Package: MCMCglmm 2.36

Jarrod Hadfield

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

MCMCglmm_2.36.tar.gz
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MCMCglmm.pdf |MCMCglmm.html✨
MCMCglmm/json (API)

# Install 'MCMCglmm' in R:
install.packages('MCMCglmm', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • BTdata - Blue Tit Data for a Quantitative Genetic Experiment
  • BTped - Blue Tit Pedigree
  • 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.
  • SShorns - Horn type and genders of Soay Sheep

On CRAN:

42 exports 2 stars 6.51 score 10 dependencies 12 dependents 477 mentions 1.1k scripts 4.3k downloads

Last updated 3 months agofrom:dcea602900. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKAug 28 2024
R-4.5-win-x86_64OKAug 28 2024
R-4.5-linux-x86_64OKAug 28 2024
R-4.4-win-x86_64OKAug 28 2024
R-4.4-mac-x86_64OKAug 28 2024
R-4.4-mac-aarch64OKAug 28 2024
R-4.3-win-x86_64OKAug 28 2024
R-4.3-mac-x86_64OKAug 28 2024
R-4.3-mac-aarch64OKAug 28 2024

Exports:at.levelat.setbuildVcommutationdcmvnormDdivergenceDexpressionsDtensorevalDtensorgelman.priorinverseAknormKPPMkrzanowski.testkuniflist2bdiagMCMCglmmmemult.membpathpkkplot.MCMCglmmplotsubspaceposterior.anteposterior.corposterior.evalsposterior.inverseposterior.modepredict.MCMCglmmprunePedPtensorrbvresiduals.MCMCglmmrIWrtcmvnormrtnormsimulate.MCMCglmmsirsm2asremlsplsummary.MCMCglmmTri2M

Dependencies:apecodacorpcorcubaturedigestlatticeMatrixnlmeRcpptensorA

Readme and manuals

Help Manual

Help pageTopics
Multivariate Generalised Linear Mixed ModelsMCMCglmm-package
Incidence Matrix of Levels within a Factorat.level
Incidence Matrix of Combined Levels within a Factorat.set
Blue Tit Data for a Quantitative Genetic ExperimentBTdata
Blue Tit PedigreeBTped
Forms expected (co)variances for GLMMs fitted with MCMCglmmbuildV
Commutation Matrixcommutation
Density of a (conditional) multivariate normal variatedcmvnorm
d-divergenceDdivergence
List of unevaluated expressions for (mixed) partial derivatives of fitness with respect to linear predictors.Dexpressions
Tensor of (mixed) partial derivativesDtensor
Evaluates a list of (mixed) partial derivativesevalDtensor
Prior Covariance Matrix for Fixed Effects.gelman.prior
Inverse Relatedness Matrix and Phylogenetic Covariance MatrixinverseA
(Mixed) Central Moments of a Multivariate Normal Distributionknorm
Kronecker Product Permutation MatrixKPPM
Krzanowski's Comparison of Subspaceskrzanowski.test
Central Moments of a Uniform Distributionkunif
Forms the direct sum from a list of matriceslist2bdiag
Multivariate Generalised Linear Mixed ModelsMCMCglmm
Design Matrix for Measurement Error Modelme
Design Matrices for Multiple Membership Modelsmult.memb
Design Matrix for Path Analysespath
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.mcmcplot.MCMCglmm
Plots covariance matricesplotsubspace
Posterior distribution of ante-dependence parametersposterior.ante
Transforms posterior distribution of covariances into correlationsposterior.cor
Posterior distribution of eigenvaluesposterior.evals
Posterior distribution of matrix inverseposterior.inverse
Estimates the marginal parameter modes using kernel density estimationposterior.mode
Predict method for GLMMs fitted with MCMCglmmpredict.MCMCglmm
Pedigree pruningprunePed
Tensor of Sample (Mixed) Central MomentsPtensor
Random Generation of MVN Breeding Values and Phylogenetic Effectsrbv
Residuals form a GLMM fitted with MCMCglmmresiduals.MCMCglmm
Random Generation from the Conditional Inverse Wishart DistributionrIW
Random Generation from a Truncated Conditional Normal Distributionrtcmvnorm
Random Generation from a Truncated Normal Distributionrtnorm
Simulate method for GLMMs fitted with MCMCglmmsimulate.MCMCglmm
Design Matrix for Simultaneous and Recursive Relationships between Responsessir
Converts sparseMatrix to asreml's giv formatsm2asreml
Orthogonal Spline Design Matrixspl
Horn type and genders of Soay SheepSShorns
Summarising GLMM Fits from MCMCglmmprint.MCMCglmm print.summary.MCMCglmm summary.MCMCglmm
Lower/Upper Triangle Elements of a MatrixTri2M