Extended Mixed Models Using Latent Classes and Latent Processes

Documentation for package ‘lcmm’ version 2.1.0

Help Pages

B C D E F G H I J L M P R S U V W X misc

lcmm-package

Estimation of extended mixed models using latent classes and latent processes.

-- B --

Brandom

For internal use only ...

-- C --

coef.externSurv	Standard methods for estimated models
coef.externX	Standard methods for estimated models
coef.hlme	Standard methods for estimated models
coef.Jointlcmm	Standard methods for estimated models
coef.lcmm	Standard methods for estimated models
coef.mpjlcmm	Standard methods for estimated models
coef.multlcmm	Standard methods for estimated models
cuminc	Predicted cumulative incidence of event according to a profile of covariates
C_calculustransfo	For internal use only ...
C_cvpl	For internal use only ...
C_hetmixcont	For internal use only ...
C_hetmixcontmult	For internal use only ...
C_hetmixlin	For internal use only ...
C_hetmixord	For internal use only ...
C_jointhet	For internal use only ...
C_postprob2	For internal use only ...
C_predictcont	For internal use only ...
C_predictmult	For internal use only ...

-- D --

data_hlme	Simulated dataset for hlme function
data_lcmm	Simulated dataset for lcmm and Jointlcmm functions
Diffepoce	Difference of expected prognostic cross-entropy (EPOCE) estimators and its 95% tracking interval between two joint latent class models estimated with 'Jointlcmm'
dynpred	Individual dynamic predictions from a joint latent class model

-- E --

epoce	Estimators of the Expected Prognostic Observed Cross-Entropy (EPOCE) for evaluating predictive accuracy of joint latent class models estimated using 'Jointlcmm'
estimates	Maximum likelihood estimates
estimates.externSurv	Maximum likelihood estimates
estimates.externX	Maximum likelihood estimates
estimates.hlme	Maximum likelihood estimates
estimates.Jointlcmm	Maximum likelihood estimates
estimates.lcmm	Maximum likelihood estimates
estimates.mpjlcmm	Maximum likelihood estimates
estimates.multlcmm	Maximum likelihood estimates
externVar	Estimation of secondary regression models after the estimation of a primary latent class model

-- F --

factor.names	For internal use only ...
fitted.hlme	Standard methods for estimated models
fitted.Jointlcmm	Standard methods for estimated models
fitted.lcmm	Standard methods for estimated models
fitted.multlcmm	Standard methods for estimated models
fitY	Marginal predictions of the longitudinal outcome(s) in their natural scale from 'lcmm', 'Jointlcmm' or 'multlcmm' objects
fitY.Jointlcmm	Marginal predictions of the longitudinal outcome(s) in their natural scale from 'lcmm', 'Jointlcmm' or 'multlcmm' objects
fitY.lcmm	Marginal predictions of the longitudinal outcome(s) in their natural scale from 'lcmm', 'Jointlcmm' or 'multlcmm' objects
fitY.multlcmm	Marginal predictions of the longitudinal outcome(s) in their natural scale from 'lcmm', 'Jointlcmm' or 'multlcmm' objects
fixef.hlme	Standard methods for estimated models
fixef.Jointlcmm	Standard methods for estimated models
fixef.lcmm	Standard methods for estimated models
fixef.multlcmm	Standard methods for estimated models
ForInternalUse	For internal use only ...

-- G --

gridsearch

Automatic grid search

-- H --

hlme	Estimation of latent class linear mixed models

-- I --

ItemInfo

Conditional probabilities and item information given specified latent process values for 'lcmm' or 'multlcmm' object with ordinal outcomes.

