We present a short tutorial and introduction to using the R package TDA, which provides some tools for Topological Data Analysis. In particular, it includes implementations of functions that, given some data, provide topological information about the underlying space, such as the distance function, the distance to a measure, the kNN density estimator, the kernel density estimator, and the kerne...

The R package clValid contains functions for validating the results of a clustering analysis. There are three main types of cluster validation measures available, “internal”, “stability”, and “biological”. The user can choose from nine clustering algorithms in existing R packages, including hierarchical, K-means, self-organizing maps (SOM), and model based clustering. In addition, we provide a ...

10 We introduce phylodyn, an R package for phylodynamic analysis based on gene 11 genealogies. The package main functionality is Bayesian nonparametric estimation of 12 effective population size fluctuations over time. Our implementation includes sev13 eral Markov chain Monte Carlo-based methods and an integrated nested Laplace 14 approximation-based approach for phylodynamic inference that hav...

Nowadays, molecular data analyses for biodiversity studies often require advanced bioinformatics skills, preventing many life scientists from analyzing their own data autonomously. BITE R package provides complete and user-friendly functions to handle SNP data and third-party software results (i.e. Admixture, TreeMix), facilitating their visualization, interpretation and use. Furthermore, BITE ...

In this manuscript we present various robust statistical methods and show how to apply them in R using the WRS2 package. We elaborate on robust location measures and present robust t-test versions for independent and dependent samples. We focus on robust one-way and higher order ANOVA strategies including mixed designs (“betweenwithin subjects”). Finally, we elaborate on running interval smooth...

This vignette demonstrates how to use the Structural Topic Model, stm, R package. The Structural Topic Model (STM) allows researchers to estimate a topic model which includes document-level meta-data. The stm package provides a range of features from model selection to extensive plotting and visualization options.

The structure of the package apt and the implementation of models for asymmetric price transmission (APT) are explained in this note. This type of economic analysis is typically time series analysis with the steps of unit root test, cointegration test, and finally error correction model. APT studies have evolved with several distinct stages: pre-cointegration, linear cointegration, nonlinear th...

In this paper, we describe the R package mediation for conducting causal mediation analysis in applied empirical research. In many scientific disciplines, the goal of researchers is not only estimating causal effects of a treatment but also understanding the process in which the treatment causally affects the outcome. Causal mediation analysis is frequently used to assess potential causal mecha...