Last updated: 2021-03-29

Checks: 2 0

Knit directory: uci_covid_modeling2/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2.9000). 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 cd13e00. 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:    data/.DS_Store
    Ignored:    data/from_OCHCA/
    Ignored:    renv/

Untracked files:
    Untracked:  alissa_missingness.R
    Untracked:  analysis/2021-02-10_2021-03-17.Rmd
    Untracked:  analysis/2021-02-10_2021-03-17_anaheim.Rmd
    Untracked:  analysis/2021-02-10_2021-03-17_irvine.Rmd
    Untracked:  analysis/2021-02-10_2021-03-17_santa-ana.Rmd
    Untracked:  analysis/2021-02-17_2021-03-24.Rmd
    Untracked:  analysis/2021-02-17_2021-03-24_anaheim.Rmd
    Untracked:  analysis/2021-02-17_2021-03-24_irvine.Rmd
    Untracked:  analysis/2021-02-17_2021-03-24_santa-ana.Rmd
    Untracked:  code/results/2021-02-10_2021-03-17/
    Untracked:  code/results/2021-02-17_2021-03-24/
    Untracked:  redo_february.R
    Untracked:  redo_february_anaheim.R
    Untracked:  redo_february_irvine.R
    Untracked:  redo_february_santa_ana.R

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   code/process_ochca_data.R
    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/license.Rmd) and HTML (docs/license.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 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
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.

Site Content

This work is licensed under the Creative Commons Attribution 4.0 International License.

Source Code

The source code is licensed under the MIT License.

MIT License

Copyright (c) UCI-NIH Covid Modeling Group

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.