Last updated: 2020-08-18

Checks: 2 0

Knit directory: uci_covid19_dashboard/

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.


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 bf27c21. 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:    .Renviron

Untracked files:
    Untracked:  r_env.yml
    Untracked:  rebuild

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 ae98627 vnminin 2020-08-14 daily date pull
html 24e4ed4 vnminin 2020-08-13 data update
html 616ee7e vnminin 2020-08-12 daily data update
html 8db6eb5 vnminin 2020-08-11 pushed a note about reporting system problems
html 0803f2b vnminin 2020-08-11 data update
html 19f2315 vnminin 2020-08-10 push with updated data
html a5927e7 vnminin 2020-08-09 rebuilding with new data
html 751c46f vnminin 2020-08-08 forgot to rebuild
Rmd 597d802 vnminin 2020-08-08 added Suellen Hopfer and Markelle Kelly to the group member list, swapped Andrew for Suellen as spokesperson
html fb0028a vnminin 2020-08-08 ca portal got data
html 9589b6d vnminin 2020-08-07 two time stamps
html 9648fc7 vnminin 2020-08-07 something
html 60756e0 Damon Bayer 2020-08-07 data update
html b3f0a7a vnminin 2020-08-06 rebuilding to fix testing not linking to itself
html 35e30c1 vnminin 2020-08-06 daily data update; I am a good robot
html 7334400 vnminin 2020-08-05 data update
html 6466f12 vnminin 2020-08-04 data pull and fixed the last date being cut off
html 5db0d2e vnminin 2020-08-03 data update
html 4afb037 vnminin 2020-08-02 forgot to republish
html e3847ed vnminin 2020-08-02 added testing maps
Rmd a2c2c61 vnminin 2020-08-01 added Software section to About
html a2c2c61 vnminin 2020-08-01 added Software section to About
html a873dd5 vnminin 2020-08-01 data update
html 8d0b6ce vnminin 2020-08-01 daily date update
html e024ad3 Damon Bayer 2020-07-31 Positivity Maps + Navigation Updates
html d621638 Damon Bayer 2020-07-31 Icons in navigation
html 490ebde vnminin 2020-07-31 daily data pull
html 4b572aa vnminin 2020-07-30 fixing Trends navigation
Rmd a8b89cf vnminin 2020-07-30 added maps sectio to About page
html a8b89cf vnminin 2020-07-30 added maps sectio to About page
html acc591d vnminin 2020-07-30 time stamp for maps
html a93ad42 vnminin 2020-07-30 now really changing filel name
html b785fc2 Damon Bayer 2020-07-30 Wider Maps page
html 7e4cb79 vnminin 2020-07-30 republishing just in case
html 244103f vnminin 2020-07-30 rebuilt just in case
html 9b1533f Damon Bayer 2020-07-30 Separate Maps Page
html cb818d8 Damon Bayer 2020-07-30 Added maps
html a4d0d51 vnminin 2020-07-29 pulling the most recent data from ca portal
Rmd c394748 vnminin 2020-07-28 not happy, but tired
html c394748 vnminin 2020-07-28 not happy, but tired
html cdd3081 vnminin 2020-07-28 still not happy
Rmd b03bd2f vnminin 2020-07-28 still not happy
Rmd c124229 vnminin 2020-07-28 not happy with mobile version
html c124229 vnminin 2020-07-28 not happy with mobile version
Rmd d9d640e vnminin 2020-07-28 making stat logo a little smaller
html d9d640e vnminin 2020-07-28 making stat logo a little smaller
Rmd 7d0bcf4 vnminin 2020-07-28 experimenting with spacing and sizing of logos
html 7d0bcf4 vnminin 2020-07-28 experimenting with spacing and sizing of logos
html 0590a7c Damon Bayer 2020-07-28 Even better colors
html a5a62c9 Damon Bayer 2020-07-28 Better Colors
Rmd db476c1 vnminin 2020-07-28 small About grammar edit
html db476c1 vnminin 2020-07-28 small About grammar edit
Rmd f770300 vnminin 2020-07-28 added links to logos
html f770300 vnminin 2020-07-28 added links to logos
Rmd 68acc48 vnminin 2020-07-28 added IDS logo
html 68acc48 vnminin 2020-07-28 added IDS logo
html 86b4d4a vnminin 2020-07-28 Build site.
Rmd d871090 vnminin 2020-07-27 completing merge
Rmd a00bcdd vnminin 2020-07-27 resized logos
html a00bcdd vnminin 2020-07-27 resized logos
Rmd 711a308 igoldsteinh 2020-07-27 proofreading
Rmd 1aad469 vnminin 2020-07-27 corrected typo
html 1aad469 vnminin 2020-07-27 corrected typo
html 7fbdfe8 vnminin 2020-07-27 completing merge
Rmd 0ec36bf vnminin 2020-07-27 added media bit to contact
html 0ec36bf vnminin 2020-07-27 added media bit to contact
html bb1619b Damon Bayer 2020-07-27 Some UCI Colors
Rmd 2964ef6 vnminin 2020-07-27 added joining the group to about
Rmd 7e96a35 vnminin 2020-07-27 added members to About page and more playing with logos
html 7e96a35 vnminin 2020-07-27 added members to About page and more playing with logos
Rmd 1f6de11 vnminin 2020-07-27 playing with logos
html 1f6de11 vnminin 2020-07-27 playing with logos
html abd9c55 Damon Bayer 2020-07-27 Update HTML
Rmd 01f6052 vnminin 2020-07-27 edits of About text
html 01f6052 vnminin 2020-07-27 edits of About text
html 84ab7e1 vnminin 2020-07-27 july 27 ca data update
html bab42bc vnminin 2020-07-26 triggering an update with latest data
Rmd 32001f7 igoldsteinh 2020-07-24 hopefully commented methods section
html f08c6cc Damon Bayer 2020-07-24 Watermark & Legend Fix
html eb680ce vnminin 2020-07-24 republishing to update plots
Rmd f07587a vnminin 2020-07-23 all plots start on the same date; moved subtitle to title
html f07587a vnminin 2020-07-23 all plots start on the same date; moved subtitle to title
html 9aa359e vnminin 2020-07-23 shortenting title for friendlier mobile version
html c14824c Damon Bayer 2020-07-23 Remove Home text
Rmd 4d981d1 vnminin 2020-07-22 started editing about
html 4d981d1 vnminin 2020-07-22 started editing about
html b4fb3ae Damon Bayer 2020-07-21 update 2020-07-21
html c95cee3 Damon Bayer 2020-07-20 Hide Workflowr buttons
html 5369804 Damon Bayer 2020-07-19 Update 2020-07-19
html 65c7195 Damon Bayer 2020-07-16 theme change
html 66110a1 Damon Bayer 2020-07-14 Initial Proof of Concept
Rmd 6151dc8 Damon Bayer 2020-07-14 Start workflowr project.

