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MCMCglmm (version 2.30)

MCMC Generalised Linear Mixed Models

Description

Fits Multi-response Generalised Linear Mixed Models (and related models) using Markov chain Monte Carlo techniques.

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Version

Install

install.packages('MCMCglmm')

Monthly Downloads

5,558

Version

2.30

License

GPL (>= 2)

Maintainer

Jarrod Hadfield

Last Published

January 7th, 2021

Functions in MCMCglmm (2.30)

Dtensor

Tensor of (mixed) partial derivatives
PlodiaPO

Phenoloxidase measures on caterpillars of the Indian meal moth.
Ddivergence

d-divergence
MCMCglmm-package

Multivariate Generalised Linear Mixed Models
KPPM

Kronecker Product Permutation Matrix
MCMCglmm

Multivariate Generalised Linear Mixed Models
BTdata

Blue Tit Data for a Quantitative Genetic Experiment
PlodiaR

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

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

Blue Tit Pedigree
knorm

(Mixed) Central Moments of a Multivariate Normal Distribution
kunif

Central Moments of a Uniform Distribution
dcmvnorm

Density of a (conditional) multivariate normal variate
evalDtensor

Evaluates a list of (mixed) partial derivatives
list2bdiag

Forms the direct sum from a list of matrices
inverseA

Inverse Relatedness Matrix and Phylogenetic Covariance Matrix
Ptensor

Tensor of Sample (Mixed) Central Moments
at.set

Incidence Matrix of Combined Levels within a Factor
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
posterior.ante

Posterior distribution of ante-dependence parameters
mult.memb

Design Matrices for Multiple Membership Models
me

Design Matrix for Measurement Error Model
gelman.prior

Prior Covariance Matrix for Fixed Effects.
commutation

Commutation Matrix
at.level

Incidence Matrix of Levels within a Factor
path

Design Matrix for Path Analyses
rIW

Random Generation from the Conditional Inverse Wishart Distribution
sir

Design Matrix for Simultaneous and Recursive Relationships between Responses
prunePed

Pedigree pruning
simulate.MCMCglmm

Simulate method for GLMMs fitted with MCMCglmm
posterior.evals

Posterior distribution of eigenvalues
spl

Orthogonal Spline Design Matrix
sm2asreml

Converts sparseMatrix to asreml's giv format
posterior.cor

Transforms posterior distribution of covariances into correlations
pkk

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

Krzanowski's Comparison of Subspaces
plot.MCMCglmm

Plots MCMC chains from MCMCglmm using plot.mcmc
posterior.mode

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

Posterior distribution of matrix inverse
predict.MCMCglmm

Predict method for GLMMs fitted with MCMCglmm
rtcmvnorm

Random Generation from a Truncated Conditional Normal Distribution
rbv

Random Generation of MVN Breeding Values and Phylogenetic Effects
plotsubspace

Plots covariance matrices
residuals.MCMCglmm

Residuals form a GLMM fitted with MCMCglmm
rtnorm

Random Generation from a Truncated Normal Distribution
Tri2M

Lower/Upper Triangle Elements of a Matrix
summary.MCMCglmm

Summarising GLMM Fits from MCMCglmm
SShorns

Horn type and genders of Soay Sheep