Other packages > Find by keyword >

slendr  

A Simulation Framework for Spatiotemporal Population Genetics
View on CRAN: Click here


Download and install slendr package within the R console
Install from CRAN:
install.packages("slendr")

Install from Github:
library("remotes")
install_github("cran/slendr")

Install by package version:
library("remotes")
install_version("slendr", "1.0.0")



Attach the package and use:
library("slendr")
Maintained by
Martin Petr
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-08-09
Latest Update: 2023-08-08
Description:
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.
How to cite:
Martin Petr (2022). slendr: A Simulation Framework for Spatiotemporal Population Genetics. R package version 1.0.0, https://cran.r-project.org/web/packages/slendr. Accessed 18 Feb. 2025.
Previous versions and publish date:
0.2.0 (2022-08-09 14:00), 0.3.0 (2022-08-19 11:20), 0.4.0 (2022-09-30 22:40), 0.5.0 (2023-02-03 00:20), 0.5.1 (2023-03-09 20:40), 0.6.0 (2023-06-07 12:20), 0.7.0 (2023-06-26 18:30), 0.7.1 (2023-07-14 21:10), 0.7.2 (2023-08-08 11:50), 0.8.0 (2023-12-07 11:50), 0.8.1 (2024-01-15 16:20), 0.9.0 (2024-02-08 09:10), 0.9.1 (2024-02-22 00:20)
Other packages that cited slendr R package
View slendr citation profile
Other R packages that slendr depends, imports, suggests or enhances
Complete documentation for slendr
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

RobustBayesianCopas  
Robust Bayesian Copas Selection Model
Fits the robust Bayesian Copas (RBC) selection model of Bai et al. (2020) for cor ...
Download / Learn more Package Citations See dependency  
readxlsb  
Read 'Excel' Binary (.xlsb) Workbooks
Import data from 'Excel' binary (.xlsb) workbooks into R. ...
Download / Learn more Package Citations See dependency  
fclust  
Fuzzy Clustering
Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visuali ...
Download / Learn more Package Citations See dependency  
ppmf  
Read Census Privacy Protected Microdata Files
Implements data processing described in to align modern differentially ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
OptGS  
Near-Optimal Group-Sequential Designs for Continuous Outcomes
Optimal group-sequential designs minimise some function of the expected and maximum sample size whil ...
Download / Learn more Package Citations See dependency  

23,712

R Packages

205,795

Dependencies

64,332

Author Associations

23,631

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA