LCAextend: Latent Class Analysis (LCA) with familial dependence in extended pedigrees

This package performs a Latent Class Analysis of phenotypic measurements in pedigrees and a model selection based on one of two methods: likelihood-based cross-validation and Bayesian Information Criterion. It computes also individual and triplet child-parents weights in a pedigree using an upward-downward algorithm. It takes into account the familial dependence defined by the pedigree structure by considering that a class of a child depends on his parents classes via triplet-transition probabilities of the classes. The package handles the case where measurements are available on all subjects and the case where measurements are available only on symptomatic (i.e. affected) subjects. Distributions for discrete (or ordinal) and continuous data are currently implemented. The package can deal with missing data.

Author
Arafat TAYEB <arafat.tayeb@ircm.qc.ca>, Alexandre BUREAU <alexandre.bureau@msp.ulaval.ca> and Aurelie Labbe <aurelie.labbe@mcgill.ca>
Date of publication
2012-03-18 16:07:12
Maintainer
Alexandre BUREAU <alexandre.bureau@msp.ulaval.ca>
License
GPL
Version
1.2
URLs

View on CRAN

Man pages

alpha.compute
computes cumulative logistic coefficients using probabilities
attrib.dens
associates to a function of density parameter optimization an...
dens.norm
computes the multinormal density of a given continuous...
dens.prod.ordi
computes the probability of a given discrete measurement...
downward
performs the downward step of the peeling algorithm and...
downward.connect
performs a downward step for a connector
e.step
performs the E step of the EM algorithm for a single pedigree...
init.norm
computes initial values for the EM algorithm in the case of...
init.ordi
computes the initial values for EM algorithm in the case of...
init.p.trans
initializes the transition probabilities
LCAextend-package
Latent Class Analysis (LCA) and model selection for pedigree...
lca.model
fits latent class models for phenotypic measurements in...
model.select
selects a latent class model for pedigree data
n.param
computes the number of parameters of a model
optim.const.ordi
performs the M step for the measurement distribution...
optim.diff.norm
performs the M step for measurement density parameters in...
optim.equal.norm
performs the M step for measurement density parameters in...
optim.gene.norm
performs the M step for measurement density parameters in...
optim.indep.norm
performs the M step for measurement density parameters in...
optim.noconst.ordi
performs the M step for the measurement distribution...
optim.probs
performs the M step of the EM algorithm for the probability...
param.cont
parameters to be used for examples in the case of continuous...
param.ordi
parameters to be used for examples in the case of discrete or...
p.compute
computes the probability vector using logistic coefficients
ped.cont
pedigrees with continuous data to be used for examples
ped.ordi
pedigrees with discrete or ordinal data to be used for...
peel
peeling order of pedigrees and couples in pedigrees
p.post.child
computes the posterior probability of observations of a child
p.post.found
computes the posterior probability of observations of a...
probs
probabilities parameters to be used for examples
upward
performs the upward step of the peeling algorithm of a...
upward.connect
performs the upward step for a connector
weight.famdep
performs the computation of triplet and individual weights...
weight.nuc
performs the computation of unnormalized triplet and...

Files in this package

LCAextend
LCAextend/MD5
LCAextend/man
LCAextend/man/weight.nuc.Rd
LCAextend/man/weight.famdep.Rd
LCAextend/man/upward.connect.Rd
LCAextend/man/upward.Rd
LCAextend/man/probs.Rd
LCAextend/man/peel.Rd
LCAextend/man/ped.ordi.Rd
LCAextend/man/ped.cont.Rd
LCAextend/man/param.ordi.Rd
LCAextend/man/param.cont.Rd
LCAextend/man/p.post.found.Rd
LCAextend/man/p.post.child.Rd
LCAextend/man/p.compute.Rd
LCAextend/man/optim.probs.Rd
LCAextend/man/optim.noconst.ordi.Rd
LCAextend/man/optim.indep.norm.Rd
LCAextend/man/optim.gene.norm.Rd
LCAextend/man/optim.equal.norm.Rd
LCAextend/man/optim.diff.norm.Rd
LCAextend/man/optim.const.ordi.Rd
LCAextend/man/n.param.Rd
LCAextend/man/model.select.Rd
LCAextend/man/lca.model.Rd
LCAextend/man/init.p.trans.Rd
LCAextend/man/init.ordi.Rd
LCAextend/man/init.norm.Rd
LCAextend/man/e.step.Rd
LCAextend/man/downward.connect.Rd
LCAextend/man/downward.Rd
LCAextend/man/dens.prod.ordi.Rd
LCAextend/man/dens.norm.Rd
LCAextend/man/attrib.dens.Rd
LCAextend/man/alpha.compute.Rd
LCAextend/man/LCAextend-package.Rd
LCAextend/data
LCAextend/data/probs.rda
LCAextend/data/peel.rda
LCAextend/data/ped.ordi.rda
LCAextend/data/ped.cont.rda
LCAextend/data/param.ordi.rda
LCAextend/data/param.cont.rda
LCAextend/R
LCAextend/R/weight.nuc.R
LCAextend/R/weight.famdep.R
LCAextend/R/upward.connect.R
LCAextend/R/upward.R
LCAextend/R/p.post.found.R
LCAextend/R/p.post.child.R
LCAextend/R/p.compute.R
LCAextend/R/optim.probs.R
LCAextend/R/optim.noconst.ordi.R
LCAextend/R/optim.indep.norm.R
LCAextend/R/optim.gene.norm.R
LCAextend/R/optim.equal.norm.R
LCAextend/R/optim.diff.norm.R
LCAextend/R/optim.const.ordi.R
LCAextend/R/n.param.R
LCAextend/R/model.select.R
LCAextend/R/lca.model.R
LCAextend/R/init.p.trans.R
LCAextend/R/init.ordi.R
LCAextend/R/init.norm.R
LCAextend/R/e.step.R
LCAextend/R/downward.connect.R
LCAextend/R/downward.R
LCAextend/R/dens.prod.ordi.R
LCAextend/R/dens.norm.R
LCAextend/R/attrib.dens.R
LCAextend/R/alpha.compute.R
LCAextend/NAMESPACE
LCAextend/DESCRIPTION