Discrete Laplace mixture model with applications in forensic genetics
Discrete Laplace mixture model with applications in forensic genetics - Published in JOSS (2018)
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Published in Journal of Open Source Software
Repository
Discrete Laplace Mixture Inference using the EM Algorithm
Basic Info
- Host: GitHub
- Owner: mikldk
- License: gpl-2.0
- Language: R
- Default Branch: master
- Size: 1.55 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 2
- Releases: 5
Metadata Files
README.md
disclapmix
An R package (https://www.r-project.org/) to perform inference in a mixture of discrete Laplace distributions using the EM algorithm. Intended for forensic Y chromosomal STR (Y-STR) haplotype analyses.
See documentation included in package (vignettes and manual) at https://mikldk.github.io/disclapmix/.
Installation
You first need R (https://www.r-project.org/).
Then you can install disclapmix from CRAN using
r
install.packages("disclapmix")
You can also install the development version from GitHub by using the remotes package (https://CRAN.R-project.org/package=remotes):
```r
install.packages("remotes")
remotes::install_github("mikldk/disclapmix") ```
Getting started
Refer to the included vignettes. You can get an overview of the included vignettes by the following R command:
r
vignette(package = "disclapmix")
To read a vignette, type:
r
vignette("introduction", package = "disclapmix")
Running tests
Note that to also install the tests, you need to install the package as follows:
``` r
install.packages("remotes")
remotes::installgithub("mikldk/disclapmix", INSTALLopts="--install-tests") ```
You can now run the tests:
r
library(disclapmix)
library(testthat)
test_package('disclapmix')
Contribute, issues, and support
Please use the issue tracker at https://github.com/mikldk/disclapmix/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.
References
Andersen MM, PS Eriksen, N Morling (2013). The discrete Laplace exponential family and estimation of Y-STR haplotype frequencies. Journal of Theoretical Biology 329. https://doi.org/10.1016/j.jtbi.2013.03.009
Andersen MM, PS Eriksen, N Morling (2013). A gentle introduction to the discrete Laplace method for estimating Y-STR haplotype frequencies. arXiv:1304.2129. https://arxiv.org/abs/1304.2129
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:
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Owner
- Name: Mikkel Meyer Andersen
- Login: mikldk
- Kind: user
- Location: Denmark
- Repositories: 64
- Profile: https://github.com/mikldk
JOSS Publication
Discrete Laplace mixture model with applications in forensic genetics
Authors
Department of Mathematical Sciences, Aalborg University, Denmark
Editor
Pjotr Prins
Tags
Y-chromosome forensic genetics population genetics weight of evidenceCodeMeta (codemeta.json)
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"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/disclapmix",
"datePublished": "2018-04-23",
"dateModified": "2018-04-23",
"dateCreated": "2018-04-23",
"description": "An R package to perform inference in a mixture of discrete Laplace distributions using the EM algorithm. This can e.g. be used in forensic genetics to evaluate the evidential strength of a Y chromosomal match by modelling the distribution of Y chromosomal haplotypes.",
"keywords": "forensic genetics, STR loci, Y-chromosome, population genetics",
"license": "GPL v2.0",
"title": "Discrete Laplace mixture model with applications in forensic genetics",
"version": ""
}GitHub Events
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Dependencies
- MASS * imports
- Rcpp >= 0.11 imports
- cluster >= 1.14.4 imports
- disclap >= 1.4 imports
- graphics * imports
- methods * imports
- stats * imports
- utils * imports
- dplyr * suggests
- fwsim * suggests
- ggdendro * suggests
- ggplot2 * suggests
- gridExtra * suggests
- knitr * suggests
- rmarkdown * suggests
- scales * suggests
- seriation * suggests
- testthat * suggests