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.
# install.packages("remotes") remotes::install_github("mikldk/malan")
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.
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
vignette(package = "malan")
To read a vignette, type:
vignette("introduction", package = "malan")
Note that to also install the tests, you need to install the package as follows:
# install.packages("remotes") remotes::install_github("mikldk/malan", INSTALL_opts="--install-tests")
You can now run the tests:
library(malan) library(testthat) test_package('malan')
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.
This package depends on R (https://www.r-project.org/) and the following R packages:
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.
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