mrc-ide. To fix this you can add URL: https://plasmogenepi.r-universe.dev/PlasmoSim to the package DESCRIPTION file. See also theR-universe documentation.Package: PlasmoSim 1.0.1
Bob Verity
PlasmoSim: Simulation of Plasmodium genetic data
A basic Plasmodium simulator. Contains functions to simulate epidemiological and genetic data from a simple model of Plasmodium falciparum transmission.
Authors:
PlasmoSim_1.0.1.tar.gz
PlasmoSim_1.0.1.zip(r-4.7)PlasmoSim_1.0.1.zip(r-4.6)PlasmoSim_1.0.1.zip(r-4.5)
PlasmoSim_1.0.1.tgz(r-4.6-x86_64)PlasmoSim_1.0.1.tgz(r-4.6-arm64)PlasmoSim_1.0.1.tgz(r-4.5-x86_64)PlasmoSim_1.0.1.tgz(r-4.5-arm64)
PlasmoSim_1.0.1.tar.gz(r-4.7-arm64)PlasmoSim_1.0.1.tar.gz(r-4.7-x86_64)PlasmoSim_1.0.1.tar.gz(r-4.6-arm64)PlasmoSim_1.0.1.tar.gz(r-4.6-x86_64)
PlasmoSim_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
PlasmoSim/json (API)
| # Install 'PlasmoSim' in R: |
| install.packages('PlasmoSim', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mrc-ide/plasmosim/issues
Last updated from:08586e1631. Checks:11 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | NOTE | 175 | ||
| linux-devel-x86_64 | NOTE | 170 | ||
| source / vignettes | OK | 283 | ||
| linux-release-arm64 | NOTE | 160 | ||
| linux-release-x86_64 | NOTE | 183 | ||
| macos-release-arm64 | NOTE | 93 | ||
| macos-release-x86_64 | NOTE | 195 | ||
| macos-oldrel-arm64 | NOTE | 91 | ||
| macos-oldrel-x86_64 | NOTE | 235 | ||
| windows-devel | NOTE | 156 | ||
| windows-release | NOTE | 155 | ||
| windows-oldrel | NOTE | 131 | ||
| wasm-release | OK | 139 |
Exports:check_PlasmoSim_loadedget_haplotype_identityget_identity_matrixget_spatial_distancelonlat_to_bearingplasmosim_filesim_falciparum
Dependencies:askpassclidplyrgenericsglueknitrProgressBarlamWlifecyclemagrittropensslpillarpkgconfigR.methodsS3R.ooR6RcppRcppParallelrlangsystibbletidyselectutf8vctrswithr
Basic tutorial
Rendered fromtutorial_basic.Rmdusingknitr::rmarkdownon May 25 2026.Last update: 2026-04-25
Started: 2023-12-11
Installation
Rendered frominstallation.Rmdusingknitr::knitron May 25 2026.Last update: 2026-04-25
Started: 2023-12-11
Space and human movement
Rendered fromtutorial_movement.Rmdusingknitr::rmarkdownon May 25 2026.Last update: 2026-04-25
Started: 2023-12-11
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Check that PlasmoSim package has loaded successfully | check_PlasmoSim_loaded |
| Get proportion identical between two haplotype matrices | get_haplotype_identity |
| Get pairwise genetic identity matrix | get_identity_matrix |
| Get great circle distance between spatial points | get_spatial_distance |
| Calculate great circle distance and bearing between coordinates | lonlat_to_bearing |
| PlasmoSim | PlasmoSim-package PlasmoSim |
| Import file | plasmosim_file |
| Simulate genetic data from simple P. falciparum model | sim_falciparum |
