a2bcovid: introduction | Times of symptom onset | Genome sequence alignment data | Patient location data | Staff location data | Example analysis | Using just the symptom onset times | Using symptom onset times and sequence data | Using symptom onset times, sequence data and patient location data | Using symptom onset times, sequence data, patient location and staff location data | Additional plotting options
Package: a2bcovid 0.1.0
Chris Illingworth
a2bcovid: Inferring COVID-19 Transmission Events from Sequence and Location Data
A tool which combines genome sequence and the locations of infected individuals, using a statistical and evolutionary model, to estimate the likelihood that transmission occurred between particular individuals, and then to identify clusters of infections. It is currently designed to apply to COVID-19 infection dynamics on hospital wards.
Authors:
a2bcovid_0.1.0.tar.gz
a2bcovid_0.1.0.zip(r-4.7)a2bcovid_0.1.0.zip(r-4.6)a2bcovid_0.1.0.zip(r-4.5)
a2bcovid_0.1.0.tgz(r-4.6-x86_64)a2bcovid_0.1.0.tgz(r-4.6-arm64)a2bcovid_0.1.0.tgz(r-4.5-x86_64)a2bcovid_0.1.0.tgz(r-4.5-arm64)
a2bcovid_0.1.0.tar.gz(r-4.7-arm64)a2bcovid_0.1.0.tar.gz(r-4.7-x86_64)a2bcovid_0.1.0.tar.gz(r-4.6-arm64)a2bcovid_0.1.0.tar.gz(r-4.6-x86_64)
a2bcovid_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
a2bcovid/json (API)
| # Install 'a2bcovid' in R: |
| install.packages('a2bcovid', repos = c('https://chjackson.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/chjackson/a2bcovid/issues
Last updated from:bd1f41d86d. Checks:7 NOTE, 2 OK, 4 WARNING. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | NOTE | 167 | ||
| linux-devel-x86_64 | NOTE | 169 | ||
| source / vignettes | OK | 262 | ||
| linux-release-arm64 | NOTE | 181 | ||
| linux-release-x86_64 | NOTE | 172 | ||
| macos-release-arm64 | WARNING | 146 | ||
| macos-release-x86_64 | WARNING | 236 | ||
| macos-oldrel-arm64 | WARNING | 112 | ||
| macos-oldrel-x86_64 | WARNING | 225 | ||
| windows-devel | NOTE | 190 | ||
| windows-release | NOTE | 158 | ||
| windows-oldrel | NOTE | 145 | ||
| wasm-release | OK | 144 |
Exports:a2bcovida2bcovid_applong_to_wideplot_a2bcovidwide_to_long
Dependencies:base64encbslibcachemclicommonmarkcpp11curldigestdplyrfarverfastmapfontawesomefsgenericsggplot2ggtextgluegridtextgtablehtmltoolshttpuvisobandjpegjquerylibjsonlitelabelinglaterlifecyclelitedownmagrittrmarkdownmemoisemimeotelpillarpkgconfigpngpromisespurrrR6rappdirsRColorBrewerRcpprlangrstudioapiS7sassscalesshinyshinyBSsourcetoolsstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithrxfunxml2xtable
