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 results in this page were generated with repository version 6be6e72. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    code/workflow/.ipynb_checkpoints/
    Ignored:    data/

Untracked files:
    Untracked:  analysis/simulation-susieI-ukbWG-gtex.adipose.Rmd
    Untracked:  code/cis_expr.R
    Untracked:  code/run_impute_expr.R
    Untracked:  code/run_simulate_pheno.R
    Untracked:  code/susieI_parallel_test.R
    Untracked:  code/workflow/submit_parallel_master_run2.sh.sh
    Untracked:  code/workflow/submit_parallel_{masterfile}.sh

Unstaged changes:
    Modified:   analysis/description.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/simulation-susieI-ukbchr17to22B-gtex.adipose.Rmd
    Modified:   code/gwas.R
    Modified:   code/run_UKB_process.R
    Modified:   code/run_gwas_expr.R
    Modified:   code/run_gwas_snp.R
    Deleted:    code/run_simulate_phenotype.R
    Modified:   code/run_test_susieI.R
    Modified:   code/run_test_susieI_temp.R
    Modified:   code/simulate_phenotype.R
    Modified:   code/susie_filter.R
    Deleted:    code/workflow/master_run.sh
    Deleted:    code/workflow/param-20200915-1-1.R
    Deleted:    code/workflow/submit_parallel_master_run.sh.sh
    Deleted:    code/workflow/submit_parallel_master_run1-x.sh.sh
    Modified:   code/workflow/workflow-ashtest-20200915.ipynb
    Modified:   code/workflow/workflow-ashtest-20201001.ipynb
    Modified:   code/workflow/workflow-data.ipynb
    Modified:   code/workflow/workflow-susieI-20200915.ipynb
    Modified:   code/workflow/workflow-susieI-20201001.ipynb

Staged changes:
    Renamed1:   code/run_simulate_data.R
    Renamed2:   code/run_simulate_phenotype.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.