Transformation Models with Mixed Effects


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Documentation for package ‘tramME’ version 1.0.0

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.cctm Create a 'conditional' ctm model with random effects as offsets
.idx Get parameter indices of various structures
.parallel_default Boilerplate parallel-handling function, modified from 'glmmTMB'
anova.tramME Comparison of nested tramME models.
BoxCoxME Mixed-effects version of 'BoxCox'
coef.LmME Extract the coefficients of the fixed effects terms of an LmME model.
coef.SurvregME Extract the coefficients of the fixed effects terms of an SurvregME model.
coef.tramME Extract the coefficients of the fixed effects terms.
coef<-.tramME Set coefficients of a tramME model.
ColrME Mixed-effects version of 'Colr'
confint.LmME Confidence intervals for LmME model parameters
confint.tramME Confidence intervals for tramME model parameters
CoxphME Mixed-effects version of 'Coxph'
duplicate Generic for copying objects that are (partly) modified in place
duplicate.tramTMB Create a duplicate of the tramTMB object
edf_smooth Calculate edf for smooth terms
edf_smooth.tramME EDFs of smooth shift terms
fitmod Fit the model.
fitmod.tramME Call the optimizer on a tramME object
is.pd Check positive definiteness
LehmannME Mixed-effects version of 'Lehmann'
LmME Mixed-effects version of 'Lm'
logLik.tramME Get the log-likelihood of the tramME model
model.frame.tramME Extract model frame from a tramME model
model.matrix.tramME Model matrices for 'tramME' models
offset Generic method for '"offset"'
offset.default Default method for '"offset"'
offset.tramME Get the offset vector of a tramME object.
offset<- Generic method for '"offset<-"'
offset<-.tramME Set the values of the offsets of a tramME model.
optim_control Set up and control optimization parameters
optim_tramTMB Optimize the tramTMB object
plot.smooth.tramME Plot smooth terms of a tramME model.
plot.tramME Plotting method for tramME objects
PolrME Mixed-effects version of 'Polr'
predict.tramME Predict method for tramME objects
predict.tramTMB Post-estimation calculations in a tramTMB model
print.anova.tramME Printing 'anova.tramME' table
print.summary.tramME Print method for tramME model summary
print.tramME Print tramME model
print.VarCorr.tramME Print method for the variance-correlation parameters of a tramME object
ranef Point estimates and conditional variances of random effects.
ranef.LmME Extract the conditional modes of random effects of an LmME model
ranef.tramME Point estimates and conditional variances of random effects.
residuals.LmME Residuals of a LmME model
residuals.tramME Residuals of a tramME model
sigma.LmME Extract the SD of the error term of an LmME model.
smooth_terms Get smooth terms.
smooth_terms.LmME Evaluate smooth terms of a 'LmME' model.
smooth_terms.tramME Extract and evaluate the smooth terms of a tramME model
summary.tramME Summary method for tramME model
SurvregME Mixed-effects version of 'Survreg'
tramME General function to define and fit tramME models
tramME_model Create an object that defines a tramME_model
tramTMB Create a tramTMB object
VarCorr Variances and correlation matrices of random effects
VarCorr.LmME Variances and correlation matrices of random effects of an LmME object
VarCorr.tramME Variances and correlation matrices of random effects
varcov Generic method for 'varcov'
varcov.LmME Extract the variance-covariance matrix of the random effects of an LmME model
varcov.tramME Extract the variance-covariance matrix of the random effects
varcov<- Generic method for '"varcov<-"'
varcov<-.tramME Set the values of the random effects covariance matrices of a tramME model.
variable.names.tramME Return variable names.
vcov.LmME Get the variance-covariance matrix of the parameters of an LmME model
vcov.tramME Calculate the variance-covariance matrix of the parameters
vcov.tramTMB Variance-covariance matrix of the parameters
weights.tramME Get the observation weight vector of a tramME object.
weights<- Generic method for '"weights<-"'
weights<-.tramME Set the values of the observation weights of a tramME model.