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MCMCglmm (version 2.35)

MCMC Generalised Linear Mixed Models

Description

Fits Multivariate Generalised Linear Mixed Models (and related models) using Markov chain Monte Carlo techniques (Hadfield 2010 J. Stat. Soft.).

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Version

Install

install.packages('MCMCglmm')

Monthly Downloads

9,015

Version

2.35

License

GPL (>= 2)

Maintainer

Jarrod Hadfield

Last Published

June 30th, 2023

Functions in MCMCglmm (2.35)

dcmvnorm

Density of a (conditional) multivariate normal variate
PlodiaRB

Resistance (as a binary trait) of Indian meal moth caterpillars to the granulosis virus PiGV.
buildV

Forms expected (co)variances for GLMMs fitted with MCMCglmm
krzanowski.test

Krzanowski's Comparison of Subspaces
Ptensor

Tensor of Sample (Mixed) Central Moments
knorm

(Mixed) Central Moments of a Multivariate Normal Distribution
mult.memb

Design Matrices for Multiple Membership Models
evalDtensor

Evaluates a list of (mixed) partial derivatives
path

Design Matrix for Path Analyses
pkk

Probability that all multinomial categories have a non-zero count.
me

Design Matrix for Measurement Error Model
plot.MCMCglmm

Plots MCMC chains from MCMCglmm using plot.mcmc
SShorns

Horn type and genders of Soay Sheep
Tri2M

Lower/Upper Triangle Elements of a Matrix
at.level

Incidence Matrix of Levels within a Factor
at.set

Incidence Matrix of Combined Levels within a Factor
inverseA

Inverse Relatedness Matrix and Phylogenetic Covariance Matrix
prunePed

Pedigree pruning
commutation

Commutation Matrix
rIW

Random Generation from the Conditional Inverse Wishart Distribution
posterior.ante

Posterior distribution of ante-dependence parameters
gelman.prior

Prior Covariance Matrix for Fixed Effects.
simulate.MCMCglmm

Simulate method for GLMMs fitted with MCMCglmm
posterior.mode

Estimates the marginal parameter modes using kernel density estimation
posterior.cor

Transforms posterior distribution of covariances into correlations
summary.MCMCglmm

Summarising GLMM Fits from MCMCglmm
predict.MCMCglmm

Predict method for GLMMs fitted with MCMCglmm
sir

Design Matrix for Simultaneous and Recursive Relationships between Responses
rbv

Random Generation of MVN Breeding Values and Phylogenetic Effects
residuals.MCMCglmm

Residuals form a GLMM fitted with MCMCglmm
rtnorm

Random Generation from a Truncated Normal Distribution
kunif

Central Moments of a Uniform Distribution
posterior.inverse

Posterior distribution of matrix inverse
plotsubspace

Plots covariance matrices
sm2asreml

Converts sparseMatrix to asreml's giv format
spl

Orthogonal Spline Design Matrix
posterior.evals

Posterior distribution of eigenvalues
list2bdiag

Forms the direct sum from a list of matrices
rtcmvnorm

Random Generation from a Truncated Conditional Normal Distribution
KPPM

Kronecker Product Permutation Matrix
MCMCglmm-package

Multivariate Generalised Linear Mixed Models
Dexpressions

List of unevaluated expressions for (mixed) partial derivatives of fitness with respect to linear predictors.
PlodiaPO

Phenoloxidase measures on caterpillars of the Indian meal moth.
PlodiaR

Resistance of Indian meal moth caterpillars to the granulosis virus PiGV.
Ddivergence

d-divergence
BTped

Blue Tit Pedigree
BTdata

Blue Tit Data for a Quantitative Genetic Experiment
MCMCglmm

Multivariate Generalised Linear Mixed Models
Dtensor

Tensor of (mixed) partial derivatives