MCMCglmm: MCMC Generalised Linear Mixed Models

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MCMC Generalised Linear Mixed Models.

Author
Jarrod Hadfield
Date of publication
2016-11-14 13:22:11
Maintainer
Jarrod Hadfield <j.hadfield@ed.ac.uk>
License
GPL (>= 2)
Version
2.24

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