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R Statistics With MongoDB

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MongoDB
MongoDB

Big Data is on every CIO’s mind. It is presently synonymous with open source technologies like Hadoop, and the ‘NoSQL’ class of databases. Another technology that is shaking things up in Big Data is R (www.r-project.org, #rstats). R is an open source programming language and software environment designed for statistical computing and visualisation. The statistical software R is the fastest growing analytics platform in the world, and is established in both academia and companies for robustness, reliability and accuracy. For real big data analyses you have to access your data in your preferred database on the fly. In this talk I will give a short overview about R, the available connection to MongoDB and present some big data analyses using R and mongoDB.

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R Statistics with MongoDB R Statistics with Mon‐ goDB Dr. Markus Schmidberger October 14th, 2013 Munich, Germany Email: markus@mongosoup.de Twitter: @cloudHPC 1 von 36
Dr. Markus Schmidberger R Statistics with MongoDB 2 von 36
R Statistics with MongoDB Outline Introduction to Big Data, MongoSoup and R R statistics with MongoDB and Examples Summary & Questions 3 von 36
R Statistics with MongoDB Big Data Wikipedia: … a collection of data sets so large and complex that it becomes difficult to process using on-hand database management tools or traditional data processing. … storing processing 4 von 36
Storing: NoSQL - MongoDB R Statistics with MongoDB databases using looser consistency models to store data German MongoDB as a Service: MongoSoup cloudControl Add-On currently running on AWS EU-Region (Ireland) all features available: shared / dedicated hosting, replica set, sharding 24/7 support available 5 von 36
R Statistics with MongoDB MongoSoup in < 5 min go to cloudControl: www.cloudcontrol.com add an account and a billing address create a new app, e.g. “rmongodb” install cloudControl command line tools: cctrlapp enable your preferred MongoSoup hosting: cctrlapp rmongodb/default addon.add mongosoup.medium go to the cloudControl Web-Console-AddOns and get your credentials https://www.cloudcontrol.com/console/app/rmongodb 6 von 36
Processing: Analyzing with R and Hadoop R Statistics with MongoDB backward-looking analysis is outdated today: quasi real-time analysis tomorrow: forward-looking predictive analysis more complex methods, more data available, more processing time required Check my Strata London Tutorial “Big Data Analyses with R” 7 von 36
R Statistics with MongoDB Introduction to R R is a free software environment for statistical computing and graphics offers tools to manage and analyze data standard statistical methods are implemented compiles and runs under different OS support via huge community www.r-project.org 8 von 36
huge online-libraries with > 5000 R-packages: R Statistics with MongoDB http://cran.r-project.org possibility to write personalized code and to contribute new packages really famous since January 6, 2009: The New York Times, “Data Analysts Captivated by R's Power” 9 von 36
R Statistics with MongoDB RStudio IDE http://www.rstudio.com 10 von 36
R Statistics with MongoDB R as calculator (5+5) - 1 * 3 [1] 7 x <- 3 x [1] 3 x^2 + 4 [1] 13 11 von 36
R Statistics with MongoDB y <- c(1,2,3) y [1] 1 2 3 x <- 1:10 x [1] 1 2 3 4 5 6 7 8 9 10 x < 5 [1] TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE 12 von 36
R Statistics with MongoDB x[3:7] [1] 3 4 5 6 7 mean(x) [1] 5.5 help("mean") ?mean 13 von 36
