Chapter 16

Specialized Machine Learning Topics

This chapter presents some technical details about data formats, streaming, optimization
of computation, and distributed deployment of optimized learning algorithms.
Chapter 22 provides additional optimization details. We show format conversion and
working with XML, SQL, JSON, 15 CSV, SAS and other data objects. In addition, we
illustrate SQL server queries, describe protocols for managing, classifying and predicting
outcomes from data streams, and demonstrate strategies for optimization, improvement
of computational performance, parallel (MPI) and graphics (GPU) computing.
The Internet of Things (IoT) leads to a paradigm shift of scientific inference –
from static data interrogated in a batch or distributed environment to on-demand
service-based Cloud computing. Here, we will demonstrate how to work with
specialized data, data-streams, and SQL databases, as well as develop and assess
on-the-fly data modeling, classification, prediction and forecasting methods. Impor-
tant examples to keep in mind throughout this chapter include high-frequency data
delivered real time in hospital ICU’s (e.g., microsecond Electroencephalography
signals, EEGs), dynamically changing stock market data (e.g., Dow Jones Industrial
Average Index, DJI), and weather patterns.
We will present (1) format conversion of XML, SQL, JSON, CSV, SAS and other
data objects, (2) visualization of bioinformatics and network data, (3) protocols for
managing, classifying and predicting outcomes from data streams, (4) strategies for
optimization, improvement of computational performance, parallel (MPI) and
graphics (GPU) computing, and (5) processing of very large datasets.

16.1 Working with Specialized Data and Databases

Unlike the case studies we saw in the previous chapters, some real world data may
not always be nicely formatted, e.g., as CSV files. We must collect, arrange, wrangle,
and harmonize scattered information to generate computable data objects that can be
further processed by various techniques. Data wrangling and preprocessing may take

© Ivo D. Dinov 2018 513

I. D. Dinov, Data Science and Predictive Analytics,
https://doi.org/10.1007/978-3-319-72347-1_16
514 16 Specialized Machine Learning Topics

over 80% of the time researchers spend interrogating complex multi-source data
archives. The following procedures will enhance your skills in collecting and han-
dling heterogeneous real world data. Multiple examples of handling long-and-wide
data, messy and tidy data, and data cleaning strategies can be found in this JSS Tidy
Data article by Hadley Wickham.

16.1.1 Data Format Conversion

The R package rio imports and exports various types of file formats, e.g.,
tab-separated (.tsv), comma-separated (.csv), JSON (.json), Stata (.dta),
SPSS (.sav and .por), Microsoft Excel (.xls and .xlsx), Weka (.arff), and
SAS (.sas7bdat and .xpt).
rio provides three important functions import(), export() and convert().
They are intuitive, easy to understand, and efficient to execute. Take Stata (.dta) files
as an example. First, we can download 02_Nof1_Data.dta from our datasets folder.

# install.packages("rio")
library(rio)
# Download the SAS .DTA file first locally
# Local data can be loaded by:
#nof1<-import("02_Nof1_Data.dta")
# the data can also be loaded from the server remotely as well:
nof1<-read.csv("https://umich.instructure.com/files/330385/download?download
_frd=1")
str(nof1)

## 'data.frame': 900 obs. of 10 variables:

## $ ID : int 1 1 1 1 1 1 1 1 1 1 ...
## $ Day : int 1 2 3 4 5 6 7 8 9 10 ...
## $ Tx : int 1 1 0 0 1 1 0 0 1 1 ...
## $ SelfEff : int 33 33 33 33 33 33 33 33 33 33 ...
## $ SelfEff25: int 8 8 8 8 8 8 8 8 8 8 ...
## $ WPSS : num 0.97 -0.17 0.81 -0.41 0.59 -1.16 0.3 -0.34 -0.74 -0.38
...
## $ SocSuppt : num 5 3.87 4.84 3.62 4.62 2.87 4.33 3.69 3.29 3.66 ...
## $ PMss : num 4.03 4.03 4.03 4.03 4.03 4.03 4.03 4.03 4.03 4.03 ...
## $ PMss3 : num 1.03 1.03 1.03 1.03 1.03 1.03 1.03 1.03 1.03 1.03 ...
## $ PhyAct : int 53 73 23 36 21 0 21 0 73 114 ...

The data are automatically stored as a data frame. Note that rio sets
stingAsFactors¼FALSE as default.
rio can help us export files into any other format we choose. To do this we have
to use the export() function.

#Sys.getenv("R_ZIPCMD", "zip") # Get the C Zip application

Sys.setenv(R_ZIPCMD="E:/Tools/ZIP/bin/zip.exe")
Sys.getenv("R_ZIPCMD", "zip")
## [1] "E:/Tools/ZIP/bin/zip.exe"

export(nof1, "02_Nof1.xlsx")
16.1 Working with Specialized Data and Databases 515

This line of code exports the Nof1 data in xlsx format located in the R working
directory. Mac users may have a problem exporting *.xslx files using rio
because of a lack of a zip tool, but still can output other formats such as ".csv".
An alternative strategy to save an xlsx file is to use package xlsx with default
row.name¼TRUE.
rio also provides a one step process to convert and save data into alternative
formats. The following simple code allows us to convert and save the
02_Nof1_Data.dta file we just downloaded into a CSV file.

# convert("02_Nof1_Data.dta", "02_Nof1_Data.csv")
convert("02_Nof1.xlsx",
"02_Nof1_Data.csv")

You can see a new CSV file popup in the current working directory. Similar
transformations are available for other data formats and types.

16.1.2 Querying Data in SQL Databases

Let’s use as an example the CDC Behavioral Risk Factor Surveillance System
(BRFSS) Data, 2013-2015. This file for the combined landline and cell phone data
set was exported from SAS V9.3 in the XPT transport format. This file contains
330 variables and can be imported into SPSS or STATA. Please note: some of the
variable labels get truncated in the process of converting to the XPT format.
Be careful – this compressed (ZIP) file is over 315MB in size!

# install.packages("Hmisc")
library(Hmisc)
memory.size(max=T)

## [1] 115.81
pathToZip <- tempfile()
download.file("http://www.socr.umich.edu/data/DSPA/BRFSS_2013_2014_2015.zip"
, pathToZip)
# let's just pull two of the 3 years of data (2013 and 2015)
brfss_2013 <- sasxport.get(unzip(pathToZip)[1])

## Processing SAS dataset LLCP2013 ..

brfss_2015 <- sasxport.get(unzip(pathToZip)[3])

## Processing SAS dataset LLCP2015 ..

dim(brfss_2013); object.size(brfss_2013)

## [1] 491773 336

## 685581232 bytes
516 16 Specialized Machine Learning Topics

# summary(brfss_2013[1:1000, 1:10]) # subsample the data

# report the summaries for

summary(brfss_2013$has_plan)

## Length Class Mode

## 0 NULL NULL

brfss_2013$x.race <- as.factor(brfss_2013$x.race)

summary(brfss_2013$x.race)
## 1 2 3 4 5 6 7 8 9 NA's
## 376451 39151 7683 9510 1546 2693 9130 37054 8530 25

# clean up
unlink(pathToZip)

Let’s try to use logistic regression to find out if self-reported race/ethnicity

predicts the binary outcome of having a health care plan.

brfss_2013$has_plan <- brfss_2013$hlthpln1 == 1

system.time(
gml1 <- glm(has_plan ~ as.factor(x.race), data=brfss_2013,
family=binomial)
) # report execution time

## user system elapsed

## 2.20 0.23 2.46
summary(gml1)

##
## Call:
## glm(formula = has_plan ~ as.factor(x.race), family = binomial,
## data = brfss_2013)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.1862 0.4385 0.4385 0.4385 0.8047
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 2.293549 0.005649 406.044 <2e-16 ***
## as.factor(x.race)2 -0.721676 0.014536 -49.647 <2e-16 ***
## as.factor(x.race)3 -0.511776 0.032974 -15.520 <2e-16 ***
## as.factor(x.race)4 -0.329489 0.031726 -10.386 <2e-16 ***
## as.factor(x.race)5 -1.119329 0.060153 -18.608 <2e-16 ***
## as.factor(x.race)6 -0.544458 0.054535 -9.984 <2e-16 ***
## as.factor(x.race)7 -0.510452 0.030346 -16.821 <2e-16 ***
## as.factor(x.race)8 -1.332005 0.012915 -103.138 <2e-16 ***
## as.factor(x.race)9 -0.582204 0.030604 -19.024 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
16.1 Working with Specialized Data and Databases 517

## Null deviance: 353371 on 491747 degrees of freedom

## Residual deviance: 342497 on 491739 degrees of freedom
## (25 observations deleted due to missingness)
## AIC: 342515
##
## Number of Fisher Scoring iterations: 5

Next, we’ll examine the odds (rather the log odds ratio, LOR) of having a health
care plan (HCP) by race (R). The LORs are calculated for two array dimensions,
separately for each race level (presence of health care plan (HCP) is binary, whereas
race (R) has 9 levels, R1, R2, . . ., R9). For example, the odds ratio of having a HCP
for R1 : R2 is:
PðHCPjR1Þ
1 PðHCPjR1Þ
ORðR1 : R2Þ ¼ PðHCPjR2Þ
:
1 PðHCPjR2Þ

#load the vcd package to compute the LOR

library("vcd")

## Loading required package: grid

lor_HCP_by_R <- loddsratio(has_plan ~ as.factor(x.race), data = brfss_2013)
lor_HCP_by_R

## log odds ratios for has_plan and as.factor(x.race)

##
## 1:2 2:3 3:4 4:5 5:6 6:7
## -0.72167619 0.20990061 0.18228646 -0.78984000 0.57487142 0.03400611
## 7:8 8:9
## -0.82155382 0.74980101

Now, let’s see an example of querying a database containing structured relational

collection of data records. A query is a machine instruction (typically represented as
text) sent by a user to a remote database requesting a specific database operation
(e.g., search or summary). One database communication protocol relies on SQL
(Structured query language). MySQL is an instance of a database management
system that supports SQL communication and is utilized by many web applications,
e.g., YouTube, Flickr, Wikipedia, biological databases like GO, ensembl, etc. Below
is an example of an SQL query using the package RMySQL. An alternative way to
interface an SQL database is using the package RODBC.

