From 67d5b6391ce76956b38370788e6475a1da6450ff Mon Sep 17 00:00:00 2001 From: "George G. Vega Yon" Date: Sat, 15 Aug 2026 21:08:42 -0600 Subject: [PATCH 1/4] Add network analysis packages --- NetworkAnalysis.md | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/NetworkAnalysis.md b/NetworkAnalysis.md index adb3e66..77548e6 100644 --- a/NetworkAnalysis.md +++ b/NetworkAnalysis.md @@ -3,7 +3,7 @@ name: NetworkAnalysis topic: Network Analysis maintainer: Fabio Ashtar Telarico, Pavel N. Krivitsky, James Hollway email: Fabio-Ashtar.Telarico@fdv.uni-lj.si -version: 2025-12-05 +version: 2026-08-15 source: https://github.com/cran-task-views/NetworkAnalysis/ --- @@ -215,6 +215,11 @@ lists, `r pkg("network")` and `r pkg("igraph")` objects) as ASCII strings and vice versa using `graph6`, `sparse6`, and `digraph6` [formats](http://users.cecs.anu.edu.au/~bdm/data/formats.txt). +- `r pkg("rgexf")` creates, reads, and writes graphs in the GEXF exchange +format used by Gephi. It supports node and edge attributes, visualization +attributes, dynamic networks, and edge weights, and interoperates with +`r pkg("igraph")` objects. + - `r pkg("tidygraph")` is designed for handling and manipulating graph data within the [_tidyverse_](https://www.tidyverse.org/) framework. It does not make it into "core" packages because it lacks a comprehensive set of tools for @@ -308,6 +313,10 @@ and Cayley graphs with various layout options. - `r pkg("ggraph")` allows to plot `r pkg("igraph")` objects by building up plots layer by layer. +- `r pkg("netplot")` draws `r pkg("igraph")` and `r pkg("network")` objects +using the grid graphics system, with aesthetically oriented defaults for +out-of-the-box network visualizations. + - `r pkg("ggsom")` offers functions to plot self-organizing maps (SOMs). - `r pkg("roughnet")` leverages the _rough.js_ library to draw sketchy, @@ -531,6 +540,7 @@ several specialized extensions are available. | Samples of small networks | `r pkg("ergmito")` | | Large hierarchical ERGMs | `r pkg("bigergm")` | | Bayesian methods for ERGMs | `r pkg("Bergm")` | + | Publication-ready tables of ERGM terms (non-CRAN) | `r github("gvegayon/tabulergm")` | | Template for implementing custom network effects (non-CRAN) | `r github("statnet/ergm.userterms")` | | User-contributed network effects (non-CRAN) | `r github("statnet/ergm.terms.contrib")` | @@ -657,6 +667,11 @@ contagion processes. It implements algorithms for calculating network diffusion statistics such as transmission rate, hazard rates, exposure models, network threshold levels, infectiousness (contagion), and susceptibility. +- `r pkg("epiworldR")` provides a fast and flexible framework for simulating +agent-based epidemic models on networks. It includes common compartmental +models such as SIS, SIR, and SEIR and supports user-defined disease processes, +interventions, and multiple-disease simulations. + ### Others - `r pkg("graphon")` provides methods for estimating the *graphon* of a network based on tis adjacency matrix using empirical degree-sorting for stochastic blockmodel (SBM), SBM approximation, universal singular value thresholding, or neighborhood smoothing. Also, on the basis of the estiamted model, it can complete a matrix from a partially observed data. Additionally, it includes function to generate binary graph given an arbitrary graphon, Erdos-Renyi random graphs, and SBMs. Besides including 10 graphon models for simulation. From f6404ff19b7598cb7175423af4d99c7f34c86f9e Mon Sep 17 00:00:00 2001 From: "George G. Vega Yon" Date: Wed, 2 Sep 2026 00:09:28 -0600 Subject: [PATCH 2/4] The tabulergm package is now on CRAN --- NetworkAnalysis.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/NetworkAnalysis.md b/NetworkAnalysis.md index 77548e6..909c2bb 100644 --- a/NetworkAnalysis.md +++ b/NetworkAnalysis.md @@ -540,7 +540,6 @@ several specialized extensions are available. | Samples of small networks | `r pkg("ergmito")` | | Large hierarchical ERGMs | `r pkg("bigergm")` | | Bayesian methods for ERGMs | `r pkg("Bergm")` | - | Publication-ready tables of ERGM terms (non-CRAN) | `r github("gvegayon/tabulergm")` | | Template for implementing custom network effects (non-CRAN) | `r github("statnet/ergm.userterms")` | | User-contributed network effects (non-CRAN) | `r github("statnet/ergm.terms.contrib")` | @@ -676,6 +675,8 @@ interventions, and multiple-disease simulations. - `r pkg("graphon")` provides methods for estimating the *graphon* of a network based on tis adjacency matrix using empirical degree-sorting for stochastic blockmodel (SBM), SBM approximation, universal singular value thresholding, or neighborhood smoothing. Also, on the basis of the estiamted model, it can complete a matrix from a partially observed data. Additionally, it includes function to generate binary graph given an arbitrary graphon, Erdos-Renyi random graphs, and SBMs. Besides including 10 graphon models for simulation. +- `r pkg("tabulergm")` provides functions to create publication-ready tables of ERGM terms, their mathematical definitions, descriptions, and graphical representations (figures). Tables generated by `tabulergm` can be used in Quarto and R Markdown documents. + ## Field packages As an interdisciplinary approach, network analysis is used in a number of From a96086ab38363078ad105f9dcacf8429dbef4686 Mon Sep 17 00:00:00 2001 From: "F. A. Telarico" <100512813+FATelarico@users.noreply.github.com> Date: Wed, 2 Sep 2026 08:38:49 +0200 Subject: [PATCH 3/4] Add network analysis packages (#24) Updated version number and re-positioned some of the packages added with the referred issue. Closes #24 --- NetworkAnalysis.md | 27 +++++++++++++-------------- 1 file changed, 13 insertions(+), 14 deletions(-) diff --git a/NetworkAnalysis.md b/NetworkAnalysis.md index 909c2bb..0f8211c 100644 --- a/NetworkAnalysis.md +++ b/NetworkAnalysis.md @@ -3,7 +3,7 @@ name: NetworkAnalysis topic: Network Analysis maintainer: Fabio Ashtar Telarico, Pavel N. Krivitsky, James Hollway email: Fabio-Ashtar.Telarico@fdv.uni-lj.si -version: 2026-08-15 +version: 2026-09-02 source: https://github.com/cran-task-views/NetworkAnalysis/ --- @@ -188,6 +188,11 @@ allows to easily convert objects produced by Statnet packages into leveraging multiple packages' functionalities and ensuring compatibility between several users' workflows too many additional functionalities. +- `r pkg("rgexf")` creates, reads, and writes graphs in the GEXF exchange +format used by Gephi. It supports node and edge attributes, visualization +attributes, dynamic networks, and edge weights, and interoperates with +`r pkg("igraph")` objects. + - Similarly, `r pkg("netUtils")` supplies a collection of helper functions for working with network objects including the extraction of sub‑graphs, computing basic statistics, converting between common network classes (not least @@ -215,11 +220,6 @@ lists, `r pkg("network")` and `r pkg("igraph")` objects) as ASCII strings and vice versa using `graph6`, `sparse6`, and `digraph6` [formats](http://users.cecs.anu.edu.au/~bdm/data/formats.txt). -- `r pkg("rgexf")` creates, reads, and writes graphs in the GEXF exchange -format used by Gephi. It supports node and edge attributes, visualization -attributes, dynamic networks, and edge weights, and interoperates with -`r pkg("igraph")` objects. - - `r pkg("tidygraph")` is designed for handling and manipulating graph data within the [_tidyverse_](https://www.tidyverse.org/) framework. It does not make it into "core" packages because it lacks a comprehensive set of tools for @@ -290,6 +290,10 @@ providing function to easily produce hierarchical clustering (`neatmaps::hierarchy`), consensus clustering (`neatmaps::consClustResTable`) and heatmaps of multiple networks (`neatmaps::neatmap`). +- `r pkg("netplot")` draws `r pkg("igraph")` and `r pkg("network")` objects +using the grid graphics system, with aesthetically oriented defaults for +out-of-the-box network visualizations. + - `r pkg("autograph")` builds on `r pkg("ggraph")` for drawing graphs and plots of network objects with sensible defaults and consistent theming in a range of institutional styles. @@ -313,10 +317,6 @@ and Cayley graphs with various layout options. - `r pkg("ggraph")` allows to plot `r pkg("igraph")` objects by building up plots layer by layer. -- `r pkg("netplot")` draws `r pkg("igraph")` and `r pkg("network")` objects -using the grid graphics system, with aesthetically oriented defaults for -out-of-the-box network visualizations. - - `r pkg("ggsom")` offers functions to plot self-organizing maps (SOMs). - `r pkg("roughnet")` leverages the _rough.js_ library to draw sketchy, @@ -543,6 +543,8 @@ several specialized extensions are available. | Template for implementing custom network effects (non-CRAN) | `r github("statnet/ergm.userterms")` | | User-contributed network effects (non-CRAN) | `r github("statnet/ergm.terms.contrib")` | +- `r pkg("tabulergm")` provides functions to create publication-ready tables of ERGM terms, their mathematical definitions, descriptions, and graphical representations (figures). Tables generated by `tabulergm` can be used in Quarto and R Markdown documents + - `r pkg("amen")` offers additive and multiplicative effect (AME) models with regression terms, covariance structure