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-x86_64)a2bcovid_0.1.0.zip(r-4.7-arm64)a2bcovid_0.1.0.zip(r-4.6-x86_64)a2bcovid_0.1.0.zip(r-4.6-arm64)a2bcovid_0.1.0.zip(r-4.5-x86_64)
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

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

cpp

3.18 score 3 stars 5 exports 63 dependencies

Last updated from:bd1f41d86d. Checks:7 NOTE, 2 OK, 6 WARNING. Indexed: yes.

Target	Result	Time
linux-devel-arm64	NOTE	135
linux-devel-x86_64	NOTE	215
source / vignettes	OK	227
linux-release-arm64	NOTE	120
linux-release-x86_64	NOTE	160
macos-release-arm64	WARNING	131
macos-release-x86_64	WARNING	244
macos-oldrel-arm64	WARNING	153
macos-oldrel-x86_64	WARNING	196
windows-devel-arm64	WARNING	255
windows-devel-x86_64	NOTE	177
windows-release-arm64	WARNING	272
windows-release-x86_64	NOTE	154
windows-oldrel-x86_64	NOTE	142
wasm-release	OK	125

Exports:a2bcovid a2bcovid_app long_to_wide plot_a2bcovid wide_to_long

Dependencies:base64enc bslib cachem cli commonmark cpp11 curl digest dplyr farver fastmap fontawesome fs generics ggplot2 ggtext glue gridtext gtable htmltools httpuv isoband jpeg jquerylib jsonlite labeling later lifecycle litedown magrittr markdown memoise mime otel pillar pkgconfig png promises purrr R6 rappdirs RColorBrewer Rcpp rlang rstudioapi S7 sass scales shiny shinyBS sourcetools stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr xfun xml2 xtable

A2BCovid: example analysis

Rendered fromexample.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Identifying clusters of COVID-19 infections from genome sequence and individual location data	a2bcovid
Web app interface to a2bcovid	a2bcovid_app
Convert patient location data for an a2bcovid analysis from long to wide format	long_to_wide
Plot results of an a2bcovid analysis	plot_a2bcovid
Convert patient location data for an a2bcovid analysis from wide to long format	wide_to_long