Last updated: 2021-06-02

Checks: 2 0

Knit directory: uci_covid_modeling2/

This reproducible R Markdown analysis was created with workflowr (version The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 2a1089e. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/.DS_Store
    Ignored:    code/.DS_Store
    Ignored:    code/.Rhistory
    Ignored:    code/models/.DS_Store
    Ignored:    code/models/model_death_reporting_delay/.DS_Store
    Ignored:    code/models/model_death_reporting_delay/.Rhistory
    Ignored:    code/models/model_no_reporting_delay/.DS_Store
    Ignored:    code/results/.DS_Store
    Ignored:    code/results/2020-11-01_2020-12-06/.DS_Store
    Ignored:    code/results/2020-11-08_2020-12-13/.DS_Store
    Ignored:    code/results/2020-11-15_2020-12-20/.DS_Store
    Ignored:    code/results/2020-11-22_2020-12-27/.DS_Store
    Ignored:    code/results/2020-12-02_2021-01-06/.DS_Store
    Ignored:    code/results/2020-12-16_2021-01-20/.DS_Store
    Ignored:    code/results/2020-12-23_2021-01-27/.DS_Store
    Ignored:    code/results/2021-02-10_2021-03-17/.DS_Store
    Ignored:    code/results/2021-02-17_2021-03-24/.DS_Store
    Ignored:    data/.DS_Store
    Ignored:    data/from_OCHCA/
    Ignored:    renv/

Untracked files:
    Untracked:  analysis/2021-04-21_2021-05-26.Rmd
    Untracked:  analysis/2021-04-21_2021-05-26_anaheim.Rmd
    Untracked:  analysis/2021-04-21_2021-05-26_irvine.Rmd
    Untracked:  analysis/2021-04-21_2021-05-26_santa-ana.Rmd
    Untracked:  code/results/2021-04-21_2021-05-26/

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   code/process_ochca_data.R
    Modified:   data/data_for_calcat.csv
    Modified:   data/death_delay_ecdf.rds
    Modified:   data/oc_city_data.csv
    Modified:   data/oc_data.csv

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/about.Rmd) and HTML (docs/about.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html 2a1089e Damon Bayer 2021-05-24 2021-05-24 Update
html 3557813 Damon Bayer 2021-05-17 2021-05-17 Update
html 44473d0 Damon Bayer 2021-05-10 2021-05-10 Update
html 9e38bb8 Damon Bayer 2021-05-04 2021-05-03 Update
html 8994d5e Damon Bayer 2021-04-27 2021-04-26 Update
html bdae734 Damon Bayer 2021-04-19 2021-04-19 Update
html 391f6a1 Damon Bayer 2021-04-12 2021-04-12 Update
html ed4a33e Damon Bayer 2021-04-05 2021-04-05 Update
html b33b72f Damon Bayer 2021-03-29 2021-03-29 Update
html cd13e00 Damon Bayer 2021-03-16 2021-03-15 Update
html 4d1bc4d Damon Bayer 2021-03-01 2021-03-01 Update
html 0eccc36 Damon Bayer 2021-02-22 2021-02-15 Backfill
html 31485c4 Damon Bayer 2021-02-22 2021-02-22 Update
html 20a5e54 Damon Bayer 2021-02-16 Revert “2021-02-16 Update”
html 0f96253 Damon Bayer 2021-02-16 2021-02-16 Update
html 5c63d55 Damon Bayer 2021-02-09 2021-02-08 Update
html 436e286 Damon Bayer 2021-02-01 2021-02-01 Update
html 8bc06d3 Damon Bayer 2021-01-27 Backfill 2020-01-18 Update
html 8da4f62 Damon Bayer 2021-01-27 Fix historical cumulative deaths
html 28db989 Damon Bayer 2021-01-26 2020-01-25 Update
html 11f4456 Damon Bayer 2021-01-20 Revert “2020-01-18 Update”
html 847f3bd Damon Bayer 2021-01-19 2020-01-18 Update
html 518b7bf Damon Bayer 2021-01-12 Small plot tweaks
html b3e230f Damon Bayer 2021-01-12 Show Probability of Death Reporting in Model Inputs Plots
html 63bcbfd Damon Bayer 2021-01-11 2021-01-11 Update, Close #2, Account for Death Reporting Delays
html 68805a0 Damon Bayer 2021-01-06 Fix Icons
html f70916b Damon Bayer 2021-01-06 2021-01-14 City & County Updates
Rmd d4cbb1a Damon Bayer 2020-12-29 about page update (Close #5)
html d4cbb1a Damon Bayer 2020-12-29 about page update (Close #5)
html 5c9b537 Damon Bayer 2020-12-29 City Reports
Rmd dcffe20 Damon Bayer 2020-12-16 Initial Commit
html dcffe20 Damon Bayer 2020-12-16 Initial Commit
Rmd 6e35bec Damon Bayer 2020-12-09 Start workflowr project.


This website provides reports on the dynamics and future trends of spread of SARS-CoV-2 in Orange County, CA. Please visit the github for details on the code, and read the manuscript associated with this endeavor for further methodological details.



Damon Bayer, Isaac Goldstein, and Vladimir N. Minin
Department of Statistics, University of California, Irvine

Jon Fintzi, Keith Lumbard, and Emily Ricotta
National Institute of Allergy and Infectious Diseases

Richard Chhuon, Alissa Dratch, Matthew Zahn
Orange County Health Care Agency


Vladimir Minin



We use data provided by OCHCA. An aggregated version of our data is available in the github. Crucially, we exclude repeat tests given to patients who test positive (which happens when patients are hospitalized). Our data may not correspond with publicly available data.

We also do not analyze data in real time. This is because case, test, and death counts are often updated retroactively, and we wish to give data collectors time to provide complete results. Typically, there will be at least a ten day gap between the present day and the final date analyzed in the most recent report.

Statistical methodology

Our analysis relies on a six compartment mechanistic model of the pandemic. We then use Bayesian inference to provide inference on key disease dynamics and make predictions on future observed cases and deaths. Further descriptions of the methodology are available in the manuscript.


We used the R software environment, tidyverse and workflowr packages for this website. Our analysis was conducted in stemr.