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

Files in this package

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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