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:
WhiteLabRt_1.01.tar.gz
WhiteLabRt_1.01.zip(r-4.5)WhiteLabRt_1.01.zip(r-4.4)WhiteLabRt_1.01.zip(r-4.3)
WhiteLabRt_1.01.tgz(r-4.4-x86_64)WhiteLabRt_1.01.tgz(r-4.4-arm64)WhiteLabRt_1.01.tgz(r-4.3-x86_64)WhiteLabRt_1.01.tgz(r-4.3-arm64)
WhiteLabRt_1.01.tar.gz(r-4.5-noble)WhiteLabRt_1.01.tar.gz(r-4.4-noble)
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
- 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
Last updated 3 months agofrom:f11f923678. Checks:OK: 2 NOTE: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 14 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 14 2024 |
| R-4.5-linux-x86_64 | OK | Nov 14 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 14 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 14 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 14 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 14 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 14 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 14 2024 |
Exports:convert_to_linelistcreate_caseCountscreate_linelistrun_backnowsispatialRt
Dependencies:abindbackportsBHcallrcheckmateclicolorspacedescdistributionalfansifarvergenericsggplot2gluegridExtragtableinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr
Backcalculating Reporting Delays Distributions from Linelist Data
Rendered frombackcalc.Rmdusingknitr::rmarkdownon Nov 14 2024.Last update: 2024-07-29
Started: 2024-07-19
Spatial R(t) estimation with transfer estimates
Rendered fromspatialRt.Rmdusingknitr::rmarkdownon Nov 14 2024.Last update: 2024-07-29
Started: 2024-07-22
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 |
