R statistics with mongo db

R Statistics with MongoDB

R Statistics with Mon‐
goDB
Dr. Markus Schmidberger
October 14th, 2013 Munich, Germany
Email: markus@mongosoup.de
Twitter: @cloudHPC

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Dr. Markus Schmidberger


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Outline

Introduction to Big Data, MongoSoup and R
R statistics with MongoDB and Examples
Summary & Questions

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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

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Storing: NoSQL - 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

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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

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Processing: Analyzing with R and Hadoop

backward-looking analysis is outdated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”

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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

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huge online-libraries with > 5000 R-packages:


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”

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RStudio IDE

http://www.rstudio.com

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R as calculator

(5+5) - 1 * 3
[1] 7
x <- 3
x
[1] 3
x^2 + 4
[1] 13

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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

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x[3:7]

[1] 3 4 5 6 7
mean(x)
[1] 5.5
help("mean")
?mean

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Many Statistical Functions


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"

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plot(dat, col = cl$cluster, cex=2, pch=16)
points(cl$centers, col = 1:4, pch = 13, cex
= 4)

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R Shiny - easy web application


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/

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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)

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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"

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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

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Other relational R package


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

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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

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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)

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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

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mongo.get.database.collections(mongo,
"cc_JwQcDLJSYQJb")
[1] "cc_JwQcDLJSYQJb.zips"
"cc_JwQcDLJSYQJb.ccp" "cc_JwQcDLJSYQJb.test"
mongo <- mongo.disconnect(mongo)

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buf <- mongo.bson.buffer.create()
mongo.bson.buffer.append(buf, "state", "AL")
[1] TRUE
query <- mongo.bson.from.buffer(buf)
query
state : 2

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AL


res <- mongo.find.one(mongo,
"cc_JwQcDLJSYQJb.zips", query)
res
city : 2
loc : 4
0 : 1
1 : 1
pop : 16
state : 2
_id : 2

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ACMAR

6055
AL
35004

-86.515570
33.584132


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"

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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"

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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


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"

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?mongo.bson
?mongo.bson.buffer.append
?mongo.bson.buffer.start.array
?mongo.bson.buffer.start.object
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")
"totalPop")
mongo.bson.buffer.append(buf, "$sum",
"$pop")
mongo.bson.buffer.finish.object(buf)
mongo.bson.buffer.start.object(buf, "$match")
"totalPop")
mongo.bson.buffer.append(buf, "$gte",
"10000")

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CCP Web Analytics Challenge


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)
}

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boxplot( as.integer(table(unlist(res[,2]))
), cex=4, horizontal=TRUE, main="Number of
actions per user")

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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

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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

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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

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R statistics with mongo db

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