# MCMC Generalised Linear Mixed Models

## Documentation for package ‘MCMCglmm’ version 2.32

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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
buildV | Forms expected (co)variances for GLMMs fitted with MCMCglmm
commutation | Commutation Matrix
dcmvnorm | Density of a (conditional) multivariate normal variate
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
gelman.prior | Prior Covariance Matrix for Fixed Effects.
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
list2bdiag | Forms the direct sum from a list of matrices
MCMCglmm | Multivariate Generalised Linear Mixed Models
me | Design Matrix for Measurement Error Model
mult.memb | Design Matrices for Multiple Membership Models
path | Design Matrix for Path Analyses
pkk | Probability that all multinomial categories have a non-zero count.
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.ante | Posterior distribution of ante-dependence parameters
posterior.cor | Transforms posterior distribution of covariances into correlations
posterior.evals | Posterior distribution of eigenvalues
posterior.inverse | Posterior distribution of matrix inverse
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
rtcmvnorm | Random Generation from a Truncated Conditional Normal Distribution
rtnorm | Random Generation from a Truncated Normal Distribution
simulate.MCMCglmm | Simulate method for GLMMs fitted with MCMCglmm
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