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:Chris Illingworth [aut, cre], Chris Jackson [aut]

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✨
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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

3.18 score 3 stars 5 exports 63 dependencies

Last updated from:bd1f41d86d. Checks:7 NOTE, 2 OK, 4 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE167
linux-devel-x86_64NOTE169
source / vignettesOK262
linux-release-arm64NOTE181
linux-release-x86_64NOTE172
macos-release-arm64WARNING146
macos-release-x86_64WARNING236
macos-oldrel-arm64WARNING112
macos-oldrel-x86_64WARNING225
windows-develNOTE190
windows-releaseNOTE158
windows-oldrelNOTE145
wasm-releaseOK144

Exports:a2bcovida2bcovid_applong_to_wideplot_a2bcovidwide_to_long

Dependencies:base64encbslibcachemclicommonmarkcpp11curldigestdplyrfarverfastmapfontawesomefsgenericsggplot2ggtextgluegridtextgtablehtmltoolshttpuvisobandjpegjquerylibjsonlitelabelinglaterlifecyclelitedownmagrittrmarkdownmemoisemimeotelpillarpkgconfigpngpromisespurrrR6rappdirsRColorBrewerRcpprlangrstudioapiS7sassscalesshinyshinyBSsourcetoolsstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithrxfunxml2xtable

A2BCovid: example analysis

Rendered fromexample.Rmdusingknitr::rmarkdownon May 31 2026.

Last update: 2020-12-16
Started: 2020-10-11