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Fostering the next gen of open science with R
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Karthik Ram
December 18, 2013
Science
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150
Fostering the next gen of open science with R
My talk at the American Geophysical Union meeting in SF, December 2013.
Karthik Ram
December 18, 2013
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Transcript
OPEN SCIENCE fostering NEXT GEN . . . . .
. . with . . . . . . .
@_inundata
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None
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MOST OF THESE DATA ARE NOT EASILY ACCESSIBLE
The data life cycle
IT LEADS TO THIS
A RESEARCH PAPER THE NARRATIVE THE DATA THE CODE
THE NARRATIVE THE DATA THE CODE A RESEARCH PAPER
Scientists don’t share code or data few incentives
But incentive structures are slowly changing
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:
community:
community:
Programmatic workflows increase reproducibility
None
glm(y ~ -1 + a + c + z +
a:z, data = mydata, maxit = 30) This is reproducible, repeatable and can serve as a analytic workflow
INCORPORATE OPEN SCIENCE INTO existing workflows
R + open science
Why R? 5,000 + Packages Widely used by environmental scientists
Our mission is to develop tools (mostly around R) to
access scientific data repositories, full-text of articles, and science metrics.
ACQUIRE DATA { 50+ CURRENT OFFERINGS packages ADD METADATA DEPOSIT
DATA
Search over 100K articles rplos
Retrieve data underlying papers in 200+ journals rdryad
Validate results from papers treebase
Past and future climate projections rWBclimate
Map biodiversity data spocc Danaus plexippus
Model species distributions
Deposit data into permanent archives library(figshare) fs_auth() id <- fs_create()
fs_upload(id, r_object) rfigshare
A RESEARCH PAPER THE NARRATIVE THE DATA THE CODE
CODE/ DATA Acquisition Analysis Documentation Deposition
DATA SHOULD BE machine readable
AUTOMATE BORING TASKS paint drying adding metadata
dryaddat <- download_url("10255/dryad.1759") ! dat <- dryad_getfile(dryaddat) ! eml_write(dat =
dat, meta, title = "Landings Data", description = description, creator = "Karthik Ram <
[email protected]
>", file = "landings.xml") ! ! eml_publish("landings.xml", description = description, categories = "Ecology", tags = "fisheries", destination = "figshare", visibility = "public")
A RESEARCH PAPER THE NARRATIVE THE DATA THE CODE
None
ropensci.org @ropensci