MCMCglmm: MCMC Generalised Linear Mixed Models
Version 2.24

MCMC Generalised Linear Mixed Models.

AuthorJarrod Hadfield
Date of publication2016-11-14 13:22:11
MaintainerJarrod Hadfield <j.hadfield@ed.ac.uk>
LicenseGPL (>= 2)
Version2.24
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MCMCglmm")

Popular man pages

gelman.prior: Prior Covariance Matrix for Fixed Effects.
inverseA: Inverse Relatedness Matrix and Phylogenetic Covariance Matrix
MCMCglmm: Multivariate Generalised Linear Mixed Models
MCMCglmmPackage: Multivariate Generalised Linear Mixed Models
mult.memb: Design Matrices for Multiple Membership Models
predict.MCMCglmm: Predict method for GLMMs fitted with MCMCglmm
residuals.MCMCglmm: Residuals form a GLMM fitted with MCMCglmm
See all...

All man pages Function index File listing

Man pages

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...
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
MCMCglmmPackage: Multivariate Generalised Linear Mixed Models
mult.memb: Design Matrices for Multiple Membership Models
path: Design Matrix for Path Analyses
PlodiaPO: Phenoloxidase measures on caterpillars of the Indian meal...
PlodiaR: Resistance of Indian meal moth caterpillars to the granulosis...
PlodiaRB: Resistance (as a binary trait) of Indian meal moth...
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...
posterior.evals: Posterior distribution of eigenvalues
posterior.inverse: Posterior distribution of matrix inverse
posterior.mode: Estimates the marginal parameter modes using kernel density...
predict.MCMCglmm: Predict method for GLMMs fitted with MCMCglmm
prunePed: Pedigree pruning
Ptensor: Tensor of Sample (Mixed) Central Moments
rbv: Random Generation of MVN Breeding Values and Phylogenetic...
residuals.MCMCglmm: Residuals form a GLMM fitted with MCMCglmm
rIW: Random Generation from the Conditional Inverse Wishart...
rtcmvnorm: Random Generation from a Truncated Conditional Normal...
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...
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

