Last updated: 2019-07-09

Checks: 1 1

Knit directory: HHVtransmission/

This reproducible R Markdown analysis was created with workflowr (version 1.3.0). 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 version displayed above was the version of the Git repository at the time these results were generated.

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/.Rhistory
    Ignored:    data/.DS_Store
    Ignored:    docs/.DS_Store
    Ignored:    docs/figure/.DS_Store
    Ignored:    docs/figure/general-statistics.Rmd/.DS_Store

Unstaged changes:
    Modified:   analysis/_site.yml
    Modified:   analysis/index.Rmd
    Modified:   analysis/transmission-risk.Rmd
    Modified:   code/build_all.R
    Modified:   code/risk_fit_functions.R

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 R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
html ccb8544 Bryan Mayer 2019-07-04 updated analysis through exposure overview
Rmd 94e6618 Bryan Mayer 2019-06-06 update through transmission risk
html 94e6618 Bryan Mayer 2019-06-06 update through transmission risk
html 9987890 Bryan Mayer 2019-04-12 updated through exposure assessment
html 6021a9c Bryan Mayer 2019-04-08 Build site.
html 37f0c94 Bryan Mayer 2019-04-08 Build site.
html 2f57367 Bryan Mayer 2019-04-07 Build site.
html 5af6494 Bryan Mayer 2019-03-20 Build site.
Rmd 510405b Bryan Mayer 2019-03-20 wflow_git_commit(all = T)
Rmd bdcc098 Bryan Mayer 2019-03-18 Start workflowr project.

Authors: Mayer BT, Krantz E, Wald A, Corey L, Casper C, Gantt S, and Schiffer JT

Analysis Roadmap:

  1. General statistics: Overview of the data, survival analysis, and descriptive analysis of exposures.
  2. Transmission modeling: Results of weekly risk estimation for transmission using the survival likelihood optimization.