相关论文: A complex network analysis of the Comprehensive R …

Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical…

Exponential-family random graph models (ERGMs) are probabilistic network models that are parametrized by sufficient statistics based on structural (i.e., graph-theoretic) properties. The ergm package for the R statistical computing system…

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…

The popularity of Python has risen rapidly over the past 15 years. It is a major language in some of the most exciting technologies today. This popularity has led to a large ecosystem of third-party packages available via the pip package…

Uncovering modular structure in networks is fundamental for systems in biology, physics, and engineering. Community detection identifies candidate modules as hypotheses, which then need to be validated through experiments, such as…

The rise of the programmable web offers new opportunities for the empirically driven social sciences. The access, compilation and preparation of data from the programmable web for statistical analysis can, however, involve substantial…

Networks or graphs are widely used across the sciences to represent relationships of many kinds. igraph (https://igraph.org) is a general-purpose software library for graph construction, analysis, and visualisation, combining fast and…

Despite the importance of scientific software for research, it is often not formally recognized and rewarded. This is especially true for foundational libraries, which are hidden below packages visible to the users (and thus doubly hidden,…

Microbiome data analyses require statistical tools that can simultaneously decode microbes' reactions to the environment and interactions among microbes. We introduce CARlasso, the first user-friendly open-source and publicly available R…

As the complexity and size of software projects increases in real-world environments, maintaining and creating maintainable and dependable code becomes harder and more costly. Refactoring is considered as a method for enhancing the internal…

Closed Loop Supply Chain (CLSC) networks are an attractive topic in both industry and academic research due to their positive environmental effects and waste reduction. Performance evaluation of CLSC networks is challenging due to the…

A community of developers has formed to modernize the Fortran ecosystem. In this article, we describe the high-level features of Fortran that continue to make it a good choice for scientists and engineers in the 21st century. Ongoing…

We introduce NetworKit, an open-source software package for analyzing the structure of large complex networks. Appropriate algorithmic solutions are required to handle increasingly common large graph data sets containing up to billions of…

The R software has become popular among researchers due to its flexibility and open-source nature. However, researchers in the fields of public health and epidemiological studies are more customary to commercial statistical softwares such…

CONTEXT The R programming language has a huge and active community, especially in the area of statistical computing. Its interpreted nature allows for several interesting constructs, like the manipulation of functions at run-time, that…

Advancements in medical informatics tools and high-throughput biological experimentation make large-scale biomedical data routinely accessible to researchers. Competing risks data are typical in biomedical studies where individuals are at…

\pkg{multiplex} is a computer program that provides algebraic tools for the analysis of multiple network structures within the \proglang{R} environment. Apart from the possibility to create and manipulate multivariate data representing…

Recently, the number of malicious open-source packages in package repositories has been increasing dramatically. While major security scanners focus on identifying known Common Vulnerabilities and Exposures (CVEs) in open-source packages,…

Much of the current software depends on open-source components, which in turn have complex dependencies on other open-source libraries. Vulnerabilities in open source therefore have potentially huge impacts. The goal of this work is to get…

We introduce ICON, an R package that contains 1075 complex network datasets in a standard edgelist format. All provided datasets have associated citations and have been indexed by the Colorado Index of Complex Networks - also referred to as…