Related papers: phylodyn: an R package for phylodynamic simulation…
Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models that extend common…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical…
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in…
We introduce an R package, PCMBase, to rapidly calculate the likelihood for multivariate phylogenetic comparative methods. The package is not specific to particular models but offers the user the functionality to very easily implement a…
The R package merlin performs flexible joint modelling of hierarchical multi-outcome data. Increasingly, multiple longitudinal biomarker measurements, possibly censored time-to-event outcomes and baseline characteristics are available.…
We describe an R package developed by the research group Turbulence, Wind energy and Stochastics (TWiSt) at the Carl von Ossietzky University of Oldenburg, which extracts the (stochastic) evolution equation underlying a set of data or…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
Phylodynamics is used to estimate epidemic dynamics from phylogenetic trees or genomic sequences of pathogens, but the likelihood calculations needed can be challenging for complex models. We present a neural Bayes estimator (NBE) for key…
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…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
The increasing risk of epidemics and a fast-growing world population has contributed to a great investment in phylogenetic analysis, in order to track numerous diseases and conceive effective medication and treatments. Phylogenetic analysis…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene…
In silico evolution instantiates the processes of heredity, variation, and differential reproductive success (the three "ingredients" for evolution by natural selection) within digital populations of computational agents. Consequently,…
Background: Determining an adequate sample size is essential for developing reliable and generalisable clinical prediction models, yet practical guidance on selecting appropriate methods remains limited. Existing analytical and…
Recent developments in data science and big data research have produced an abundance of large data sets that are too big to be analyzed in their entirety, due to limits on either computer memory or storage capacity. Here, we introduce our R…
Identifying individuals who are at high risk of cancer due to inherited germline mutations is critical for effective implementation of personalized prevention strategies. Most existing models to identify these individuals focus on specific…
Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume…
The dirichletprocess package provides software for creating flexible Dirichlet process objects. Users can perform nonparametric Bayesian analysis using Dirichlet processes without the need to program their own inference algorithms. Instead,…
Extensions in the field of joint modeling of correlated data and dynamic predictions improve the development of prognosis research. The R package frailtypack provides estimations of various joint models for longitudinal data and survival…