-- J --

jlcmm	Estimation of joint latent class models for longitudinal and time-to-event data
Jointlcmm	Estimation of joint latent class models for longitudinal and time-to-event data

-- L --

lcmm	Estimation of mixed-effect models and latent class mixed-effect models for different types of outcomes (continuous Gaussian, continuous non-Gaussian or ordinal)
loglik	Wrapper to the Fortran subroutines computing the log-likelihood
loglikhlme	Wrapper to the Fortran subroutines computing the log-likelihood
loglikJointlcmm	Wrapper to the Fortran subroutines computing the log-likelihood
logliklcmm	Wrapper to the Fortran subroutines computing the log-likelihood
loglikmpjlcmm	Wrapper to the Fortran subroutines computing the log-likelihood
loglikmultlcmm	Wrapper to the Fortran subroutines computing the log-likelihood

-- M --

mixture	For internal use only ...
mlcmm	Estimation of multivariate mixed-effect models and multivariate latent class mixed-effect models for multivariate longitudinal outcomes of possibly multiple types (continuous Gaussian, continuous non-Gaussian/curvilinear, ordinal) that measure the same underlying latent process.
mpjlcmm	Estimation of multivariate joint latent class mixed models
multlcmm	Estimation of multivariate mixed-effect models and multivariate latent class mixed-effect models for multivariate longitudinal outcomes of possibly multiple types (continuous Gaussian, continuous non-Gaussian/curvilinear, ordinal) that measure the same underlying latent process.

