# MCMC Generalised Linear Mixed Models

## Documentation for package ‘MCMCglmm’ version 2.15

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

MCMCglmm-package | Multivariate Generalised Linear Mixed Models
at.level | Incidence Matrix of Levels within a Factor
at.set | Incidence Matrix of Combined Levels within a Factor
BTdata | Blue Tit Data for a Quantitative Genetic Experiment
BTped | Blue Tit Pedigree
commutation | Commutation Matrix
Ddivergence | d-divergence
Dexpressions | List of unevaluated expressions for (mixed) partial derivatives of fitness with respect to linear predictors.
Dtensor | Tensor of (mixed) partial derivatives
evalDtensor | Evaluates a list of (mixed) partial derivatives
inverseA | Inverse Relatedness Matrix and Phylogenetic Covariance Matrix
knorm | (Mixed) Central Moments of a Multivariate Normal Distribution
KPPM | Kronecker Product Permutation Matrix
krzanowski.test | Krzanowski's Comparison of Subspaces
kunif | Central Moments of a Uniform Distribution
leg | Evaluates Orthogonal Legendre Polynomials
list2bdiag | Forms the direct sum from a list of matrices
MCMCglmm | Multivariate Generalised Linear Mixed Models
mult.memb | Design Matrices for Multiple Membership Models
PlodiaPO | Phenoloxidase measures on caterpillars of the Indian meal moth.
PlodiaR | Resistance of Indian meal moth caterpillars to the granulosis virus PiGV.
PlodiaRB | Resistance (as a binary trait) of Indian meal moth caterpillars to the granulosis virus PiGV.
plot.MCMCglmm | Plots MCMC chains from MCMCglmm using plot.mcmc
plotsubspace | Plots covariance matrices
posterior.cor | Transforms posterior distribution of covariances into correlations
posterior.evals | Posterior distribution of eigenvalues
posterior.mode | Estimates the marginal parameter modes using kernel density estimation
predict.MCMCglmm | Predict method for GLMMs fitted with MCMCglmm
print.MCMCglmm | Summarising GLMM Fits from MCMCglmm
print.summary.MCMCglmm | Summarising GLMM Fits from MCMCglmm
prunePed | Pedigree pruning
Ptensor | Tensor of Sample (Mixed) Central Moments
rbv | Random Generation of MVN Breeding Values and Phylogenetic Effects
residuals.MCMCglmm | Residuals form a GLMM fitted with MCMCglmm
rIW | Random Generation from the Conditional Inverse Wishart Distribution
rtnorm | Random Generation from a Truncated Normal Distribution
sir | Design Matrix for Simultaneous and Recursive Relationships between Responses
sm2asreml | Converts sparseMatrix to asreml's giv format
spl | Orthogonal Spline Design Matrix
SShorns | Horn type and genders of Soay Sheep
summary.MCMCglmm | Summarising GLMM Fits from MCMCglmm
Tri2M | Lower/Upper Triangle Elements of a Matrix