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", "0.9.1")



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 0.9.1, https://cran.r-project.org/web/packages/slendr. Accessed 21 Nov. 2024.
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)
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

SCBiclust  
Identifies Mean, Variance, and Hierarchically Clustered Biclusters
Identifies a bicluster, a submatrix of the data such that the features and observations within the s ...
Download / Learn more Package Citations See dependency  
RcppHNSW  
'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors
'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This package provides a minimal R int ...
Download / Learn more Package Citations See dependency  
crossrun  
Joint Distribution of Number of Crossings and Longest Run
Joint distribution of number of crossings and the longest run in a series of independent Bernoulli ...
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  
pkgdepends  
Package Dependency Resolution and Downloads
Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain ...
Download / Learn more Package Citations See dependency  
kgschart  
KGS Rank Graph Parser
Restore underlining numeric data from rating history graph of KGS (an online platform of the game o ...
Download / Learn more Package Citations See dependency  

23,229

R Packages

199,929

Dependencies

62,984

Author Associations

23,230

Publication Badges

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