Transformation Models with Mixed Effects


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Documentation for package ‘tramME’ version 0.1.3

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.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)
.model_name Generates proper model name for the tramME model
.mod_negative Helper function to figure out if negative = TRUE in a given 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'
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.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
LehmannME Mixed-effects version of 'Lehmann'
LmME ME version of tram::Lm
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
PolrME Mixed-effects version of 'Polr'
predict.tramME Predict method for tramME objects
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
print.VarCorr.tramME Print method for the variance-correlation parameters of a tramME object
ranef Extract the conditional modes and conditional variances of random effects
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
residuals.LmME Residuals of a LmME model
residuals.tramME Residuals of a tramME model
re_terms Create random effects data and initial paramaters
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
SurvregME Mixed-effects version of 'Survreg'
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
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.