Last updated: 2019-06-25

workflowr checks: (Click a bullet for more information)

  • ✔ R Markdown file: up-to-date

    Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

  • ✔ Repository version: b78e77f

    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:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/figure/
    Untracked:  analysis/ldl_cad_cache/
    Untracked:  example_data/CAD_META.gz
    Untracked:  example_data/genome_wide_pruned_vars.1.RDS
    Untracked:  example_data/glg_ldl__vanderHarst_cad_cause.RDS
    Untracked:  example_data/glg_ldl__vanderHarst_cad_data.RDS
    Untracked:  example_data/glg_ldl__vanderHarst_cad_grid.RDS
    Untracked:  example_data/jointGwasMc_LDL.txt.gz
    Untracked:  example_data/ld_data.tar.gz
    Untracked:  example_data/ld_data/
    Untracked:  example_data/ldl_cad_cause.RDS
    Untracked:  example_data/ldl_cad_cause.old_grid.RDS
    Untracked:  example_data/ldl_cad_params.RDS
    Untracked:  example_data/snp_overlap.txt
    Untracked:  example_data/snp_overlap_ldpruned.txt
    Untracked:  example_data/top_ldl_pruned_vars.1.RDS
    Untracked:  ll_v7_notes.Rmd
    Untracked:  matrix_lik.RDS
    Untracked:  quantile_sampling.R
    Untracked:  simulations/
    Untracked:  src/RcppExports.o
    Untracked:  src/log_likelihood_functions.o
    Untracked:  test_data/

Unstaged changes:
    Modified:   analysis/index.Rmd
    Modified:   analysis/ldl_cad.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.
Expand here to see past versions:
    File Version Author Date Message
    Rmd b78e77f Jean Morrison 2019-06-25 wflow_publish(files = c(“analysis/simulations.Rmd”))
    html 286f4e9 Jean Morrison 2019-06-25 Build site.
    Rmd 8f3b82e Jean Morrison 2019-06-25 wflow_publish(files = c(“analysis/about.Rmd”, “analysis/index.Rmd”, “analysis/ldl_cad.Rmd”, “analysis/license.Rmd”,

Simulated Data Experiments

Simulations are run using the causeSims R package. The package can be downloaded using

devtools::install_github("jean997/causeSims")

This package relies on multiple R packages that are not on CRAN, so you will need to download these separately. For detailed installation instructions including installation of supporting R packages for other methods and a detailed description of the package see here. There you can also find a detailed walk through of a single simulation and explanations of the functions contained in the package.

We conduct simulations using the Dynamical Statisical Comparisons software. DSC files for executing the experiments presented in the paper can be found here: power, false positives

To execute them, use the following commands (on a compute cluster)

nohup dsc --replicate 100 --host config.yml -c 4 pwr.dsc > pwr_dsc.out &
nohup dsc --replicate 100 --host config.yml -c 4 false_positives.dsc > fp_dsc.out &

You will need to modify the config.yml file to be specific to your compute cluster.

Coming Soon

  • Plotting

This reproducible R Markdown analysis was created with workflowr 1.1.1