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

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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 d242e92 Bryan 2019-11-10 separate pre-process model data and update index
Rmd e6ddfc5 Bryan Mayer 2019-07-09 analysis through first-final draft
html e6ddfc5 Bryan Mayer 2019-07-09 analysis through first-final draft
html ccb8544 Bryan Mayer 2019-07-04 updated analysis through exposure overview
Rmd 94e6618 Bryan Mayer 2019-06-07 update through transmission risk
html 94e6618 Bryan Mayer 2019-06-07 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 2019-04-08 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.

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: Code that fits transmission models using the survival likelihood optimization and sensitivity analysis.
  3. Transmission model analysis: Results from the final transmission model: weekly risk estimation by exposure source and dose-response curves.

Data and other code