Approximate False Positive Rate Control in Selection Frequency for Random Forest

Approximate false positive rate control in selection frequency for random forest using the methods described by Ender Konukoglu and Melanie Ganz (2014) . Methods for calculating the selection frequency threshold at false positive rates and selection frequency false positive rate feature selection.

Modeling and Map Production using Random Forest and Related Stochastic Models

Creates sophisticated models of training data and validates the models with an independent test set, cross validation, or Out Of Bag (OOB) predictions on the training data. Create graphs and tables of the model validation results. Applies these models to GIS .img files of predictors to create detailed prediction surfaces. Handles large predictor files for map making, by reading in the .img files in chunks, and output to the .txt file the prediction for each data chunk, before reading the next chunk of data.

Joint Random Forest (JRF) for the Simultaneous Estimation of Multiple Related Networks

Simultaneous estimation of multiple related networks.

Performing Monte Carlo Expectation Maximization Random Forest Imputation for Biological Data

Perform missing value imputation for biological data using the random forest algorithm, the imputation aim to keep the original mean and standard deviation consistent after imputation.

Innovative Complex Split Procedures in Random Forests Through Candidate Split Sampling

Implementations of three diversity forest (DF) (Hornung, 2022, ) variants. The DF algorithm is a split-finding approach that allows complex split procedures to be realized in random forest variants. The three DF variants implemented are: 1. interaction forests (IFs) (Hornung & Boulesteix, 2022, ): Model quantitative and qualitative interaction effects using bivariable splitting. Come with the Effect Importance Measure (EIM), which can be used to identify variable pairs that have well-interpretable quantitative and qualitative interaction effects with high predictive relevance. 2. multi forests (MuFs) (Hornung & Hapfelmeier, 2024, ): Model multi-class outcomes using multi-way and binary splitting. Come with two variable importance measures (VIMs): The multi-class VIM measures the degree to which the variables are specifically associated with one or more outcome classes, and the discriminatory VIM, similar to conventional VIMs, measures the overall influence strength of the variables. 3. the basic form of diversity forests that uses conventional univariable, binary splitting (Hornung, 2022). Except for multi forests, which are tailored for multi-class outcomes, all included diversity forest variants support categorical, metric, and survival outcomes. The package also includes plotting functions that make it possible to learn about the forms of the effects identified using IFs and MuFs. This is a fork of the R package 'ranger' (main author: Marvin N. Wright), which implements random forests using an efficient C++ implementation.

R Interface for the 'H2O' Scalable Machine Learning Platform

R interface for 'H2O', the scalable open source machine learning platform that offers parallelized implementations of many supervised and unsupervised machine learning algorithms such as Generalized Linear Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests, Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection, Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).

Nested Cross-Validation to Compare Cox-PH, Cox-Lasso, Survival Random Forests

Performs repeated nested cross-validation for Cox Proportionate Hazards, Cox Lasso, Survival Random Forest, and their ensemble. Returns internally validated concordance index, time-dependent area under the curve, Brier score, calibration slope, and statistical testing of non-linear ensemble outperforming the baseline Cox model. In this, it helps researchers to quantify the gain of using a more complex survival model, or justify its redundancy. Equally, it shows the performance value of the non-linear and interaction terms, and may highlight the need of further feature transformation. Further details can be found in Shamsutdinova, Stamate, Roberts, & Stahl (2022) "Combining Cox Model and Tree-Based Algorithms to Boost Performance and Preserve Interpretability for Health Outcomes" , where the method is described as Ensemble 1.

A Laboratory for Recursive Partytioning

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) , Zeileis et al. (2008) and Strobl et al. (2007) .

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, ) and 'Top-Down Transformation Choice' (Hothorn, 2018, ).

RF Variable Importance for Arbitrary Measures

Computes the random forest variable importance (VIMP) for the conditional inference random forest (cforest) of the 'party' package. Includes a function (varImp) that computes the VIMP for arbitrary measures from the 'measures' package. For calculating the VIMP regarding the measures accuracy and AUC two extra functions exist (varImpACC and varImpAUC).