About

This is an effort to provide timely and understandable COVID-19 data visualizations to the public in Orange County, California. The effort is coordinated by the UC Irvine COVID Awareness Group, consisting of students and faculty from the following units at UC Irvine.

                   

UC Irvine COVID Awareness Group Members:

Damon Bayer, Bernadette Boden-Albala, Isaac Goldstein, Suellen Hopfer, Markelle Kelly, Rachel Longjohn, Vladimir Minin, Andrew Noymer, Daniel M. Parker, Padhraic Smyth.

Contact information:

If you would like to know more about technical details and/or to join the group, get in touch with Prof. Vladimir Minin. For general media inquiries contact Prof. Suellen Hopfer. If you are a media organization and would like to use our images, you do not need to ask for permission. Just don’t forget to acknowledge UC Irvine COVID Awareness Group. The content of this site is licensed under the most permissive creative commons license (click on License tab in the navigation bar to learn more).

Methodology

Moving Averages

Our figures present 7 day moving averages. This means that, for cases on July 7th, for example, we report the average number of cases per million people during the period July 1st to July 7th. On July 8th, we report the average number of cases per million people during the period July 2nd to July 8th, etc. We use moving averages as opposed to raw data (such as the actual number of cases per million people on July 7th) because cases can increase or decrease dramatically on a particular day, making it difficult to see trends in the time series of interest. Moving averages help highlight these trends more clearly.

In order to calculate, for example, cases per million people, we take the number of cases reported in a county for a day, divide by the 2019 census population for that county and then multiply by 1 million. We do this because different counties have very different population sizes (Los Angeles County has approximately 10 million while Orange County has approximately 3 million) and we want to provide numbers which are comparable across counties.

Testing Data

The number of daily new cases depends not only on the number of infected individuals in the population, but also on the number of tests performed. It would be much better to plot the positivity ratio (positive cases divided by the total number of tests) instead of cases. Unfortunately, the number of Covid-19 diagnostic tests performed in a day is not available at a county level from the California Open Data Portal at this time. LA and OC counties do have testing data available (LA COVID-19 data, OC COVID-19 Data), but we prefer to use one data source for now.

Maps

Maps of cases have been created with data provided by the Orange County Health Care Agency. If an individual tested multiple times, only the first postive test was counted as a case.

Software

We used R software environment, tidyverse collection of R packages, workflowr R package, and QGIS geographic information system software.