R Statistics with MongoDB 14 von 36
Many Statistical Functions R Statistics with MongoDB kmeans(dat, 4) K-means clustering with 4 clusters of sizes 21, 18, 30, 31 Cluster means: [,1] [,2] 1 0.7755 0.8509 2 -0.1557 -0.2305 3 1.2299 1.1472 4 0.1510 0.1507 Clustering vector: [1] 4 2 4 4 2 4 4 2 2 4 4 4 2 4 2 4 4 [36] 4 4 4 4 4 4 4 3 1 3 3 3 1 1 3 3 3 [71] 1 3 1 1 3 3 3 1 3 1 3 3 3 3 1 3 3 4 2 4 3 3 3 2 4 2 1 1 4 2 4 3 1 4 2 2 1 3 4 4 2 3 3 2 2 4 4 1 4 2 4 4 2 2 1 1 1 1 3 1 1 1 3 3 3 3 Within cluster sum of squares by cluster: [1] 3.318 1.166 4.019 3.195 (between_SS / total_SS = 83.0 %) Available components: [1] "cluster" "centers" "totss" "withinss" [5] "tot.withinss" "betweenss" "size" 15 von 36
R Statistics with MongoDB plot(dat, col = cl$cluster, cex=2, pch=16) points(cl$centers, col = 1:4, pch = 13, cex = 4) 16 von 36
R Shiny - easy web application R Statistics with MongoDB developed by RStudio turns R analyses into interactive web applications that anyone can use let your users choose input parameters using friendly controls like sliders, drop-downs, and text fields easily incorporate any number of outputs like plots, tables, and summaries no HTML or JavaScript knowledge is necessary, only R http://www.rstudio.com/shiny/ 17 von 36
R Statistics with MongoDB R and Databases SQL provides a standard language to filter, aggregate, group, sort data SQL in new places: Hive, Impala, … ODBC provides SQL interface to non-database data (Excel, CSV, text files) R stores relational data in data.frames (extended lists) 18 von 36
R Statistics with MongoDB data(iris) head(iris, n=3) Sepal.Length Sepal.Width Petal.Length Petal.Width Species 1 5.1 3.5 1.4 0.2 setosa 2 4.9 3.0 1.4 0.2 setosa 3 4.7 3.2 1.3 0.2 setosa class(iris) [1] "data.frame" 19 von 36
R Statistics with MongoDB R package: sqldf running SQL statements on R data frames library(sqldf) sqldf("select * from iris limit 2") Sepal_Length Sepal_Width Petal_Length Petal_Width Species 1 5.1 3.5 1.4 0.2 setosa 2 4.9 3.0 1.4 0.2 setosa sqldf("select count(*) from iris") count(*) 1 150 20 von 36
Other relational R package R Statistics with MongoDB RMySQL package provides an interface to MySQL RPostgreSQL package provides an interface to PostgreSQL ROracle package provides an interface for Oracle RJDBC package provides access to databases through a JDBC interface RSQLite package provides access to SQLite (SQLite engine is included) One big problem: all packages read the full result in R memory 21 von 36
R Statistics with MongoDB R and MongoDB on CRAN there are two packages to connect R with MongoDB rmongodb supported by MongoDB, Inc. powerful for big data difficult to use due to BSON objects RMongo easy to use limited functionality reads full results in R memory does not work on MAC OS X 22 von 36
R Statistics with MongoDB R package: RMongo library(Rmongo) mongo <- mongoDbConnect("cc_JwQcDLJSYQJb", "dbs001.mongosoup.de", 27017) dbAuthenticate(mongo, username="JwQcDLJSYQJb", password="RSXPkUkXXXXX") dbShowCollections(mongo) dbGetQuery(mongo, "zips","{'state':'AL'}") dbInsertDocument(mongo, "test_data", '{"foo": "bar", "size": 5 }') dbDisconnect(mongo) 23 von 36
R Statistics with MongoDB R package: rmongodb developed on top of the MongoDB supported C driver library(rmongodb) mongo <mongo.create(host="dbs001.mongosoup.de", db="cc_JwQcDLJSYQJb", username="JwQcDLJSYQJb", password="RSXPkUkXXXXX") mongo [1] 0 attr(,"mongo") <pointer: 0x105a1de80> attr(,"class") [1] "mongo" attr(,"host") [1] "dbs001.mongosoup.de" attr(,"name") [1] "" attr(,"username") [1] "JwQcDLJSYQJb" attr(,"password") [1] "RSXPkUkxRdOX" attr(,"db") [1] "cc_JwQcDLJSYQJb" attr(,"timeout") [1] 0 24 von 36
