CMA - Synthesis of microarray-based classification

This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.

Last updated 23 days ago

classificationdecisiontree

5.09 score 61 scripts 324 downloads

prioritylasso - Analyzing Multiple Omics Data with an Offset Approach

Priority-LASSO (Klau et al., 2018) fits successive Lasso models for several blocks of (omics) data with different priorities and takes the predicted values as an offset for the next block. Also offers options to deal with block-wise missingness in multi-omics data. Reference: Klau, S., Jurinovic, V., Hornung, R., Herold, T., Boulesteix, A.-L. (2018) Priority-Lasso: a simple hierarchical approach to the prediction of clinical outcome using multi-omics data. BMC Bioinformatics 19:322, <doi:10.1186/s12859-018-2344-6>.

Last updated 2 years ago

4.36 score 23 scripts 318 downloads

ordinalForest - Ordinal Forests: Prediction and Variable Ranking with Ordinal Target Variables

The ordinal forest (OF) method allows ordinal regression with high-dimensional and low-dimensional data. After having constructed an OF prediction rule using a training dataset, it can be used to predict the values of the ordinal target variable for new observations. Moreover, by means of the (permutation-based) variable importance measure of OF, it is also possible to rank the covariates with respect to their importance in the prediction of the values of the ordinal target variable. OF is presented in Hornung (2020). NOTE: Starting with package version 2.4, it is also possible to obtain class probability predictions in addition to the class point predictions. Moreover, the variable importance values can also be based on the class probability predictions. Preliminary results indicate that this might lead to a better discrimination between influential and non-influential covariates. The main functions of the package are: ordfor() (construction of OF) and predict.ordfor() (prediction of the target variable values of new observations). References: Hornung R. (2020) Ordinal Forests. Journal of Classification 37, 4–17. <doi:10.1007/s00357-018-9302-x>.

Last updated 23 days ago

2.09 score 4 stars 31 scripts 745 downloads

rfvimptest - Sequential Permutation Testing of Random Forest Variable Importance Measures

Sequential permutation testing for statistical significance of predictors in random forests. The main function of the package is rfvimptest(), which allows to test for the statistical significance of predictors in random forests using different (sequential) permutation test strategies [1]. The advantage of sequential over conventional permutation tests is that they are computationally considerably less intensive, as the sequential procedure is stopped as soon as there is sufficient evidence for either the null or the alternative hypothesis. Reference: [1] Hapfelmeier, A., Hornung, R. & Haller, B. (2023) Efficient permutation testing of variable importance measures by the example of random forests. Computational Statistics & Data Analysis 181:107689, <doi:10.1016/j.csda.2022.107689>.

Last updated 1 years ago

2.00 score 2 scripts 178 downloads

diversityForest - Innovative Complex Split Procedures in Random Forests Through Candidate Split Sampling

Implements interaction forests [1], which are specific diversity forests and the basic form of diversity forests that uses univariable, binary splitting [2]. Interaction forests (IFs) are ensembles of decision trees that model quantitative and qualitative interaction effects using bivariable splitting. IFs come with the Effect Importance Measure (EIM), which can be used to identify variable pairs that feature quantitative and qualitative interaction effects with high predictive relevance. IFs and EIM focus on well interpretable forms of interactions. The package also offers plot functions for visualising the estimated forms of interaction effects. Categorical, metric, and survival outcomes are supported. This is a fork of the R package 'ranger' (main author: Marvin N. Wright) that implements random forests using an efficient C++ implementation. References: [1] Hornung, R. & Boulesteix, A.-L. (2022) Interaction Forests: Identifying and exploiting interpretable quantitative and qualitative interaction effects. Computational Statistics & Data Analysis 171:107460, <doi:10.1016/j.csda.2022.107460>. [2] Hornung, R. (2022) Diversity forests: Using split sampling to enable innovative complex split procedures in random forests. SN Computer Science 3(2):1, <doi:10.1007/s42979-021-00920-1>.

Last updated 2 years ago

2.00 score 5 scripts 373 downloads

bapred - Batch Effect Removal and Addon Normalization (in Phenotype Prediction using Gene Data)

Various tools dealing with batch effects, in particular enabling the removal of discrepancies between training and test sets in prediction scenarios. Moreover, addon quantile normalization and addon RMA normalization (Kostka & Spang, 2008) is implemented to enable integrating the quantile normalization step into prediction rules. The following batch effect removal methods are implemented: FAbatch, ComBat, (f)SVA, mean-centering, standardization, Ratio-A and Ratio-G. For each of these we provide an additional function which enables a posteriori ('addon') batch effect removal in independent batches ('test data'). Here, the (already batch effect adjusted) training data is not altered. For evaluating the success of batch effect adjustment several metrics are provided. Moreover, the package implements a plot for the visualization of batch effects using principal component analysis. The main functions of the package for batch effect adjustment are ba() and baaddon() which enable batch effect removal and addon batch effect removal, respectively, with one of the seven methods mentioned above. Another important function here is bametric() which is a wrapper function for all implemented methods for evaluating the success of batch effect removal. For (addon) quantile normalization and (addon) RMA normalization the functions qunormtrain(), qunormaddon(), rmatrain() and rmaaddon() can be used.

Last updated 2 years ago

1.78 score 20 scripts 271 downloads