Package: PlasmoSim 1.0.0
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_1.0.0.tar.gz
PlasmoSim_1.0.0.zip(r-4.5)PlasmoSim_1.0.0.zip(r-4.4)PlasmoSim_1.0.0.zip(r-4.3)
PlasmoSim_1.0.0.tgz(r-4.4-x86_64)PlasmoSim_1.0.0.tgz(r-4.4-arm64)PlasmoSim_1.0.0.tgz(r-4.3-x86_64)PlasmoSim_1.0.0.tgz(r-4.3-arm64)
PlasmoSim_1.0.0.tar.gz(r-4.5-noble)PlasmoSim_1.0.0.tar.gz(r-4.4-noble)
PlasmoSim_1.0.0.tgz(r-4.4-emscripten)PlasmoSim_1.0.0.tgz(r-4.3-emscripten)
PlasmoSim.pdf |PlasmoSim.html✨
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 11 months agofrom:40ce6af570. Checks:OK: 1 NOTE: 8. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 06 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 06 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 06 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 06 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 06 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 06 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 06 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 06 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 06 2024 |
Exports:check_PlasmoSim_loadedget_haplotype_identityget_identity_matrixget_spatial_distancelonlat_to_bearingplasmosim_filesim_falciparum
Dependencies:askpassclidplyrfansigenericsglueknitrProgressBarlifecyclemagrittropensslpillarpkgconfigR.methodsS3R.ooR6Rcpprlangsystibbletidyselectutf8vctrswithr
Basic tutorial
Rendered fromtutorial_basic.Rmdusingknitr::rmarkdownon Nov 06 2024.Last update: 2023-12-12
Started: 2023-12-11
Installation
Rendered frominstallation.Rmdusingknitr::knitron Nov 06 2024.Last update: 2023-12-12
Started: 2023-12-11
Space and human movement
Rendered fromtutorial_movement.Rmdusingknitr::rmarkdownon Nov 06 2024.Last update: 2023-12-12
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 |
| Import file | plasmosim_file |
| Simulate genetic data from simple P. falciparum model | sim_falciparum |
