Accessing Ecological and evolutionary datasets in R

Karthik Ram, Carl Boettiger, and Scott Chamberlain

esa2012@ropensci.org


Shortcuts: M =   ,   G =


Most science is not reproducible or repeatable, even within the same lab group over time.


Science

Data Life Cycle

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source: Michener, 2006 Ecoinformatics.



Open Science


Open data + code

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Source: Wolkovich et al. GCB 2012.



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Source: PLOS, 2007



R Open Science



Open Science needs open source tools

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Source: Revolution Analytics, 2010, Nature editorial, 2012

Why R?

The old way...

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Why R?

A better way



glm(y ~ -1 + a + c + z + a:z, data = mydata, maxit = 30)


This is reproducible, repeatable and can serve as a analytic workflow.




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Wrapping all science APIs



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Development team


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Carl Boettiger
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Karthik Ram
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Scott Chamberlain
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Advisory team


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Duncan
Temple Lang
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Hadley Wickham

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JJ Allaire

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Bertram
Ludascher
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Matt Jones

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R and APIs

API keys can be stored in a users.rprofile

 
	options(MendeleyKey = "uf5daib7wyil7ag5buc")
	options(MendeleyPrivateKey = "faj2os5dyd7jop2fok6")
	options(PlosApiKey = "ef3vip9yak7od3hud4g")
	options(SpringerMetdataKey = "ri9hi7woc6jax4vaf8w")





Note: These keys aren't real.

Public Library of Science full text - rplos


library(rplos)
plot_throughtime(list("reproducible science"), 500)
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Managing bibliography - RMendeley

Manage libraries and measure impact of research

groupDocInfo(mc, 530031, 4344945792)

$abstract
[1] "SUMMARY: Modern biological experiments create vast amounts of data which are geographically distributed. These datasets consist of petabytes of raw data and billions of documents. Yet to the best of our knowledge, a search engine technology that searches and cross-links all different data types in life sciences does not exist.....

$authors
$authors[[1]]
      forename        surname
   "Dominic S" 	"L\xfctjohann" 
# ....


Accessing data behind papers - rdryad

# Get the URL for a data file
dryaddat <- download_url("10255/dryad.1759")

# Get a file given the URL
file <- dryad_getfile(dryaddat)


Tracking altmetrics - raltmet

Tracks altmetrics across various sources such as GitHub, Total impact, CitedIn, CiteULike, Stackoverflow.

GitHub(userorg = "ropensci", repo = "rmendeley")

totimp(id = "10.5061/dryad.8671")

stackexchange(ids = 16632)

Mapping biodiversity data - rgbif

distribution <- occurrencelist(sciname = "Danaus plexippus", coordinatestatus = TRUE, maxresults = 1000, latlongdf = TRUE)
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Also see Cartodb's powerful mapping capabilites and R package.


Sharing unpublished data - (rfigshare)

Using Figshare's new API, it is now possible to share figures, data, and any other object generated in R directly to one's figshare account.


> figshare(data)
# code isn't ready yet but once it is, it will return a persistent identifier






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DataONE

DataONE creates all the necessary components to support persistent and secure access to earth observation data.




DataONE's upcoming R package will allow users to submit and access data to/from member nodes directly from the console.




Git + Science

Does your version control look like this?

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Using Git with a GUI

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Rapid peer-peer sharing of code is great for science



R packages early in development can easily be tested, rapidly deployed from GitHub using devtools and revised before submitting to a persistent repository such as CRAN.


library(devtools)
install_github("RMendeley", "ropensci")



R + collaborative writing


knitr + Markdown


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Xie Y (2012). knitr: A general-purpose package for dynamic report generation in R.

knitr + Markdown + GitHub

GitHub automatically renders Markdown and even provides syntax highlighting


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knitr + Markdown + GitHub = executible paper


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knitr + Markdown + GitHub = pre publication review


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Incorporate citations with R + Markdown


knitcitations

citet(c(Halpern2006 = "10.1111/j.1461-0248.2005.00827.x"))
# then cite in your markdown file
citet("Halpern2006")


# or read citations from a bibtex file which can be automatically generated and updated from services like Mendeley

bib <- read.bibtex("example.bib")
# then cite inline
citet(bib[["knitr"]])

- knitcitations on Carl Boettiger's GitHub
- tutorial

  esa.ropensci.org

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