-- P --

paquid	Longitudinal data on cognitive and physical aging in the elderly
permut	Permutation of the latent classes
plot	Plot of a fitted model
plot.cuminc	Plot of predicted cumulative incidences according to a profile of covariates
plot.Diffepoce	Plots
plot.dynpred	Plot of individual dynamic predictions
plot.epoce	Plots
plot.externSurv	Plot of a fitted model
plot.externX	Plot of a fitted model
plot.hlme	Plot of a fitted model
plot.ItemInfo	Plot of information functions
plot.Jointlcmm	Plot of a fitted model
plot.lcmm	Plot of a fitted model
plot.mpjlcmm	Plot of a fitted model
plot.multlcmm	Plot of a fitted model
plot.pred.accuracy	Plots
plot.predict	Plot of predicted trajectories and link functions
plot.predictL	Plot of predicted trajectories and link functions
plot.predictL.Jointlcmm	Plot of predicted trajectories and link functions
plot.predictL.lcmm	Plot of predicted trajectories and link functions
plot.predictL.multlcmm	Plot of predicted trajectories and link functions
plot.predictlink	Plot of predicted trajectories and link functions
plot.predictlink.Jointlcmm	Plot of predicted trajectories and link functions
plot.predictlink.lcmm	Plot of predicted trajectories and link functions
plot.predictlink.multlcmm	Plot of predicted trajectories and link functions
plot.predictY	Plot of predicted trajectories and link functions
plot.predictY.hlme	Plot of predicted trajectories and link functions
plot.predictY.Jointlcmm	Plot of predicted trajectories and link functions
plot.predictY.lcmm	Plot of predicted trajectories and link functions
plot.predictY.multlcmm	Plot of predicted trajectories and link functions
plot.predictYcond	Plot of predicted trajectories and link functions
postprob	Posterior classification stemmed from a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' estimation
postprob.externSurv	Posterior classification stemmed from a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' estimation
postprob.externX	Posterior classification stemmed from a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' estimation
postprob.hlme	Posterior classification stemmed from a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' estimation
postprob.Jointlcmm	Posterior classification stemmed from a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' estimation
postprob.lcmm	Posterior classification stemmed from a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' estimation
postprob.mpjlcmm	Posterior classification stemmed from a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' estimation
postprob.multlcmm	Posterior classification stemmed from a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' estimation
predictClass	Posterior classification and class-membership probabilities
predictL	Class-specific marginal predictions in the latent process scale for 'lcmm', 'Jointlcmm' and 'multlcmm' objects
predictL.Jointlcmm	Class-specific marginal predictions in the latent process scale for 'lcmm', 'Jointlcmm' and 'multlcmm' objects
predictL.lcmm	Class-specific marginal predictions in the latent process scale for 'lcmm', 'Jointlcmm' and 'multlcmm' objects
predictL.multlcmm	Class-specific marginal predictions in the latent process scale for 'lcmm', 'Jointlcmm' and 'multlcmm' objects
predictlink	Confidence intervals for the estimated link functions from 'lcmm', 'Jointlcmm' and 'multlcmm'
predictlink.Jointlcmm	Confidence intervals for the estimated link functions from 'lcmm', 'Jointlcmm' and 'multlcmm'
predictlink.lcmm	Confidence intervals for the estimated link functions from 'lcmm', 'Jointlcmm' and 'multlcmm'
predictlink.multlcmm	Confidence intervals for the estimated link functions from 'lcmm', 'Jointlcmm' and 'multlcmm'
predictRE	Predictions of the random-effects
predictY	Predictions (marginal and possibly subject-specific in some cases) of a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' object in the natural scale of the longitudinal outcome(s) computed from a profile of covariates (marginal) or individual data (subject specific in case of 'hlme').
predictY.hlme	Predictions (marginal and possibly subject-specific in some cases) of a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' object in the natural scale of the longitudinal outcome(s) computed from a profile of covariates (marginal) or individual data (subject specific in case of 'hlme').
predictY.Jointlcmm	Predictions (marginal and possibly subject-specific in some cases) of a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' object in the natural scale of the longitudinal outcome(s) computed from a profile of covariates (marginal) or individual data (subject specific in case of 'hlme').
predictY.lcmm	Predictions (marginal and possibly subject-specific in some cases) of a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' object in the natural scale of the longitudinal outcome(s) computed from a profile of covariates (marginal) or individual data (subject specific in case of 'hlme').
predictY.multlcmm	Predictions (marginal and possibly subject-specific in some cases) of a 'hlme', 'lcmm', 'multlcmm' or 'Jointlcmm' object in the natural scale of the longitudinal outcome(s) computed from a profile of covariates (marginal) or individual data (subject specific in case of 'hlme').
predictYcond	Conditional predictions of a 'lcmm', 'multlcmm' or 'Jointlcmm' object in the natural scale of the longitudinal outcome(s) for specified latent process values.
print.Diffepoce	Brief summary of a 'hlme', 'lcmm', 'Jointlcmm','multlcmm', 'epoce' or 'Diffepoce' objects
print.epoce	Brief summary of a 'hlme', 'lcmm', 'Jointlcmm','multlcmm', 'epoce' or 'Diffepoce' objects
print.externSurv	Brief summary of a 'hlme', 'lcmm', 'Jointlcmm','multlcmm', 'epoce' or 'Diffepoce' objects
print.externX	Brief summary of a 'hlme', 'lcmm', 'Jointlcmm','multlcmm', 'epoce' or 'Diffepoce' objects
print.hlme	Brief summary of a 'hlme', 'lcmm', 'Jointlcmm','multlcmm', 'epoce' or 'Diffepoce' objects
print.Jointlcmm	Brief summary of a 'hlme', 'lcmm', 'Jointlcmm','multlcmm', 'epoce' or 'Diffepoce' objects
print.lcmm	Brief summary of a 'hlme', 'lcmm', 'Jointlcmm','multlcmm', 'epoce' or 'Diffepoce' objects
print.mpjlcmm	Brief summary of a 'hlme', 'lcmm', 'Jointlcmm','multlcmm', 'epoce' or 'Diffepoce' objects
print.multlcmm	Brief summary of a 'hlme', 'lcmm', 'Jointlcmm','multlcmm', 'epoce' or 'Diffepoce' objects

-- R --

ranef.hlme	Standard methods for estimated models
ranef.Jointlcmm	Standard methods for estimated models
ranef.lcmm	Standard methods for estimated models
ranef.multlcmm	Standard methods for estimated models
residuals.hlme	Standard methods for estimated models
residuals.Jointlcmm	Standard methods for estimated models
residuals.lcmm	Standard methods for estimated models
residuals.multlcmm	Standard methods for estimated models
risqcum_spl	For internal use only ...
risq_spl	For internal use only ...

