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Rtsne

R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding

https://github.com/jkrijthe/rtsne

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 7 committers (28.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.3%) to scientific vocabulary

Keywords from Contributors

visualisation
Last synced: 10 months ago · JSON representation

Repository

R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding

Basic Info
  • Host: GitHub
  • Owner: jkrijthe
  • License: other
  • Language: C++
  • Default Branch: master
  • Size: 618 KB
Statistics
  • Stars: 263
  • Watchers: 18
  • Forks: 66
  • Open Issues: 4
  • Releases: 1
Created over 12 years ago · Last pushed about 2 years ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output:
  github_document:
    html_preview: false
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```
[![CRAN version](http://www.r-pkg.org/badges/version/Rtsne)](https://cran.r-project.org/package=Rtsne/)
[![R-CMD-check](https://github.com/jkrijthe/Rtsne/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jkrijthe/Rtsne/actions/workflows/R-CMD-check.yaml)
[![codecov.io](https://codecov.io/github/jkrijthe/Rtsne/coverage.svg?branch=master)](https://app.codecov.io/github/jkrijthe/Rtsne?branch=master)
[![CRAN mirror downloads](http://cranlogs.r-pkg.org/badges/Rtsne)](https://cran.r-project.org/package=Rtsne/)


# R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding 

## Installation

To install from CRAN:
```{r, eval = FALSE}
install.packages("Rtsne") # Install Rtsne package from CRAN
```
To install the latest version from the github repository, use:
```{r, eval = FALSE}
if(!require(devtools)) install.packages("devtools") # If not already installed
devtools::install_github("jkrijthe/Rtsne")
```


## Usage
After installing the package, use the following code to run a simple example (to install, see below).
```{r example, fig.path="tools/"}
library(Rtsne) # Load package
iris_unique <- unique(iris) # Remove duplicates
set.seed(42) # Sets seed for reproducibility
tsne_out <- Rtsne(as.matrix(iris_unique[,1:4])) # Run TSNE
plot(tsne_out$Y,col=iris_unique$Species,asp=1) # Plot the result
```


# Details
This R package offers a wrapper around the Barnes-Hut TSNE C++ implementation of [2] [3]. Changes were made to the original code to allow it to function as an R package and to add additional functionality and speed improvements.

# References
[1] L.J.P. van der Maaten and G.E. Hinton. "Visualizing High-Dimensional Data Using t-SNE." Journal of Machine Learning Research 9(Nov):2579-2605, 2008.

[2] L.J.P van der Maaten. "Accelerating t-SNE using tree-based algorithms." Journal of Machine Learning Research 15.1:3221-3245, 2014.

[3] https://lvdmaaten.github.io/tsne/

Owner

  • Name: Jesse Krijthe
  • Login: jkrijthe
  • Kind: user
  • Company: Delft University of Technology

GitHub Events

Total
  • Watch event: 6
Last Year
  • Watch event: 6

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 144
  • Total Committers: 7
  • Avg Commits per committer: 20.571
  • Development Distribution Score (DDS): 0.264
Past Year
  • Commits: 4
  • Committers: 1
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Jesse Krijthe j****e@g****m 106
Aaron Lun a****n@c****k 24
daniel-wells d****s 6
Richard Cotton r****s@g****m 4
by321 b****1@h****m 2
Laurent l****0@c****k 1
Tal Galili t****i@g****m 1
Committer Domains (Top 20 + Academic)
cam.ac.uk: 1 cruk.cam.ac.uk: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 45
  • Total pull requests: 12
  • Average time to close issues: 7 months
  • Average time to close pull requests: about 2 months
  • Total issue authors: 39
  • Total pull request authors: 9
  • Average comments per issue: 4.58
  • Average comments per pull request: 4.42
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • 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
View more stats
Top Authors
Issue Authors
  • zachmayer (4)
  • SamGG (2)
  • lgatto (2)
  • kickbox (2)
  • lcougnaud (1)
  • kevinwkc (1)
  • PhrenoVermouth (1)
  • sami10007 (1)
  • ekinda (1)
  • Ivy-ops (1)
  • ChenMorSays (1)
  • daniel-wells (1)
  • sky-peng (1)
  • vjcitn (1)
  • karigunnarsson (1)
Pull Request Authors
  • LTLA (3)
  • richierocks (2)
  • MichaelChirico (2)
  • by321 (1)
  • zachmayer (1)
  • daniel-wells (1)
  • alyst (1)
  • talgalili (1)
  • lgatto (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 41,138 last-month
  • Total docker downloads: 188,188
  • Total dependent packages: 65
    (may contain duplicates)
  • Total dependent repositories: 377
    (may contain duplicates)
  • Total versions: 13
  • Total maintainers: 1
cran.r-project.org: Rtsne

T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation

  • Versions: 10
  • Dependent Packages: 55
  • Dependent Repositories: 368
  • Downloads: 41,138 Last month
  • Docker Downloads: 188,188
Rankings
Dependent repos count: 0.8%
Forks count: 1.1%
Dependent packages count: 1.6%
Stargazers count: 1.7%
Downloads: 1.8%
Average: 4.0%
Docker downloads count: 17.3%
Maintainers (1)
jkrijthe@gmail.com
Last synced: 11 months ago
conda-forge.org: r-rtsne
  • Versions: 3
  • Dependent Packages: 10
  • Dependent Repositories: 9
Rankings
Dependent packages count: 5.9%
Dependent repos count: 11.6%
Average: 16.0%
Forks count: 22.4%
Stargazers count: 24.2%
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • Rcpp >= 0.11.0 imports
  • stats * imports
  • irlba * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite