Showing 3 of total 3 results (show query)
bodkan
slendr:A Simulation Framework for Spatiotemporal Population Genetics
A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis.
Maintained by Martin Petr. Last updated 6 days ago.
popgenpopulation-geneticssimulationsspatial-statistics
56 stars 9.13 score 88 scripts
martinschobben
oceanexplorer:Explore Our Planet's Oceans with NOAA
Provides tools for easy exploration of the world ocean atlas of the US agency National Oceanic and Atmospheric Administration (NOAA). It includes functions to extract NetCDF data from the repository and code to visualize several physical and chemical parameters of the ocean. A Shiny app further allows interactive exploration of the data. The methods for data collecting and quality checks are described in several papers, which can be found here: <https://www.ncei.noaa.gov/products/world-ocean-atlas>.
Maintained by Martin Schobben. Last updated 1 years ago.
earthearth-observationearth-sciencenoaanoaa-dataoceanocean-sciencesoceanographyopen-datashinyspatialspatial-analysisspatial-data
9 stars 5.01 score 23 scripts
f-rousset
Infusion:Inference Using Simulation
Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated. The package implements more advanced methods than the ones first described in: Rousset, Gouy, Almoyna and Courtiol (2017) <doi:10.1111/1755-0998.12627>.
Maintained by François Rousset. Last updated 6 months ago.
1.18 score 15 scripts