Package: tramME 1.0.4

Balint Tamasi

tramME: Transformation Models with Mixed Effects

Likelihood-based estimation of mixed-effects transformation models using the Template Model Builder ('TMB', Kristensen et al., 2016) <doi:10.18637/jss.v070.i05>. The technical details of transformation models are given in Hothorn et al. (2018) <doi:10.1111/sjos.12291>. 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 (Tamasi & Hothorn, 2021) <doi:10.32614/RJ-2021-075>. Penalized smooth shift terms can be defined using 'mgcv'.

Authors:Balint Tamasi [aut, cre], Torsten Hothorn [ctb]

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tramME.pdf |tramME.html✨
tramME/json (API)
NEWS

# Install 'tramME' in R:
install.packages('tramME', repos = c('https://r-forge.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://r-forge.r-project.org/projects/ctm

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

5.46 score 323 downloads 20 exports 32 dependencies

Last updated 1 months agofrom:8a7cbb914a. Checks:OK: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-win-x86_64OKNov 11 2024
R-4.5-linux-x86_64OKNov 08 2024
R-4.4-win-x86_64OKNov 18 2024
R-4.4-mac-x86_64OKNov 18 2024
R-4.4-mac-aarch64OKNov 18 2024

Exports:.tramME2ctmBoxCoxMEColrMECoxphMEduplicateedf_smoothLehmannMELmMEoptim_controlPolrMEranefRespsmooth_termsSurvregMEtramMEtramME_modeltramTMBVarCorrvarcovvarcov<-

Dependencies:alabamabasefunBBbootcodetoolsconeprojFormulalatticelme4MASSMatrixmgcvminqamltmultcompmvtnormnlmenloptrnumDerivorthopolynompolynomquadprogRcppRcppArmadilloRcppEigensandwichsurvivalTH.dataTMBtramvariableszoo

Examples in statistical ecology

Rendered frommixed-effects-additive-models.Rnwusingknitr::knitron Nov 18 2024.

Last update: 2023-04-04
Started: 2022-04-11

R Journal 2021

Rendered fromRJ-2021-075.Rnwusingutils::Sweaveon Nov 18 2024.

Last update: 2022-04-11
Started: 2022-04-11

Readme and manuals

Help Manual

Help pageTopics
Comparison of nested tramME models.anova.tramME
Mixed-effects version of 'BoxCox'BoxCoxME
Extract the coefficients of the fixed effects terms of an LmME model.coef.LmME
Extract the coefficients of the fixed effects terms of an SurvregME model.coef.SurvregME
Extract the coefficients of the fixed effects terms.coef.tramME
Set coefficients of a tramME model.coef<-.tramME
Mixed-effects version of 'Colr'ColrME
Confidence intervals for LmME model parametersconfint.LmME
Confidence intervals for tramME model parametersconfint.tramME
Mixed-effects version of 'Coxph'CoxphME
Generic for copying objects that are (partly) modified in placeduplicate
Create a duplicate of the tramTMB objectduplicate.tramTMB
EDFs of smooth shift termsedf_smooth edf_smooth.tramME
Mixed-effects version of 'Lehmann'LehmannME
Mixed-effects version of 'Lm'LmME
Get the log-likelihood of the tramME modellogLik.tramME
Extract model frame from a tramME modelmodel.frame.tramME
Model matrices for 'tramME' modelsmodel.matrix.tramME
Set up and control optimization parametersoptim_control
Plot smooth terms of a tramME model.plot.smooth.tramME
Plotting method for tramME objectsplot.tramME
Mixed-effects version of 'Polr'PolrME
Predict method for tramME objectspredict.tramME
Post-estimation calculations in a tramTMB modelpredict.tramTMB
Printing 'anova.tramME' tableprint.anova.tramME
Print method for tramME model summaryprint.summary.tramME
Print tramME modelprint.tramME
Print method for the variance-correlation parameters of a tramME objectprint.VarCorr.tramME
Extract the conditional modes of random effects of an LmME modelranef.LmME
Point estimates and conditional variances of random effects.ranef ranef.tramME
Residuals of a LmME modelresiduals.LmME
Residuals of a tramME modelresiduals.tramME
Response objectsformat.Resp is.na.Resp length.Resp print.Resp R.Resp Resp [.Resp
Extract the SD of the error term of an LmME model.sigma.LmME
Simulate from a 'tramME' modelsimulate.tramME
Evaluate smooth terms of a 'LmME' model.smooth_terms.LmME
Extract and evaluate the smooth terms of a tramME modelsmooth_terms smooth_terms.tramME
Summary method for tramME modelsummary.tramME
Mixed-effects version of 'Survreg'SurvregME
General function to define and fit tramME modelstramME
Create an object that defines a tramME_modeltramME_model
Create a tramTMB objecttramTMB
Variances and correlation matrices of random effects of an LmME objectVarCorr.LmME
Variances and correlation matrices of random effectsVarCorr VarCorr.tramME
Generic method for 'varcov'varcov
Extract the variance-covariance matrix of the random effects of an LmME modelvarcov.LmME
Extract the variance-covariance matrix of the random effectsvarcov.tramME
Generic method for '"varcov<-"'varcov<-
Set the values of the random effects covariance matrices of a tramME model.varcov<-.tramME
Return variable names.variable.names.tramME
Get the variance-covariance matrix of the parameters of an LmME modelvcov.LmME
Calculate the variance-covariance matrix of the parametersvcov.tramME