-- S --

simdataHADS	Simulated dataset simdataHADS
simulate.lcmm	Data simulation according to models from lcmm package
StandardMethods	Standard methods for estimated models
summary.Diffepoce	Summary of a 'hlme', 'lcmm', 'Jointlcmm', 'multlcmm', 'mpjlcmm', 'externSurv', 'externX', 'epoce' or 'Diffepoce' objects
summary.epoce	Summary of a 'hlme', 'lcmm', 'Jointlcmm', 'multlcmm', 'mpjlcmm', 'externSurv', 'externX', 'epoce' or 'Diffepoce' objects
summary.externSurv	Summary of a 'hlme', 'lcmm', 'Jointlcmm', 'multlcmm', 'mpjlcmm', 'externSurv', 'externX', 'epoce' or 'Diffepoce' objects
summary.externX	Summary of a 'hlme', 'lcmm', 'Jointlcmm', 'multlcmm', 'mpjlcmm', 'externSurv', 'externX', 'epoce' or 'Diffepoce' objects
summary.hlme	Summary of a 'hlme', 'lcmm', 'Jointlcmm', 'multlcmm', 'mpjlcmm', 'externSurv', 'externX', 'epoce' or 'Diffepoce' objects
summary.Jointlcmm	Summary of a 'hlme', 'lcmm', 'Jointlcmm', 'multlcmm', 'mpjlcmm', 'externSurv', 'externX', 'epoce' or 'Diffepoce' objects
summary.lcmm	Summary of a 'hlme', 'lcmm', 'Jointlcmm', 'multlcmm', 'mpjlcmm', 'externSurv', 'externX', 'epoce' or 'Diffepoce' objects
summary.mpjlcmm	Summary of a 'hlme', 'lcmm', 'Jointlcmm', 'multlcmm', 'mpjlcmm', 'externSurv', 'externX', 'epoce' or 'Diffepoce' objects
summary.multlcmm	Summary of a 'hlme', 'lcmm', 'Jointlcmm', 'multlcmm', 'mpjlcmm', 'externSurv', 'externX', 'epoce' or 'Diffepoce' objects
summaryplot	Summary of models
summarytable	Summary of models

-- U --

update.mpjlcmm

Update the longitudinal submodels

-- V --

VarCov	Variance-covariance of the estimates
VarCovRE	Estimates, standard errors and Wald test for the parameters of the variance-covariance matrix of the random effects.
VarCovRE.hlme	Estimates, standard errors and Wald test for the parameters of the variance-covariance matrix of the random effects.
VarCovRE.Jointlcmm	Estimates, standard errors and Wald test for the parameters of the variance-covariance matrix of the random effects.
VarCovRE.lcmm	Estimates, standard errors and Wald test for the parameters of the variance-covariance matrix of the random effects.
VarCovRE.multlcmm	Estimates, standard errors and Wald test for the parameters of the variance-covariance matrix of the random effects.
VarExpl	Percentage of variance explained by the (latent class) linear mixed model regression
VarExpl.hlme	Percentage of variance explained by the (latent class) linear mixed model regression
VarExpl.Jointlcmm	Percentage of variance explained by the (latent class) linear mixed model regression
VarExpl.lcmm	Percentage of variance explained by the (latent class) linear mixed model regression
VarExpl.multlcmm	Percentage of variance explained by the (latent class) linear mixed model regression
vcov.externSurv	Standard methods for estimated models
vcov.externX	Standard methods for estimated models
vcov.hlme	Standard methods for estimated models
vcov.Jointlcmm	Standard methods for estimated models
vcov.lcmm	Standard methods for estimated models
vcov.mpjlcmm	Standard methods for estimated models
vcov.multlcmm	Standard methods for estimated models

-- W --

WaldMult

Multivariate Wald Test

-- X --

xclass

Cross classifications

-- misc --

.Contlcmm	For internal use only ...
.Ordlcmm	For internal use only ...
.plotbaselinerisk	For internal use only ...
.plotfit	For internal use only ...
.plotlinkfunctionmult	For internal use only ...
.plotlinkfuntion	For internal use only ...
.plotpostprob	For internal use only ...
.plotresid	For internal use only ...
.plotsurvival	For internal use only ...