About

Last updated: 2019-12-30

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.

R Markdown file: uncommitted changes

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.

Repository version: 9ec3ff2

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/.Rhistory
    Ignored:    docs/.DS_Store
    Ignored:    docs/figure/.DS_Store
    Ignored:    docs/figure/transmission-risk-sensitivity.Rmd/.DS_Store
    Ignored:    docs/figure/transmission-risk.Rmd/.DS_Store
    Ignored:    output/.DS_Store

Untracked files:
    Untracked:  analysis/project-functions.Rmd
    Untracked:  output/final-model/
    Untracked:  output/preprocess-model-data/
    Untracked:  output/results-tables/combined_risk_tab.csv
    Untracked:  output/results-tables/hhv6_id50_tab.csv
    Untracked:  output/results-tables/individual_risk_tab.csv
    Untracked:  output/results-tables/supp_table1.csv
    Untracked:  output/results-tables/supp_table2.csv
    Untracked:  output/results-tables/supp_table4.csv

Unstaged changes:
    Modified:   analysis/about.Rmd
    Modified:   analysis/general-statistics.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/setup-exposure-data.Rmd
    Modified:   analysis/setup-model-data.Rmd
    Modified:   analysis/transmission-risk-sensitivity.Rmd
    Modified:   analysis/transmission-risk.Rmd
    Modified:   code/build_all.R
    Deleted:    output/final_model.rds
    Deleted:    output/model_data.RData
    Deleted:    output/supp_table1.csv
    Deleted:    output/supp_table2.csv
    Deleted:    output/supp_table3.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 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	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.