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tramME (version 0.1.3)

Transformation Models with Mixed Effects

Description

Likelihood-based estimation of mixed-effects transformation models using the Template Model Builder (TMB, Kristensen et al., 2016, ). The technical details of transformation models are given in Hothorn et al. (2018, ). Likelihood contributions of exact, randomly censored (left, right, interval) and truncated observations are supported. The random effects are assumed to be normally distributed on the scale of the transformation function, the marginal likelihood is evaluated using the Laplace approximation, and the gradients are calculated with automatic differentiation (AD).

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Version

Install

install.packages('tramME')

Monthly Downloads

684

Version

0.1.3

License

GPL-2

Maintainer

Balint Tamasi

Last Published

March 8th, 2022

Functions in tramME (0.1.3)

Mixed-effects version of Survreg

Mixed-effects version of Coxph

Mixed-effects version of BoxCox

Mixed-effects version of Colr

Variances and correlation matrices of random effects

Mixed-effects version of Polr

Mixed-effects version of Aareg

Variances and correlation matrices of random effects of an LmME object

Mixed-effects version of Lehmann

Helper function to check parameter constarints

Comparison of nested tramME models.

Generates proper model name for the tramME model

Set up and control optimization parameters

Get the log-likelihood of the model

Generic method for extracting terms of the linear predictor

Set coefficients of a tramME model.

Add names to the vc matrix

Generator for param closure

.combine_formulas

Combine a set of formulas into one (similar to nlme::asOneFormula)

Get the coefficient vector

Optimize the tramTMB object

Convert from theta vector to vc matrix

Confidence intervals for LmME model parameters

Extract the coefficients of the fixed effects terms.

Confidence intervals for tramME model parameters

duplicate.tramME

Duplicate a tramME object

Generic method for "offset<-"

Create a corresponding ctm model for a tramME model

ME version of tram::Lm

duplicate.tramTMB

Create a duplicate of the tramTMB object

Check whether formula contains bars (RE parts)

Extract the coefficients of the fixed effects terms of an LmME model.

Helper function to figure out if negative = TRUE in a given model

Set the parameters of the random effect covariance matrix

Extract the coefficients of the fixed effects terms of an SurvregME model.

print.VarCorr.tramME

Print method for the variance-correlation parameters of a tramME object

print.anova.tramME

Printing anova.tramME table

Extract the SD of the error term of an LmME model.

Generic method for "offset"

Generic method for "weights<-"

Residuals of a LmME model

residuals.tramME

Residuals of a tramME model

Add names to the vector of theta parameters

Get parameter indices of various structures

Helper function to extract formatted parameters

Extract the variance-covariance matrix of the random effects

simulate.tramME

Simulate from a tramME model

Create a 'conditional' ctm model with random effects as offsets

Helper function to adjust the constraints consistently with the parameter restrictions

Create a dummy fromula from a ctm object

Format random effects

.parallel_default

Boilerplate parallel-handling function, modified from glmmTMB

variable.names.tramME

Return variable names.

Get the observation weight vector of a tramME object.

Calculates the size of the random effect vector implied by the model and the data

Variance-covariance matrix of the parameters

Set the coefficient vector

Create fixed effects data and initial parameters

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

Simulates random effects vector from a tramME object

Create random effects data and initial paramaters

Print tramME model

Extract the conditional modes and conditional variances of random effects

Extract the conditional modes of random effects of an LmME model

Remove random effects terms from full formulas or calls

Call the optimizer on a tramME object

weights<-.tramME

Set the values of the observation weights of a tramME model.

Check positive definiteness

offset<-.tramME

Set the values of the offsets of a tramME model.

Get the baseline transformation function and its confidence interval

plot.trafo.tramME

Plotting method for trafo.tramME objects

Create an object that defines a tramME_model

Do parametric bootsrap using a tarmME model

Convert from vc matrix to theta vector

Create a tramTMB object

varcov<-.tramME

Set the values of the random effects covariance matrices of a tramME model.

Default method for "offset"

Generic for copying objects that are (partly) modified in place

Generic method for "varcov<-"

Create inputs of the tramTMB model

print.simulate.tramME

Print method for simulate.tramME objects

print.summary.tramME

Print method for tramME model summary

Get the variance-covariance matrix of the parameters of an LmME model

Get the offset vector of a tramME object.

Predict method for tramME objects

Plotting method for tramME objects

Summary method for tramME model

Generic method for varcov

Generic method for extracting baseline transformations

Extract the variance-covariance matrix of the random effects of an LmME model

Calculate the variance-covariance matrix of the parameters