# install.packages("DBI"); install.packages("RMySQL")
# install.packages("RODBC"); library(RODBC)
library(DBI)
library(RMySQL)

ucscGenomeConn <- dbConnect(MySQL(),

user='genome',
dbname='hg38',
host='genome-mysql.cse.ucsc.edu')
518 16 Specialized Machine Learning Topics

result <- dbGetQuery(ucscGenomeConn,"show databases;");

# List the DB tables

allTables <- dbListTables(ucscGenomeConn); length(allTables)

# Get dimensions of a table, read and report the head

dbListFields(ucscGenomeConn, "affyU133Plus2")
affyData <- dbReadTable(ucscGenomeConn, "affyU133Plus2"); head(affyData)

# Select a subset, fetch the data, and report the quantiles

subsetQuery <- dbSendQuery(ucscGenomeConn, "select * from affyU133Plus2
where misMatches between 1 and 3")
affySmall <- fetch(subsetQuery); quantile(affySmall$misMatches)

# Get repeat mask

bedFile <- 'repUCSC.bed'
df <- dbSendQuery(ucscGenomeConn,'select genoName,genoStart,genoEnd,
repName,swScore, strand,repClass, repFamily from rmsk') %>%
dbFetch(n=-1) %>%
mutate(genoName = str_replace(genoName,'chr','')) %>%
tbl_df %>%
write_tsv(bedFile,col_names=F)
message('written ', bedFile)

# Once done, close the connection

dbDisconnect(ucscGenomeConn)

To complete the above database SQL commands, it requires access to the remote
UCSC SQL Genome server and user-specific credentials. You can see this functional
example on the DSPA website. Below is another example that can be done by all
readers, as it relies only on local services.

# install.packages("RSQLite")
library("RSQLite")

# generate an empty DB and store it in RAM

myConnection <- dbConnect(RSQLite::SQLite(), ":memory:")
myConnection

## <SQLiteConnection>
## Path: :memory:
## Extensions: TRUE
dbListTables(myConnection)

## character(0)
# Add tables to the local SQL DB
data(USArrests); dbWriteTable(myConnection, "USArrests", USArrests)

## [1] TRUE

dbWriteTable(myConnection, "brfss_2013", brfss_2013)

## [1] TRUE

dbWriteTable(myConnection, "brfss_2015", brfss_2015)

## [1] TRUE
16.1 Working with Specialized Data and Databases 519

# Check again the DB content

dbListFields(myConnection, "brfss_2013")

## [1] "x.state" "fmonth" "idate" "imonth" "iday"

## [6] "iyear" "dispcode" "seqno" "x.psu" "ctelenum"
## [11] "pvtresd1" "colghous" "stateres" "cellfon3" "ladult"
## [16] "numadult" "nummen" "numwomen" "genhlth" "physhlth"
## [21] "menthlth" "poorhlth" "hlthpln1" "persdoc2" "medcost"
…
## [331] "rcsbrac1" "rcsrace1" "rchisla1" "rcsbirth" "typeinds"
## [336] "typework" "has_plan"

dbListTables(myConnection);

## [1] "USArrests" "brfss_2013" "brfss_2015"

# Retrieve the entire DB table (for the smaller USArrests table)

dbGetQuery(myConnection, "SELECT * FROM USArrests")

## Murder Assault UrbanPop Rape

## 1 13.2 236 58 21.2
## 2 10.0 263 48 44.5
## 3 8.1 294 80 31.0
## 4 8.8 190 50 19.5
## 5 9.0 276 91 40.6
## 6 7.9 204 78 38.7
## 7 3.3 110 77 11.1
## 8 5.9 238 72 15.8
## 9 15.4 335 80 31.9
## 10 17.4 211 60 25.8
## 11 5.3 46 83 20.2
## 12 2.6 120 54 14.2
## 13 10.4 249 83 24.0
## 14 7.2 113 65 21.0
## 15 2.2 56 57 11.3
## 16 6.0 115 66 18.0
## 17 9.7 109 52 16.3
## 18 15.4 249 66 22.2
## 19 2.1 83 51 7.8
## 20 11.3 300 67 27.8
## 21 4.4 149 85 16.3
## 22 12.1 255 74 35.1
## 23 2.7 72 66 14.9
## 24 16.1 259 44 17.1
## 25 9.0 178 70 28.2
## 26 6.0 109 53 16.4
## 27 4.3 102 62 16.5
## 28 12.2 252 81 46.0
## 29 2.1 57 56 9.5
## 30 7.4 159 89 18.8
## 31 11.4 285 70 32.1
## 32 11.1 254 86 26.1
## 33 13.0 337 45 16.1
## 34 0.8 45 44 7.3
## 35 7.3 120 75 21.4
## 36 6.6 151 68 20.0
## 37 4.9 159 67 29.3
## 38 6.3 106 72 14.9
520 16 Specialized Machine Learning Topics

## 39 3.4 174 87 8.3

## 40 14.4 279 48 22.5
## 41 3.8 86 45 12.8
## 42 13.2 188 59 26.9
## 43 12.7 201 80 25.5
## 44 3.2 120 80 22.9
## 45 2.2 48 32 11.2
## 46 8.5 156 63 20.7
## 47 4.0 145 73 26.2
## 48 5.7 81 39 9.3
## 49 2.6 53 66 10.8
## 50 6.8 161 60 15.6

# Retrieve just the average of one feature

myQuery <- dbGetQuery(myConnection, "SELECT avg(Assault) FROM USArrests"); m
yQuery

## avg(Assault)
## 1 170.76
myQuery <- dbGetQuery(myConnection, "SELECT avg(Assault) FROM USArrests GROU
P BY UrbanPop"); myQuery
## avg(Assault)
## 1 48.00
## 2 81.00
## 3 152.00
## 4 211.50
## 5 271.00
## 6 190.00
## 7 83.00
## 8 109.00
## 9 109.00
## 10 120.00
## 11 57.00
## 12 56.00
## 13 236.00
## 14 188.00
## 15 186.00
## 16 102.00
## 17 156.00
## 18 113.00
## 19 122.25
## 20 229.50
## 21 151.00
## 22 231.50
## 23 172.00
## 24 145.00
## 25 255.00
## 26 120.00
## 27 110.00
## 28 204.00
## 29 237.50
## 30 252.00
## 31 147.50
## 32 149.00
## 33 254.00
## 34 174.00
## 35 159.00
## 36 276.00
16.1 Working with Specialized Data and Databases 521

# Or do it in batches (for the much larger brfss_2013 and brfss_2015 tables)

myQuery <- dbGetQuery(myConnection, "SELECT * FROM brfss_2013")

# extract data in chunks of 2 rows, note: dbGetQuery vs. dbSendQuery

# myQuery <- dbSendQuery(myConnection, "SELECT * FROM brfss_2013")
# fetch2 <- dbFetch(myQuery, n = 2); fetch2
# do we have other cases in the DB remaining?
# extract all remaining data
# fetchRemaining <- dbFetch(myQuery, n = -1);fetchRemaining
# We should have all data in DB now
# dbHasCompleted(myQuery)
# compute the average (poorhlth) grouping by Insurance (hlthpln1)
# Try some alternatives: numadult nummen numwomen genhlth physhlth menthlth
poorhlth hlthpln1
myQuery1_13 <- dbGetQuery(myConnection, "SELECT avg(poorhlth) FROM brfss_201
3 GROUP BY hlthpln1"); myQuery1_13

## avg(poorhlth)
## 1 56.25466
## 2 53.99962
## 3 58.85072
## 4 66.26757

# Compare 2013 vs. 2015: Health grouping by Insurance

myQuery1_15 <- dbGetQuery(myConnection, "SELECT avg(poorhlth) FROM brfss_201
5 GROUP BY hlthpln1"); myQuery1_15
## avg(poorhlth)
## 1 55.75539
## 2 55.49487
## 3 61.35445
## 4 67.62125

myQuery1_13 - myQuery1_15

## avg(poorhlth)
## 1 0.4992652
## 2 -1.4952515
## 3 -2.5037326
## 4 -1.3536797
# reset the DB query
# dbClearResult(myQuery)

# clean up
dbDisconnect(myConnection)

## [1] TRUE

16.1.3 Real Random Number Generation

We are already familiar with (pseudo) random number generation (e.g., rnorm
(100, 10, 4) or runif(100, 10,20)), which generate algorithmically
computer values subject to specified distributions. There are also web services,
e.g., random.org, that can provide true random numbers based on atmospheric
522 16 Specialized Machine Learning Topics

noise, rather than using a pseudo random number generation protocol. Below is one
example of generating a total of 300 numbers arranged in 3 columns, each of
100 rows of random integers (in decimal format) between 100 and 200.

#https://www.random.org/integers/?num=300&min=100&max=200&col=3&base=10&
format=plain&rnd=new
siteURL <- "http://random.org/integers/" # base URL
shortQuery<-"num=300&min=100&max=200&col=3&base=10&format=plain&rnd=new"
completeQuery <- paste(siteURL, shortQuery, sep="?") # concat url and
submit query string
rngNumbers <- read.table(file=completeQuery) # and read the data
rngNumbers

## V1 V2 V3
## 1 144 179 131
## 2 127 160 150
## 3 142 169 109
…
## 98 178 103 134
## 99 173 178 156
## 100 117 118 110

16.1.4 Downloading the Complete Text of Web Pages

RCurl package provides an amazing tool for extracting and scraping information
from websites. Let’s install it and extract information from a SOCR website.

# install.packages("RCurl")
library(RCurl)

## Loading required package: bitops

web<-getURL("http://wiki.socr.umich.edu/index.php/SOCR_Data", followlocation
= TRUE)
str(web, nchar.max = 200)

## chr "<!DOCTYPE html>\n<html lang=\"en\" dir=\"ltr\" class=\"client-nojs\

">\n<head>\n<meta charset=\"UTF-8\" />\n<title>SOCR Data - SOCR</title>\n<me
ta http-equiv=\"X-UA-Compatible\" content=\"IE=EDGE\" />"| __truncated__

The web object looks incomprehensible. This is because most websites are
wrapped in XML/HTML hypertext or include JSON formatted metadata. RCurl
deals with special HTML tags and website metadata.
To deal with the web pages only, httr package would be a better choice than
RCurl. It returns a list that makes much more sense.

#install.packages("httr")
library(httr)
web<-GET("http://wiki.socr.umich.edu/index.php/SOCR_Data")
str(web[1:3])
## List of 3
## $ url : chr "http://wiki.socr.umich.edu/index.php/SOCR_Data"
## $ status_code: int 200
16.1 Working with Specialized Data and Databases 523

## $ headers :List of 12
## ..$ date : chr "Mon, 03 Jul 2017 19:09:56 GMT"
## ..$ server : chr "Apache/2.2.15 (Red Hat)"
## ..$ x-powered-by : chr "PHP/5.3.3"
## ..$ x-content-type-options: chr "nosniff"
## ..$ content-language : chr "en"
## ..$ vary : chr "Accept-Encoding,Cookie"
## ..$ expires : chr "Thu, 01 Jan 1970 00:00:00 GMT"
## ..$ cache-control : chr "private, must-revalidate, max-age=0"
## ..$ last-modified : chr "Sat, 22 Oct 2016 21:46:21 GMT"
## ..$ connection : chr "close"
## ..$ transfer-encoding : chr "chunked"
## ..$ content-type : chr "text/html; charset=UTF-8"
## ..- attr(*, "class")= chr [1:2] "insensitive" "list"

16.1.5 Reading and Writing XML with the XML Package

A combination of the RCurl and the XML packages could help us extract only the
plain text in our desired webpages. This would be very helpful to get information
from heavy text-based websites.

web<-getURL("http://wiki.socr.umich.edu/index.php/SOCR_Data", followlocation
= TRUE)
#install.packages("XML")
library(XML)
web.parsed<-htmlParse(web, asText = T)
plain.text<-xpathSApply(web.parsed, "//p", xmlValue)
cat(paste(plain.text, collapse = "\n"))
## The links below contain a number of datasets that may be used for demonst
ration purposes in probability and statistics education. There are two types
of data - simulated (computer-generated using random sampling) and observed
(research, observationally or experimentally acquired).
##
## The SOCR resources provide a number of mechanisms to simulate data using
computer random-number generators. Here are some of the most commonly used S
OCR generators of simulated data:
##
## The following collections include a number of real observed datasets from
different disciplines, acquired using different techniques and applicable in
different situations.
##
## In addition to human interactions with the SOCR Data, we provide several
machine interfaces to consume and process these data.
##
## Translate this page:
##
## (default)
##
## Deutsch
…
## România
##
## Sverige
524 16 Specialized Machine Learning Topics

Here we extracted all plain text between the starting and ending paragraph
HTML tags, <p> and </p>.
More information about extracting text from XML/HTML to text via XPath is
available online.

16.1.6 Web-Page Data Scraping

The process that extracting data from complete web pages and storing it in structured
data format is called scraping. However, before starting a data scrape from a
website, we need to understand the underlying HTML structure for that specific
website. Also, we have to check the terms of that website to make sure that scraping
from this site is allowed.
The R package rvest is a very good place to start “harvesting” data from
websites.
To start with, we use read_html() to store the SOCR data website into a
xmlnode object.

library(rvest)
SOCR<-read_html("http://wiki.socr.umich.edu/index.php/SOCR_Data")
SOCR

## {xml_document}
## <html lang="en" dir="ltr" class="client-nojs">
## [1] <head>\n<meta http-equiv="Content-Type" content="text/html; charset=
...
## [2] <body class="mediawiki ltr sitedir-ltr ns-0 ns-subject page-SOCR_Dat
...

From the summary structure of SOCR, we can discover that there are two important
hypertext section markups <head> and <body>. Also, notice that the SOCR data
website uses <title> and </title> tags to separate title in the <head> section.
Let’s use html_node() to extract title information based on this knowledge.

SOCR %>% html_node("head title") %>% html_text()

## [1] "SOCR Data - SOCR"

Here we used %>% operator, or pipe, to connect two functions. The above line of
code creates a chain of functions to operate on the SOCR object. The first function in
the chain html_node() extracts the title from head section. Then,
html_text() translates HTML formatted hypertext into English. More on R
piping can be found in the magrittr package.
Another function, rvest::html_nodes() can be very helpful in scraping.
Similar to html_node(), html_nodes() can help us extract multiple nodes in
an xmlnode object. Assume that we want to obtain the meta elements (usually page
16.1 Working with Specialized Data and Databases 525

description, keywords, author of the document, last modified, and other metadata)
from the SOCR data website. We apply html_nodes() to the SOCR object to
extract the hypertext data, e.g., lines starting with <meta> in the <head> section of
the HTML page source. It is optional to use html_attrs(), which extracts
attributes, text and tag names from HTML, obtain the main text attributes.

meta<-SOCR %>% html_nodes("head meta") %>% html_attrs()

meta

## [[1]]
## http-equiv content
## "Content-Type" "text/html; charset=UTF-8"
##
## [[2]]
## charset
## "UTF-8"
##
## [[3]]
## http-equiv content
## "X-UA-Compatible" "IE=EDGE"
##
## [[4]]
## name content
## "generator" "MediaWiki 1.23.1"
##
## [[5]]
## name content
## "ResourceLoaderDynamicStyles" ""

16.1.7 Parsing JSON from Web APIs

Application Programming Interfaces (APIs) allow web-accessible functions to com-

municate with each other. Today most API is stored in JSON (JavaScript Object
Notation) format.
JSON represents a plain text format used for web applications, data structures or
objects. Online JSON objects could be retrieved by packages like RCurl and httr.
Let’s see a JSON formatted dataset first. We can use 02_Nof1_Data.json in the class
file as an example.

library(httr)
nof1<-GET("https://umich.instructure.com/files/1760327/download?download_frd
=1")
nof1

## Response [https://instructure-uploads.s3.amazonaws.com/account_1770000000
0000001/attachments/1760327/02_Nof1_Data.json?response-content-disposition=a
ttachment%3B%20filename%3D%2202_Nof1_Data.json%22%3B%20filename%2A%3DUTF-8%2
7%2702%255FNof1%255FData.json&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credent
ial=AKIAJFNFXH2V2O7RPCAA%2F20170703%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Da
te=20170703T190959Z&X-Amz-Expires=86400&X-Amz-SignedHeaders=host&X-Amz-Signa
ture=ceb3be3e71d9c370239bab558fcb0191bc829b98a7ba61ac86e27a2fc3c1e8ce]
526 16 Specialized Machine Learning Topics

## Date: 2017-07-03 19:10

## Status: 200
## Content-Type: application/json
## Size: 109 kB
## [{"ID":1,"Day":1,"Tx":1,"SelfEff":33,"SelfEff25":8,"WPSS"...
## {"ID":1,"Day":2,"Tx":1,"SelfEff":33,"SelfEff25":8,"WPSS"...
## {"ID":1,"Day":3,"Tx":0,"SelfEff":33,"SelfEff25":8,"WPSS"...
## {"ID":1,"Day":4,"Tx":0,"SelfEff":33,"SelfEff25":8,"WPSS"...
## {"ID":1,"Day":5,"Tx":1,"SelfEff":33,"SelfEff25":8,"WPSS"...
## {"ID":1,"Day":6,"Tx":1,"SelfEff":33,"SelfEff25":8,"WPSS"...
## {"ID":1,"Day":7,"Tx":0,"SelfEff":33,"SelfEff25":8,"WPSS"...
## {"ID":1,"Day":8,"Tx":0,"SelfEff":33,"SelfEff25":8,"WPSS"...
## {"ID":1,"Day":9,"Tx":1,"SelfEff":33,"SelfEff25":8,"WPSS"...
## {"ID":1,"Day":10,"Tx":1,"SelfEff":33,"SelfEff25":8,"WPSS"...
## ...

We can see that JSON objects are very simple. The data structure is organized
using hierarchies marked by square brackets. Each piece of information is formatted
as a {key:value} pair.
The package jsonlite is a very useful tool to import online JSON formatted
datasets into data frame directly. Its syntax is very straight-forward.

#install.packages("jsonlite")
library(jsonlite)
nof1_lite<-
fromJSON("https://umich.instructure.com/files/1760327/download?download_frd=1")
class(nof1_lite)
## [1] "data.frame"

16.1.8 Reading and Writing Microsoft Excel Spreadsheets

Using XLSX

We can transfer a xlsx dataset into CSV and use read.csv() to load this kind of
dataset. However, R provides an alternative read.xlsx() function in package
xlsx to simplify this process. Take our 02_Nof1_Data.xls data in the class file
as an example. We need to download the file first.

# install.packages("xlsx")
library(xlsx)

nof1<-read.xlsx("C:/Users/Folder/02_Nof1.xlsx", 1)
str(nof1)
## 'data.frame': 900 obs. of 10 variables:
## $ ID : num 1 1 1 1 1 1 1 1 1 1 ...
## $ Day : num 1 2 3 4 5 6 7 8 9 10 ...
## $ Tx : num 1 1 0 0 1 1 0 0 1 1 ...
16.2 Working with Domain-Specific Data 527

## $ SelfEff : num 33 33 33 33 33 33 33 33 33 33 ...

## $ SelfEff25: num 8 8 8 8 8 8 8 8 8 8 ...
## $ WPSS : num 0.97 -0.17 0.81 -0.41 0.59 -1.16 0.3 -0.34 -0.74 -0.38
...
## $ SocSuppt : num 5 3.87 4.84 3.62 4.62 2.87 4.33 3.69 3.29 3.66 ...
## $ PMss : num 4.03 4.03 4.03 4.03 4.03 4.03 4.03 4.03 4.03 4.03 ...
## $ PMss3 : num 1.03 1.03 1.03 1.03 1.03 1.03 1.03 1.03 1.03 1.03 ...
## $ PhyAct : num 53 73 23 36 21 0 21 0 73 114 ...

The last argument, 1, stands for the first excel sheet, as any excel file may include
a large number of tables in it. Also, we can download the xls or xlsx file into our
R working directory so that it is easier to find the file path.
Sometimes more complex protocols may be necessary to ingest data from XLSX
documents. For instance, if the XLSX doc is large, includes many tables and is only
accessible via HTTP protocol from a web-server. Below is an example of
downloading the second table, ABIDE_Aggregated_Data, from the multi-
table Autism/ABIDE XLSX dataset:

# install.packages("openxlsx"); library(openxlsx)
tmp = tempfile(fileext = ".xlsx")
download.file(url = "https://umich.instructure.com/files/3225493/download?do
wnload_frd=1",
destfile = tmp, mode="wb") df_Autism <- openxlsx::read.xlsx(xlsxFile = tmp,
sheet = "ABIDE_Aggregated_Data", skipEmptyRows = TRUE)
dim(df_Autism)

## [1] 1098 2145

16.2 Working with Domain-Specific Data

Powerful machine-learning methods have already been applied in many applica-

tions. Some of these techniques are very specialized and some applications require
unique approaches to address the corresponding challenges.

16.2.1 Working with Bioinformatics Data

Genetic data are stored in widely varying formats and usually have more feature
variables than observations. They could have 1,000 columns and only 200 rows. One
of the commonly used pre-processng steps for such datasets is variable selection. We
will talk about this in Chap. 17.
The Bioconductor project created powerful R functionality (packages and tools)
for analyzing genomic data, see Bioconductor for more detailed information.
528 16 Specialized Machine Learning Topics

16.2.2 Visualizing Network Data

Social network data and graph datasets describe the relations between nodes (verti-
ces) using connections (links or edges) joining the node objects. Assume we have
N objects, we can have N ∗ (N 1) directed links establishing paired associations
between the nodes. Let’s use an example with N¼4 to demonstrate a simple graph
potentially modeling the node linkage Table 16.1.
If we change the a ! b to an indicator variable (0 or 1) capturing whether we
have an edge connecting a pair of nodes, then we get the graph adjacency matrix.
Edge lists provide an alternative way to represent network connections. Every
line in the list contains a connection between two nodes (objects) (Table 16.2).
The edge list on Table 16.2 lists three network connections: object 1 is linked to
object 2; object 1 is linked to object 3; and object 2 is linked to object 3. Note that
edge lists can represent both directed as well as undirected networks or graphs.
We can imagine that if N is very large, e.g., social networks, the data represen-
tation and analysis may be resource intense (memory or computation). In R, we have
multiple packages that can deal with social network data. One user-friendly example
is provided using the igraph package. First, let’s build a toy example and visualize
it using this package (Fig. 16.1).

#install.packages("igraph")
library(igraph)

g<-graph(c(1, 2, 1, 3, 2, 3, 3, 4), n=10)

plot(g)

Here c(1, 2, 1, 3, 2, 3, 3, 4) is an edge list with 4 rows and n¼10

indicates that we have 10 nodes (objects) in total. The small arrows in the graph
show the directed network connections. We might notice that 5-10 nodes are
scattered out in the graph. This is because they are not included in the edge list, so
there are no network connections between them and the rest of the network.

Table 16.1 Schematic matrix Objects 1 2 3 4

representation of network
1 ..... 1!2 1!3 1!4
connectivity
2 2!1 ..... 2!3 2!4
3 3!1 3!2 ..... 3!4
4 4!1 4!2 4!3 .....

Table 16.2 List-based Vertex Vertex

representation of network
1 2
connectivity
1 3
2 3
16.2 Working with Domain-Specific Data 529

Fig. 16.1 A simple 8

example of a social network
as a graph object
9
6

4 7

3
2

10
1

Now let’s examine the co-appearance network of Facebook circles. The data
contains anonymized circles (friends lists) from Facebook collected from survey
participants using a Facebook app. The dataset only includes edges (circles, 88,234)
connecting pairs of nodes (users, 4,039) in the member social networks.
The values on the connections represent the number of links/edges within a circle.
We have a huge edge-list made of scrambled Facebook user IDs. Let’s load this
dataset into R first. The data is stored in a text file. Unlike CSV files, text files in table
format need to be imported using read.table(). We are using the header¼F
option to let R know that we don’t have a header in the text file that contains only
tab-separated node pairs (indicating the social connections, edges, between
Facebook users).

soc.net.data<-read.table("https://umich.instructure.com/files/2854431/downlo
ad?download_frd=1", sep=" ", header=F)
head(soc.net.data)

## V1 V2
## 1 0 1
## 2 0 2
## 3 0 3
## 4 0 4
## 5 0 5
## 6 0 6

Now the data is stored in a data frame. To make this dataset ready for igraph
processing and visualization, we need to convert soc.net.data into a matrix
object.

soc.net.data.mat <- as.matrix(soc.net.data, ncol=2)

530 16 Specialized Machine Learning Topics

By using ncol¼2, we made a matrix with two columns. The data is now ready
and we can apply graph.edgelist().

# remove the first 347 edges (to wipe out the degenerate "0" node)
graph_m<-graph.edgelist(soc.net.data.mat[-c(0:347), ], directed = F)

Before we display the social network graph we may want to examine our model
first.

summary(graph_m)

## IGRAPH U--- 4038 87887 --

This is an extremely brief yet informative summary. The first line U--- 4038
87887 includes potentially four letters and two numbers. The first letter could be U
or D indicating undirected or directed edges. A second letter N would mean that the
objects set has a “name” attribute. A third letter is for weighted (W) graph. Since we
didn’t add weight in our analysis the third letter is empty (“-“). A fourth character is
an indicator for bipartite graphs, whose vertices can be divided into two disjoint
sets where each vertex from one set connects to one vertex in the other set. The
two numbers following the 4 letters represent the number of nodes and the
number of edges, respectively. Now let’s render the graph (Fig. 16.2).

plot(graph_m)

This graph is very complicated. We can still see that some words are surrounded
by more nodes than others. To obtain such information we can use the degree()
function, which lists the number of edges for each node.

degree(graph_m)

Skimming the table we can find that the 107-th user has as many as 1,044
connections, which makes the user a highly-connected hub. Likely, this node may
have higher social relevance.
Some edges might be more important than other edges because they serve as a
bridge to link a cloud of nodes. To compare their importance, we can use the
betweenness centrality measurement. Betweenness centrality measures centrality in
a network. High centrality for a specific node indicates influence. betweenness
() can help us to calculate this measurement.

betweenness(graph_m)

Again, the 107-th node has the highest betweenness centrality

(3.556221e + 06).
16.2 Working with Domain-Specific Data 531

Fig. 16.2 Social network connectivity of Facebook users

http://socr.umich.edu/html/Navigators.html
http://socr.ucla.edu/SOCR_HyperTree.json

Fig. 16.3 Live demo: a dynamic graph representation of the SOCR resources

We can try another example using SOCR hierarchical data, which is also avail-
able for dynamic exploration as a tree graph. Let’s read its JSON data source using
the jsonlite package (Fig. 16.3).
532 16 Specialized Machine Learning Topics

tree.json<-fromJSON("http://socr.ucla.edu/SOCR_HyperTree.json",
simplifyDataFrame = FALSE)

This generates a list object representing the hierarchical structure of the

network. Note that this is quite different from an edge list. There is one root node,
its sub nodes are called children nodes, and the terminal nodes are call leaf nodes.
Instead of presenting the relationship between nodes in pairs, this hierarchical
structure captures the level for each node. To draw the social network graph, we
need to convert it as a Node object. We can utilize the as.Node() function in the
data.tree package to do so.

# install.packages("data.tree")
library(data.tree)
tree.graph<-as.Node(tree.json, mode = "explicit")

Here we use mode¼"explicit" option to allow “children” nodes to have

their own “children” nodes. Now, the tree.json object has been separated into
four different node structures – "About SOCR", "SOCR Resources", "Get
Started", and "SOCR Wiki". Let’s plot the first one using igraph package
(Fig. 16.4).

Fig. 16.4 The SOCR resourceome network plotted as a static R graph

16.3 Data Streaming 533

plot(as.igraph(tree.graph$`About SOCR`), edge.arrow.size=5, edge.label.font=

0.05)

In this graph, "About SOCR", which is located at the center, represents the root
node of the tree graph.

16.3 Data Streaming

The proliferation of Cloud services and the emergence of modern technology in all
aspects of human experiences leads to a tsunami of data much of which is streamed
real-time. The interrogation of such voluminous data is an increasingly important
area of research. Data streams are ordered, often unbounded sequences of data
points created continuously by a data generator. All of the data mining, interrogation
and forecasting methods we discuss here are also applicable to data streams.

16.3.1 Definition

Mathematically, a data stream in an ordered sequence of data points

Y ¼ fy1 ; y2 ; y3 ;


; yt ;


g,

where the (time) index, t, reflects the order of the observation/record, which may be
single numbers, simple vectors in multidimensional space, or objects, e.g., structured
Ann Arbor Weather (JSON) and its corresponding structured form. Some streaming
data is streamed because it’s too large to be downloaded shotgun style and some is
streamed because it’s continually generated and serviced. This presents the potential
problem of dealing with data streams that may be unlimited.
Notes:
• Data sources: Real or synthetic stream data can be used. Random simulation
streams may be created by rstream. Real stream data may be piped from
financial data providers, the WHO, World Bank, NCAR and other sources.
• Inference Techniques: Many of the data interrogation techniques we have seen
can be employed for dynamic stream data, e.g., factas, for PCA, rEMM and
birch for clustering, etc. Clustering and classification methods capable of
processing data streams have been developed, e.g., Very Fast Decision Trees
(VFDT), time window-based Online Information Network (OLIN), On-demand
Classification, and the APRIORI streaming algorithm.
• Cloud distributed computing: Hadoop2/HadoopStreaming, SPARK, Storm3/
RStorm provide an environments to expand batch/script-based R tools to the
Cloud.
534 16 Specialized Machine Learning Topics

16.3.2 The stream Package

The R stream package provides data stream mining algorithms using fpc, clue,
cluster, clusterGeneration, MASS, and proxy packages. In addition, the
package streamMOA provides an rJava interface to the Java-based data stream
clustering algorithms available in the Massive Online Analysis (MOA) framework
for stream classification, regression and clustering.
If you need a deeper exposure to data streaming in R, we recommend you go over
the stream vignettes.

16.3.3 Synthetic Example: Random Gaussian Stream

This example shows the creation and loading of a mixture of 5 random 2D Gauss-
ians, centers at (x_coords, y_coords) with paired correlations rho_corr, representing
a simulated data stream.
Generate the stream:

# install.packages("stream")
library("stream")

x_coords <- c(0.2,0.3, 0.5, 0.8, 0.9)

y_coords <- c(0.8,0.3, 0.7, 0.1, 0.5)
p_weight <- c(0.1, 0.9, 0.5, 0.4, 0.3) # A vector of probabilities that dete
rmines the likelihood of generated a data point from a particular
cluster set.seed(12345)
stream_5G <- DSD_Gaussians(k = 5, d = 2, mu=cbind(x_coords, y_coords),
p=p_weight)

k-Means Clustering

We will now try k-means and density-based data stream clustering algorithm,
D-Stream, where micro-clusters are formed by grid cells of size gridsize with density
of a grid cell (Cm) is least 1.2 times the average cell density. The model is updated
with the next 500 data points from the stream.

dstream <- DSC_DStream(gridsize = .1, Cm = 1.2)

update(dstream, stream_5G, n = 500)

First, let’s run the k-means clustering with k ¼ 5 clusters and plot the resulting
micro- and macro-clusters (Fig. 16.5).
16.3 Data Streaming 535

Fig. 16.5 Micro and macro clusters of a 5-means clustering of the first 500 points of the streamed
simulated 2D Gaussian kernels

kmc <- DSC_Kmeans(k = 5)

recluster(kmc, dstream)
plot(kmc, stream_5G, type = "both", xlab="X-axis", ylab="Y-axis")

In this clustering plot, micro-clusters are shown as circles and macro-clusters are
shown as crosses and their sizes represent the corresponding cluster weight
estimates.
Next try the density-based data stream clustering algorithm D-Stream. Prior to
updating the model with the next 1,000 data points from the stream, we specify the
grid cells as micro-clusters, grid cell size (gridsize¼0.1), and a micro-cluster
(Cm¼1.2) that specifies the density of a grid cell as a multiple of the average cell
density.

dstream <- DSC_DStream(gridsize = 0.1, Cm = 1.2)

update(dstream, stream_5G, n=1000)

We can re-cluster the data using k-means with 5 clusters and plot the resulting
micro- and macro-clusters (Fig. 16.6).

km_G5 <- DSC_Kmeans(k = 5)

recluster(km_G5, dstream)
plot(km_G5, stream_5G, type = "both")

Note the subtle changes in the clustering results between kmc and km_G5.
536 16 Specialized Machine Learning Topics

Fig. 16.6 Micro- and macro- clusters of a 5-means clustering of the next 1,000 points of the
streamed simulated 2D Gaussian kernels

16.3.4 Sources of Data Streams

Static Structure Streams

• DSD_BarsAndGaussians generates two uniformly filled rectangular and two

Gaussian clusters with different density.
• DSD_Gaussians generates randomly placed static clusters with random multi-
variate Gaussian distributions.
• DSD_mlbenchData provides streaming access to machine learning benchmark
data sets found in the mlbench package.
• DSD_mlbenchGenerator interfaces the generators for artificial data sets defined
in the mlbench package.
• DSD_Target generates a ball in circle data set.
• DSD_UniformNoise generates uniform noise in a d-dimensional (hyper) cube.

Concept Drift Streams

• DSD_Benchmark provides a collection of simple benchmark problems including

splitting and joining clusters, and changes in density or size, which can be used as
a comprehensive benchmark set for algorithm comparison.
• DSD_MG is a generator to specify complex data streams with concept drift. The
shape as well as the behavior of each cluster over time can be specified using
keyframes.
• DSD_RandomRBFGeneratorEvents generates streams using radial base func-
tions with noise. Clusters move, merge and split.
16.3 Data Streaming 537

Real Data Streams

• DSD_Memory provides a streaming interface to static, matrix-like data (e.g., a

data frame, a matrix) in memory which represents a fixed portion of a data stream.
Matrix-like objects also include large objects potentially stored on disk like ff::
ffdf.
• DSD_ReadCSV reads data line by line in text format from a file or an open
connection and makes it available in a streaming fashion. This way data that is
larger than the available main memory can be processed.
• DSD_ReadDB provides an interface to an open result set from a SQL query to a
relational database.

16.3.5 Printing, Plotting and Saving Streams

For DSD objects, some basic stream functions include print(), plot(), and
write_stream(). These can save part of a data stream to disk. DSD_Memory
and DSD_ReadCSV objects also include member functions like reset_stream()
to reset the position in the stream to its beginning.
To request a new batch of data points from the stream we use get_points().
This chooses a random cluster (based on the probability weights in p_weight) and
a point is drawn from the multivariate Gaussian distribution (mean ¼ mu, covariance
matrix ¼ Σ) of that cluster. Below, we pull n ¼ 10 new data points from the stream
(Fig. 16.7).

Fig. 16.7 Scatterplot of the next batch of 700 random Gaussian points in 2D
538 16 Specialized Machine Learning Topics

new_p <- get_points(stream_5G, n = 10)

new_p

## X1 X2
## 1 0.4017803 0.2999017
## 2 0.4606262 0.5797737
## 3 0.4611642 0.6617809
## 4 0.3369141 0.2840991
## 5 0.8928082 0.5687830
## 6 0.8706420 0.4282589
## 7 0.2539396 0.2783683
## 8 0.5594320 0.7019670
## 9 0.5030676 0.7560124
## 10 0.7930719 0.0937701
new_p <- get_points(stream_5G, n = 100, class = TRUE)
head(new_p, n = 20)

## X1 X2 class
## 1 0.7915730 0.09533001 4
## 2 0.4305147 0.36953997 2
## 3 0.4914093 0.82120395 3
## 4 0.7837102 0.06771246 4
## 5 0.9233074 0.48164544 5
## 6 0.8606862 0.49399269 5
## 7 0.3191884 0.27607324 2
## 8 0.2528981 0.27596700 2
## 9 0.6627604 0.68988585 3
## 10 0.7902887 0.09402659 4
## 11 0.7926677 0.09030248 4
## 12 0.9393515 0.50259344 5
## 13 0.9333770 0.62817482 5
## 14 0.7906710 0.10125432 4
## 15 0.1798662 0.24967850 2
## 16 0.7985790 0.08324688 4
## 17 0.5247573 0.57527380 3
## 18 0.2358468 0.23087585 2
## 19 0.8818853 0.49668824 5
## 20 0.4255094 0.81789418 3

plot(stream_5G, n = 700, method = "pc")

Note that if you add noise to your stream, e.g., stream_Noise <-
DSD_Gaussians(k ¼ 5, d ¼ 4, noise ¼ .1, p ¼ c(0.1, 0.5, 0.3,
0.9, 0.1)), then the noise points that are not classified as part of any cluster will
have an NA class label.

16.3.6 Stream Animation

Clusters can be animated over time by animate_data(). Use reset_stream

() to start the animation at the beginning of the stream and note that this method is
not implemented for streams of class DSD_Gaussians, DSD_R, DSD_data.
frame, and DSD. We’ll create a new DSD_Benchmark data stream (Fig. 16.8).
16.3 Data Streaming 539

Fig. 16.8 Discrete snapshots of the animated stream clustering process

set.seed(12345)
stream_Bench <- DSD_Benchmark(1)
stream_Bench

## Benchmark 1: Two clusters moving diagonally from left to right, meeting

in
## the center (5% noise).
## Class: DSD_MG, DSD_R, DSD_data.frame, DSD
## With 2 clusters in 2 dimensions. Time is 1
library("animation")
reset_stream(stream_Bench)
animate_data(stream_Bench,n=10000,horizon=100,xlim=c(0,1), ylim=c(0,1))

This benchmark generator creates two 2D clusters moving in 2D. One moves
from top-left to bottom-right, the other from bottom-left to top-right. Then they meet
at the center of the domain, the 2 clusters overlap and then split again.
Concept drift in the stream can be depicted by requesting (10) times 300 data
points from the stream and animating the plot. Fast-forwarding the stream can be
accomplished by requesting, but ignoring, (2000) points in between the (10) plots.
The output of the animation below is suppressed to save space.

for(i in 1:10) {
plot(stream_Bench, 300, xlim = c(0, 1), ylim = c(0, 1))
tmp <- get_points(stream_Bench, n = 2000)
}
540 16 Specialized Machine Learning Topics

reset_stream(stream_Bench)
animate_data(stream_Bench,n=8000,horizon=120, xlim=c(0,1), ylim=c(0,1))
# Animations can be saved as HTML or GIF
#saveHTML(ani.replay(), htmlfile = "stream_Bench_Animation.html")
#saveGIF(ani.replay())

Streams can also be saved locally by write_stream(stream_Bench,

"dataStreamSaved.csv", n ¼ 100, sep¼",") and loaded back in R by
DSD_ReadCSV().

16.3.7 Case-Study: SOCR Knee Pain Data

These data represent the X and Y spatial knee-pain locations for over 8,000 patients,
along with labels about the knee Front, Back, Left and Right. Let’s try to read the
SOCR Knee Pain Dataset as a stream.

library("XML"); library("xml2"); library("rvest")

wiki_url <- read_html("http://wiki.socr.umich.edu/index.php/SOCR_Data_KneePa

inData_041409")
html_nodes(wiki_url, "#content")

## {xml_nodeset (1)}
## [1] <div id="content" class="mw-body-primary" role="main">\n\t<a id="top
...

kneeRawData <- html_table(html_nodes(wiki_url, "table")[[2]])

normalize<-function(x){
return((x-min(x))/(max(x)-min(x)))
}
kneeRawData_df <- as.data.frame(cbind(normalize(kneeRawData$x),
normalize(kneeRawData$Y), as.factor(kneeRawData$View)))
colnames(kneeRawData_df) <- c("X", "Y", "Label")
# randomize the rows of the DF as RF, RB, LF and LB labels of classes are
sequential
set.seed(1234)
kneeRawData_df <- kneeRawData_df[sample(nrow(kneeRawData_df)), ]
summary(kneeRawData_df)
## X Y Label
## Min. :0.0000 Min. :0.0000 Min. :1.000
## 1st Qu.:0.1331 1st Qu.:0.4566 1st Qu.:2.000
## Median :0.2995 Median :0.5087 Median :3.000
## Mean :0.3382 Mean :0.5091 Mean :2.801
## 3rd Qu.:0.3645 3rd Qu.:0.5549 3rd Qu.:4.000
## Max. :1.0000 Max. :1.0000 Max. :4.000

# View(kneeRawData_df)

We can use the DSD::DSD_Memory class to get a stream interface for matrix or
data frame objects, like the Knee pain location dataset. The number of true clusters
k ¼ 4 in this dataset.
16.3 Data Streaming 541

# use data.frame to create a stream (3rd column contains label assignment)

kneeDF <- data.frame(x=kneeRawData_df[,1], y=kneeRawData_df[,2],
class=as.factor(kneeRawData_df[,3]))
head(kneeDF)
## x y class
## 1 0.1188590 0.5057803 4
## 2 0.3248811 0.6040462 2
## 3 0.3153724 0.4971098 2
## 4 0.3248811 0.4161850 2
## 5 0.6941363 0.5289017 1
## 6 0.3217116 0.4595376 2

streamKnee <- DSD_Memory(kneeDF[,c("x", "y")], class=kneeDF[,"class"],

loop=T)
streamKnee

## Memory Stream Interface

## Class: DSD_Memory, DSD_R, DSD_data.frame, DSD
## With NA clusters in 2 dimensions
## Contains 8666 data points - currently at position 1 - loop is TRUE

# Each time we get a point from *streamKnee*, the stream pointer moves
to the next position (row) in the data.
get_points(streamKnee, n=10)

## x y
## 1 0.11885895 0.5057803
## 2 0.32488114 0.6040462
## 3 0.31537242 0.4971098
## 4 0.32488114 0.4161850
## 5 0.69413629 0.5289017
## 6 0.32171157 0.4595376
## 7 0.06497623 0.4913295
## 8 0.12519810 0.4682081
## 9 0.32329635 0.4942197
## 10 0.30744849 0.5086705
streamKnee

## Memory Stream Interface

## Class: DSD_Memory, DSD_R, DSD_data.frame, DSD
## With NA clusters in 2 dimensions
## Contains 8666 data points - currently at position 11 - loop is TRUE

# Stream pointer is in position 11 now

# We can redirect the current position of the stream pointer by:

reset_stream(streamKnee, pos = 200)
get_points(streamKnee, n=10)
## x y
## 200 0.9413629 0.5606936
## 201 0.3217116 0.5664740
## 202 0.3122029 0.6416185
## 203 0.1553090 0.6040462
## 204 0.3645008 0.5346821
## 205 0.3122029 0.5000000
## 206 0.3549921 0.5404624
## 207 0.1473851 0.5260116
## 208 0.1870048 0.6329480
## 209 0.1220285 0.4132948
542 16 Specialized Machine Learning Topics

streamKnee

## Memory Stream Interface

## Class: DSD_Memory, DSD_R, DSD_data.frame, DSD
## With NA clusters in 2 dimensions
## Contains 8666 data points - currently at position 210 - loop is TRUE

16.3.8 Data Stream Clustering and Classification (DSC)

Let’s demonstrate clustering using DSC_DStream, which assigns points to cells in

a grid. First, initialize the clustering, as an empty cluster and then use the update()
function to implicitly alter the mutable DSC object (Fig. 16.9).

dsc_streamKnee <- DSC_DStream(gridsize = 0.1, Cm = 0.4, attraction=T)

dsc_streamKnee
## DStream
## Class: DSC_DStream, DSC_Micro, DSC_R, DSC
## Number of micro-clusters: 0
## Number of macro-clusters: 0

# stream::update
reset_stream(streamKnee, pos = 1)
update(dsc_streamKnee, streamKnee, n = 500)
dsc_streamKnee

## DStream
## Class: DSC_DStream, DSC_Micro, DSC_R, DSC
## Number of micro-clusters: 16
## Number of macro-clusters: 11

Fig. 16.9 Data stream clustering and classification of the SOCR knee-pain dataset (n¼500)
16.3 Data Streaming 543

Fig. 16.10 5-Means stream clustering of the SOCR knee pain data

head(get_centers(dsc_streamKnee))
## [,1] [,2]
## [1,] 0.05 0.45
## [2,] 0.05 0.55
## [3,] 0.15 0.35
## [4,] 0.15 0.45
## [5,] 0.15 0.55
## [6,] 0.15 0.65

plot(dsc_streamKnee, streamKnee, xlim=c(0,1), ylim=c(0,1))

# plot(dsc_streamKnee, streamKnee, grid = TRUE)

# Micro-clusters are plotted in red on top of gray stream data points
# The size of the micro-clusters indicates their weight - it's proportional
to the number of data points represented by each micro-cluster.
# Micro-clusters are shown as dense grid cells (density is coded with gray
values).

The purity metric represents an external evaluation criterion of cluster

quality, which is the proportion of the total number of points that were correctly
classified:

1 Xk
0  Purity ¼ maxj ci \ t j  1,
N i¼1

where N¼number of observed data points, k ¼ number of clusters, ci is the ith cluster,
and tj is the classification that has the maximum number of points with ci class labels.
High purity suggests that we correctly label points (Fig. 16.10).
544 16 Specialized Machine Learning Topics

Next, we can use K-means clustering.

kMeans_Knee <- DSC_Kmeans(k=5) # use 4-5 clusters matching the 4 knee labels
recluster(kMeans_Knee, dsc_streamKnee)
plot(kMeans_Knee, streamKnee, type = "both")

Again, the graphical output of the animation sequence of frames is suppressed,

however, the readers are encouraged to run the command line and inspect the
graphical outcome (Figs. 16.11 and 16.12).

