Man pages for stevencarlislewalker/lme4ord
Generalized Linear Mixed Models with Flexible (Co)Variance Structures
| 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 |
