LCAextend: Latent Class Analysis (LCA) with familial dependence in extended pedigrees
Version 1.2

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.

Browse man pages Browse package API and functions Browse package files

AuthorArafat TAYEB <arafat.tayeb@ircm.qc.ca>, Alexandre BUREAU <alexandre.bureau@msp.ulaval.ca> and Aurelie Labbe <aurelie.labbe@mcgill.ca>
Date of publication2012-03-18 16:07:12
MaintainerAlexandre BUREAU <alexandre.bureau@msp.ulaval.ca>
LicenseGPL
Version1.2
URL http://www.r-project.org http://www.crulrg.ulaval.ca/pages_perso_chercheurs/bureau_a/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("LCAextend")

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...

Functions

LCAextend Man page
LCAextend-package Man page
alpha.compute Man page Source code
attrib.dens Man page Source code
dens.norm Man page Source code
dens.prod.ordi Man page Source code
downward Man page Source code
downward.connect Man page Source code
e.step Man page Source code
init.norm Man page Source code
init.ordi Man page Source code
init.p.trans Man page Source code
lca.model Man page Source code
model.select Man page Source code
n.param Man page Source code
optim.const.ordi Man page Source code
optim.diff.norm Man page Source code
optim.equal.norm Man page Source code
optim.gene.norm Man page Source code
optim.indep.norm Man page Source code
optim.noconst.ordi Man page Source code
optim.probs Man page Source code
p.compute Man page Source code
p.post.child Man page Source code
p.post.found Man page Source code
param.cont Man page
param.ordi Man page
ped.cont Man page
ped.ordi Man page
peel Man page
probs Man page
upward Man page Source code
upward.connect Man page Source code
weight.famdep Man page Source code
weight.nuc Man page Source code

Files

MD5
man
man/weight.nuc.Rd
man/weight.famdep.Rd
man/upward.connect.Rd
man/upward.Rd
man/probs.Rd
man/peel.Rd
man/ped.ordi.Rd
man/ped.cont.Rd
man/param.ordi.Rd
man/param.cont.Rd
man/p.post.found.Rd
man/p.post.child.Rd
man/p.compute.Rd
man/optim.probs.Rd
man/optim.noconst.ordi.Rd
man/optim.indep.norm.Rd
man/optim.gene.norm.Rd
man/optim.equal.norm.Rd
man/optim.diff.norm.Rd
man/optim.const.ordi.Rd
man/n.param.Rd
man/model.select.Rd
man/lca.model.Rd
man/init.p.trans.Rd
man/init.ordi.Rd
man/init.norm.Rd
man/e.step.Rd
man/downward.connect.Rd
man/downward.Rd
man/dens.prod.ordi.Rd
man/dens.norm.Rd
man/attrib.dens.Rd
man/alpha.compute.Rd
man/LCAextend-package.Rd
data
data/probs.rda
data/peel.rda
data/ped.ordi.rda
data/ped.cont.rda
data/param.ordi.rda
data/param.cont.rda
R
R/weight.nuc.R
R/weight.famdep.R
R/upward.connect.R
R/upward.R
R/p.post.found.R
R/p.post.child.R
R/p.compute.R
R/optim.probs.R
R/optim.noconst.ordi.R
R/optim.indep.norm.R
R/optim.gene.norm.R
R/optim.equal.norm.R
R/optim.diff.norm.R
R/optim.const.ordi.R
R/n.param.R
R/model.select.R
R/lca.model.R
R/init.p.trans.R
R/init.ordi.R
R/init.norm.R
R/e.step.R
R/downward.connect.R
R/downward.R
R/dens.prod.ordi.R
R/dens.norm.R
R/attrib.dens.R
R/alpha.compute.R
NAMESPACE
DESCRIPTION
LCAextend documentation built on May 19, 2017, 10:20 p.m.