding for structured sparse... |
changeSparseFormat | Changing sparse format |
chol | Cholesky decomposition of structured sparse matrices |
compressStrucGlmer | Compress strucGlmer object |
count | Count unique values |
covExpDecay | Exponentially decaying covariances |
denseInds | Indices for square dense matrices |
edgeTipIndicator | Relationships between tips and edges |
factors | Extract factors |
familySimFun | Family simulation functions |
family.strucGlmer | Extract family object |
flattenIntVec | Flatten an integer vector |
getInit | Get and set initial parameter values for structured sparse... |
getModMatAndGrpFac | Get model matrix and grouping factor |
getRepPattern | Get repetition pattern of a structured sparse matrix |
getReTrm | Get random effects structures from a strucGlmer object |
kron | Kronecker and Khatri-Rao products for structured sparse... |
langOps | Tools for constructing formula terms |
laplace | Laplace approximation |
listOfSubscriptingCallsWithListOfIndices | List of subscripting calls with a list of indices |
listTranspose | Transpose a list |
lme4ord | 'lme4ord': Generalized Linear Mixed Models with Flexible... |
mkGeneralGlmerDevfun | Make a general (Laplace) glmer deviance function |
mkParInds | Make parameter indices |
mkPenaltyFun | Make penalty function |
mkReTrmStructs | Construct random effects structures |
mkSparseTrans | Make transformation function to be used with a... |
mkTrans | Construct functions for transforming a parameter vector to... |
nChoose2Inv | Inverse of the n-choose-2 function |
Ops.strucMatrix | Structured sparse matrix multiplication (and other binary... |
orthProcrustesRotMat | Orthogonal procrustean rotation matrix |
packReTrm | Package up a random effects term structure |
parLength | Lengths of parameter vectors |
pars | Parameter retrieval for structured generalized linear mixed... |
printReTrm | Print random effects term |
resetTransConst | Constant structured sparse matrix |
rStrucMatrix | Random structured sparse matrices |
scalarMult | Add scalar multiple to a structured sparse matrix |
setLowerUpperDefault | Get defaults choices for lower and/or upper bound of a model... |
setReTrm | Set model matrix slice and relative covariance factor block... |
setReTrm.cooccur | Random effects term for cooccurence model (experimental) |
setReTrm.expDecay | Random effects term with exponential decay in distance-based... |
setReTrm.factAnal | Random effects term for factor analysis |
setReTrm.flexvar | Random effects term for a flexible variance function |
setReTrm.identity | Random effects term for covariance proportional to identity... |
setReTrm.lme4 | lme4 emulator |
setReTrm.nlmeCorStruct | Random effects term from an 'nlme'-style 'corStruct' object |
setReTrm.obslev | Random effects term with observation level random effects |
setReTrm.phyloEdge | Random effects term for edge-based model of tree-induced... |
setReTrm.sem | Random effects term for structural equation model |
setReTrm.varExp | Random effects term with exponential variance structure |
setReTrm.varIdent | Random effects term with constant variance within groups |
showSkeleton | Show skeleton for some type of function |
simAddArgs | Simulate additional arguments (experimental) |
simplifyFacList | Simplify factor list over random effects terms (not currently... |
simplifyStrucMatrix | Simplify structured sparse matrices |
simReTrm | Simulate from a random effects term |
simStrucParsedForm | Simulate from a parsed formula |
sortedBind | Bind repeated sparse matrices and sort their indices to be... |
sort.strucMatrix | Sort the indices of a structured sparse matrix |
splitForm | Split a formula |
stanCov | Standardize covariance matrix to determinant one |
strucGlmer | Generalized linear mixed model with structured (co)variance... |
strucGlmer-class | Structured GLMM class |
strucMatrix | Structured sparse matrices |
strucMatrixBlank | Blank structured sparse matrix |
strucMatrix-class | A structured sparse matrix class |
strucMatrixCol | Column vector as structured sparse matrix |
strucMatrixCompSymm | Structured sparse matrix with compound symmetry |
strucMatrixConstVarChol | Structured sparse Cholesky factor leading to constant... |
strucMatrixCorFactor | Construct a structured sparse upper Cholesky factor from an... |
strucMatrixCorMatChol | Structured sparse Cholesky factor of a correlation matrix |
strucMatrixDiag | Diagonal structured sparse matrix |
strucMatrixExpChol | Cholesky factor of a structured sparse covariance matrix... |
strucMatrixFull | Full structured sparse matrix |
strucMatrixGenFullTri | General and full triangular structured sparse matrix |
strucMatrixIdent | Identity structured sparse matrix |
strucMatrixInd | Structured sparse indicator matrix |
strucMatrixOneOffDiag | Structured sparse matrix with only one non-zero value off the... |
strucMatrixOnes | Structured sparse matrix of ones |
strucMatrixSymm | Symmetric structured sparse matrix |
strucMatrixTri | Triangular structured sparse matrix |
strucMatrixVarWithCovariate | Structured sparse diagonal covariance matrix with a covariate... |
strucMkDevfun | Make a (Laplace) glmer deviance function from a parsed... |
strucOpt | Optimize a structured GLMM deviance function |
strucParseFormula | Parse a mixed model formula |
subset | Subsetting structured sparse matices |
tipNodeRelationship | Tip-node bigraph adjacency matrix |
triInds | Convert row and column indices to vector indices, for a... |
update.reTrmStruct | Update a random effects term structure with new parameters |
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