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
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polySimIBD_1.1.0.tgz(r-4.4-x86_64)polySimIBD_1.1.0.tgz(r-4.4-arm64)polySimIBD_1.1.0.tgz(r-4.3-x86_64)polySimIBD_1.1.0.tgz(r-4.3-arm64)
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polySimIBD.pdf |polySimIBD.html✨
polySimIBD/json (API)
NEWS

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

Peer review:

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

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

On CRAN:

3.95 score 1 stars 10 scripts 8 exports 31 dependencies

Last updated 2 months agofrom:3eb603e9de. Checks:OK: 1 NOTE: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64NOTEOct 31 2024
R-4.5-linux-x86_64NOTEOct 31 2024
R-4.4-win-x86_64NOTEOct 31 2024
R-4.4-mac-x86_64NOTEOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64NOTEOct 31 2024
R-4.3-mac-x86_64NOTEOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

Exports:%>%bvtreeToNewickget_argget_bvibdget_effective_coiget_within_ibdsim_swfsubset_bvtree

Dependencies:clicolorspacefansifarverggplot2gluegoodegggtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr

Discrete-Time Discrete-Loci Structured Wright Fisher Malaria Model Overview

Rendered fromorig_mod_framework.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Extension of Structured Model for Spacee

Rendered fromspatial_extension.Rmdusingknitr::rmarkdownon Oct 31 2024.

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

Installing polySimIBD

Rendered frominstallation.Rmdusingknitr::rmarkdownon Oct 31 2024.

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