相关论文: 'coexist': an R package for performing species coe…
Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new…
We present properties of Lotka-Volterra equations describing ecological competition among a large number of competing species. First we extend to the case of a non-homogeneous niche space stability conditions for solutions representing…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
Despite the general acknowledgment of the role of niche and fitness differences in community dynamics, species abundance has been coined as a relevant feature not just regarding niche perspectives, but also according to neutral…
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…
Multivariate spatio-temporal models are widely applicable, but specifying their structure is complicated and may inhibit wider use. We introduce the R package tinyVAST from two viewpoints: the software user and the statistician. From the…
Survival data is encountered in a range of disciplines, most notably health and medical research. Although Bayesian approaches to the analysis of survival data can provide a number of benefits, they are less widely used than classical (e.g.…
Background. The bootComb R package allows researchers to derive confidence intervals with correct target coverage for arbitrary combinations of arbitrary numbers of independently estimated parameters. Previous versions (< 1.1.0) of bootComb…
The increasing complexity of data requires methods and models that can effectively handle intricate structures, as simplifying them would result in loss of information. While several analytical tools have been developed to work with complex…
How do landscape fragmentation affects ecosystems diversity and stability is an important and complex question in ecology with no simple answer, as spatially separated habitats where species live are highly dynamic rather than just static.…
Species do not merely evolve, they also coevolve with other organisms. Coevolution is a major force driving interacting species to continuously evolve ex- ploring their fitness landscapes. Coevolution involves the coupling of species fit-…
Causal analyses for observational studies are often complicated by covariate imbalances among treatment groups, and matching methodologies alleviate this complication by finding subsets of treatment groups that exhibit covariate balance. It…
Interacting proteins coevolve at multiple but interconnected scales, from the residue-residue over the protein-protein up to the family-family level. The recent accumulation of enormous amounts of sequence data allows for the development of…
Nowadays, the analysis of dynamics in networks represents a great deal in the Social Network Analysis research area. To support students, teachers, developers, and researchers in this work we introduce a novel R package, namely DynComm. It…
Microarray technology is still an important way to assess gene expression in molecular biology, mainly because it measures expression profiles for thousands of genes simultaneously, what makes this technology a good option for some studies…
Scientific advancement relies on the ability to share and reproduce results. When data analysis or calculations are carried out using software written by scientists there are special challenges around code versions, quality and code…
We introduce the concept of 'dynamical phase coexistence' to provide a simple solution for a long-standing problem in theoretical ecology, the so-called "savanna problem". The challenge is to understand why in savanna ecosystems trees and…
Cooperative Co-evolution, through the decomposition of the problem space, is a primary approach for solving large-scale global optimization problems. Typically, when the subspaces are disjoint, the algorithms demonstrate significantly both…
Evaluating forecasts is essential to understand and improve forecasting and make forecasts useful to decision makers. A variety of R packages provide a broad variety of scoring rules, visualisations and diagnostic tools. One particular…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…