Last updated: 2020-04-27
Checks: 1 1
Knit directory: lieb/
This reproducible R Markdown analysis was created with workflowr (version 1.6.1). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.
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 3d86b68. 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/.Rhistory
Ignored: analysis/pairwise_fitting_cache/
Ignored: analysis/running_mcmc_cache/
Ignored: data/.DS_Store
Ignored: output/.DS_Store
Ignored: output/chip_shiny/.DS_Store
Ignored: output/chip_shiny/Data/.DS_Store
Ignored: output/vision_shiny/.DS_Store
Ignored: output/vision_shiny/.Rhistory
Ignored: output/vision_shiny/Data/.DS_Store
Untracked files:
Untracked: output/chain.rds
Unstaged changes:
Modified: analysis/downstream.Rmd
Modified: analysis/running_mcmc.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/downstream.Rmd) and HTML (docs/downstream.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 | cc98d2b | hillarykoch | 2020-04-24 | replace cache and update to describe flex_mu |
| Rmd | 717e762 | hillarykoch | 2020-04-23 | add placeholder for downstream analyses |
| html | 717e762 | hillarykoch | 2020-04-23 | add placeholder for downstream analyses |
| Rmd | 2a75de4 | hillarykoch | 2020-02-20 | remove too-big header |
| html | 2a5b7c0 | hillarykoch | 2020-02-20 | Build site. |
| html | 3a9bf9d | hillarykoch | 2020-02-20 | Build site. |
| Rmd | a99d063 | hillarykoch | 2020-02-20 | add new page about downstream analysis |
| html | a99d063 | hillarykoch | 2020-02-20 | add new page about downstream analysis |
CLIMB’s output is effectively the posterior MCMC samples of the parameters of the normal mixture. These samples can be used for clustering/classification, visualizations, and statistical inference. Here, we show implementations of several of the analyses used in the CLIMB manuscript.
First, let’s load in the MCMC we briefly ran on simulated data in the running the MCMC section.