malan

malan: MAle Lineage ANalysis - Published in JOSS (2018)

https://github.com/mikldk/malan

Science Score: 93.0%

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

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CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 15 DOI reference(s) in README and JOSS metadata
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Academic publication links
Links to: joss.theoj.org, zenodo.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Scientific Fields

Sociology Social Sciences - 87% confidence

Last synced: 4 months ago · JSON representation

Repository

MAle Lineage ANalysis

Basic Info

Host: GitHub
Owner: mikldk
License: gpl-2.0
Language: C++
Default Branch: master
Homepage:
Size: 10.4 MB

Statistics

Stars: 0
Watchers: 1
Forks: 3
Open Issues: 1
Releases: 6

Created about 9 years ago · Last pushed 5 months ago

Metadata Files

Readme Changelog License Codemeta

malan: MAle Lineage ANalysis

An R package (https://www.r-project.org/) to perform MAle Lineage ANalysis by simulating genealogies backwards and imposing short tandem repeats (STR) mutations forwards. Intended for forensic Y chromosomal STR (Y-STR) haplotype analyses. Numerous analyses are possible, e.g. number of matches and meiotic distance to matches.

Refer to papers mentioned in citation("malan") (DOI's: https://doi.org/10.1371/journal.pgen.1007028, https://doi.org/10.21105/joss.00684 and https://doi.org/10.1016/j.fsigen.2018.10.004).

Installation

You first need R (https://www.r-project.org/). Then you can install malan from GitHub by using the remotes package (https://CRAN.R-project.org/package=remotes):

``` r

install.packages("remotes")

remotes::install_github("mikldk/malan") ```

For Mac OS users

Some Mac OSX configurations may have installation problems (for example missing gfortran libraries). In such cases, it may help to use Conda package management system. See also the discussion in issue #14.

Getting started

See documentation included in package (vignettes and manual) at https://mikldk.github.io/malan/. The introduction vignette is available at https://mikldk.github.io/malan/articles/introduction.html.

You can also get an overview of the included vignettes by the following R command:

r vignette(package = "malan")

To read a vignette, type:

r vignette("introduction", package = "malan")

Running tests

Note that to also install the tests, you need to install the package as follows:

``` r

install.packages("remotes")

remotes::installgithub("mikldk/malan", INSTALLopts="--install-tests") ```

You can now run the tests:

r library(malan) library(testthat) test_package('malan')

Contribute, issues, and support

Please use the issue tracker at https://github.com/mikldk/malan/issues if you want to notify us of an issue or need support. If you want to contribute, please either create an issue or make a pull request.

Dependencies

This package depends on R (https://www.r-project.org/) and the following R packages: Rcpp, RcppProgress, RcppArmadillo, igraph, tibble, magrittr, dplyr, and tidygraph.

References

Andersen MM, Balding DJ (2017). How convincing is a matching Y-chromosome profile?. PLoS Genet 13(11): e1007028. https://doi.org/10.1371/journal.pgen.1007028.

Disclaimer

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

License

License: GPL-2.

Badges

The Journal of Open Source Software:

Zenodo:

Travis CI:

Owner

Name: Mikkel Meyer Andersen
Login: mikldk
Kind: user
Location: Denmark

Repositories: 64
Profile: https://github.com/mikldk

JOSS Publication

malan: MAle Lineage ANalysis

Published

May 07, 2018

DOI

10.21105/joss.00684

Volume 3, Issue 25, Page 684

Authors

Mikkel Meyer Andersen

Department of Mathematical Sciences, Aalborg University, Denmark

Editor

Roman Valls Guimera

CodeMeta (codemeta.json)