R Statistics with MongoDB mongo.get.database.collections(mongo, "cc_JwQcDLJSYQJb") [1] "cc_JwQcDLJSYQJb.zips" "cc_JwQcDLJSYQJb.ccp" "cc_JwQcDLJSYQJb.test" mongo <- mongo.disconnect(mongo) 25 von 36
R Statistics with MongoDB buf <- mongo.bson.buffer.create() mongo.bson.buffer.append(buf, "state", "AL") [1] TRUE query <- mongo.bson.from.buffer(buf) query state : 2 26 von 36 AL
R Statistics with MongoDB res <- mongo.find.one(mongo, "cc_JwQcDLJSYQJb.zips", query) res city : 2 loc : 4 0 : 1 1 : 1 pop : 16 state : 2 _id : 2 27 von 36 ACMAR 6055 AL 35004 -86.515570 33.584132
R Statistics with MongoDB out <- mongo.bson.to.list(res) out$loc [1] -86.52 33.58 typeof(out$loc) [1] "double" out$pop [1] 6055 out$state [1] "AL" 28 von 36
R Statistics with MongoDB cursor <- mongo.find(mongo, "cc_JwQcDLJSYQJb.zips", query) res <- NULL while (mongo.cursor.next(cursor)){ value <- mongo.cursor.value(cursor) Rvalue <- mongo.bson.to.list(value) res <- rbind(res, Rvalue) } err <- mongo.cursor.destroy(cursor) head(res, n=4) city _id Rvalue "ACMAR" "35004" Rvalue "ADAMSVILLE" "35005" Rvalue "ADGER" "35006" Rvalue "KEYSTONE" "35007" 29 von 36 loc pop Numeric,2 6055 state "AL" Numeric,2 10616 "AL" Numeric,2 3205 "AL" Numeric,2 14218 "AL"
It is all about creating BSON query or field objects R Statistics with MongoDB b <- mongo.bson.from.list( list(name="Fred", age=29, city="Boston")) b name : 2 age : 1 city : 2 Fred 29.000000 Boston mongo.bson.to.list(b) $name [1] "Fred" $age [1] 29 $city [1] "Boston" 30 von 36
R Statistics with MongoDB ?mongo.bson ?mongo.bson.buffer.append ?mongo.bson.buffer.start.array ?mongo.bson.buffer.start.object buf <- mongo.bson.buffer.create() mongo.bson.buffer.append(buf, "aggregate", "zips") mongo.bson.buffer.start.array(buf, "pipeline") mongo.bson.buffer.start.object(buf, "$group") mongo.bson.buffer.append(buf, "_id", "$state") mongo.bson.buffer.start.object(buf, "totalPop") mongo.bson.buffer.append(buf, "$sum", "$pop") mongo.bson.buffer.finish.object(buf) mongo.bson.buffer.finish.object(buf) mongo.bson.buffer.start.object(buf, "$match") mongo.bson.buffer.start.object(buf, "totalPop") mongo.bson.buffer.append(buf, "$gte", "10000") mongo.bson.buffer.finish.object(buf) mongo.bson.buffer.finish.object(buf) mongo.bson.buffer.finish.object(buf) query <- mongo.bson.from.buffer(buf) 31 von 36
CCP Web Analytics Challenge R Statistics with MongoDB buf <- mongo.bson.buffer.create() query <- mongo.bson.from.buffer(buf) buf <- mongo.bson.buffer.create() err <- mongo.bson.buffer.append(buf, "user", 1) err <- mongo.bson.buffer.append(buf, "type", 1) field <- mongo.bson.from.buffer(buf) out <- mongo.find(mongo, "cc_JwQcDLJSYQJb.ccp", query, fields=field, limit=1000) res <- NULL while (mongo.cursor.next(out)){ value <- mongo.cursor.value(out) Rvalue <- mongo.bson.to.list(value) res <- rbind(res, Rvalue) } 32 von 36
R Statistics with MongoDB boxplot( as.integer(table(unlist(res[,2])) ), cex=4, horizontal=TRUE, main="Number of actions per user") 33 von 36
R Statistics with MongoDB Shiny Mongo R based MongoDB User Interface R packages shiny and rmongodb less than 200 lines of code DEMO: http://localhost:8100 https://github.com/comsysto/ShinyMongo 34 von 36
R Statistics with MongoDB Summary R is a powerful statistical tool to analyse many different kind of data R can access databases MongoDB and rmongodb ready for Big Data start playing around with R, Big Data and MongoDB http://www.r-project.org http://www.mongodb.org http://www.mongosoup.de  35 von 36
R Statistics with MongoDB See you soon thanks a lot for your attention there are R trainings in December 2013 in Munich http://comsysto.com/events.html#r we are hosting many events and meetups meet you at the MongoSoup booth Email: markus@mongosoup.de Twitter: @cloudHPC 36 von 36

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R Statistics With MongoDB

  • 1. R Statistics with MongoDB R Statistics with Mon‐ goDB Dr. Markus Schmidberger October 14th, 2013 Munich, Germany Email: markus@mongosoup.de Twitter: @cloudHPC 1 von 36
  • 2. Dr. Markus Schmidberger R Statistics with MongoDB 2 von 36
  • 3. R Statistics with MongoDB Outline Introduction to Big Data, MongoSoup and R R statistics with MongoDB and Examples Summary & Questions 3 von 36
  • 4. R Statistics with MongoDB Big Data Wikipedia: … a collection of data sets so large and complex that it becomes difficult to process using on-hand database management tools or traditional data processing. … storing processing 4 von 36
  • 5. Storing: NoSQL - MongoDB R Statistics with MongoDB databases using looser consistency models to store data German MongoDB as a Service: MongoSoup cloudControl Add-On currently running on AWS EU-Region (Ireland) all features available: shared / dedicated hosting, replica set, sharding 24/7 support available 5 von 36
  • 6. R Statistics with MongoDB MongoSoup in < 5 min go to cloudControl: www.cloudcontrol.com add an account and a billing address create a new app, e.g. “rmongodb” install cloudControl command line tools: cctrlapp enable your preferred MongoSoup hosting: cctrlapp rmongodb/default addon.add mongosoup.medium go to the cloudControl Web-Console-AddOns and get your credentials https://www.cloudcontrol.com/console/app/rmongodb 6 von 36
  • 7. Processing: Analyzing with R and Hadoop R Statistics with MongoDB backward-looking analysis is outdated today: quasi real-time analysis tomorrow: forward-looking predictive analysis more complex methods, more data available, more processing time required Check my Strata London Tutorial “Big Data Analyses with R” 7 von 36
  • 8. R Statistics with MongoDB Introduction to R R is a free software environment for statistical computing and graphics offers tools to manage and analyze data standard statistical methods are implemented compiles and runs under different OS support via huge community www.r-project.org 8 von 36
  • 9. huge online-libraries with > 5000 R-packages: R Statistics with MongoDB http://cran.r-project.org possibility to write personalized code and to contribute new packages really famous since January 6, 2009: The New York Times, “Data Analysts Captivated by R's Power” 9 von 36
  • 10. R Statistics with MongoDB RStudio IDE http://www.rstudio.com 10 von 36
  • 11. R Statistics with MongoDB R as calculator (5+5) - 1 * 3 [1] 7 x <- 3 x [1] 3 x^2 + 4 [1] 13 11 von 36
  • 12. R Statistics with MongoDB y <- c(1,2,3) y [1] 1 2 3 x <- 1:10 x [1] 1 2 3 4 5 6 7 8 9 10 x < 5 [1] TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE 12 von 36
  • 13. R Statistics with MongoDB x[3:7] [1] 3 4 5 6 7 mean(x) [1] 5.5 help("mean") ?mean 13 von 36
  • 14. R Statistics with MongoDB 14 von 36
  • 15. Many Statistical Functions R Statistics with MongoDB kmeans(dat, 4) K-means clustering with 4 clusters of sizes 21, 18, 30, 31 Cluster means: [,1] [,2] 1 0.7755 0.8509 2 -0.1557 -0.2305 3 1.2299 1.1472 4 0.1510 0.1507 Clustering vector: [1] 4 2 4 4 2 4 4 2 2 4 4 4 2 4 2 4 4 [36] 4 4 4 4 4 4 4 3 1 3 3 3 1 1 3 3 3 [71] 1 3 1 1 3 3 3 1 3 1 3 3 3 3 1 3 3 4 2 4 3 3 3 2 4 2 1 1 4 2 4 3 1 4 2 2 1 3 4 4 2 3 3 2 2 4 4 1 4 2 4 4 2 2 1 1 1 1 3 1 1 1 3 3 3 3 Within cluster sum of squares by cluster: [1] 3.318 1.166 4.019 3.195 (between_SS / total_SS = 83.0 %) Available components: [1] "cluster" "centers" "totss" "withinss" [5] "tot.withinss" "betweenss" "size" 15 von 36
