# Torsten Hothorn

#### mvtnorm

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Computes multivariate normal and t probabilities, quantiles, random deviates and densities.

#### multcomp

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Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book "Multiple Comparisons Using R" (Bretz, Hothorn, Westfall, 2010, CRC Press).

#### modeltools

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A collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future. The documentation is rather terse, but packages coin' and party' have some working examples. However, if you find the implemented ideas interesting we would be very interested in a discussion of this proposal. Contributions are more than welcome!

#### ipred

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Improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.

#### TH.data

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Contains data sets used in other packages Torsten Hothorn maintains.

#### coin

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Conditional inference procedures for the general independence problem including two-sample, K-sample (non-parametric ANOVA), correlation, censored, ordered and multivariate problems.

#### party

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A computational toolbox for recursive partitioning. The core of the package is ctree(), an implementation of conditional inference trees which embed tree-structured regression models into a well defined theory of conditional inference procedures. This non-parametric class of regression trees is applicable to all kinds of regression problems, including nominal, ordinal, numeric, censored as well as multivariate response variables and arbitrary measurement scales of the covariates. Based on conditional inference trees, cforest() provides an implementation of Breiman's random forests. The function mob() implements an algorithm for recursive partitioning based on parametric models (e.g. linear models, GLMs or survival regression) employing parameter instability tests for split selection. Extensible functionality for visualizing tree-structured regression models is available. The methods are described in Hothorn et al. (2006) <doi:10.1198/106186006X133933>, Zeileis et al. (2008) <doi:10.1198/106186008X319331> and Strobl et al. (2007) <doi:10.1186/1471-2105-8-25>.

#### partykit

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A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This unified infrastructure can be used for reading/coercing tree models from different sources ('rpart', 'RWeka', 'PMML') yielding objects that share functionality for print()/plot()/predict() methods. Furthermore, new and improved reimplementations of conditional inference trees (ctree()) and model-based recursive partitioning (mob()) from the 'party' package are provided based on the new infrastructure. A description of this package was published by Hothorn and Zeileis (2015) <http://jmlr.org/papers/v16/hothorn15a.html>.

#### inum

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Enum-type representation of vectors and representation of intervals, including a method of coercing variables in data frames.

#### libcoin

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Basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999) <http://epub.wu.ac.at/102/>. This package must not be used by end-users. CRAN package 'coin' implements all user interfaces and is ready to be used by anyone.

#### exactRankTests

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Computes exact conditional p-values and quantiles using an implementation of the Shift-Algorithm by Streitberg & Roehmel.

#### maxstat

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Maximally selected rank statistics with several p-value approximations.

#### HSAUR2

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Functions, data sets, analyses and examples from the second edition of the book ''A Handbook of Statistical Analyses Using R'' (Brian S. Everitt and Torsten Hothorn, Chapman & Hall/CRC, 2008). The first chapter of the book, which is entitled ''An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available. In addition, the package contains Sweave code for producing slides for selected chapters (see HSAUR2/inst/slides).

#### HSAUR

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Functions, data sets, analyses and examples from the book ''A Handbook of Statistical Analyses Using R'' (Brian S. Everitt and Torsten Hothorn, Chapman & Hall/CRC, 2006). The first chapter of the book, which is entitled ''An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available.

#### HSAUR3

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Functions, data sets, analyses and examples from the third edition of the book ''A Handbook of Statistical Analyses Using R'' (Torsten Hothorn and Brian S. Everitt, Chapman & Hall/CRC, 2014). The first chapter of the book, which is entitled ''An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available. In addition, Sweave source code for slides of selected chapters is included in this package (see HSAUR3/inst/slides). The publishers web page is '<http://www.crcpress.com/product/isbn/9781482204582>'.

#### MVA

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Functions, data sets, analyses and examples from the book `An Introduction to Applied Multivariate Analysis with R' (Brian S. Everitt and Torsten Hothorn, Springer, 2011).

#### basefun

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Some very simple infrastructure for basis functions.

#### variables

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Abstract descriptions of (yet) unobserved variables.

#### mlt

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Likelihood-based estimation of conditional transformation models via the most likely transformation approach described in Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.

#### ATR

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Plot party trees in left-right orientation instead of the classical top-down layout.

#### trtf

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Recursive partytioning of transformation models with corresponding random forest for conditional transformation models as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>) and 'Top-Down Transformation Choice' (Hothorn, 2017, <arXiv:1706.08269>).

#### mlt.docreg

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

#### tram

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Formula-based user-interfaces to specific transformation models implemented in package 'mlt'. 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>.

#### lmtest

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A collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.

#### DescTools

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A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.

#### RWeka

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An R interface to Weka (Version 3.9.2). Weka is a collection of machine learning algorithms for data mining tasks written in Java, containing tools for data pre-processing, classification, regression, clustering, association rules, and visualization. Package 'RWeka' contains the interface code, the Weka jar is in a separate package 'RWekajars'. For more information on Weka see <http://www.cs.waikato.ac.nz/ml/weka/>.

#### mboost

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Functional gradient descent algorithm (boosting) for optimizing general risk functions utilizing component-wise (penalised) least squares estimates or regression trees as base-learners for fitting generalized linear, additive and interaction models to potentially high-dimensional data.

#### stabs

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Resampling procedures to assess the stability of selected variables with additional finite sample error control for high-dimensional variable selection procedures such as Lasso or boosting. Both, standard stability selection (Meinshausen & Buhlmann, 2010, <doi:10.1111/j.1467-9868.2010.00740.x>) and complementary pairs stability selection with improved error bounds (Shah & Samworth, 2013, <doi:10.1111/j.1467-9868.2011.01034.x>) are implemented. The package can be combined with arbitrary user specified variable selection approaches.

#### bst

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Functional gradient descent algorithm for a variety of convex and non-convex loss functions, for both classical and robust regression and classification problems.

#### FDboost

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Regression models for functional data, i.e., scalar-on-function, function-on-scalar and function-on-function regression models, are fitted by a component-wise gradient boosting algorithm.

#### StatDataML

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Support for reading and writing files in StatDataML---an XML-based data exchange format.

#### model4you

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Model-based trees for subgroup analyses in clinical trials and model-based forests for the estimation and prediction of personalised treatment effects (personalised models). Currently partitioning of linear models, lm(), generalised linear models, glm(), and Weibull models, survreg(), is supported. Advanced plotting functionality is supported for the trees and a test for parameter heterogeneity is provided for the personalised models. For details on model-based trees for subgroup analyses see Seibold, Zeileis and Hothorn (2016) <doi:10.1515/ijb-2015-0032>; for details on model-based forests for estimation of individual treatment effects see Seibold, Zeileis and Hothorn (2017) <doi:10.1177/0962280217693034>.

#### globalboosttest

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'globalboosttest' implements a permutation-based testing procedure to globally test the (additional) predictive value of a large set of predictors given that a small set of predictors is already available. Currently, 'globalboosttest' supports binary outcomes (via logistic regression) and survival outcomes (via Cox regression). It is based on boosting regression as implemented in the package 'mboost'.

#### palmtree

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This is an implementation of model-based trees with global model parameters (PALM trees). The PALM tree algorithm is an extension to the MOB algorithm (implemented in the 'partykit' package), where some parameters are fixed across all groups. Details about the method can be found in Seibold, Hothorn, Zeileis (2016) <arXiv:1612.07498>. The package offers coef(), logLik(), plot(), and predict() functions for PALM trees.

#### mobForest

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Functions to implements random forest method for model based recursive partitioning. The mob() function, developed by Zeileis et al. (2008), within 'party' package, is modified to construct model-based decision trees based on random forests methodology. The main input function mobforest.analysis() takes all input parameters to construct trees, compute out-of-bag errors, predictions, and overall accuracy of forest. The algorithm performs parallel computation using cluster functions within 'parallel' package.