Last updated: 2018-07-19

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• ✔ 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: eb264b1

  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:    .DS_Store
      Ignored:    .Rhistory
      Ignored:    .Rproj.user/
      Ignored:    docs/.DS_Store
      Ignored:    docs/figure/.DS_Store
  
  Unstaged changes:
      Modified:   analysis/flash_em.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	eb264b1	Jason Willwerscheid	2018-07-19	wflow_publish(“analysis/index.Rmd”)
html	36a6312	Jason Willwerscheid	2018-07-19	Build site.
Rmd	a9f8cc6	Jason Willwerscheid	2018-07-19	wflow_publish(“analysis/index.Rmd”)
html	c420802	Jason Willwerscheid	2018-07-17	Build site.
Rmd	38942eb	Jason Willwerscheid	2018-07-17	wflow_publish(“analysis/index.Rmd”)
html	e2e1286	Jason Willwerscheid	2018-07-16	Build site.
Rmd	55f42ca	Jason Willwerscheid	2018-07-16	wflow_publish(“analysis/index.Rmd”)
html	de8f823	Jason Willwerscheid	2018-07-16	Build site.
Rmd	f5379fa	Jason Willwerscheid	2018-07-16	wflow_publish(“analysis/index.Rmd”)
html	7db12a1	Jason Willwerscheid	2018-07-16	Build site.
html	873da40	Jason Willwerscheid	2018-07-16	Build site.
html	58e136a	Jason Willwerscheid	2018-07-15	Build site.
Rmd	82c7cdd	Jason Willwerscheid	2018-07-15	wflow_publish(c(“analysis/index.Rmd”, “analysis/about.Rmd”))
html	76eacb7	Jason Willwerscheid	2018-07-15	Build site.
Rmd	f6928cc	Jason Willwerscheid	2018-07-15	wflow_publish(c(“analysis/index.Rmd”, “analysis/about.Rmd”))
Rmd	56d7ded	Jason Willwerscheid	2018-07-14	Start workflowr project.

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Investigation 1. The FLASH objective function appears to behave erratically.

Investigation 2. This problem only occurs when using ebnm_pn, not ebnm_ash.

Investigation 3. The objective can continue to get worse as loadings are repeatedly updated. Nonetheless, convergence takes place (from above!).

Notes on computing the FLASH objective.

An alternate algorithm for updating loadings.

Investigation 4. The alternate algorithm yields much different results from FLASH. In particular, the fits of the priors on the loadings are visibly different.

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This reproducible R Markdown analysis was created with workflowr 1.0.1

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