Last updated: 2021-10-24

Checks: 7 0

Knit directory: BreedingSchemeOpt/

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.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20210422)

The command set.seed(20210422) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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Cache: none

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

File paths: relative

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Repository version: e0ca345

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 e0ca345. 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:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  analysis/archive/
    Untracked:  code/runSchemesPostBurnIn_dev.R
    Untracked:  code/scrap.R
    Untracked:  data/baselineScheme.gsheet
    Untracked:  output/Icon
    Untracked:  output/benchmark_sim.rds
    Untracked:  output/benchmark_sims5.rds
    Untracked:  output/burnInSims_bsp1_iita_2021Aug27.rds
    Untracked:  output/burnInSims_bsp2_iita_2021Aug27.rds
    Untracked:  output/burnInSims_bsp3_iita_2021Aug27.rds
    Untracked:  output/burnInSims_iita_2021Aug27.rds
    Untracked:  output/burnIn_test.rds
    Untracked:  output/postBurnInGMS_test_DirDom_UCparent.rds
    Untracked:  output/postBurnInGMS_test_newBSP1.rds
    Untracked:  output/postBurnInGMS_test_newBSP2.rds
    Untracked:  output/postBurnInGMS_test_newBSP3.rds
    Untracked:  output/postBurnInGMS_test_newBSP3_GS.rds
    Untracked:  output/postBurnInGMS_test_newBSP3_PS.rds
    Untracked:  output/postBurnInGS_test.rds
    Untracked:  output/postBurnIn_test.rds
    Untracked:  output/testSims_GMS_DirDom_MeanTGV_2021Sep18.rds
    Untracked:  output/testSims_GMS_DirDom_MeanTGV_50parents_2021Sep18.rds
    Untracked:  output/testSims_GMS_DirDom_UCvariety_2021Sep18.rds
    Untracked:  output/testSims_GMS_ModelA_MeanBV_2021Sep15.rds
    Untracked:  output/testSims_GMS_ModelA_MeanBV_2021Sep18.rds
    Untracked:  output/testSims_GMS_ModelA_UCparent_propSelpt05_2021Sep18.rds
    Untracked:  output/test_burnInSims_2021Sep17.rds
    Untracked:  output/test_burnInSims_GS_2021Sep17.rds
    Untracked:  output/test_burnInSims_GS_noAYT_2021Sep17.rds
    Untracked:  output/test_burnInSims_PS_2021Sep17.rds
    Untracked:  output/test_burnInSims_PS_noAYT_2021Sep17.rds
    Untracked:  output/test_burnIn_sim.rds
    Untracked:  output/test_inputs_for_mmer.Rdata

Unstaged changes:
    Modified:   analysis/AlphaSimHlpR_firstSteps.Rmd
    Modified:   analysis/baselineSim.Rmd
    Modified:   analysis/genomicMateSelSims.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.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/workflowr_workflow.Rmd) and HTML (docs/workflowr_workflow.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 e0d20bd wolfemd 2021-08-27 Build site.
Rmd c2e379e wolfemd 2021-08-13 Rebuild repo removing the “Group” part. Project is to contain BOTH the “Group” and a separate section just for the actual simulation analyses.
html 9f8bd55 wolfemd 2021-04-22 Build site.
Rmd 4c85d1a wolfemd 2021-04-22 Publish the workflowr workflow itself.
html 92bd15b wolfemd 2021-04-22 Build site.
Rmd aac97a0 wolfemd 2021-04-22 Publish the workflowr workflow itself.
html 1d503b6 wolfemd 2021-04-22 Build site.
Rmd bf9f68c wolfemd 2021-04-22 Publish the workflowr workflow itself.

Below, I document the process of creating and publishing a workflowr documentation for the Breeding Scheme Opt. Group.

To implement yourself, also recommend you check out the getting started page for workflowr.

I work in Rstudio. I use the Rstudio GUI to create the project and do a few other tasks that don’t need automation.

File > New Project > New Directory > Create workflowr project

Enter your Git / GitHub user name and email address to facilitate version control set-up.

The project get’s set up automatically.

Get presented with initial files and file structure.

File in a super brief description or other relevant information in the README.md; this will appear on the main GitHub repository for the project.

Next index.Rmd. This is the home / landing page for the project. Combined with the top navigation bar (which is edited in the _site.yml).

Change the theme and syntax highlighting in _site.yml to yeti and breezedark because I like them.

From here, content creation begins.

I add new Rmd’s in the analysis/ directory as I go. I also subsequently link new documents in the index.Rmd main page and on the navbar (_site.yml) as desired.

Once the structure is in place, it’s pretty straightforward to build on.

You can add and automatically open a new Rmd using

workflowr::wflow_open("analysis/AlphaSimHlpR_firstSteps.Rmd")

Automatically adds a bit of yaml at the top to connect it to the rest of the project. Customize the title, author name, etc as desired.

---
title: "First steps - Install and Run AlphaSimHlpR tutorial"
author: "Marnin Wolfe"
date: "2021-04-22"
output: workflowr::wflow_html
editor_options:
  chunk_output_type: console
---

Now I’m ready to do an initial “publish” of the project, which means the *.Rmd files will be compiled into *.html in the docs/ directory. Also a Git commit will occur.

I like to manually record each Rmd I publish for precision, but you can compile everything if you want.

workflowr::wflow_publish(c("analysis/AlphaSimHlpR_firstSteps.Rmd",
                           "analysis/example-simulation-reducing-error-with-new-tools.Rmd",
                           "analysis/index.Rmd", 
                           "analysis/about.Rmd", 
                           "analysis/license.Rmd",
                           "analysis/_site.yml"),
                         "Publish the initial files for the Breeding Scheme Optimization Group project")
workflowr::wflow_use_github(username="wolfemd", create_on_github = T)
workflowr::wflow_git_push(usename="wolfemd")

Now the repository is uploaded to GitHub.

Last step to make it live on GitHub Pages

In GitHub repository –> “Settings” (approx top right")

Choose Pages (left side bar) –> Choose Source branch “master” and directory /docs

Site is now published to: https://wolfemd.github.io/BreedingSchemeOptGroup/

Might take a few moments to be live.

Last step, add this page to the workflowR project.

workflowr::wflow_open("analysis/workflowr_workflow.Rmd")
workflowr::wflow_publish(c("analysis/index.Rmd", 
                           "analysis/_site.yml",
                           "analysis/workflowr_workflow.Rmd"),
                         republish = T, # republish=T since we updated _site.yml
                         message = "Publish the workflowr workflow itself.")

sessionInfo()