Last updated: 2020-05-09
Checks: 2 0
Knit directory: drift-workflow/analysis/
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.
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.
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 d8ba76d. 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: .snakemake/
Ignored: data/datasets/
Ignored: data/raw/
Ignored: data/simulations/
Ignored: nb-log-1080241.err
Ignored: nb-log-1080241.out
Ignored: output/
Ignored: sandbox/.ipynb_checkpoints/
Untracked files:
Untracked: notebooks/
Untracked: plots/drift-K10-scaled.png
Untracked: plots/drift-K10-unscaled.png
Untracked: start-jupyter.sbatch
Untracked: start-rstudio.sbatch
Unstaged changes:
Modified: README.md
Deleted: analysis/hoa_global_bimodal.Rmd
Modified: code/structure_plot.R
Deleted: plots/africa_admixture-K8.png
Deleted: plots/africa_drift-K12.png
Deleted: plots/africa_drift-K3.png
Deleted: plots/africa_drift-K9.png
Deleted: plots/africa_flash_backfit-K9.png
Deleted: plots/africa_flash_greedy-K9.png
Deleted: plots/america_admixture-K8.png
Deleted: plots/america_drift-K12.png
Deleted: plots/america_drift-K3.png
Deleted: plots/america_drift-K9.png
Deleted: plots/america_flash_backfit-K9.png
Deleted: plots/america_flash_greedy-K9.png
Deleted: plots/central_asia_siberia_admixture-K8.png
Deleted: plots/central_asia_siberia_drift-K12.png
Deleted: plots/central_asia_siberia_drift-K3.png
Deleted: plots/central_asia_siberia_drift-K9.png
Deleted: plots/central_asia_siberia_flash_backfit-K9.png
Deleted: plots/central_asia_siberia_flash_greedy-K9.png
Deleted: plots/east_asia_admixture-K8.png
Deleted: plots/east_asia_drift-K12.png
Deleted: plots/east_asia_drift-K3.png
Deleted: plots/east_asia_drift-K9.png
Deleted: plots/east_asia_flash_backfit-K9.png
Deleted: plots/east_asia_flash_greedy-K9.png
Deleted: plots/local_west_eurasia_drift-K12.png
Deleted: plots/local_west_eurasia_drift-K3.png
Deleted: plots/local_west_eurasia_drift-K8.png
Deleted: plots/local_west_eurasia_flash_greedy-K12.png
Deleted: plots/local_west_eurasia_flash_greedy-K3.png
Deleted: plots/local_west_eurasia_flash_greedy-K8.png
Deleted: plots/marcus_et_al_2020_ancient_drift-K10.png
Deleted: plots/marcus_et_al_2020_ancient_drift-K11.png
Deleted: plots/marcus_et_al_2020_ancient_drift-K7.png
Deleted: plots/marcus_et_al_2020_ancient_drift-K9.png
Deleted: plots/marcus_et_al_2020_ancient_flash_greedy-K10.png
Deleted: plots/marcus_et_al_2020_ancient_flash_greedy-K8.png
Deleted: plots/marcus_et_al_2020_modern_drift-K10.png
Deleted: plots/marcus_et_al_2020_modern_drift-K11.png
Deleted: plots/marcus_et_al_2020_modern_drift-K7.png
Deleted: plots/marcus_et_al_2020_modern_drift-K9.png
Deleted: plots/marcus_et_al_2020_modern_flash_greedy-K10.png
Deleted: plots/marcus_et_al_2020_modern_flash_greedy-K8.png
Deleted: plots/oceania_admxiture-K8.png
Deleted: plots/oceania_drift-K12.png
Deleted: plots/oceania_drift-K3.png
Deleted: plots/oceania_drift-K9.png
Deleted: plots/oceania_flash_backfit-K9.png
Deleted: plots/oceania_flash_greedy-K9.png
Deleted: plots/south_asia_admixture-K8.png
Deleted: plots/south_asia_drift-K12.png
Deleted: plots/south_asia_drift-K3.png
Deleted: plots/south_asia_drift-K9.png
Deleted: plots/south_asia_flash_backfit-K9.png
Deleted: plots/south_asia_flash_greedy-K9.png
Deleted: plots/west_eurasia_admixture-K8.png
Deleted: plots/west_eurasia_drift-K12.png
Deleted: plots/west_eurasia_drift-K3.png
Deleted: plots/west_eurasia_drift-K9.png
Deleted: plots/west_eurasia_flash_backfit-K9.png
Deleted: plots/west_eurasia_flash_greedy-K9.png
Deleted: start-nb.sbatch
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 |
|---|---|---|---|---|
| html | d8ba76d | Joseph Marcus | 2020-05-09 | Build site. |
| Rmd | ab45cd4 | Joseph Marcus | 2020-05-09 | wflow_publish(“index.Rmd”) |
| html | 1cf93f3 | Joseph Marcus | 2020-05-09 | Build site. |
| Rmd | ceffc2b | Joseph Marcus | 2020-05-09 | wflow_publish(“index.Rmd”) |
| Rmd | eb53ef2 | Joseph Marcus | 2020-05-05 | simplified plotting code and updating analysis with new plots |
| html | 2dd9256 | Jason Willwerscheid | 2020-01-18 | Build site. |
| Rmd | aec23d2 | Jason Willwerscheid | 2020-01-18 | wflow_publish(“analysis/index.Rmd”) |
| html | a9a33bc | Jason Willwerscheid | 2020-01-16 | Build site. |
| Rmd | b0090a0 | Jason Willwerscheid | 2020-01-16 | wflow_publish(“analysis/index.Rmd”) |
| html | 92ea5bb | Jason Willwerscheid | 2020-01-16 | Build site. |
| Rmd | 7128cb0 | Jason Willwerscheid | 2020-01-16 | wflow_publish(“analysis/index.Rmd”) |
| html | 3c8a921 | Jason Willwerscheid | 2020-01-15 | Build site. |
| Rmd | fc51e9b | Jason Willwerscheid | 2020-01-15 | wflow_publish(“analysis/index.Rmd”) |
| html | 7b056d2 | Jason Willwerscheid | 2020-01-14 | Build site. |
| Rmd | 3b38211 | Jason Willwerscheid | 2020-01-14 | wflow_publish(“analysis/index.Rmd”) |
| html | 63c9d16 | Jason Willwerscheid | 2020-01-10 | Build site. |
| Rmd | 885767b | Jason Willwerscheid | 2020-01-10 | wflow_publish(“analysis/index.Rmd”) |
| html | ad7400b | Jason Willwerscheid | 2020-01-10 | Build site. |
| Rmd | 6d7cf9e | Jason Willwerscheid | 2020-01-10 | workflowr::wflow_publish(“analysis/index.Rmd”) |
| html | 0bb6732 | jhmarcus | 2019-12-21 | Build site. |
| Rmd | 7b7b6d4 | jhmarcus | 2019-12-19 | added init drift alpha application to simulation |
| html | 7b7b6d4 | jhmarcus | 2019-12-19 | added init drift alpha application to simulation |
| Rmd | e3936bc | jhmarcus | 2019-12-01 | pushing 2 pop analysis |
| html | e3936bc | jhmarcus | 2019-12-01 | pushing 2 pop analysis |
| Rmd | 221956b | jhmarcus | 2019-05-23 | added exploration of using bernoulli prior for enbm |
| html | 221956b | jhmarcus | 2019-05-23 | added exploration of using bernoulli prior for enbm |
| Rmd | c03180c | jhmarcus | 2019-05-22 | added 2 pop tree |
| html | c03180c | jhmarcus | 2019-05-22 | added 2 pop tree |
| Rmd | 2ded9d3 | jhmarcus | 2019-05-20 | added bimodal prior sim |
| html | 2ded9d3 | jhmarcus | 2019-05-20 | added bimodal prior sim |
| Rmd | 44a10f7 | jhmarcus | 2019-05-05 | added bimodal ash exploration |
| html | 44a10f7 | jhmarcus | 2019-05-05 | added bimodal ash exploration |
| html | 89ee553 | jhmarcus | 2019-05-03 | added github link |
| Rmd | 912c5ff | jhmarcus | 2019-05-03 | added simpler tree sim |
| html | 912c5ff | jhmarcus | 2019-05-03 | added simpler tree sim |
| Rmd | e32adcc | jhmarcus | 2019-04-19 | init badmixture sim |
| html | e32adcc | jhmarcus | 2019-04-19 | init badmixture sim |
| Rmd | 0a3374d | jhmarcus | 2019-04-15 | added simple sim |
| html | 0a3374d | jhmarcus | 2019-04-15 | added simple sim |
| html | 71e0580 | Peter Carbonetto | 2019-03-14 | Re-built home page with correct top-right link. |
| html | 820a40e | Peter Carbonetto | 2019-03-14 | Added link to hoa_global_alt analysis in home page. |
| Rmd | 4c8921b | Peter Carbonetto | 2019-03-14 | wflow_publish(“index.Rmd”) |
| html | 9d521a9 | jhmarcus | 2019-03-06 | Build site. |
| Rmd | d2573ea | jhmarcus | 2019-03-05 | updated idx |
| html | d2573ea | jhmarcus | 2019-03-05 | updated idx |
| html | 9a69c08 | jhmarcus | 2019-03-05 | updated data hoa |
| Rmd | a1580ed | jhmarcus | 2019-03-04 | added data exploration |
| html | a1580ed | jhmarcus | 2019-03-04 | added data exploration |
| html | c203e00 | jhmarcus | 2019-03-03 | Build site. |
| html | 90a0a02 | jhmarcus | 2019-02-28 | updated to autosomes and added manhatten plot |
| html | 38a461d | jhmarcus | 2019-02-25 | built all |
| html | 7644d40 | jhmarcus | 2019-02-24 | updated index |
| Rmd | 38b57c5 | jhmarcus | 2019-02-24 | simplified greedy flash global analysis |
| html | 403bc6b | jhmarcus | 2019-02-15 | added hide code blocks |
| html | b4749ac | jhmarcus | 2019-02-15 | fixed some typos |
| html | 7a2b6c7 | jhmarcus | 2019-02-15 | added backfit |
| Rmd | f5ef1af | jhmarcus | 2019-02-15 | added workflows for human origins datasets |
| html | f5ef1af | jhmarcus | 2019-02-15 | added workflows for human origins datasets |
| html | 31a16c6 | jhmarcus | 2019-02-14 | added hists of factors |
| html | 9538510 | jhmarcus | 2019-02-14 | switched to struct style plot |
| html | 63c2b75 | jhmarcus | 2019-02-13 | added softimpute |
| html | 7b6ecbc | jhmarcus | 2019-02-13 | made fig size bigger |
| Rmd | 5c0f91a | jhmarcus | 2019-02-12 | init flash proof of principle |
| html | 5c0f91a | jhmarcus | 2019-02-12 | init flash proof of principle |
| Rmd | 46105ee | jhmarcus | 2019-02-11 | Start workflowr project. |
Authors: Joe Marcus and Jason Willwerscheid
Advisors: John Novembre, Peter Carbonetto, and Matthew Stephens
Less simple admixture event:
Before 2019-12-01:
These vignettes describe results on simulated / empirical data: