Last updated: 2020-06-24

Checks: 2 0

Knit directory: rss/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). 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: 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: 1e806af

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 1e806af. 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:    .Rproj.user/
    Ignored:    .spelling
    Ignored:    examples/example5/.Rhistory
    Ignored:    examples/example5/Aseg_chr16.mat
    Ignored:    examples/example5/example5_simulated_data.mat
    Ignored:    examples/example5/example5_simulated_results.mat
    Ignored:    examples/example5/ibd2015_path2641_genes_results.mat

Untracked files:
    Untracked:  docs_old/

Unstaged changes:
    Modified:   rmd/_site.yml

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 repository in which changes were made to the R Markdown (rmd/setup.Rmd) and HTML (docs/setup.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html f6e93e6 Xiang Zhu 2020-06-23 Build site.
Rmd 6cafbc3 Xiang Zhu 2020-06-23 wflow_publish(“rmd/setup.Rmd”)
html 0a1d1e9 Xiang Zhu 2020-06-23 Build site.
Rmd a4c0020 Xiang Zhu 2020-06-23 wflow_publish(“rmd/setup.Rmd”)

Below are instructions for installing RSS software. In a standard computing environment with internet connection, the installation time is typically less than 10 minutes.

RSS based on MCMC

This page shows how to install the Monte Carlo Markov chain (MCMC) scripts in rss/src/.

These MCMC scripts have been tested in the following environments:

RSS based on VB

This page shows how to install the Variational Bayes (VB) scripts in rss/src_vb/.

These VB scripts have been tested in the following environments: