Fostering the next gen of open science with R

My talk at the American Geophysical Union meeting in SF, December 2013.

Transcript

1. OPEN SCIENCE fostering NEXT GEN . . . . . . . with . . . . . . .
2. @_inundata
6. MOST OF THESE DATA ARE NOT EASILY ACCESSIBLE
7. The data life cycle
8. IT LEADS TO THIS
9. A RESEARCH PAPER THE NARRATIVE THE DATA THE CODE
10. THE NARRATIVE THE DATA THE CODE A RESEARCH PAPER
11. Scientists don’t share code or data few incentives
12. But incentive structures are slowly changing
13. Instructions for preparation of the Biographical Sketch have been revised to rename the "Publications" section to "Products" and amend terminology and instructions accordingly. This change makes clear that products may include, but are not limited to, publications, data sets, software, patents, and copyrights. Funders:
14. community:
15. community:
16. Programmatic workflows increase reproducibility
18. glm(y ~ -1 + a + c + z + a:z, data = mydata, maxit = 30) This is reproducible, repeatable and can serve as a analytic workflow
19. INCORPORATE OPEN SCIENCE INTO existing workflows
20. R + open science
21. Why R? 5,000 + Packages Widely used by environmental scientists
22. Our mission is to develop tools (mostly around R) to access scientific data repositories, full-text of articles, and science metrics.
23. ACQUIRE DATA { 50+ CURRENT OFFERINGS packages ADD METADATA DEPOSIT DATA
24. Search over 100K articles rplos
25. Retrieve data underlying papers in 200+ journals rdryad
26. Validate results from papers treebase
27. Past and future climate projections rWBclimate
28. Map biodiversity data spocc Danaus plexippus
29. Model species distributions
30. Deposit data into permanent archives library(figshare) fs_auth() id <- fs_create() fs_upload(id, r_object) rfigshare
31. A RESEARCH PAPER THE NARRATIVE THE DATA THE CODE
32. CODE/ DATA Acquisition Analysis Documentation Deposition
33. DATA SHOULD BE machine readable
34. AUTOMATE BORING TASKS paint drying adding metadata
35. dryaddat <- download_url("10255/dryad.1759") ! dat <- dryad_getfile(dryaddat) ! eml_write(dat = dat, meta, title = "Landings Data", description = description, creator = "Karthik Ram <karthik@ropensci.org>", file = "landings.xml") ! ! eml_publish("landings.xml", description = description, categories = "Ecology", tags = "fisheries", destination = "figshare", visibility = "public")
36. A RESEARCH PAPER THE NARRATIVE THE DATA THE CODE
38. ropensci.org @ropensci