Functions

Files

inst
inst/CITATION
inst/doc
inst/doc/CourseNotes.Rnw
inst/doc/CourseNotes.pdf
inst/doc/Overview.Rnw
inst/doc/Overview.pdf
src
src/cs_house.c
src/cs_directsum.c
src/cs_ipvec.c
src/cs_dmvnorm.c
src/cs_addR.c
src/rtcmvnorm.c
src/cs_qr.c
src/cs_post.c
src/cs_rCinvwishart.c
src/cs_invR.c
src/cs_cbind.c
src/cs_omega.c
src/cs_permute.c
src/cs_ereach.c
src/cs_sortdv.c
src/MCMCglmm.cc
src/dcmvnormR.cc
src/rIW.cc
src/cs_multiply.c
src/cs_leaf.c
src/cs_inv.c
src/cs_ltsolve.c
src/cs_updown.c
src/cs_util.c
src/cs_cumsum.c
src/cs_rRsubinvwishart.c
src/cs_rR.c
src/cs_fkeep.c
src/cs_chol.c
src/cs_randperm.c
src/cs_rinvwishart.c
src/cs_dcmvnorm.c
src/cs_cov2cor.c
src/cs_rAnte.c
src/cs_counts.c
src/cs_cholsol.c
src/cs_norm.c
src/cs_kroneckerI.c
src/cs_print.c
src/pcmvnorm.c
src/cs_kroneckerIupdate.c
src/cs_kroneckerIadd.c
src/cs_etree.c
src/cs_kroneckerAupdate.c
src/cs_entry.c
src/rante.cc
src/cs_load.c
src/cs_droptol.c
src/cs_kroneckerSIupdate.c
src/cs_qrsol.c
src/cs_add.c
src/cs_usolve.c
src/cs_malloc.c
src/cs_lu.c
src/rtcmvnormR.cc
src/cs_maxtrans.c
src/cs_symperm.c
src/cs_omegaupdate.c
src/cs_lusol.c
src/cs_schol.c
src/MCMCglmm.h
src/cs_schur.c
src/cs_transpose.c
src/cs.h
src/cs_spsolve.c
src/cs_kroneckerA.c
src/inverseA.cc
src/cs_kroneckerDI.c
src/cs_happly.c
src/cs_kroneckerDA.c
src/rtnorm.c
src/rbv.cc
src/cs_compress.c
src/cs_reach.c
src/cs_kroneckerSI.c
src/cs_pvec.c
src/cs_dfs.c
src/cs_directsumupdate.c
src/dcutpoints.c
src/cs_rSinvwishart.c
src/cs_dupl.c
src/rtnormR.cc
src/MCMCglmmcc.h
src/cs_tdfs.c
src/cs_amd.c
src/cs_scatter.c
src/cs_pinv.c
src/cs_rwishart.c
src/cs_lsolve.c
src/cs_utsolve.c
src/cs_dmperm.c
src/cs_dropzeros.c
src/cs_scc.c
src/cs_gaxpy.c
src/cs_sqr.c
NAMESPACE
data
data/PlodiaRB.tab.gz
data/BTdata.tab.gz
data/SShorns.tab.gz
data/PlodiaR.tab.gz
data/BTped.tab.gz
data/PlodiaPO.tab.gz
R
R/posterior.inverse.R
R/posterior.cor.R
R/rbv.R
R/buildV.R
R/Tri2M.R
R/plot.MCMCglmm.R
R/priorformat.R
R/Dexpressions.R
R/krzanowski.test.R
R/Dtensor.R
R/mterms.R
R/rante.R
R/spl.R
R/simulate.MCMCglmm.R
R/rIW.R
R/summary.MCMCglmm.R
R/sir.R
R/list2bdiag.R
R/Ptensor.R
R/mult.memb.R
R/MCMCglmm.R
R/Ddivergence.R
R/plotsubspace.R
R/dcmvnorm.R
R/sm2asreml.R
R/residuals.MCMCglmm.R
R/buildZ.R
R/rtnorm.R
R/inverseA.R
R/path.R
R/commutation.R
R/find.components.R
R/rtcmvnorm.R
R/posterior.mode.R
R/kunif.R
R/posterior.evals.R
R/KPPM.R
R/close.bracket.R
R/prunePed.R
R/posterior.ante.R
R/gelman.prior.R
R/split.direct.sum.R
R/knorm.R
R/predict.MCMCglmm.R
vignettes
vignettes/CourseNotes.bib
vignettes/Lecture4-005.pdf
vignettes/Overview.bib
vignettes/Lecture5-046.pdf
vignettes/Lecture1-034.pdf
vignettes/Lecture3-028.pdf
vignettes/Lecture5-043.pdf
vignettes/Lecture2-019.pdf
vignettes/Figures
vignettes/Figures/buildCN.R
vignettes/Figures/defaults.R
vignettes/Figures/TEST.R
vignettes/Figures/CourseNotes.Rnw
vignettes/Figures/Overview.Rnw
