Related papers: Visually pleasing knot projections in R
In the package corr2D two-dimensional correlation analysis is implemented in R. This paper describes how two-dimensional correlation analysis is done in the package and how the mathematical equations are translated into R code. The paper…
While the problem of knot classification is far from solved, it is possible to create computer programs that can be used to tabulate knots up to a desired degree of complexity. Here we discuss the main ideas on which such programs can be…
The R programming language is built on an ecosystem of packages, some that allow analysts to accomplish the same tasks. For example, there are at least two clear workflows for creating data visualizations in R: using the base graphics…
Knot diagrams are among the most common visual tools in topology. Computer programs now make it possible to draw, manipulate and render them digitally, which proves to be useful in knot theory teaching and research. Still, an openly…
Nonlinear dimension reduction methods provide a low-dimensional representation of high-dimensional data by applying a Nonlinear transformation. However, the complexity of the transformations and data structures can create wildly different…
This article describes a software named "KnotPortal" for visualization of branched covers of knots based on an idea by Bill Thurston to view a knot as a portal to other universes. Our implementation allows users to explore these knotted…
This paper introduces GephiForR, an R package designed to replicate Java-based Gephi's key plotting tools in R. The package is accessible to those with minimal R experience and, in particular, implements ForceAtlas2, the key layout feature…
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…
Motivation Network visualization is critical for effective communication in various fields of knowledge. Currently, a gap separates network manipulation from network visualization in programming environments. Users often export network data…
This paper presents the R package gRapHD for efficient selection of high-dimensional undirected graphical models. The package provides tools for selecting trees, forests and decomposable models minimizing information criteria such as AIC or…
Networks are useful for representing phenomena in a broad range of domains. Although their ability to represent complexity can be a virtue, it is sometimes useful to focus on a simplified network that contains only the most important edges:…
We introduce KnotMosaics, a SageMath package for constructing, visualizing, and analyzing knot mosaic diagrams. The package represents an n-mosaic as a matrix of standard tile labels and implements the local connectivity rules needed to…
Bipartite projections are used in a wide range of network contexts including politics (bill co-sponsorship), genetics (gene co-expression), economics (executive board co-membership), and innovation (patent co-authorship). However, because…
This note introduces a code snippet in R aiming to generate necklaces as well as bracelets. Among various uses, necklaces are useful tools to manage traces of products of random matrices. Functionality for necklaces and bracelets is…
The xdvir package provides functions for rendering LaTeX fragments as labels, annotations, and data symbols in R plots. There are convenient high-level functions for rendering LaTeX fragments, including labels on ggplot2 plots, plus…
We make use of the 3D nature of knots and links to find savings in computational complexity when computing knot invariants such as the linking number and, in general, most finite type invariants. These savings are achieved in comparison…
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…
Here I present the freegroup package for working with the free group on a finite set of symbols. The package is vectorised; internally it uses an efficient matrix-based representation for free group objects but uses a configurable print…
Discovering patterns of the complex high-dimensional data is a long-standing problem. Dimension Reduction (DR) and Intrinsic Dimension Estimation (IDE) are two fundamental thematic programs that facilitate geometric understanding of the…
R is a programming language and environment that is a central tool in the applied sciences for writing program. Its impact on the development of modern statistics is inevitable. Current research, especially for big data may not be done…