Related papers: Fast likelihood evaluation for multivariate phylog…
Label switching is a well-known and fundamental problem in Bayesian estimation of mixture or hidden Markov models. In case that the prior distribution of the model parameters is the same for all states, then both the likelihood and…
Recent advances in computational methods for intractable models have made network data increasingly amenable to statistical analysis. Exponential random graph models (ERGMs) emerged as one of the main families of models capable of capturing…
Despite their promise and ubiquity, Gaussian processes (GPs) can be difficult to use in practice due to the computational impediments of fitting and sampling from them. Here we discuss a short R package for efficient multivariate normal…
We implemented several multilabel classification algorithms in the machine learning package mlr. The implemented methods are binary relevance, classifier chains, nested stacking, dependent binary relevance and stacking, which can be used…
The random-effects or normal-normal hierarchical model is commonly utilized in a wide range of meta-analysis applications. A Bayesian approach to inference is very attractive in this context, especially when a meta-analysis is based only on…
We introduce PolyLinkR, an R package for gene set enrichment analysis that implements a novel null-model that accounts for linkage disequilibrium between genes belonging to the same gene set - a potential cause of false positives that is…
Symmetric positive definite (SPD) matrices arising from functional connectivity analysis of neuroimaging data can be endowed with a Riemannian geometric structure that standard methods fail to respect. While existing R packages provide some…
This article introduces the bpcs R package (Bayesian Paired Comparison in Stan) and the statistical models implemented in the package. This package aims to facilitate the use of Bayesian models for paired comparison data in behavioral…
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…
Mixed-effects models are among the most commonly used statistical methods for the exploration of multispecies data. In recent years, also Joint Species Distribution Models and Generalized Linear Latent Variale Models have gained in…
The numerical availability of statistical inference methods for a modern and robust analysis of longitudinal- and multivariate data in factorial experiments is an essential element in research and education. While existing approaches that…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
We propose a multiple imputation method based on principal component analysis (PCA) to deal with incomplete continuous data. To reflect the uncertainty of the parameters from one imputation to the next, we use a Bayesian treatment of the…
In this paper we consider a variety of procedures for numerical statistical inference in the family of univariate and multivariate stable distributions. In connection with univariate distributions (i) we provide approximations by finite…
Graphical models are a powerful tool in modelling and analysing complex biological associations in high-dimensional data. The R-package netgwas implements the recent methodological development on copula graphical models to (i) construct…
Compatibilized polymer blends are a complex, yet versatile and widespread category of material. When the components of a binary blend are immiscible, they are typically driven towards a macrophase-separated state, but with the introduction…
The R Package IBMPopSim aims to simulate the random evolution of heterogeneous populations using stochastic Individual-Based Models (IBMs). The package enables users to simulate population evolution, in which individuals are characterized…
BPEC is an R package for Bayesian Phylogeographic and Ecological Clustering which allows geographical, environmental and phenotypic measurements to be combined with DNA sequences in order to reveal clustered structure resulting from…
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide…
Complex systems of polynomial equations have to be set up and solved algebraically in order to obtain analytic solutions for maximum likelihood on phylogenetic trees. This has restricted the types of systems previously resolved to the…