  • 16. R Statistics with MongoDB plot(dat, col = cl$cluster, cex=2, pch=16) points(cl$centers, col = 1:4, pch = 13, cex = 4) 16 von 36
  • 17. R Shiny - easy web application R Statistics with MongoDB developed by RStudio turns R analyses into interactive web applications that anyone can use let your users choose input parameters using friendly controls like sliders, drop-downs, and text fields easily incorporate any number of outputs like plots, tables, and summaries no HTML or JavaScript knowledge is necessary, only R http://www.rstudio.com/shiny/ 17 von 36
  • 18. R Statistics with MongoDB R and Databases SQL provides a standard language to filter, aggregate, group, sort data SQL in new places: Hive, Impala, … ODBC provides SQL interface to non-database data (Excel, CSV, text files) R stores relational data in data.frames (extended lists) 18 von 36
  • 19. R Statistics with MongoDB data(iris) head(iris, n=3) Sepal.Length Sepal.Width Petal.Length Petal.Width Species 1 5.1 3.5 1.4 0.2 setosa 2 4.9 3.0 1.4 0.2 setosa 3 4.7 3.2 1.3 0.2 setosa class(iris) [1] "data.frame" 19 von 36
  • 20. R Statistics with MongoDB R package: sqldf running SQL statements on R data frames library(sqldf) sqldf("select * from iris limit 2") Sepal_Length Sepal_Width Petal_Length Petal_Width Species 1 5.1 3.5 1.4 0.2 setosa 2 4.9 3.0 1.4 0.2 setosa sqldf("select count(*) from iris") count(*) 1 150 20 von 36
  • 21. Other relational R package R Statistics with MongoDB RMySQL package provides an interface to MySQL RPostgreSQL package provides an interface to PostgreSQL ROracle package provides an interface for Oracle RJDBC package provides access to databases through a JDBC interface RSQLite package provides access to SQLite (SQLite engine is included) One big problem: all packages read the full result in R memory 21 von 36
  • 22. R Statistics with MongoDB R and MongoDB on CRAN there are two packages to connect R with MongoDB rmongodb supported by MongoDB, Inc. powerful for big data difficult to use due to BSON objects RMongo easy to use limited functionality reads full results in R memory does not work on MAC OS X 22 von 36
  • 23. R Statistics with MongoDB R package: RMongo library(Rmongo) mongo <- mongoDbConnect("cc_JwQcDLJSYQJb", "dbs001.mongosoup.de", 27017) dbAuthenticate(mongo, username="JwQcDLJSYQJb", password="RSXPkUkXXXXX") dbShowCollections(mongo) dbGetQuery(mongo, "zips","{'state':'AL'}") dbInsertDocument(mongo, "test_data", '{"foo": "bar", "size": 5 }') dbDisconnect(mongo) 23 von 36
  • 24. R Statistics with MongoDB R package: rmongodb developed on top of the MongoDB supported C driver library(rmongodb) mongo <mongo.create(host="dbs001.mongosoup.de", db="cc_JwQcDLJSYQJb", username="JwQcDLJSYQJb", password="RSXPkUkXXXXX") mongo [1] 0 attr(,"mongo") <pointer: 0x105a1de80> attr(,"class") [1] "mongo" attr(,"host") [1] "dbs001.mongosoup.de" attr(,"name") [1] "" attr(,"username") [1] "JwQcDLJSYQJb" attr(,"password") [1] "RSXPkUkxRdOX" attr(,"db") [1] "cc_JwQcDLJSYQJb" attr(,"timeout") [1] 0 24 von 36
  • 25. R Statistics with MongoDB mongo.get.database.collections(mongo, "cc_JwQcDLJSYQJb") [1] "cc_JwQcDLJSYQJb.zips" "cc_JwQcDLJSYQJb.ccp" "cc_JwQcDLJSYQJb.test" mongo <- mongo.disconnect(mongo) 25 von 36
