MCMCglmm: MCMC Generalised Linear Mixed Models

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

View on CRAN

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

at.level Man page
at.set Man page
BTdata Man page
BTped Man page
buildV Man page
commutation Man page
dcmvnorm Man page
Ddivergence Man page
Dexpressions Man page
Dtensor Man page
evalDtensor Man page
gelman.prior Man page
inverseA Man page
knorm Man page
KPPM Man page
krzanowski.test Man page
kunif Man page
list2bdiag Man page
MCMCglmm Man page
MCMCglmm-package Man page
mult.memb Man page
path Man page
PlodiaPO Man page
PlodiaR Man page
PlodiaRB Man page
plot.MCMCglmm Man page
plotsubspace Man page
posterior.ante Man page
posterior.cor Man page
posterior.evals Man page
posterior.inverse Man page
posterior.mode Man page
predict.MCMCglmm Man page
print.MCMCglmm Man page
print.summary.MCMCglmm Man page
prunePed Man page
Ptensor Man page
rbv Man page
residuals.MCMCglmm Man page
rIW Man page
rtcmvnorm Man page
rtnorm Man page
simulate.MCMCglmm Man page
sir Man page
sm2asreml Man page
spl Man page
SShorns Man page
summary.MCMCglmm Man page
Tri2M Man page

Files

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

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