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  "@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
  "@type": "Code",
  "author": [
    {
      "@id": "https://orcid.org/0000-0002-0234-0266",
      "@type": "Person",
      "email": "mikl@math.aau.dk",
      "name": "Mikkel Meyer Andersen",
      "affiliation": "Department of Mathematical Sciences, Aalborg University, Denmark"
    }
  ],
  "identifier": "",
  "codeRepository": "https://github.com/mikldk/malan",
  "datePublished": "2018-05-06",
  "dateModified": "2018-05-06",
  "dateCreated": "2018-05-06",
  "description": "An R package to perform MAle Lineage ANalysis by simulating genealogies backwards and imposing short tandem repeats (STR) mutations forwards. Intended for forensic Y chromosomal STR (Y-STR) haplotype analyses. Numerous analyses are possible, e.g. number of matches and meiotic distance to matches.",
  "keywords": "forensic genetics, STR loci, Y-chromosome, population genetics",
  "license": "GPL v2.0",
  "title": "malan: MAle Lineage ANalysis",
  "version": "1.0.0"
}

Papers & Mentions

Total mentions: 3

How many individuals share a mitochondrial genome?

DOI: 10.1371/journal.pgen.1007774
OpenAlex ID: https://openalex.org/W2952866684
Published: November 2018

Last synced: 3 months ago

How convincing is a matching Y-chromosome profile?

DOI: 10.1371/journal.pgen.1007028
OpenAlex ID: https://openalex.org/W2952968127
Published: November 2017

Last synced: 3 months ago

Assessing the Forensic Value of DNA Evidence from Y Chromosomes and Mitogenomes

DOI: 10.3390/genes12081209
OpenAlex ID: https://openalex.org/W3191595166
Published: August 2021

Last synced: 3 months ago

GitHub Events

Total

Release event: 1
Push event: 1
Create event: 1

Last Year

Release event: 1
Push event: 1
Create event: 1

Committers

Last synced: 5 months ago

All Time

Total Commits: 257
Total Committers: 2
Avg Commits per committer: 128.5
Development Distribution Score (DDS): 0.004

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Mikkel Meyer Andersen	m**l@m**k	256
olivroy	5****y	1

Committer Domains (Top 20 + Academic)

mikl.dk: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 11
Total pull requests: 8
Average time to close issues: 5 days
Average time to close pull requests: 4 days
Total issue authors: 4
Total pull request authors: 2
Average comments per issue: 3.82
Average comments per pull request: 0.25
Merged pull requests: 8
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

afrubin (6)
ajank (3)
szhorvat (1)
mikldk (1)

Pull Request Authors

mikldk (7)
olivroy (2)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 283 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 3
Total maintainers: 1

cran.r-project.org: malan

MAle Lineage ANalysis

Homepage: https://mikldk.github.io/malan/
Documentation: http://cran.r-project.org/web/packages/malan/malan.pdf
License: GPL-2 | file LICENSE
Latest release: 1.0.4
published 5 months ago

Versions: 3
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 283 Last month

Rankings

Forks count: 14.9%

Dependent packages count: 29.8%

Stargazers count: 35.2%

Dependent repos count: 35.5%

Average: 39.3%

Downloads: 81.2%

Maintainers (1)

mikl@math.aau.dk

Last synced: 4 months ago

Dependencies

DESCRIPTION cran

R >= 2.10 depends
dplyr >= 0.7.3 depends
tidygraph >= 1.0.0.9999 depends
Rcpp >= 0.12.7 imports
RcppArmadillo >= 0.9.880.1.0 imports
RcppProgress >= 0.2.1 imports
igraph >= 1.0.1 imports
magrittr >= 1.5 imports
methods * imports
tibble >= 1.1 imports
Rmpfr * suggests
dirmult * suggests
ggraph * suggests
knitr * suggests
rmarkdown * suggests
testthat * suggests

malan

Science Score: 93.0%

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.md

malan: MAle Lineage ANalysis

Installation

install.packages("remotes")

For Mac OS users

Getting started

Running tests

install.packages("remotes")

Contribute, issues, and support

Dependencies

References

Disclaimer

License

Badges

Owner

JOSS Publication

malan: MAle Lineage ANalysis

Authors

Editor

Tags

CodeMeta (codemeta.json)

Papers & Mentions

How many individuals share a mitochondrial genome?

How convincing is a matching Y-chromosome profile?

Assessing the Forensic Value of DNA Evidence from Y Chromosomes and Mitogenomes

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: malan

Rankings

Maintainers (1)

Dependencies