An R package that provides read/write access to data and metadata from the DataONE network of Member Node data repositories. Member Nodes in DataONE are independent data repositories that have adopted the DataONE services for interoperability, making each of the repositories accessible to client tools such as the DataONE R Client using a standard interface. The DataONE R Client can be used to access data files and to write new data and metadata files to nodes in the DataONE network.
The currently supported version requires two R packages, dataone and dataonelibs (which provides the Java libraries necessary for the dataone package to function):
- DataONE R Client (dataone_1.0.0.tar.gz)
- DataONE Libraries (dataonelibs_1.0.0.tar.gz)
Documentation for the DataONE R Client is provided as help files within the R framework, and is downloadable in PDF format:
- DataONE R Client Manual (dataone_1.0.0-manual.pdf)
The easiest way to install the client is via the GitHub repository:
> devtools::install_github("DataONEorg/rdataone/dataonelibs", ref="D1_CLIENT_R_v1.0.0")
> devtools::install_github("DataONEorg/rdataone/dataone", ref="D1_CLIENT_R_v1.0.0")
Alternatively, you can download and install the package manually from this web site above and, after downloading the package, install it using:
$ R CMD install dataonelibs_1.0.0.tar.gz $ R CMD install dataone_1.0.0.tar.gz
This package uses rJava to bind to the Java client libraries. Be sure to install rJava for your particular version of R and Java.
See the full manual for documentation, but once installed, the package can be run in R using:
$ R > library(dataone) Loading required package: rJava Loading required package: XML Loading required package: dataonelibs > help(dataone)
Reading a CSV data file from a DataONE node is as simple as:
> library(dataone) > cli <- D1Client() > d1o <- getD1Object(cli, "doi:10.5063/AA/hstuar01.10.1") > mydf <- asDataFrame(d1o)
Writing a CSV file to a DataONE Member Node requires authentication via CILogon, but is similarly simple:
> library(uuid)
> mn_nodeid <- "urn:node:mnTestKNB"
> cli <- D1Client("STAGING2")
> id <- paste("urn:uuid:", UUIDgenerate(), sep="")
> testdf <- data.frame(x=1:10,y=11:20)
> csvdata <- convert.csv(cli, testdf)
> format <- "text/csv"
## Build a D1Object containing the csv, and upload it to the MN
> d1Object <- new(Class="D1Object", id, csvdata, format, mn_nodeid)
> setPublicAccess(d1Object)
> createD1Object(cli, d1Object)
We are currently working on a version 2 release milestone that removes the dependency on rJava. This work is almost complete and significantly changes the base API to correspond to the published DataONE API. Previous methods for accessing DataONE will be maintained, but new methods will be added. Consequently, the current development snapshot in the master branch is quite different from the 1.0.0 release. Be aware that there are API differences that are not fully finalized.
Because the v2 package has not been released to CRAN, nor have its dependencies, you need to install the dependencies manually before installing the package itself. The main dependency is the redland R package which must be installed on your OS prior to installing the R code.
Before the redland R package can be installed, the Redland C libraries must be installed.
On Mac OS X you can use the package management system HomeBrew to install the necessary libraries. The HomeBrew software can be installed with the following command entered at a terminal window:
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
Once HomeBrew has been installed, you can then enter the following command to install the Redland C libraries:
brew install redland
Next, use the CRAN 'drat' package and the NCEAS repository to install all of the R dependencies needed:
$ R
> install.packages("drat")
> library(drat)
> addRepo("NCEAS")
> install.packages("redland", type="binary")
> install.packages("dataone")
For ubuntu, install the required Redland C libraies:
$ sudo apt-get install librdf0 librdf0-dev
Then install the R packages:
$ R
> install.packages("drat")
> library(drat)
> addRepo("NCEAS")
> install.packages("dataone")
For developers interested in getting an email for each push to the rdataone repository, you can subscribe to our mailing list:
rdataone-dev: List Info
The DataONE R Client is licensed as open source software under the Apache 2.0 license.
- Matthew Jones <[email protected]>
- Rob Nahf <[email protected]>
- Chris Jones <[email protected]>
- Carl Boettiger <[email protected]>
- Lauren Walker <[email protected]>
- Scott Chamberlain <[email protected]>
- Edmund Hart <[email protected]>
- Jordan Read <[email protected]>
- Peter Slaughter <slaughter.nceas.ucsb.edu>