Nested Loop Cross Validation (nlcv)
Nested loop cross validation for classification purposes for misclassification error rate estimation. The package supports several methodologies for feature selection: random forest, Student t-test, limma, and provides an interface to the following classification methods in the ‘MLInterfaces’ package: linear, quadratic discriminant analyses, random forest, bagging, prediction analysis for microarray, generalized linear model, support vector machine (svm and ksvm). Visualizations to assess the quality of the classifier are included: plot of the ranks of the features, scores plot for a specific classification algorithm and number of features, misclassification rate for the different number of features and classification algorithms tested and ROC plot. For further details about the methodology, please check: Markus Ruschhaupt, Wolfgang Huber, Annemarie Poustka, and Ulrich Mansmann (2004) <doi:10.2202/1544-6115.1078>.

Estimated Marginal Means, aka Least-Squares Means (emmeans)
Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and compact letter displays. Least-squares means are discussed, and the term ‘estimated marginal means’ is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.

Highlight Lines and Points in ‘ggplot2’ (gghighlight)
Make it easier to explore data with highlights.

Diversity Measures on Tripartite Graphs (triversity)
Computing diversity measures on tripartite graphs. This package first implements a parametrized family of such diversity measures which apply on probability distributions. Sometimes called ‘True Diversity’, this family contains famous measures such as the richness, the Shannon entropy, the Herfindahl-Hirschman index, and the Berger-Parker index. Second, the package allows to apply these measures on probability distributions resulting from random walks between the levels of tripartite graphs. By defining an initial distribution at a given level of the graph and a path to follow between the three levels, the probability of the walker’s position within the final level is then computed, thus providing a particular instance of diversity to measure.

Rename and Encode Data Frames Using External Crosswalk Files (crosswalkr)
A pair of functions for renaming and encoding data frames using external crosswalk files. It is especially useful when constructing master data sets from multiple smaller data sets that do not name or encode variables consistently across files. Based on similar commands in ‘Stata’.

Meta-CART: A Flexible Approach to Identify Moderators in Meta-Analysis (metacart)
Fits meta-CART by integrating classification and regression trees (CART) into meta-analysis. Meta-CART is a flexible approach to identify interaction effects between moderators in meta-analysis. The methods are described in Dusseldorp et al. (2014) <doi:10.1037/hea0000018> and Li et al. (2017) <doi:10.1111/bmsp.12088>.

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