Example: lineList data | Example: Case Count data
This package is considered a duplicate. The official version of this package is found at:https://cmilando.r-universe.dev/WhiteLabRt
Package: WhiteLabRt 1.0.1
Chad Milando
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:
WhiteLabRt_1.0.1.tar.gz
WhiteLabRt_1.0.1.zip(r-4.7-x86_64)WhiteLabRt_1.0.1.zip(r-4.7-arm64)WhiteLabRt_1.0.1.zip(r-4.6-x86_64)WhiteLabRt_1.0.1.zip(r-4.6-arm64)
WhiteLabRt_1.0.1.tar.gz(r-4.7-arm64)WhiteLabRt_1.0.1.tar.gz(r-4.7-x86_64)WhiteLabRt_1.0.1.tar.gz(r-4.6-arm64)WhiteLabRt_1.0.1.tar.gz(r-4.6-x86_64)
WhiteLabRt_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
WhiteLabRt/json (API)
| # Install 'WhiteLabRt' in R: |
| install.packages('WhiteLabRt', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
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
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:bc88bdaca2. Checks:10 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 293 | ||
| linux-devel-x86_64 | OK | 353 | ||
| source / vignettes | OK | 547 | ||
| linux-release-arm64 | OK | 302 | ||
| linux-release-x86_64 | OK | 311 | ||
| windows-devel-arm64 | OK | 294 | ||
| windows-devel-x86_64 | OK | 370 | ||
| windows-release-arm64 | OK | 431 | ||
| windows-release-x86_64 | OK | 429 | ||
| wasm-release | OK | 222 |
Exports:convert_to_linelistcreate_caseCountscreate_linelistrun_backnowsispatialRt
Dependencies:abindbackportsBHcallrcheckmateclicpp11descdistributionalfarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglifecycleloomagrittrmatrixStatsnumDerivotelpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsS7scalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr
Backcalculating Reporting Delays Distributions from Linelist Data
Last update: 2024-08-01
Started: 2024-08-01
Spatial R(t) estimation with transfer estimates
Example of 2 states:
Last update: 2024-08-01
Started: 2024-08-01
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 |