rmongodb
This is an R (www.r-project.org) extension supporting access to MongoDB (www.mongodb.org) using the mongodb-c-driver (http://docs.mongodb.org/ecosystem/drivers/c/).
The latest stable version is available on CRAN: http://cran.r-project.org/package=rmongodb
Thanks to Gerald Lindsly and MongoDB, Inc. (formerly 10gen) for the initial work.
In October 2013, MongoSoup and Markus Schmidberger have overtaken the development and maintenance of the R package.
Since October 2014 package is maintained by Dmitriy Selivanov. Please feel free to send us issues or pull requests via github: https://github.com/mongosoup/rmongodb
Furthermore, I'm happy to get your feedback personally via email: selivanov.dmitriy (at) gmail.com.
Usage
Once you have installed the package, it may be loaded from within R like any other package:
library("rmongodb")
# connect to your local mongodb
mongo <- mongo.create()
# create query object
query <- mongo.bson.from.JSON('{"age": 27}')
# Find the first 100 records
# in collection people of database test where age == 27
cursor <- mongo.find(mongo, "test.people", query, limit=100L)
# Step though the matching records and display them
while (mongo.cursor.next(cursor))
print(mongo.cursor.value(cursor))
mongo.cursor.destroy(cursor)
res <- mongo.find.batch(mongo, "test.people", query, limit=100L)
mongo.disconnect(mongo)
mongo.destroy(mongo)
There is also one demo available:
library("rmongodb")
demo(teachers_aid)
Supported Functionality by rmongodb
- Connecting and disconnecting to MongoDB
- Querying, inserting and updating to MongoDB including with JSON and BSON
- Creating and handling BSON objects
- Dropping collections and databases on MongoDB
- Creating indices on MongoDB collections
- Error handling
- Executing commands on MongoDB
- Adding, removing, handling files on a "Grid File System" (GridFS) on a
MongoDB server
- High Level functionality as mongo.apply, mongo.summary, mongo.get.keys, ...
- Aggregation pipeline
Good ressources to Get Started with rmongodb
Basic Overview of using the rmongodb package for R - December 2013, Brock Tibert
code examples: https://gist.github.com/Btibert3/7751989R with MongoDB - MongoDB Munich conference, October 2013, Markus Schmidberger
Accessing mongodb from R - January 2012, Sean Davis
code examples: http://watson.nci.nih.gov/~sdavis/blog/rmongodb-using-R-with-mongo/R and MongoDB - June 2013, WenSui
example comparing rmongodb and RMongo: http://www.r-bloggers.com/r-and-mongodb/rmongodb – R Driver for MongoDB - September 2011, Gerald Lindsly
blog post: http://www.r-bloggers.com/rmongodb-r-driver-for-mongodb/Stackoverflow questions and answers:
http://stackoverflow.com/questions/tagged/rmongodb
Good ressources to Install and Get Started with MongoDB
Installing MongoDB, MongoDB Doku
http://docs.mongodb.org/manual/installation/Getting Started with MongoDB, MongoDB Doku
http://docs.mongodb.org/manual/tutorial/getting-started/MongoDB - Getting Started Guide, April 2013, Satish
Good ressources for working with JSON-Data in R:
- There are three R packages on CRAN: RJSONIO, jsonlite (used by rmongodb) and rjson
- jsonlite vignette for using JSON in R: http://cran.r-project.org/web/packages/jsonlite/vignettes/json-mapping.pdf
Development
To install the development version of rmongodb, it's easiest to use the devtools package:
# install.packages("devtools")
library(devtools)
install_github("mongosoup/rmongodb")
We advice using RStudio (www.rstudio.org) for the package development. The RStudio .Rproj file is included in the repository.
Usefull links
- BSON specification: http://bsonspec.org/#/specification
Versioning
We use a three step version number system, e.g. v1.2.1:
- first: major changes as new C libraries
- second: for each new stable CRAN release
- third: for each new github version ready for testing
General Development Rules
- we use roxygen2
- we write RUnit tests for all new functionality in tests/test_XXX.R
- for bigger changes we use branches
- run valgrid to check for memory leaks R -d "valgrind --tool=memcheck --leak-check=full" --vanilla < test_XXX.R > log.txt 2>&1
- CRAN submission:
- http://cran.r-project.org/submit.html
- create Package tar.gz via RStudio "Build Source Package"
- run R CRAN checks via: R CMD check --as-cran package.tar.gz
- run R CRAN checks without running mongodb installation
- create a tag / release on github for every CRAN submission