About
Last updated: 2020-12-16
Checks: 1 1
Knit directory: uci_covid_modeling2/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.
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 40eab34. 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: analysis/2020-03-29_2020-05-03_cache/
Ignored: analysis/2020-05-03_2020-06-07_cache/
Ignored: analysis/2020-06-07_2020-07-12_cache/
Ignored: analysis/2020-07-12_2020-08-16_cache/
Ignored: analysis/2020-08-16_2020-09-20_cache/
Ignored: analysis/2020-09-20_2020-10-25_cache/
Ignored: analysis/2020-10-25_2020-11-29_cache/
Ignored: code/.DS_Store
Ignored: data/.DS_Store
Ignored: data/from_OCHCA/
Untracked files:
Untracked: analysis/2020-03-29_2020-05-03.Rmd
Untracked: analysis/2020-05-03_2020-06-07.Rmd
Untracked: analysis/2020-06-07_2020-07-12.Rmd
Untracked: analysis/2020-07-12_2020-08-16.Rmd
Untracked: analysis/2020-08-16_2020-09-20.Rmd
Untracked: analysis/2020-09-20_2020-10-25.Rmd
Untracked: analysis/2020-10-25_2020-11-29.Rmd
Untracked: code/analysis_template.Rmd
Untracked: code/check post_prior_post transition.R
Untracked: code/check_all_fits.R
Untracked: code/fit_first_model.R
Untracked: code/forecast.R
Untracked: code/helper_functions.R
Untracked: code/process_ochca_data.R
Untracked: code/results/
Untracked: code/stemr_functions.R
Untracked: code/update_site.R
Untracked: data/oc_city_data.csv
Untracked: data/oc_data.csv
Untracked: data/oc_zips.csv
Unstaged changes:
Modified: analysis/_site.yml
Modified: analysis/about.Rmd
Modified: analysis/license.Rmd
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 |
|---|---|---|---|---|
| Rmd | 6e35bec | Damon Bayer | 2020-12-09 | Start workflowr project. |
About
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.
Contact
Methodology
Data
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.