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add citation and acknowledgements

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TomKellyGenetics committed Nov 15, 2018
1 parent 846b6b9 commit 0a7b087d1dae739496c87bd6a659ae211bc39cf5
Showing with 119 additions and 1 deletion.
  1. +5 −0 .travis.yml
  2. +3 −0 DESCRIPTION
  3. +36 −1 README.md
  4. +45 −0 appveyor.yml
  5. +12 −0 codecov.yml
  6. +18 −0 inst/CITATION
@@ -0,0 +1,5 @@
# R for travis: see documentation at https://docs.travis-ci.com/user/languages/r

language: R
sudo: false
cache: packages
@@ -2,6 +2,7 @@ Package: leiden
Type: Package
Title: R implementation of the Leiden package
Version: 0.1.0
Date: 2018
Author: Tom Kelly <tom.kelly@riken.jp>
Maintainer: Tom Kelly <tom.kelly@riken.jp>
Description: Implements the Python leidenalg module to be called in R.
@@ -12,3 +13,5 @@ License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Suggests:
covr
@@ -1,4 +1,16 @@
# Leiden Algorithm

## leiden version 0.1.0

[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/leiden)](https://cran.r-project.org/package=leiden)
[![Travis Build Status](https://travis-ci.org/TomKellyGenetics/leiden.svg?branch=master)](https://travis-ci.org/TomKellyGenetics/leiden)
[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/TomKellyGenetics/leiden?branch=master&svg=true)](https://ci.appveyor.com/project/TomKellyGenetics/leiden)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
[![codecov](https://codecov.io/gh/TomKellyGenetics/leiden/branch/master/graph/badge.svg)](https://codecov.io/gh/TomKellyGenetics/leiden)

## Clustering with the Leiden Algorithm in R

This package allows calling the Leiden algorthm for clustering on an igraph object from R. See the Python and Java implementations for more details:

https://github.com/CWTSLeiden/networkanalysis

@@ -47,6 +59,29 @@ object@meta.data$ident <- membership

### Citation

Please cite this implementation R in if you use it:

```
To cite the leiden package in publications use:
S. Thomas Kelly (2018). leiden: R implementation of the Leiden algorithm. R
package version 0.1.0 https://github.com/TomKellyGenetics/leiden
A BibTeX entry for LaTeX users is
@Manual{,
title = {leiden: R implementation of the Leiden algorithm},
author = {S. Thomas Kelly},
year = {2018},
note = {R package version 0.1.0},
url = {https://github.com/TomKellyGenetics/leiden},
}
```

Please also cite the original publication of this algorithm.

```
Traag, V.A., Waltman. L., Van Eck, N.-J. (2018). From Louvain to
Leiden: guaranteeing well-connected communities.
`arXiv:1810.08473 <https://arxiv.org/abs/1810.08473>`_
`arXiv:1810.08473 <https://arxiv.org/abs/1810.08473>`
```
@@ -0,0 +1,45 @@
# DO NOT CHANGE the "init" and "install" sections below

# Download script file from GitHub
init:
ps: |
$ErrorActionPreference = "Stop"
Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
Import-Module '..\appveyor-tool.ps1'
install:
ps: Bootstrap

cache:
- C:\RLibrary

# Adapt as necessary starting from here

build_script:
- travis-tool.sh install_deps

test_script:
- travis-tool.sh run_tests

on_failure:
- 7z a failure.zip *.Rcheck\*
- appveyor PushArtifact failure.zip

artifacts:
- path: '*.Rcheck\**\*.log'
name: Logs

- path: '*.Rcheck\**\*.out'
name: Logs

- path: '*.Rcheck\**\*.fail'
name: Logs

- path: '*.Rcheck\**\*.Rout'
name: Logs

- path: '\*_*.tar.gz'
name: Bits

- path: '\*_*.zip'
name: Bits
@@ -0,0 +1,12 @@
comment: false

coverage:
status:
project:
default:
target: auto
threshold: 1%
patch:
default:
target: auto
threshold: 1%
@@ -0,0 +1,18 @@
citHeader("To cite the leiden package in publications use:")

citEntry(entry = "Manual",
title = "leiden: R implementation of the Leiden algorithm",
author = personList(as.person("S. Thomas Kelly")),
year = "2018",
note = "R package version 0.1.0",
url = "https://github.com/TomKellyGenetics/leiden",

textVersion =
paste("S. Thomas Kelly (2018). leiden: R implementation of the Leiden algorithm. R package version 0.1.0",
"https://github.com/TomKellyGenetics/leiden")
)

citFooter(paste("Please also acknowledge the original publication: \n",
"Traag, V.A., Waltman. L., Van Eck, N.-J. (2018). \n",
"From Louvain to Leiden: guaranteeing well-connected communities. \n",
"`arXiv:1810.08473 <https://arxiv.org/abs/1810.08473>`",sep=" "))

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