Last updated: 2020-02-03
Checks: 1 1
Knit directory: HHVtransmission/
This reproducible R Markdown analysis was created with workflowr (version 1.4.0). 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: output/.DS_Store
Ignored: output/preprocess-model-data/.DS_Store
Untracked files:
Untracked: data/tmp/
Unstaged changes:
Modified: analysis/_site.yml
Modified: analysis/about.Rmd
Modified: analysis/index.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 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 | c50009c | Bryan | 2020-02-01 | Build site. |
| Rmd | a1d2e7b | Bryan | 2020-01-24 | update with documentation |
| html | a1d2e7b | Bryan | 2020-01-24 | update with documentation |
| Rmd | af2a4c1 | Bryan | 2019-12-30 | all updates after co-author review; edits to tables/figs; ID75 |
| html | af2a4c1 | Bryan | 2019-12-30 | all updates after co-author review; edits to tables/figs; ID75 |
| html | 54f6c39 | Bryan | 2019-11-10 | separate pre-process model data and update index |
| Rmd | ce0f229 | Bryan Mayer | 2019-07-09 | analysis through first-final draft |
| html | ce0f229 | Bryan Mayer | 2019-07-09 | analysis through first-final draft |
| html | 3bc1e7c | Bryan Mayer | 2019-07-04 | updated analysis through exposure overview |
| Rmd | 39e3dc0 | Bryan Mayer | 2019-06-07 | update through transmission risk |
| html | 39e3dc0 | Bryan Mayer | 2019-06-07 | update through transmission risk |
| html | c96d292 | 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 | 2019-04-08 | Build site. |
| html | 5af6494 | Bryan Mayer | 2019-03-21 | Build site. |
| Rmd | 510405b | Bryan Mayer | 2019-03-21 | wflow_git_commit(all = T) |
| Rmd | bdcc098 | Bryan Mayer | 2019-03-19 | Start workflowr project. |
Article Authors: Mayer BT, Krantz E, Wald A, Corey L, Casper C, Gantt S, and Schiffer JT
This article was published in Viruses in 2020 and the pdf is available there.
Citation: Mayer, B.T.; Krantz, E.M.; Wald, A.; Corey, L.; Casper, C.; Gantt, S.; Schiffer, J.T. Estimating the Risk of Human Herpesvirus 6 and Cytomegalovirus Transmission to Ugandan Infants from Viral Shedding in Saliva by Household Contacts. Viruses 2020, 12, 171.