Package: MCMCglmm 2.37

MCMCglmm: MCMC Generalised Linear Mixed Models

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

Authors:Jarrod Hadfield [aut, cre]

MCMCglmm_2.37.tar.gz
MCMCglmm_2.37.zip(r-4.7)MCMCglmm_2.37.zip(r-4.6)MCMCglmm_2.37.zip(r-4.5)
MCMCglmm_2.37.tgz(r-4.6-x86_64)MCMCglmm_2.37.tgz(r-4.6-arm64)MCMCglmm_2.37.tgz(r-4.5-x86_64)MCMCglmm_2.37.tgz(r-4.5-arm64)
MCMCglmm_2.37.tar.gz(r-4.7-arm64)MCMCglmm_2.37.tar.gz(r-4.7-x86_64)MCMCglmm_2.37.tar.gz(r-4.6-arm64)MCMCglmm_2.37.tar.gz(r-4.6-x86_64)
MCMCglmm_2.37.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MCMCglmm/json (API)

# Install 'MCMCglmm' in R:

install.packages('MCMCglmm', repos = c('https://jarrodhadfield.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jarrodhadfield/mcmcglmm/issues

Pkgdown/docs site:https://jarrodhadfield.github.io

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

ABPvirus - Data on Acute Bee Paralysis Virus Infections in Bumblebees from Pascall et al. (2018).
BTdata - Blue Tit Data for a Quantitative Genetic Experiment
BTped - Blue Tit Pedigree
FullGrumpy - Full Grumpy Scores of Academics
Grumpy - Grumpy Scores of Academics
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.
sigma - Infection Data for Sigma Virus in _Drosophila melanogaster_
SShorns - Horn type and genders of Soay Sheep
tufted_puffin - Diet composition of Tufted Puffin

On CRAN:

cpp

11.16 score 5 stars 12 packages 2.1k scripts 11k downloads 477 mentions 49 exports 11 dependencies

Last updated from:6291bfef47. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	176
linux-devel-x86_64	OK	177
source / vignettes	OK	226
linux-release-arm64	OK	176
linux-release-x86_64	OK	170
macos-release-arm64	OK	208
macos-release-x86_64	OK	319
macos-oldrel-arm64	OK	183
macos-oldrel-x86_64	OK	432
windows-devel	OK	170
windows-release	OK	184
windows-oldrel	OK	170
wasm-release	OK	126

Exports:at.level at.set buildV commutation dcmvnorm Ddivergence Dexpressions dprior Dtensor evalDtensor F gelman.prior IG inverseA IW knorm KPPM krzanowski.test kunif list2bdiag MCMCglmm me mult.memb path pkk plot.MCMCglmm plotsubspace posterior.ante posterior.cor posterior.evals posterior.inverse posterior.mode predict.MCMCglmm prunePed Ptensor rbv residuals.MCMCglmm resolve_prior rIW rprior rtcmvnorm rtnorm simulate.MCMCglmm sir sm2asreml spl summary.MCMCglmm Tri2M tSD

Dependencies:ape coda corpcor cubature digest lattice MASS Matrix nlme Rcpp tensorA

MCMCglmm Course Notes

Rendered fromCourseNotes.Rmdusingknitr::rmarkdown

Last update: 2026-01-05
Started: 2025-12-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Multivariate Generalised Linear Mixed Models	MCMCglmm-package
Data on Acute Bee Paralysis Virus Infections in Bumblebees from Pascall et al. (2018).	ABPvirus
Incidence Matrix of Levels within a Factor	at.level
Incidence Matrix of Combined Levels within a Factor	at.set
Blue Tit Data for a Quantitative Genetic Experiment	BTdata
Blue Tit Pedigree	BTped
Forms expected (co)variances for GLMMs fitted with MCMCglmm	buildV
Commutation Matrix	commutation
Density of a (conditional) multivariate normal variate	dcmvnorm
d-divergence	Ddivergence
List of unevaluated expressions for (mixed) partial derivatives of fitness with respect to linear predictors.	Dexpressions
Prior Density of Variance or Standard Deviation	dprior
Tensor of (mixed) partial derivatives	Dtensor
Evaluates a list of (mixed) partial derivatives	evalDtensor
Full Grumpy Scores of Academics	FullGrumpy
Prior Covariance Matrix for Fixed Effects.	gelman.prior
Grumpy Scores of Academics	Grumpy
Inverse Relatedness Matrix and Phylogenetic Covariance Matrix	inverseA
(Mixed) Central Moments of a Multivariate Normal Distribution	knorm
Kronecker Product Permutation Matrix	KPPM
Krzanowski's Comparison of Subspaces	krzanowski.test
Central Moments of a Uniform Distribution	kunif
Forms the direct sum from a list of matrices	list2bdiag
Multivariate Generalised Linear Mixed Models	MCMCglmm
Design Matrix for Measurement Error Model	me
Design Matrices for Multiple Membership Models	mult.memb
Design Matrix for Path Analyses	path
Probability that all multinomial categories have a non-zero count.	pkk
Phenoloxidase measures on caterpillars of the Indian meal moth.	PlodiaPO
Resistance of Indian meal moth caterpillars to the granulosis virus PiGV.	PlodiaR
Resistance (as a binary trait) of Indian meal moth caterpillars to the granulosis virus PiGV.	PlodiaRB
Plots MCMC chains from MCMCglmm using plot.mcmc	plot.MCMCglmm
Plots covariance matrices	plotsubspace
Posterior distribution of ante-dependence parameters	posterior.ante
Transforms posterior distribution of covariances into correlations	posterior.cor
Posterior distribution of eigenvalues	posterior.evals
Posterior distribution of matrix inverse	posterior.inverse
Estimates the marginal parameter modes using kernel density estimation	posterior.mode
Predict method for GLMMs fitted with MCMCglmm	predict.MCMCglmm
Generator Functions for Priors in MCMCglmm	F IG IW prior_generators tSD
Pedigree pruning	prunePed
Tensor of Sample (Mixed) Central Moments	Ptensor
Random Generation of MVN Breeding Values and Phylogenetic Effects	rbv
Residuals form a GLMM fitted with MCMCglmm	residuals.MCMCglmm
Resolves a Prior Specification in MCMCglmm	resolve_prior
Random Generation from the Conditional Inverse Wishart Distribution	rIW
Simulate Covariance Matrices from Prior	rprior
Random Generation from a Truncated Conditional Normal Distribution	rtcmvnorm
Random Generation from a Truncated Normal Distribution	rtnorm
Infection Data for Sigma Virus in _Drosophila melanogaster_	sigma
Simulate method for GLMMs fitted with MCMCglmm	simulate.MCMCglmm
Design Matrix for Simultaneous and Recursive Relationships between Responses	sir
Converts sparseMatrix to asreml's giv format	sm2asreml
Orthogonal Spline Design Matrix	spl
Horn type and genders of Soay Sheep	SShorns
Summarising GLMM Fits from MCMCglmm	print.MCMCglmm print.summary.MCMCglmm summary.MCMCglmm
Lower/Upper Triangle Elements of a Matrix	Tri2M
Diet composition of Tufted Puffin	tufted_puffin