Basic workflow | 1) Plot data | 2) Compute recurrence state posterior probabilities | 3) Plot per-recurrence probabilities | Exploration of relationship graphs
This package is considered a duplicate. The official version of this package is found at:https://aimeertaylor.r-universe.dev/Pv3Rs
Package: Pv3Rs 1.0.0.9000
Aimee Taylor
Pv3Rs: Estimate the Cause of Recurrent Vivax Malaria using Genetic Data
Plot malaria parasite genetic data on two or more episodes. Compute per-person posterior probabilities that each Plasmodium vivax (Pv) recurrence is a recrudescence, relapse, or reinfection (3Rs) using per-person P. vivax genetic data on two or more episodes and a statistical model described in Taylor, Foo and White (2022) <doi:10.1101/2022.11.23.22282669>. Plot per-recurrence posterior probabilities.
Authors:
Pv3Rs_1.0.0.9000.tar.gz
Pv3Rs_1.0.0.9000.zip(r-4.7)Pv3Rs_1.0.0.9000.zip(r-4.6)Pv3Rs_1.0.0.9000.zip(r-4.5)
Pv3Rs_1.0.0.9000.tgz(r-4.6-any)Pv3Rs_1.0.0.9000.tgz(r-4.5-any)
Pv3Rs_1.0.0.9000.tar.gz(r-4.7-any)Pv3Rs_1.0.0.9000.tar.gz(r-4.6-any)
Pv3Rs_1.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Pv3Rs/json (API)
| # Install 'Pv3Rs' in R: |
| install.packages('Pv3Rs', repos = c('https://plasmogenepi.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/aimeertaylor/pv3rs/issues
Pkgdown/docs site:https://aimeertaylor.github.io
Datasets:
- fs_VHX_BPD - Allele frequencies computed using example _Plasmodium vivax_ data
- ys_VHX_BPD - Example _Plasmodium vivax_ data
Last updated from:680b4c5a23. Checks:9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 133 | ||
| source / vignettes | OK | 195 | ||
| linux-release-x86_64 | OK | 146 | ||
| macos-release-arm64 | OK | 139 | ||
| macos-oldrel-arm64 | OK | 93 | ||
| windows-devel | OK | 93 | ||
| windows-release | OK | 88 | ||
| windows-oldrel | OK | 99 | ||
| wasm-release | OK | 112 |
Exports:compute_posteriordetermine_MOIsenumerate_RGsplot_dataplot_RGplot_simplexproject2DRG_to_igraphsample_RG
Dependencies:clicpp11dotCall64dplyrfieldsgenericsgluegmpigraphlatticelifecyclemagrittrmapsMatrixmatrixStatsmulticoolpartitionspillarpkgconfigpolynompurrrR6rbibutilsRColorBrewerRcppRdpackrlangsetsspamtibbletidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute posterior probabilities of _P. vivax_ recurrence states | compute_posterior |
| Determine multiplicities of infection (MOIs) | determine_MOIs |
| Enumerate relationship graphs (RGs) | enumerate_RGs |
| Allele frequencies computed using example _Plasmodium vivax_ data | fs_VHX_BPD |
| Plots the data | plot_data |
| Plot a relationship graph (RG) | plot_RG |
| Plots a 2D simplex | plot_simplex |
| Project 3D probability coordinates onto 2D simplex coordinates | project2D |
| Converts a relationship graph (RG) encoded as a list to an 'igraph' object | RG_to_igraph |
| Sample a relationship graph (RG) | sample_RG |
| Example _Plasmodium vivax_ data | ys_VHX_BPD |
