mitolina
mitolina: MITOchondrial LINeage Analysis - Published in JOSS (2019)
Science Score: 93.0%
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Published in Journal of Open Source Software
Scientific Fields
Repository
MITOchondrial LINeage Analysis
Basic Info
Statistics
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
mitolina: MITOchondrial LINeage Analysis
An R package (https://www.r-project.org/) to perform MITOchondrial LINeage Analysis by simulating genealogies backwards and imposing mtDNA including binary mutations forwards. This software operates under the maternal inheritance only model, i.e. that mtDNA is only passed on by mothers to children. Numerous analyses are possible, e.g. number of matches and meiotic distance to matches.
See documentation included in package (vignettes and manual) at https://mikldk.github.io/mitolina/.
Installation
You first need R (https://www.r-project.org/).
Then you can install mitolina from GitHub by using the remotes package (https://CRAN.R-project.org/package=remotes):
``` r
install.packages("remotes")
remotes::installgithub("mikldk/mitolina", buildopts = c("--no-resave-data", "--no-manual"), build_vignettes = TRUE) ```
The build_opts is provided to remove --no-build-vignettes such that vignettes are built.
Getting started
Refer to the included vignettes. You can get an overview of the included vignettes by the following R command:
r
browseVignettes(package = "mitolina")
To read a vignette, type:
r
vignette("introduction", package = "mitolina")
Contribute, issues, and support
Please use the issue tracker at https://github.com/mikldk/mitolina/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.
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.
Build status
Travis CI:
The Journal of Open Source Software (JOSS):
Owner
- Name: Mikkel Meyer Andersen
- Login: mikldk
- Kind: user
- Location: Denmark
- Repositories: 64
- Profile: https://github.com/mikldk
JOSS Publication
mitolina: MITOchondrial LINeage Analysis
Authors
Department of Mathematical Sciences, Aalborg University, Denmark
Editor
Lorena Pantano
Tags
simulation mtDNA mitochondrial genomes mitogenome forensic genetics population genetics weight of evidenceCodeMeta (codemeta.json)
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"@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/mitolina",
"datePublished": "2019-02-18",
"dateModified": "2019-02-18",
"dateCreated": "2019-02-18",
"description": "An R package to perform MITOchondrial LINeage Analysis by simulating genealogies backwards and imposing mtDNA/mitochondrial genomes (mitogenomes) forwards from founders with mutations. Numerous analyses are possible, e.g. number of matches and meiotic distance to matches.",
"keywords": "simulation, mtDNA, mitochondrial genomes, mitogenome, forensic genetics, population genetics, weight of evidence",
"license": "GPL v2.0",
"title": "mitolina: MITOchondrial LINeage Analysis",
"version": "0.0.1"
}GitHub Events
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Last Year
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Mikkel Meyer Andersen | m****l@m****k | 69 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 2
- Total pull requests: 1
- Average time to close issues: about 10 hours
- Average time to close pull requests: less than a minute
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 1.5
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
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- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jdeligt (2)
Pull Request Authors
- mikldk (1)
Top Labels
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Dependencies
- R >= 2.10 depends
- dplyr >= 0.7.3 depends
- tidygraph >= 1.0.0.9999 depends
- Rcpp >= 0.12.7 imports
- RcppArmadillo >= 0.7.600.1.0 imports
- RcppProgress >= 0.2.1 imports
- igraph >= 1.0.1 imports
- magrittr >= 1.5 imports
- methods * imports
- tibble >= 1.1 imports
- ggraph * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests