Last updated: 2021-08-19

Checks: 2 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.

Repository version: 5914d8d

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 5914d8d. 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/
    Ignored:    analysis/.DS_Store
    Ignored:    analysis/images/.DS_Store
    Ignored:    data/.DS_Store

Untracked files:
    Untracked:  data/baselineScheme.gsheet
    Untracked:  output/benchmark_sim.rds
    Untracked:  output/benchmark_sims5.rds

Unstaged changes:
    Modified:   data/README.md

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/index.Rmd) and HTML (docs/index.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
Rmd	5914d8d	wolfemd	2021-08-19	Publish initial sims towards a baseline set of sims using runBreedingScheme_wBurnIn
Rmd	0ebe65f	wolfemd	2021-08-13	test
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	5395509	wolfemd	2021-04-22	Build site.
html	92bd15b	wolfemd	2021-04-22	Build site.
html	1d503b6	wolfemd	2021-04-22	Build site.
Rmd	bf9f68c	wolfemd	2021-04-22	Publish the workflowr workflow itself.
html	fe3048a	wolfemd	2021-04-22	Build site.
Rmd	9df9d9b	wolfemd	2021-04-22	Publish the initial files for the Breeding Scheme Optimization Group project
Rmd	32a7aff	wolfemd	2021-04-22	Start workflowr project.

Breeding Scheme Opt Group

Group Objectives

Participants learn about the usage of empirically-parameterized simulations for decision making about optimal breeding schemes.
Generate recommendations to NGC and stakeholders regarding key breeding scheme-related questions.

2021

Meeting 1 - 2021-Mar-12

Meeting 2 - 2021-Apr-02

Meeting 3 - 2021-Apr-23

AlphaSimHlpR first steps: Installation and quickly running the AlphaSimHlpR tutorial example.

Reducing error with new tools: Run a simple example simulation of the effect of reducing error with new tools. The first part, which currently is where my progress terminated, was to try and initiate a simulation and burn-in under phenotypic selection for several cycles before switching to genomic selection. Spoiler alert: Still needs work.

Creating this workflowR page for the group:

Meeting 4 - 2021-Jul-02

Meeting Slides: Concept for empirically estimating selection error described.

NextGen Breeding Scheme Optimization