of the social relations model, and multiplicative factor models. @@ -575,7 +577,6 @@ attributes, relations between individuals, and size-related factors. - `r pkg("networkscaleup")` implements methods for estimating, among other things, degree and sizes of hidden populations based on Aggregated Relational Data (ARD) -- number of people known in a set of sub-populations. The methods include "classical" MLE estimators as well as more recent Bayesian models. - ### Multimodal and multilevel networks - `r pkg("migraph")` is an `r pkg("igraph")` extension to analyze multimodal @@ -673,9 +674,7 @@ interventions, and multiple-disease simulations. ### Others -- `r pkg("graphon")` provides methods for estimating the *graphon* of a network based on tis adjacency matrix using empirical degree-sorting for stochastic blockmodel (SBM), SBM approximation, universal singular value thresholding, or neighborhood smoothing. Also, on the basis of the estiamted model, it can complete a matrix from a partially observed data. Additionally, it includes function to generate binary graph given an arbitrary graphon, Erdos-Renyi random graphs, and SBMs. Besides including 10 graphon models for simulation. - -- `r pkg("tabulergm")` provides functions to create publication-ready tables of ERGM terms, their mathematical definitions, descriptions, and graphical representations (figures). Tables generated by `tabulergm` can be used in Quarto and R Markdown documents. +- `r pkg("graphon")` provides methods for estimating the *graphon* of a network based on tis adjacency matrix using empirical degree-sorting for stochastic blockmodel (SBM), SBM approximation, universal singular value thresholding, or neighborhood smoothing. Also, on the basis of the estiamted model, it can complete a matrix from a partially observed data. Additionally, it includes function to generate binary graph given an arbitrary graphon, Erdos-Renyi random graphs, and SBMs. Besides including 10 graphon models for simulation.. ## Field packages From 72fc130a220aa9156a4ca22048b4b0984a4b2c9c Mon Sep 17 00:00:00 2001 From: "F. A. Telarico" <100512813+FATelarico@users.noreply.github.com> Date: Wed, 2 Sep 2026 08:45:24 +0200 Subject: [PATCH 4/4] Minor fixes - typos in `graphon`; - missing final period at the end of `tabulergm`'s entry. Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- NetworkAnalysis.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/NetworkAnalysis.md b/NetworkAnalysis.md index 0f8211c..199040e 100644 --- a/NetworkAnalysis.md +++ b/NetworkAnalysis.md @@ -543,7 +543,7 @@ several specialized extensions are available. | Template for implementing custom network effects (non-CRAN) | `r github("statnet/ergm.userterms")` | | User-contributed network effects (non-CRAN) | `r github("statnet/ergm.terms.contrib")` | -- `r pkg("tabulergm")` provides functions to create publication-ready tables of ERGM terms, their mathematical definitions, descriptions, and graphical representations (figures). Tables generated by `tabulergm` can be used in Quarto and R Markdown documents +- `r pkg("tabulergm")` provides functions to create publication-ready tables of ERGM terms, their mathematical definitions, descriptions, and graphical representations (figures). Tables generated by `tabulergm` can be used in Quarto and R Markdown documents. - `r pkg("amen")` offers additive and multiplicative effect (AME) models with regression terms, covariance structure of the social relations model, @@ -674,7 +674,7 @@ interventions, and multiple-disease simulations. ### Others -- `r pkg("graphon")` provides methods for estimating the *graphon* of a network based on tis adjacency matrix using empirical degree-sorting for stochastic blockmodel (SBM), SBM approximation, universal singular value thresholding, or neighborhood smoothing. Also, on the basis of the estiamted model, it can complete a matrix from a partially observed data. Additionally, it includes function to generate binary graph given an arbitrary graphon, Erdos-Renyi random graphs, and SBMs. Besides including 10 graphon models for simulation.. +- `r pkg("graphon")` provides methods for estimating the *graphon* of a network based on its adjacency matrix using empirical degree-sorting for stochastic block model (SBM), SBM approximation, universal singular value thresholding, or neighborhood smoothing. Also, on the basis of the estimated model, it can complete a matrix from partially observed data. Additionally, it includes functions to generate a binary graph given an arbitrary graphon, Erdos-Renyi random graphs, and SBMs, and includes 10 graphon models for simulation. ## Field packages