Fig. 16.11 Animated continuous 5-means stream clustering of the knee pain data

Fig. 16.12 Continuous stream clustering and purity index across iterations
16.3 Data Streaming 545

animate_data(streamKnee, n=1000, horizon=100,xlim=c(0,1), ylim = c(0,1))

# purity <- animate_cluster(kMeans_Knee, streamKnee, n=2500, type="both",

xlim=c(0,1), ylim=c(-,1), evaluationMeasure="purity", horizon=10)

animate_cluster(kMeans_Knee, streamKnee, horizon = 100, n = 5000,

measure = "purity", plot.args = list(xlim = c(0, 1), ylim = c(0, 1)))

## points purity
## 1 1 0.9600000
## 2 101 0.9043478
## 3 201 0.9500000
…
## 49 4801 0.9047619
## 50 4901 0.8850000

16.3.9 Evaluation of Data Stream Clustering

Figure 16.13 shows the average clustering purty as we evaluate the stream clustering
across the streaming points.

# Synthetic Gaussian example

# stream <- DSD_Gaussians(k = 3, d = 2, noise = .05)
# dstream <- DSC_DStream(gridsize = .1)
# update(dstream, stream, n = 2000)
# evaluate(dstream, stream, n = 100)

evaluate(dsc_streamKnee, streamKnee, measure = c("crand", "SSQ",

"silhouette"), n = 100, type = c("auto","micro","macro"), assign="micro",
assignmentMethod = c("auto", "model", "nn"), noise = c("class","exclude"))
## Evaluation results for micro-clusters.
## Points were assigned to micro-clusters.
## cRand SSQ silhouette
## 0.3473634 0.3382900 0.1373143
clusterEval <- evaluate_cluster(dsc_streamKnee, streamKnee, measure =
c("numMicroClusters", "purity"), n = 5000, horizon = 100)
head(clusterEval)
## points numMicroClusters purity
## 1 0 16 0.9555556
## 2 100 17 0.9733333
## 3 200 18 0.9671053
## 4 300 21 0.9687500
## 5 400 21 0.9880952
## 6 500 22 0.9750000

plot(clusterEval[ , "points"], clusterEval[ , "purity"], type = "l",

ylab = "Avg Purity", xlab = "Points")

animate_cluster(dsc_streamKnee, streamKnee, horizon = 100, n = 5000,

measure = "purity", plot.args = list(xlim = c(0, 1), ylim = c(0, 1)))
546 16 Specialized Machine Learning Topics

Fig. 16.13 Average clustering purity

## points purity
## 1 1 0.9714286
## 2 101 0.9833333
## 3 201 0.9722222
…

## 49 4801 0.9772727
## 50 4901 0.9777778

The dsc_streamKnee represents the result of the stream clustering, where n is

the number of data points from the streamKnee stream. The evaluation measure
can be specified as a vector of character strings. Points are assigned to clusters in
dsc_streamKnee using get_assignment() and can be used to assess the
quality of the classification. By default, points are assigned to micro-clusters, or can
be assigned to macro-cluster centers by assign ¼ "macro". Also, new points can
be assigned to clusters by the rule used in the clustering algorithm by
assignmentMethod ¼ "model" or using nearest-neighbor assignment (nn),
Fig. 16.14.

16.4 Optimization and Improving the Computational

Performance

Here and in previous chapters, e.g., Chap. 15, we notice that R may sometimes be
slow and memory-inefficient. These problems may be severe, especially for
datasets with millions of records or when using complex functions. There are
packages for processing large datasets and memory optimization – bigmemory,
biganalytics, bigtabulate, etc.
16.4 Optimization and Improving the Computational Performance 547

Fig. 16.14 Continuous k-means stream clustering with classificaiton purity

16.4.1 Generalizing Tabular Data Structures with dplyr

We have also seen long execution times when running processes that ingest, store or
manipulate huge data.frame objects. The dplyr package, created by Hadley
Wickham and Romain Francoi, provides a faster route to manage such large datasets
in R. It creates an object called tbl, similar to data.frame, which has an
in-memory column-like structure. R reads these objects a lot faster than data frames.
To make a tbl object we can either convert an existing data frame to tbl or
connect to an external database. Converting from data frame to tbl is quite easy. All
we need to do is call the function as.tbl().

#install.packages("dplyr")
library(dplyr)

nof1_tbl<-as.tbl(nof1); nof1_tbl

## # A tibble: 900 × 10
## ID Day Tx SelfEff SelfEff25 WPSS SocSuppt PMss PMss3 PhyAct
## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 1 1 1 33 8 0.97 5.00 4.03 1.03 53
## 2 1 2 1 33 8 -0.17 3.87 4.03 1.03 73
## 3 1 3 0 33 8 0.81 4.84 4.03 1.03 23
…

## 8 1 8 0 33 8 -0.34 3.69 4.03 1.03 0

## 9 1 9 1 33 8 -0.74 3.29 4.03 1.03 73
## 10 1 10 1 33 8 -0.38 3.66 4.03 1.03 114
## # ... with 890 more rows

This looks like a normal data frame. If you are using R Studio, displaying the
nof1_tbl will show the same output as nof1.
548 16 Specialized Machine Learning Topics

16.4.2 Making Data Frames Faster with Data.Table

Similar to tbl, the data.table package provides another alternative to data

frame object representation. data.table objects are processed in R much faster
compared to standard data frames. Also, all of the functions that can accept data
frame could be applied to data.table objects as well. The function fread() is
able to read a local CSV file directly into a data.table.

#install.packages("data.table")
library(data.table)

nof1<-fread("C:/Users/Dinov/Desktop/02_Nof1_Data.csv")

Another amazing property of data.table is that we can use subscripts to

access a specific location in the dataset just like dataset[row, column]. It also
allows the selection of rows with Boolean expression and direct application of
functions to those selected rows. Note that column names can be used to call the
specific column in data.table, whereas with data frames, we have to use the
dataset$columnName syntax.

nof1[ID==1, mean(PhyAct)]

## [1] 52.66667

This useful functionality can also help us run complex operations with only a few
lines of code. One of the drawbacks of using data.table objects is that they are
still limited by the available system memory.

16.4.3 Creating Disk-Based Data Frames with ff

The ff (fast-files) package allows us to overcome the RAM limitations of finite

system memory. For example, it helps with operating datasets with billions of rows.
ff creates objects in ffdf formats, which is like a map that points to a location of
the data on a disk. However, this makes ffdf objects inapplicable for most R
functions. The only way to address this problem is to break the huge dataset into
small chunks. After processing a batch of these small chunks, we have to combine
the results to reconstruct the complete output. This strategy is relevant in parallel
computing, which will be discussed in detail in the next section. First, let’s download
one of the large datasets in our datasets archive, UQ_VitalSignsData_Case04.csv.
16.5 Parallel Computing 549

# install.packages("ff")
library(ff)
# vitalsigns<-read.csv.ffdf(file="UQ_VitalSignsData_Case04.csv", header=T)
vitalsigns<-
read.csv.ffdf(file="https://umich.instructure.com/files/366335/download?
download_frd=1", header=T)

As mentioned earlier, we cannot apply functions directly on this object.

mean(vitalsigns$Pulse)
## Warning in mean.default(vitalsigns$Pulse): argument is not numeric or
## logical: returning NA
## [1] NA

For basic calculations on such large datasets, we can use another package,
ffbase. It allows operations on ffdf objects using simple tasks like: mathemat-
ical operations, query functions, summary statistics and bigger regression models
using packages like biglm, which will be mentioned later in this chapter.

# install.packages("ffbase")
library(ffbase)
mean(vitalsigns$Pulse)
## [1] 108.7185

16.4.4 Using Massive Matrices with bigmemory

The previously introduced packages include alternatives to data.frames. For

instance, the bigmemory package creates alternative objects to 2D matrices
(second-order tensors). It can store huge datasets and can be divided into small
chunks that can be converted to data frames. However, we cannot directly apply
machine-learning methods on this type of objects. More detailed information about
the bigmemory package is available online.

16.5 Parallel Computing

In previous chapters, we saw various machine-learning techniques applied as serial

computing tasks. The traditional protocol involves: First, applying function 1 to our
raw data. Then, using the output from function 1 as an input to function 2. This
process may be iterated over a series of functions. Finally, we have the terminal
output generated by the last function. This serial or linear computing method is
straightforward but time consuming and perhaps sub-optimal.
Now we introduce a more efficient way of computing - parallel computing, which
provides a mechanism to deal with different tasks at the same time and combine the
550 16 Specialized Machine Learning Topics

outputs for all of processes to get the final answer faster. However, parallel algo-
rithms may require special conditions and cannot be applied to all problems. If two
tasks have to be run in a specific order, this problem cannot be parallelized.

16.5.1 Measuring Execution Time

To measure how much time can be saved for different methods, we can use function
system.time().

system.time(mean(vitalsigns$Pulse))
## user system elapsed
## 0 0 0

This means calculating the mean of Pulse column in the vitalsigns dataset
takes less than 0.001 seconds. These values will vary between computers, operating
systems, and states of operations.

