.cctm                   Create a 'conditional' ctm model with random
                        effects as offsets
.check_par              Helper function to check parameter constarints
.combine_formulas       Combine a set of formulas into one (similar to
                        nlme::asOneFormula)
.constr_adj             Helper function to adjust the constraints
                        consistently with the parameter restrictions
.ctm2formula            Create a dummy fromula from a ctm object
.gen_param              Generator for param closure
.get_cf                 Get the coefficient vector
.get_par                Helper function to extract formatted parameters
.idx                    Get parameter indices of various structures
.isbars                 Check whether formula contains bars (RE parts)
.mod_negative           Helper function to figure out if negative =
                        TRUE in a given model
.model_name             Generates proper model name for the tramME
                        model
.nm2mat                 Add names to the vc matrix
.nm2vec                 Add names to the vector of theta parameters
.nobars                 Remove random effects terms from full formulas
                        or calls
.parallel_default       Boilerplate parallel-handling function,
                        modified from 'glmmTMB'
.re_format              Format random effects
.re_size                Calculates the size of the random effect vector
                        implied by the model and the data
.set_cf                 Set the coefficient vector
.set_vc                 Set the parameters of the random effect
                        covariance matrix
.sim_re                 Simulates random effects vector from a tramME
                        object
.th2vc                  Convert from theta vector to vc matrix
.tramME2ctm             Create a corresponding ctm model for a tramME
                        model
.vc2th                  Convert from vc matrix to theta vector
AaregME                 Mixed-effects version of 'Aareg'
BoxCoxME                Mixed-effects version of 'BoxCox'
ColrME                  Mixed-effects version of 'Colr'
CoxphME                 Mixed-effects version of 'Coxph'
LehmannME               Mixed-effects version of 'Lehmann'
LmME                    ME version of tram::Lm
PolrME                  Mixed-effects version of 'Polr'
SurvregME               Mixed-effects version of 'Survreg'
VarCorr.LmME            Variances and correlation matrices of random
                        effects of an LmME object
VarCorr.tramME          Variances and correlation matrices of random
                        effects
anova.tramME            Comparison of nested tramME models.
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.
confint.LmME            Confidence intervals for LmME model parameters
confint.tramME          Confidence intervals for tramME model
                        parameters
duplicate               Generic for copying objects that are (partly)
                        modified in place
duplicate.tramME        Duplicate a tramME object
duplicate.tramTMB       Create a duplicate of the tramTMB object
fe_terms                Create fixed effects data and initial
                        parameters
fitmod                  Fit the model.
fitmod.tramME           Call the optimizer on a tramME object
is.pd                   Check positive definiteness
logLik.tramME           Get the log-likelihood of the model
lpterms                 Generic method for extracting terms of the
                        linear predictor
lpterms.tramME          Get inidvidual terms of the linear predictor
                        and their confidence intervals
model.frame.tramME      Extract model frame from a tramME model
model.matrix.tramME     Model matrix for tramME mdoels
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
parboot.tramME          Do parametric bootsrap using a tarmME model
plot.trafo.tramME       Plotting method for 'trafo.tramME' objects
plot.tramME             Plotting method for tramME objects
predict.tramME          Predict method for tramME objects
print.VarCorr.tramME    Print method for the variance-correlation
                        parameters of a tramME object
print.anova.tramME      Printing 'anova.tramME' table
print.simulate.tramME   Print method for 'simulate.tramME' objects
print.summary.tramME    Print method for tramME model summary
print.tramME            Print tramME model
ranef.LmME              Extract the conditional modes of random effects
                        of an LmME model
ranef.tramME            Extract the conditional modes and conditional
                        variances of random effects
re_terms                Create random effects data and initial
                        paramaters
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.
simulate.tramME         Simulate from a tramME model
summary.tramME          Summary method for tramME model
trafo                   Generic method for extracting baseline
                        transformations
trafo.tramME            Get the baseline transformation function and
                        its confidence interval
tramME_model            Create an object that defines a tramME_model
tramTMB                 Create a tramTMB object
tramTMB_inputs          Create inputs of the tramTMB model
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.
