Introduction | Identify | Get individual trees | Performance | Accuracy | Entropy | Visualisation | Augment the linelist with outbreaker2's results | Consensus tree | Maximum posterior tree | Additional analyses
Package: o2ools 0.0.1
o2ools: Tools for 'outbreaker2'
Streamlines the post-processing, summarization, and visualization of 'outbreaker2' output via a suite of helper functions. Facilitates tidy manipulation of posterior samples, integration with case metadata, generation of diagnostic plots and summary statistics.
Authors:
o2ools_0.0.1.tar.gz
o2ools_0.0.1.zip(r-4.7)o2ools_0.0.1.zip(r-4.6)o2ools_0.0.1.zip(r-4.5)
o2ools_0.0.1.tgz(r-4.6-any)o2ools_0.0.1.tgz(r-4.5-any)
o2ools_0.0.1.tar.gz(r-4.7-any)o2ools_0.0.1.tar.gz(r-4.6-any)
o2ools_0.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
o2ools/json (API)
| # Install 'o2ools' in R: |
| install.packages('o2ools', repos = c('https://cygei.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cygei/o2ools/issues
Pkgdown/docs site:https://cygei.github.io
Last updated from:3e6bc15ce7. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 181 | ||
| source / vignettes | OK | 297 | ||
| linux-release-x86_64 | OK | 154 | ||
| macos-release-arm64 | OK | 138 | ||
| macos-oldrel-arm64 | OK | 160 | ||
| windows-devel | OK | 95 | ||
| windows-release | OK | 89 | ||
| windows-oldrel | OK | 97 | ||
| wasm-release | OK | 111 |
Exports:augment_linelistfilter_chainget_accuracyget_consensusget_entropyget_Riget_siget_treesidentifysample.outbreaker_chainsttable
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Append summaries of outbreaker results to a linelist | augment_linelist |
| Filter chain by parameter threshold | filter_chain |
| Calculate the accuracy of outbreak reconstruction | get_accuracy |
| Get the consensus transmission tree | get_consensus |
| Compute the entropy of transmission trees | get_entropy |
| Compute case reproduction numbers (Ri) from outbreaker2 chains | get_Ri |
| Compute the serial interval (si) from transmission trees | get_si |
| Extract posterior transmission trees | get_trees |
| Replace integers in outbreaker2 output with unique identifiers | identify |
| Simulated linelist with group labels | linelist |
| outbreaker2 toy dataset | out |
| Sample rows from an outbreaker_chains object | sample.outbreaker_chains |
| Compute the transmission contingency table | ttable |
