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]

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WhiteLabRt.pdf |WhiteLabRt.html✨
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:

out_list_demo - Sample back-calculation output
sample_cases - Sample cases
sample_dates - Sample dates
sample_location - Sample location
sample_m_hier - Sample hierachical model output
sample_multi_site - Sample multi site
sample_onset_dates - Sample onset dates
sample_report_dates - Sample report dates
transfer_matrix - Transfer matrix

On CRAN:

6 exports 3 stars 1.26 score 53 dependencies 4 scripts 288 downloads

Last updated 1 months agofrom:f11f923678. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 15 2024
R-4.5-win-x86_64	NOTE	Sep 15 2024
R-4.5-linux-x86_64	NOTE	Sep 15 2024
R-4.4-win-x86_64	NOTE	Sep 15 2024
R-4.4-mac-x86_64	NOTE	Sep 15 2024
R-4.4-mac-aarch64	NOTE	Sep 15 2024
R-4.3-win-x86_64	NOTE	Sep 15 2024
R-4.3-mac-x86_64	NOTE	Sep 15 2024
R-4.3-mac-aarch64	NOTE	Sep 15 2024

Exports:convert_to_linelist create_caseCounts create_linelist run_backnow si spatialRt

Dependencies:abind backports BH callr checkmate cli colorspace desc distributional fansi farver generics ggplot2 glue gridExtra gtable inline isoband labeling lattice lifecycle loo magrittr MASS Matrix matrixStats mgcv munsell nlme numDeriv pillar pkgbuild pkgconfig posterior processx ps QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel rlang rstan rstantools scales StanHeaders tensorA tibble utf8 vctrs viridisLite withr

Backcalculating Reporting Delays Distributions from Linelist Data

Rendered frombackcalc.Rmdusingknitr::rmarkdownon Sep 15 2024.

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

Spatial R(t) estimation with transfer estimates

Rendered fromspatialRt.Rmdusingknitr::rmarkdownon Sep 15 2024.

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The 'WhiteLabRt' package.	WhiteLabRt-package WhiteLabRt
Convert Case Counts to a Line List	convert_to_linelist
Create a Case Counts Data Frame	create_caseCounts
Create a Line List from Report and Onset Dates	create_linelist
Sample back-calculation output	out_list_demo
Plot Estimates or Reproduction Numbers	plot.backnow
Plot Case Counts Over Time	plot.caseCounts
Run Back Calculation and Estimate Reproduction Numbers	run_backnow
Sample cases	sample_cases
Sample dates	sample_dates
Sample location	sample_location
Sample hierachical model output	sample_m_hier
Sample multi site	sample_multi_site
Sample onset dates	sample_onset_dates
Sample report dates	sample_report_dates
Calculate a Serial Interval Distribution	si
Run Spatial R(t) estimation and Estimate Reproduction Numbers	spatialRt
Transfer matrix	transfer_matrix