相关论文: 'coexist': an R package for performing species coe…

The role of species interactions in controlling the interplay between the stability of an ecosystem and its biodiversity is still not well understood. The ability of ecological communities to recover after a small perturbation of the…

The past decade has witnessed a dramatic increase in the size and scope of biological and behavioral experiments. These experiments are providing an unprecedented level of detail and depth of data. However, this increase in data presents…

R packages are the fundamental units of reproducible code in R, providing a mechanism for distributing user-developed code, documentation, and data. Docker is a virtualization technology that allows applications and their dependencies to be…

Camouflage in nature seems to arise from competition between predator and prey. To survive, predators must find prey, and prey must avoid being found. This work simulates an abstract model of that adversarial relationship. It looks at…

One key task in environmental science is to map environmental variables continuously in space or even in space and time. Machine learning algorithms are frequently used to learn from local field observations to make spatial predictions by…

The R package ecosystem is expanding fast and dependencies among packages in the ecosystem are becoming more complex. In this study, we explored the package dependencies from a new aspect. We applied a new metric named "dependency…

Genetic algorithms are stochastic iterative algorithms in which a population of individuals evolve by emulating the process of biological evolution and natural selection. The R package GA provides a collection of general purpose functions…

The matched case-control design, up until recently mostly pertinent to epidemiological studies, is becoming customary in biomedical applications as well. For instance, in omics studies, it is quite common to compare cancer and healthy…

This R package evaluates main and pair-wise interaction effect of single nucleotide polymorphisms (SNPs) via the W-test, scalable to whole genome-wide data sets. The package provides fast and accurate p-value estimation of genetic markers,…

This work describes the setup of an advanced technical infrastructure for collaborative software development (CDE) in large, distributed projects based on GitLab. We present its customization and extension, additional features and processes…

The number of available constraints on the Universe during and before cosmic reionization is rapidly growing. These are often scattered across inhomogeneous formats, unit systems and sampling strategies. In this paper, I introduce CoReCon,…

Artificial ecosystems provide an additional experimental tool to support laboratory work, field work, and theoretical development in competitive exclusion research. A novel application of a spatiotemporal agent based model is presented…

The Rocker Project provides widely used Docker images for R across different application scenarios. This article surveys downstream projects that build upon the Rocker Project images and presents the current state of R packages for managing…

Monitoring the quality of statistical processes has been of great importance, mostly in industrial applications. Control charts are widely used for this purpose, but often lack the possibility to monitor survival outcomes. Recently,…

Microbial communities harbor extensive fine-scale diversity: closely-related strains of the same species coexist alongside many distantly-related taxa. Yet strain coexistence remains poorly understood, largely because most studies neglect…

1.) Spatio-temporal datasets that are difficult to analyze are common in ecological surveys. There are software packages available to analyze these datasets, but many of them require advanced coding skills. There is a growing need for easy…

What determines biodiversity in nature is a prominent issue in ecology, especially in biotic resource systems that are typically devoid of cross-feeding. Here, we show that by incorporating pairwise encounters among consumer individuals…

This is the first of two papers where we discuss the limits imposed by competition to the biodiversity of species communities. In this first paper we study the coexistence of competing species at the fixed point of population dynamic…

Recent work draws attention to community-community encounters ("coalescence") as likely an important factor shaping natural ecosystems. This work builds on MacArthur's classic model of competitive coexistence to investigate such…

Network inference is a major field of interest for the ecological community, especially in light of the high cost and difficulty of manual observation, and easy availability of remote, long term monitoring data. In addition, comparing…