  • 26. R Statistics with MongoDB buf <- mongo.bson.buffer.create() mongo.bson.buffer.append(buf, "state", "AL") [1] TRUE query <- mongo.bson.from.buffer(buf) query state : 2 26 von 36 AL
  • 27. R Statistics with MongoDB res <- mongo.find.one(mongo, "cc_JwQcDLJSYQJb.zips", query) res city : 2 loc : 4 0 : 1 1 : 1 pop : 16 state : 2 _id : 2 27 von 36 ACMAR 6055 AL 35004 -86.515570 33.584132
  • 28. R Statistics with MongoDB out <- mongo.bson.to.list(res) out$loc [1] -86.52 33.58 typeof(out$loc) [1] "double" out$pop [1] 6055 out$state [1] "AL" 28 von 36
  • 29. R Statistics with MongoDB cursor <- mongo.find(mongo, "cc_JwQcDLJSYQJb.zips", query) res <- NULL while (mongo.cursor.next(cursor)){ value <- mongo.cursor.value(cursor) Rvalue <- mongo.bson.to.list(value) res <- rbind(res, Rvalue) } err <- mongo.cursor.destroy(cursor) head(res, n=4) city _id Rvalue "ACMAR" "35004" Rvalue "ADAMSVILLE" "35005" Rvalue "ADGER" "35006" Rvalue "KEYSTONE" "35007" 29 von 36 loc pop Numeric,2 6055 state "AL" Numeric,2 10616 "AL" Numeric,2 3205 "AL" Numeric,2 14218 "AL"
  • 30. It is all about creating BSON query or field objects R Statistics with MongoDB b <- mongo.bson.from.list( list(name="Fred", age=29, city="Boston")) b name : 2 age : 1 city : 2 Fred 29.000000 Boston mongo.bson.to.list(b) $name [1] "Fred" $age [1] 29 $city [1] "Boston" 30 von 36
  • 31. R Statistics with MongoDB ?mongo.bson ?mongo.bson.buffer.append ?mongo.bson.buffer.start.array ?mongo.bson.buffer.start.object buf <- mongo.bson.buffer.create() mongo.bson.buffer.append(buf, "aggregate", "zips") mongo.bson.buffer.start.array(buf, "pipeline") mongo.bson.buffer.start.object(buf, "$group") mongo.bson.buffer.append(buf, "_id", "$state") mongo.bson.buffer.start.object(buf, "totalPop") mongo.bson.buffer.append(buf, "$sum", "$pop") mongo.bson.buffer.finish.object(buf) mongo.bson.buffer.finish.object(buf) mongo.bson.buffer.start.object(buf, "$match") mongo.bson.buffer.start.object(buf, "totalPop") mongo.bson.buffer.append(buf, "$gte", "10000") mongo.bson.buffer.finish.object(buf) mongo.bson.buffer.finish.object(buf) mongo.bson.buffer.finish.object(buf) query <- mongo.bson.from.buffer(buf) 31 von 36
  • 32. CCP Web Analytics Challenge R Statistics with MongoDB buf <- mongo.bson.buffer.create() query <- mongo.bson.from.buffer(buf) buf <- mongo.bson.buffer.create() err <- mongo.bson.buffer.append(buf, "user", 1) err <- mongo.bson.buffer.append(buf, "type", 1) field <- mongo.bson.from.buffer(buf) out <- mongo.find(mongo, "cc_JwQcDLJSYQJb.ccp", query, fields=field, limit=1000) res <- NULL while (mongo.cursor.next(out)){ value <- mongo.cursor.value(out) Rvalue <- mongo.bson.to.list(value) res <- rbind(res, Rvalue) } 32 von 36
  • 33. R Statistics with MongoDB boxplot( as.integer(table(unlist(res[,2])) ), cex=4, horizontal=TRUE, main="Number of actions per user") 33 von 36
  • 34. R Statistics with MongoDB Shiny Mongo R based MongoDB User Interface R packages shiny and rmongodb less than 200 lines of code DEMO: http://localhost:8100 https://github.com/comsysto/ShinyMongo 34 von 36
  • 35. R Statistics with MongoDB Summary R is a powerful statistical tool to analyse many different kind of data R can access databases MongoDB and rmongodb ready for Big Data start playing around with R, Big Data and MongoDB http://www.r-project.org http://www.mongodb.org http://www.mongosoup.de  35 von 36
  • 36. R Statistics with MongoDB See you soon thanks a lot for your attention there are R trainings in December 2013 in Munich http://comsysto.com/events.html#r we are hosting many events and meetups meet you at the MongoSoup booth Email: markus@mongosoup.de Twitter: @cloudHPC 36 von 36