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tram - Transformation Models

Formula-based user-interfaces to specific transformation models implemented in package 'mlt' (<DOI:10.32614/CRAN.package.mlt>, <DOI:10.32614/CRAN.package.mlt.docreg>). Available models include Cox models, some parametric survival models (Weibull, etc.), models for ordered categorical variables, normal and non-normal (Box-Cox type) linear models, and continuous outcome logistic regression (Lohse et al., 2017, <DOI:10.12688/f1000research.12934.1>). The underlying theory is described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>. An extension to transformation models for clustered data is provided (Barbanti and Hothorn, 2022, <DOI:10.1093/biostatistics/kxac048>) and a tutorial explains applications in survival analysis (Siegfried et al., 2025, <DOI:10.48550/arXiv.2402.06428>). Multivariate conditional transformation models (Klein et al, 2022, <DOI:10.1111/sjos.12501>) and shift-scale transformation models (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>) can be fitted as well. The package contains an implementation of a doubly robust score test, described in Kook et al. (2024, <DOI:10.1080/01621459.2024.2395588>).

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8.40 score 6 dependents 203 scripts 5.9k downloads

mlt - Most Likely Transformations

Likelihood-based estimation of conditional transformation models via the most likely transformation approach described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291> and Hothorn (2020) <DOI:10.18637/jss.v092.i01>. Shift-scale (Siegfried et al, 2023, <DOI:10.1080/00031305.2023.2203177>) and multivariate (Klein et al, 2022, <DOI:10.1111/sjos.12501>) transformation models are part of this package. A package vignette is available from <DOI:10.32614/CRAN.package.mlt.docreg> and more convenient user interfaces to many models from <DOI:10.32614/CRAN.package.tram>.

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6.99 score 6 dependents 92 scripts 5.1k downloads

basefun - Infrastructure for Computing with Basis Functions

Some very simple infrastructure for basis functions.

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5.48 score 6 dependents 13 scripts 4.5k downloads

mlt.docreg - Most Likely Transformations: Documentation and Regression Tests

Additional documentation, a package vignette and regression tests for package mlt.

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5.06 score 962 downloads

tbm - Transformation Boosting Machines

Boosting the likelihood of conditional and shift transformation models as introduced in <DOI:10.1007/s11222-019-09870-4>.

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4.61 score 14 scripts 613 downloads

variables - Variable Descriptions

Abstract descriptions of (yet) unobserved variables.

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4.36 score 6 dependents 11 scripts 4.0k downloads

cotram - Count Transformation Models

Count transformation models featuring parameters interpretable as discrete hazard ratios, odds ratios, reverse-time discrete hazard ratios, or transformed expectations. An appropriate data transformation for a count outcome and regression coefficients are simultaneously estimated by maximising the exact discrete log-likelihood using the computational framework provided in package 'mlt', technical details are given in Siegfried & Hothorn (2020) <DOI:10.1111/2041-210X.13383>. The package also features joint count transformation models with covariate-dependent correlations applied to a species community of three aquatic birds <DOI:10.48550/arXiv.2201.13095>.

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4.24 score 2 dependents 8 scripts 863 downloads

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'.

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cppopenmp

3.81 score 3 scripts 797 downloads

trtf - Transformation Trees and Forests

Recursive partytioning of transformation models with corresponding random forest for conditional transformation models as described in 'Transformation Forests' (Hothorn and Zeileis, 2021, <doi:10.1080/10618600.2021.1872581>) and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).

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2.77 score 11 scripts 1.8k downloads

tramvs - Optimal Subset Selection for Transformation Models

Greedy optimal subset selection for transformation models (Hothorn et al., 2018, <doi:10.1111/sjos.12291> ) based on the abess algorithm (Zhu et al., 2020, <doi:10.1073/pnas.2014241117> ). Applicable to models from packages 'tram' and 'cotram'. Application to shift-scale transformation models are described in Siegfried et al. (2024, <doi:10.1080/00031305.2023.2203177>).

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2.00 score 9 scripts 697 downloads

tramnet - Penalized Transformation Models

Partially penalized versions of specific transformation models implemented in package 'mlt'. Available models include a fully parametric version of the Cox model, other parametric survival models (Weibull, etc.), models for binary and ordered categorical variables, normal and transformed-normal (Box-Cox type) linear models, and continuous outcome logistic regression. Hyperparameter tuning is facilitated through model-based optimization functionalities from package 'mlrMBO'. The accompanying vignette describes the methodology used in 'tramnet' in detail. Transformation models and model-based optimization are described in Hothorn et al. (2019) <doi:10.1111/sjos.12291> and Bischl et al. (2016) <doi:10.48550/arXiv.1703.03373>, respectively.

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2.00 score 2 scripts 934 downloads