README.md

In transmart/RInterface: R Client for accessing the tranSMART RESTful API

TranSMART R client package

This package enables R programmers to access to a tranSMART installation via its RESTful API. Usually this involves authentication with the tranSMART installation. The package has built-in functionality for obtaining an authentication token.

Installation

Package dependencies

Protocol Buffers

The protobuf and its accompanying c implementation package need to be installed on the machine. The Protocol Buffers must be at version 2.2.0 or newer and can be installed either via the distribution package manager.

Ubuntu:

# apt-get install libcurl4-openssl-dev libssl-dev libprotoc-dev libprotobuf-dev protobuf-c-compiler

Redhat:

# # Incomplete, you also need libcurl and libssl development packages and maybe a protobuf-compiler devel package
# yum install protobuf-compiler protobuf protobuf-devel

Or install it from source with one of the packages available at https://code.google.com/p/protobuf/downloads/list.

Curl

Windows users might need to install the curl package from http://curl.haxx.se.

Installing transmartRClient

The package can be installed directly from github using the devtools package:

require(devtools)
install_github('transmart/RInterface')

or by following the instructions in bin/installCommands.R

Demonstration of the package

The demo/demoCommands.R file contains a short demo of how to connect to tranSMART and how to retrieve data from it.

Contributing

The bin/devCommands.R file contains some pointers that might be useful to anyone interested in developing on this package.

In order to contribute a patch, follow the instructions given in https://guides.github.com/activities/contributing-to-open-source/#contributing

And: thanks for considering contributing!

transmart/RInterface documentation built on May 31, 2019, 7:45 p.m.