to be announced
Preprint (2024-04-16)
Schmid, C., Ghalichi, A., Lamnidis, T. C., Mudiyanselage, D. B. A., Haak, W., & Schiffels, S. (2024). Poseidon – A framework for archaeogenetic human genotype data management. bioRxiv. https://doi.org/10.1101/2024.04.12.589180
https://doi.org/10.17605/OSF.IO/ZUQGB at Open Science Framework (OSF)
The files in this archived storage will generate the results as found in the publication. The files hosted on GitHub are the development versions and may have changed since the paper was published.
Clemens Schmid
This repository contains the following main top level directories:
code: The R scripts necessary to reproduce the analysis and create the figures. Some scripts provide code beyond what is required to reproduce figures and results in the publication (e.g. scripts to create didactic figures for presentations).data: Intermediate data output by the scripts, not tracked by Git.data_tracked: Input data files manually or only semi-automatically created for this analysis.osf: Scripts to prepare the data upload to the Open Science Framework (OSF) long-term archive.plots: Rendered versions of the plots for the publication, not tracked by Git.schemata: Schematic drawings created for the paper.
The following versions of the Poseidon public archives downloaded on 2024-03-15 were analysed:
| archive | Git commit | Corresponding package versions |
|---|---|---|
| PCA | b159991 | archive.chron |
| PAA | 60ddda0 | archive.chron |
The archive.chron files include all present and past package versions, but only the latest ones were considered here.
The analysis was performed with R v4.3.2 using the following packages and package versions as available on CRAN (Comprehensive R Archive Network) on 2024-03-13:
Generated with this code
tibble::tibble(
package = rrtools::add_dependencies_to_description(just_packages = T),
version = purrr::map_chr(package, \(x) utils::packageVersion(x) |> as.character())
) |> knitr::kable()| package | version |
|---|---|
| bib2df | 1.1.1 |
| cowplot | 1.1.3 |
| dplyr | 1.1.4 |
| ggpattern | 1.0.1 |
| ggplot2 | 3.5.0 |
| ggrepel | 0.9.4 |
| ggsankey | 0.0.99999 |
| giscoR | 0.4.1 |
| hash | 2.2.6.3 |
| janno | 1.0.0 |
| magrittr | 2.0.3 |
| purrr | 1.0.2 |
| readr | 2.1.5 |
| scales | 1.3.0 |
| sf | 1.0.15 |
| stringr | 1.5.1 |
| tibble | 3.2.1 |
| tidyr | 1.3.1 |
| tidyselect | 1.2.1 |
| wesanderson | 0.3.7 |