16.5.2 Parallel Processing with Multiple Cores

We will introduce two packages for parallel computing multicore and snow
(their core components are included in the package parallel). They both have a
different way of multitasking. However, to run these packages, you need to have a
relatively modern multicore computer. Let’s check how many cores your computer
has. This function parallel::detectCores() provides this functionality.
parallel is a base package, so there is no need to install it prior to using it.

library(parallel); detectCores()

## [1] 8

So, there are eight (8) cores in my computer. I will be able to run up to 6-8 parallel
jobs on this computer.
The multicore package simply uses the multitasking capabilities of the kernel,
the computer’s operating system, to “fork” additional R sessions that share the same
memory. Imagine that we open several R sessions in parallel and let each of them do
part of the work. Now, let’s examine how this can save time when running complex
protocols or dealing with large datasets. To start with, we can use the mclapply()
function, which is similar to lapply(), which applies functions to a vector and
returns a vector of lists. Instead of applying functions to vectors mcapply()
divides the complete computational task and delegates portions of it to each avail-
able core. To demonstrate this procedure, we will construct a simple, yet time
16.5 Parallel Computing 551

consuming, task of generating random numbers. Also, we can use the system.
time() function to track execution time.

set.seed(123)
system.time(c1<-rnorm(10000000))

## user system elapsed

## 0.64 0.00 0.64

# Note the multi core calls may not work on Windows, but will work on
Linux/Mac.
#This shows a 2-core and 4-vore invocations
# system.time(c2<-unlist(mclapply(1:2, function(x){rnorm(5000000)},
mc.cores = 2)))
# system.time(c4<-unlist(mclapply(1:4, function(x){rnorm(2500000)},
mc.cores = 4)))

# And here is a Windows (single core invocation)

system.time(c2<-unlist(mclapply(1:2, function(x){rnorm(5000000)},
mc.cores = 1)))

## user system elapsed

## 0.65 0.00 0.65

The unlist() is used at the end to combine results from different cores into a
single vector. Each line of code creates 10,000,000 random numbers. The c1 call
took the longest time to complete. The c2 call used two cores to finish the task (each
core handled 5,000,000 numbers) and used less time than c1. Finally, c4 used all
four cores to finish the task and successfully reduced the overall time. We can see
that when we use more cores the overall time is significantly reduced.
The snow package allows parallel computing on multicore multiprocessor
machines or a network of multiple machines. It might be more difficult to use but
it’s also certainly more flexible. First we can set how many cores we want to use via
makeCluster() function.

# install.packages("snow")
library(snow)

cl<-makeCluster(2)

This call might cause your computer to pop up a message warning about access
though the firewall. To do the same task we can use parLapply() function in the
snow package. Note that we have to call the object we created with the previous
makeCluster() function.

system.time(c2<-unlist(parLapply(cl, c(5000000, 5000000), function(x) {

rnorm(x)})))

## user system elapsed

## 0.11 0.11 0.64
552 16 Specialized Machine Learning Topics

While using parLapply(), we have to specify the matrix and the function that
will be applied to this matrix. Remember to stop the cluster we made after complet-
ing the task, to release back the system resources.

stopCluster(cl)

16.5.3 Parallelization Using foreach and doParallel

The foreach package provides another option of parallel computing. It relies on a

loop-like process basically applying a specified function for each item in the set,
which again is somewhat similar to apply(), lapply() and other regular
functions. The interesting thing is that these loops can be computed in parallel
saving substantial amounts of time. The foreach package alone cannot provide
parallel computing. We have to combine it with other packages like doParallel.
Let’s reexamine the task of creating a vector of 10,000,000 random numbers. First,
register the 4 compute cores using registerDoParallel().

# install.packages("doParallel")
library(doParallel)

cl<-makeCluster(4)
registerDoParallel(cl)

Then we can examine the time saving foreach command.

#install.packages("foreach")
library(foreach)
system.time(c4<-foreach(i=1:4, .combine = 'c')
%dopar% rnorm(2500000))

## user system elapsed

## 0.11 0.18 0.54

Here we used four items (each item runs on a separate core), .combine¼c
allows foreach to combine the results with the parameter c(), generating the
aggregate result vector.
Also, don’t forget to close the doParallel by registering the sequential
backend.

unregister<-registerDoSEQ()
16.6 Deploying Optimized Learning Algorithms 553

16.5.4 GPU Computing

Modern computers have graphics cards, GPUs (Graphical Processing Units), that
consists of thousands of cores, however they are very specialized, unlike the
standard CPU chip. If we can use this feature for parallel computing, we may
reach amazing performance improvements, at the cost of complicating the
processing algorithms and increasing the constraints on the data format. Specific
disadvantages of GPU computing include reliance on proprietary manufacturer (e.g.,
NVidia) frameworks and Complete Unified Device Architecture (CUDA) program-
ming language. CUDA allows programming of GPU instructions into a common
computing language. This paper provides one example of using GPU computation to
significantly improve the performance of advanced neuroimaging and brain mapping
processing of multidimensional data.
The R package gputools is created for parallel computing using NVidia
CUDA. Detailed GPU computing in R information is available online.

16.6 Deploying Optimized Learning Algorithms

As we mentioned earlier, some tasks can be parallelized easier than others. In real
world situations, we can pick the algorithms that lend themselves well to
parallelization. Some of the R packages that allow parallel computing using ML
algorithms are listed below.

16.6.1 Building Bigger Regression Models with biglm

biglm allows training regression models with data from SQL databases or large
data chunks obtained from the ff package. The output is similar to the standard
lm() function that builds linear models. However, biglm operates efficiently on
massive datasets.

16.6.2 Growing Bigger and Faster Random Forests

with bigrf

The bigrf package can be used to train random forests combining the foreach
and doParallel packages. In Chap. 15, we presented random forests as machine
learners ensembling multiple tree learners. With parallel computing, we can split the
task of creating thousands of trees into smaller tasks that can be outsourced to each
554 16 Specialized Machine Learning Topics

available compute core. We only need to combine the results at the end. Then, we
will obtain the exact same output in a relatively shorter amount of time.

16.6.3 Training and Evaluation Models in Parallel

with caret

Combining the caret package with foreach, we can obtain a powerful method
to deal with time-consuming tasks like building a random forest learner. Utilizing the
same example we presented in Chap. 15, we can see the time difference of utilizing
the foreach package.

#library(caret)
system.time(m_rf <- train(CHARLSONSCORE ~ ., data = qol, method = "rf",
metric = "Kappa", trControl = ctrl, tuneGrid = grid_rf))

## user system elapsed

## 130.05 0.40 130.49

It took more than a minute to finish this task in standard execution model purely
relying on the regular caret function. Below, this same model training completes
much faster using parallelization (less than half the time) compared to the standard
call above.

set.seed(123)
cl<-makeCluster(4)
registerDoParallel(cl)
getDoParWorkers()

## [1] 4

system.time(m_rf <- train(CHARLSONSCORE ~ ., data = qol, method = "rf",

metric = "Kappa", trControl = ctrl, tuneGrid = grid_rf))

## user system elapsed

## 4.61 0.02 47.70

unregister<-registerDoSEQ()

16.7 Practice Problem

Try to analyze the co-appearance network in the novel “Les Miserables”. The data
contains the weighted network of co-appearances of characters in Victor Hugo’s
novel “Les Miserables”. Nodes represent characters as indicated by the labels and
edges connect any pair of characters that appear in the same chapter of the book. The
values on the edges are the number of such co-appearances.
16.8 Assignment: 16. Specialized Machine Learning Topics 555

miserables<-read.table("https://umich.instructure.com/files/330389/download?
download_frd¼1", sep¼"", header¼F) head(miserables)
Also, try to interrogate some of the larger datasets we have by using alternative
parallel computing and big data analytics.

16.8 Assignment: 16. Specialized Machine Learning Topics

16.8.1 Working with Website Data

• Download the Main SOCR Wiki Page and compare RCurl and httr.
• Read and write XML code for the SOCR Main Page.
• Scrape the data from the SOCR Main Page.

16.8.2 Network Data and Visualization

• Download 03_les_miserablese_GraphData.txt
• Visualize this undirected network.
• Summary the graph and explain the output.
• Calculate degree and the centrality of this graph.
• Find out some important characters.
• Will the result change or not if we assume the graph is directed?

16.8.3 Data Conversion and Parallel Computing

• Download CaseStudy12_ AdultsHeartAttack_Data.xlsx or require online.

• load this data as data frame.
• Use Export() or write.xlsx() to renew the xlsx file.
• Use rio package to convert this ".xlsx" "file to" ".csv".
• Generate generalizing tabular data structures.
• Generate data.table.
• Create disk-based data frames and perform basic calculation.
• Perform basic calculation on the last 5 columns as a big matrix.
• Use DIAGNOSIS, SEX, DRG, CHARGES, LOS and AGE to predict DIED with
randomForest setting ntree¼20000. Notice: sample without replacement to
get an as large as possible balanced dataset.
• Run train() in caret and detect the execute time.
• Detect cores and make proper number of clusters.
556 16 Specialized Machine Learning Topics

• Rerun train() parallelized and compare the execute time.

• Use foreach and doMC to design a parallelized random forest with
ntree¼20000 totally and compare the execute time with sequential execution.

References

Data Streams in R:https://cran.r-project.org/web/packages/stream/vignettes/stream.pdf

Dplyr:https://cran.rstudio.com/web/packages/dplyr/vignettes/introduction.html
doParallel:https://cran.rproject.org/web/packages/doParallel/vignettes/gettingstartedParallel.pdf
Mailund, T. (2017) Beginning Data Science in R: Data Analysis, Visualization, and Modelling for
the Data Scientist, Apress, ISBN 1484226712, 9781484226711