相关论文: 'coexist': an R package for performing species coe…
The Statistical Toolkit is an open source system specialized in the statistical comparison of distributions. It addresses requirements common to different experimental domains, such as simulation validation (e.g. comparison of experimental…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
In survival analysis, longitudinal information on the health status of a patient can be used to dynamically update the predicted probability that a patient will experience an event of interest. Traditional approaches to dynamic prediction…
A pair of ecological tables is made of one table containing environmental variables (in columns) and another table containing species data (in columns). The rows of these two tables are identical and correspond to the sites where…
Microbial populations generally evolve in volatile environments, under conditions fluctuating between harsh and mild, e.g. as the result of sudden changes in toxin concentration or nutrient abundance. Environmental variability thus shapes…
We present RKappa, a framework for the development and analysis of rule-based models within a mature, statistically empowered R environment. The infrastructure allows model editing, modification, parameter sampling, simulation, statistical…
Anthropogenic activity threatens biodiversity through climate change, habitat fragmentation, and increasing frequency and scale of disturbance. Various theoretical studies have sought to shed light on how these factors could promote or…
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…
In this paper, we discuss the need for an integrated software stack that unites artificial intelligence (AI) and modeling and simulation (ModSim) tools to advance scientific discovery. The authors advocate for a unified AI/ModSim software…
If two species exhibit different nonlinear responses to a single shared resource, and if each species modifies the resource dynamics such that this favors its competitor, they may stably coexist. This coexistence mechanism, known as…
A complex interplay between species governs the evolution of spatial patterns in ecology. An open problem in the biological sciences is characterising spatio-temporal data and understanding how changes at the local scale affect global…
Occupancy modeling is a common approach to assess spatial and temporal species distribution patterns, while explicitly accounting for measurement errors common in detection-nondetection data. Numerous extensions of the basic single species…
Random forests are a sensible non-parametric model to predict competing risk data according to some covariates. However, there are currently no packages that can adequately handle large datasets ($n > 100,000$). We introduce a new R…
This document describes an infra-structure provided by the R package performanceEstimation that allows to estimate the predictive performance of different approaches (workflows) to predictive tasks. The infra-structure is generic in the…
The ability to conduct reproducible research in Stata is often limited by the lack of version control for community-contributed packages. This article introduces the require command, a tool designed to ensure Stata package dependencies are…
A central goal in ecology is to understand how biodiversity is maintained. Previous theoretical works have employed the rock-paper-scissors (RPS) game as a toy model, demonstrating that population mobility is crucial in determining the…
We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric estimation of effective population size fluctuations over time. Our implementation includes…
Detecting changepoints in a time series of length $N$ entails evaluating up to $2^{N-1}$ possible changepoint models, making exhaustive enumeration computationally infeasible. Genetic algorithms (GAs) provide a stochastic way to identify…
Conducting research often involves managing multiple disconnected tools for survey design, data collection, response analysis, and report generation, leading to inefficiencies, increased error risks, and challenges in ensuring…
Estimating sample size and statistical power is an essential part of a good study design. This R package allows users to conduct power analysis based on Monte Carlo simulations in settings in which consideration of the correlations between…