# Extended Mixed Models Using Latent Classes and Latent Processes

## Documentation for package ‘lcmm’ version 2.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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 a secondary regression model 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').
predictYback | Marginal predictions in the natural scale of a pre-transformed outcome
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 ...