rsetse
This package is used to calculate the Strain Elevation Tension Spring embedding (SETSe) for networks in R
Science Score: 13.0%
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Low similarity (16.2%) to scientific vocabulary
Keywords
Repository
This package is used to calculate the Strain Elevation Tension Spring embedding (SETSe) for networks in R
Basic Info
- Host: GitHub
- Owner: JonnoB
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://jonnob.github.io/rSETSe/
- Size: 9.01 MB
Statistics
- Stars: 7
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
rSETSe 
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Importnant note
The github version of R setse has been updated so that setseautohd has been re-written in c++ using Rcpp Armadillo. This makes it much faster (between 36 -350 times) than the version on CRAN. If you have larger networks I would definately advise using installing from github not CRAN.
An R package for embedding graphs using the SETSe algorithm
This is the R package for the Strain Elevation Tension Spring embeddings (SETSe) algorithm. SETSe is a deterministic graph embeddings algorithm. It converts the node attributes of a graph into forces and the edge attributes into springs. The algorithm finds an equilibrium position when the forces of the nodes are balanced by the forces on the springs. A full description of the algorithm is given in "The spring bounces back: Introduction to Strain Elevation Tension Spring embedding for network representation" (Bourne 2020). There is a website for the package providing documentation and vignettes at https://jonnob.github.io/rSETSe/index.html . This is a very niche package so please feel free to reach out to me on twitter or through email with questions.
Installation instructions
The package is available on CRAN and can be installed by running install.packages("rsetse").Alternatively it can be installed from github using the below method.
- Open R/Rstudio and ensure that devtools has been installed
- Run the following code library(devtools); install_github("JonnoB/rSETSe")
- Load the package normally using library(rsetse)
- All functions have help files e.g ?setse_auto
The package can also be downloaded or cloned then installed locally using the install function from devtools.
Basic use
``` library(rSETSe)
prepares a graph for embedding using SETSe
set.seed(234) #set the random see for generating the network g <- generatepeelsnetwork(type = "E") %>% prepare_edges(k = 500, distance = 1) %>%
prepare the network for a binary embedding
preparecategoricalforce(., nodenames = "name", forcevar = "class")
Embedds using the bi-connected auto-parametrization algorithm.
This method is strongly reccomended, it tends to be much faster and almost always converges
embeddings <- setsebicomp(g, force = "classA", tol = sum(abs(vertexattr(g, "classA")))/1000, hypertol = 0.1, hyperiters = 3000, verbose = T)
```
Cite
To cite rsetse in publications use: Bourne, J. The spring bounces back: introducing the strain elevation tension spring embedding algorithm for network representation. Appl Netw Sci 5, 88 (2020). https://doi.org/10.1007/s41109-020-00329-4
Owner
- Name: Jonathan Bourne
- Login: JonnoB
- Kind: user
- Location: London
- Company: @UCL
- Website: https://www.somesquarederror.com/
- Twitter: sse_data
- Repositories: 62
- Profile: https://github.com/JonnoB
Mostly, Complex networks and geospatial analysis. Also some FOI stuff
GitHub Events
Total
- Issue comment event: 4
Last Year
- Issue comment event: 4
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 112
- Total Committers: 2
- Avg Commits per committer: 56.0
- Development Distribution Score (DDS): 0.009
Top Committers
| Name | Commits | |
|---|---|---|
| Jonathan Bourne | c****g@h****m | 111 |
| Jonno | J****e@g****m | 1 |
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Last synced: 9 months ago
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- Total issues: 0
- Total pull requests: 0
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- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
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Packages
- Total packages: 1
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Total downloads:
- cran 242 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
cran.r-project.org: rsetse
Strain Elevation Tension Spring Embedding
- Homepage: https://github.com/JonnoB/rSETSe
- Documentation: http://cran.r-project.org/web/packages/rsetse/rsetse.pdf
- License: GPL-3
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Latest release: 0.5.0
published over 4 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.4.0 depends
- Matrix * imports
- Rcpp * imports
- RcppArmadillo * imports
- dplyr * imports
- igraph * imports
- magrittr * imports
- methods * imports
- minpack.lm * imports
- purrr * imports
- rlang >= 0.1.2 imports
- stats * imports
- tibble * imports
- ggplot2 * suggests
- ggraph * suggests
- knitr * suggests
- rmarkdown * suggests
- roxygen2 * suggests
- tidyr * suggests