Package: polySimIBD 1.1.0

Nick Brazeau

polySimIBD: Structured Wright Fisher Simulator for Malaria Genetics

Unique features of the malaria life-cycle and transmission dynamics requires extensions of typical population genetic simulators. Using a spatial discrete-loci, discrete-time structured Wright Fisher framework, we simulate malaria population genetics forwards in time. Users are then able to capture the full Ancestral Recombination Graph.

Authors:Nick Brazeau [aut, cre], Bob Verity [aut]

polySimIBD_1.1.0.tar.gz
polySimIBD_1.1.0.zip(r-4.7)polySimIBD_1.1.0.zip(r-4.6)polySimIBD_1.1.0.zip(r-4.5)
polySimIBD_1.1.0.tgz(r-4.6-x86_64)polySimIBD_1.1.0.tgz(r-4.6-arm64)polySimIBD_1.1.0.tgz(r-4.5-x86_64)polySimIBD_1.1.0.tgz(r-4.5-arm64)
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polySimIBD_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
polySimIBD/json (API)

# Install 'polySimIBD' in R:
install.packages('polySimIBD', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nickbrazeau/polysimibd/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

3.18 score 1 stars 10 scripts 8 exports 21 dependencies

Last updated from:9046b62014. Checks:11 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE445
linux-devel-x86_64NOTE385
source / vignettesOK233
linux-release-arm64NOTE426
linux-release-x86_64NOTE312
macos-release-arm64NOTE464
macos-release-x86_64NOTE660
macos-oldrel-arm64NOTE345
macos-oldrel-x86_64NOTE752
windows-develNOTE382
windows-releaseNOTE345
windows-oldrelNOTE328
wasm-releaseOK140

Exports:%>%bvtreeToNewickget_argget_bvibdget_effective_coiget_within_ibdsim_swfsubset_bvtree

Dependencies:clicpp11farverggplot2gluegoodegggtableisobandlabelinglifecyclemagrittrpurrrR6RColorBrewerRcpprlangS7scalesvctrsviridisLitewithr

Discrete-Time Discrete-Loci Structured Wright Fisher Malaria Model Overview
Purpose | A Primer on Malaria Genetics | A Primer on the Coalescent | Model Formulation | Understanding the Simulator | Getting the ARG | bv_tree Class | Tree Conversions | Conclusion
Rendered fromorig_mod_framework.Rmdusingknitr::rmarkdown

Last update: 2024-07-01
Started: 2023-06-11

Extension of Structured Model for Spacee
Extending the Model for Space | Forwards-in-time Description | A Note on the Migration Matrix | Island Case | Conclusion
Rendered fromspatial_extension.Rmdusingknitr::rmarkdown

Last update: 2024-07-01
Started: 2023-06-11

Installing polySimIBD
Installing and Loading polySimIBD | Dependencies
Rendered frominstallation.Rmdusingknitr::rmarkdown

Last update: 2024-07-01
Started: 2023-06-11