Upgrade to Pro
— share decks privately, control downloads, hide ads and more …
Speaker Deck
Features
Speaker Deck
PRO
Sign in
Sign up for free
Search
Search
Fostering the next gen of open science with R
Search
Karthik Ram
December 18, 2013
Science
0
120
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
Tweet
Share
More Decks by Karthik Ram
See All by Karthik Ram
R summit talk
karthik
1
51
Introduction to ggplot2
karthik
11
16k
Other Decks in Science
See All in Science
構造活性フォーラム2023-山﨑担当分
yamasakih
0
310
2023-10-03-FOGBoston
lcolladotor
0
170
How we developed a data exchange format: Lessons learned from Camtrap DP
peterdesmet
1
140
KDD2023学会参加報告
tereka114
2
340
Leveraging conformal prediction for calibrated probabilistic time series forecasts to accelerate the renewable energy transition
ingevandenende
2
250
バックアップ『しながら』ランサムウェア検出も!? セキュリティ強化が満載 Veeam 12.1
climbteam
0
300
文系出身でも「アルゴリズム×数学」はスッキリ理解できた!話
wakamatsu_takumu
0
200
2023-07-18_Verge_Genomics
lcolladotor
0
110
研究・教育・産学連携の循環の実践
sshimizu2006
0
220
論文輪読会 第16回 "NeRF:Representing Scenes as Neural"
academix
0
460
統計的因果探索の方法
sshimizu2006
0
870
名古屋市立大学データサイエンス学部 夏のオープンキャンパス模擬授業20230818
ncu_ds
0
1k
Featured
See All Featured
Docker and Python
trallard
34
2.7k
YesSQL, Process and Tooling at Scale
rocio
164
13k
The Cult of Friendly URLs
andyhume
74
5.7k
No one is an island. Learnings from fostering a developers community.
thoeni
16
2.1k
It's Worth the Effort
3n
180
27k
Art, The Web, and Tiny UX
lynnandtonic
289
19k
The Brand Is Dead. Long Live the Brand.
mthomps
49
29k
Responsive Adventures: Dirty Tricks From The Dark Corners of Front-End
smashingmag
244
20k
Pencils Down: Stop Designing & Start Developing
hursman
117
11k
JavaScript: Past, Present, and Future - NDC Porto 2020
reverentgeek
40
4.4k
The Invisible Customer
myddelton
114
12k
Distributed Sagas: A Protocol for Coordinating Microservices
caitiem20
322
20k
Transcript
OPEN SCIENCE fostering NEXT GEN . . . . .
. . with . . . . . . .
@_inundata
None
None
None
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