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:    .Rproj.user/
    Ignored:    data/.DS_Store
    Ignored:    data/SD_k tests_2018_04_05.xlsx
    Ignored:    data/clean_data/.DS_Store
    Ignored:    data/data collection sheet - follow up looking at sex ratio.xlsx
    Ignored:    data/data collection sheet from Heidi.xlsx
    Ignored:    data/model_output/
    Ignored:    docs/.DS_Store
    Ignored:    docs/figure/SD_costs_analysis.Rmd/
    Ignored:    docs/figure/evolutionary_simulation_SD.Rmd/
    Ignored:    manuscript/.DS_Store

Untracked files:
    Untracked:  analysis/raw_data.Rmd
    Untracked:  figures/Edited_fig3.pdf

Unstaged changes:
    Modified:   analysis/index.Rmd
    Modified:   analysis/simulation.Rmd
    Modified:   analysis/statistics.Rmd
    Modified:   code/pdf_supplementary_material.pdf
    Modified:   data/clean_data/larval_fitness.csv
    Modified:   figures/fig1.pdf
    Modified:   figures/fig2.pdf
    Modified:   figures/fig3.pdf
    Modified:   manuscript/SD_manuscript.Rmd
    Modified:   manuscript/SD_manuscript.pdf

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.