Package: WhiteLabRt 1.01

WhiteLabRt: Novel Methods for Reproduction Number Estimation, Back-Calculation, and Forecasting

A collection of functions related to novel methods for estimating R(t), created by the lab of Professor Laura White. Currently implemented methods include two-step Bayesian back-calculation and now-casting for line-list data with missing reporting delays, adapted in 'STAN' from Li (2021) <doi:10.1371/journal.pcbi.1009210>, and calculation of time-varying reproduction number assuming a flux between various adjacent states, adapted into 'STAN' from Zhou (2021) <doi:10.1371/journal.pcbi.1010434>.

Authors:Chad Milando [aut, cre], Tenglong Li [ctb], Zhenwei Zhou [ctb], Laura White [ctb]

WhiteLabRt_1.01.tar.gz
WhiteLabRt_1.01.zip(r-4.7)WhiteLabRt_1.01.zip(r-4.6)WhiteLabRt_1.01.zip(r-4.5)
WhiteLabRt_1.01.tgz(r-4.6-x86_64)WhiteLabRt_1.01.tgz(r-4.6-arm64)WhiteLabRt_1.01.tgz(r-4.5-x86_64)WhiteLabRt_1.01.tgz(r-4.5-arm64)
WhiteLabRt_1.01.tar.gz(r-4.7-arm64)WhiteLabRt_1.01.tar.gz(r-4.7-x86_64)WhiteLabRt_1.01.tar.gz(r-4.6-arm64)WhiteLabRt_1.01.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
WhiteLabRt/json (API)

# Install 'WhiteLabRt' in R:
install.packages('WhiteLabRt', repos = c('https://cmilando.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cmilando/whitelabrt/issues

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

On CRAN:

Conda:

cpp

4.78 score 6 stars 6 scripts 280 downloads 6 exports 48 dependencies

Last updated from:7ffe631208. Checks:10 OK, 2 WARNING, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK348
linux-devel-x86_64OK384
source / vignettesOK459
linux-release-arm64OK381
linux-release-x86_64OK345
macos-release-arm64OK236
macos-release-x86_64OK489
macos-oldrel-arm64WARNING196
macos-oldrel-x86_64WARNING591
windows-develOK535
windows-releaseOK501
windows-oldrelOK504
wasm-releaseFAIL188

Exports:convert_to_linelistcreate_caseCountscreate_linelistrun_backnowsispatialRt

Dependencies:abindbackportsBHcallrcheckmateclicpp11descdistributionalfarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglifecycleloomagrittrmatrixStatsnumDerivotelpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsS7scalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr

Backcalculating Reporting Delays Distributions from Linelist Data
Example: lineList data | Example: Case Count data
Rendered frombackcalc.Rmdusingknitr::rmarkdown

Last update: 2024-07-29
Started: 2024-07-19

Spatial R(t) estimation with transfer estimates
Example of 2 states:
Rendered fromspatialRt.Rmdusingknitr::rmarkdown

Last update: 2024-07-29
Started: 2024-07-22