vignettes/Figures/Tutorial.Rnw
vignettes/Lecture4-030.pdf
vignettes/Lecture3-018.pdf
vignettes/Lecture5-024.pdf
vignettes/Lecture4-022.pdf
vignettes/Lecture1-052.pdf
vignettes/Overview-Sol.pdf
vignettes/Lecture2-038.pdf
vignettes/Lecture5-011.pdf
vignettes/Lecture2-037.pdf
vignettes/Lecture5-029.pdf
vignettes/CourseNotes.Rnw
vignettes/Lecture1-060.pdf
vignettes/Lecture8-012.pdf
vignettes/axes.pdf
vignettes/Lecture2.tex
vignettes/Lecture1-075.pdf
vignettes/Lecture1-071.pdf
vignettes/Lecture1-065.pdf
vignettes/Lecture4-011.pdf
vignettes/Lecture2-052.pdf
vignettes/Lecture8-005.pdf
vignettes/Lecture6.tex
vignettes/Lecture4-026.pdf
vignettes/Lecture1-055.pdf
vignettes/Lecture1-027.pdf
vignettes/Lecture2-068.pdf
vignettes/Overview.Rnw
vignettes/Lecture4-034.pdf
vignettes/Lecture2-066.pdf
vignettes/Lecture1-015.pdf
vignettes/Lecture4-017.pdf
vignettes/Lecture2-050.pdf
vignettes/Lecture2-007.pdf
vignettes/rgl1.pdf
vignettes/Lecture2-046.pdf
vignettes/Lecture1-041.pdf
vignettes/Lecture5.tex
vignettes/Lecture4-037.pdf
vignettes/Lecture8-023.pdf
vignettes/Lecture2-085.pdf
vignettes/Lecture4-014.pdf
vignettes/Overview-VCV.pdf
vignettes/Lecture2-074.pdf
vignettes/Lecture1-049.pdf
vignettes/Lecture4.tex
vignettes/Lecture1-011.pdf
vignettes/Lecture2-030.pdf
vignettes/Lecture8.tex
vignettes/Lecture7.tex
vignettes/Lecture8-021.pdf
vignettes/rgl2.pdf
vignettes/Lecture4-040.pdf
vignettes/Lecture8-018.pdf
vignettes/Lecture5-039.pdf
vignettes/Lecture3-005.pdf
vignettes/Lecture2-029.pdf
vignettes/Lecture1-023.pdf
vignettes/Lecture2-081.pdf
vignettes/Lecture6-006.pdf
vignettes/Lecture3-025.pdf
vignettes/Lecture3.tex
vignettes/Lecture2-072.pdf
vignettes/Lecture2-023.pdf
vignettes/Lecture8-015.pdf
vignettes/Lecture2-055.pdf
vignettes/Lecture9.tex
vignettes/Lecture1.tex
vignettes/Lecture5-016.pdf
vignettes/Lecture1-006.pdf
vignettes/Lecture1-058.pdf
vignettes/Lecture5-ZIP.pdf
vignettes/Lecture2-070.pdf
MD5
build
build/vignette.rds
DESCRIPTION
man
man/at.level.Rd
man/rbv.Rd
man/gelman.prior.Rd
man/plotsubspace.Rd
man/path.Rd
man/mult.memb.Rd
man/posterior.inverse.Rd
man/SShorns.Rd
man/inverseA.Rd
man/prunePed.Rd
man/Tri2M.Rd
man/krzanowski.test.Rd
man/plot.MCMCglmm.Rd
man/simulate.MCMCglmm.Rd
man/PlodiaPO.Rd
man/knorm.Rd
man/at.set.Rd
man/posterior.mode.Rd
man/Dtensor.Rd
man/posterior.evals.Rd
man/Ptensor.Rd
man/Ddivergence.Rd
man/PlodiaRB.Rd
man/sir.Rd
man/summary.MCMCglmm.Rd
man/posterior.ante.Rd
man/rtcmvnorm.Rd
man/KPPM.Rd
man/sm2asreml.Rd
man/buildV.Rd
man/list2bdiag.Rd
man/predict.MCMCglmm.Rd
man/rtnorm.Rd
man/dcmvnorm.Rd
man/MCMCglmm.Rd
man/commutation.Rd
man/evalDtensor.Rd
man/posterior.cor.Rd
man/spl.Rd
man/kunif.Rd
man/MCMCglmmPackage.Rd
man/BTped.Rd
man/rIW.Rd
man/PlodiaR.Rd
man/Dexpressions.Rd
man/residuals.MCMCglmm.Rd
man/BTdata.Rd
.Rinstignore
MCMCglmm documentation built on May 19, 2017, 10:32 p.m.

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