make predictions from your data using

Workshop:MakePredictions FromYourDataUsingR.UTM15July2019

Workshop Instructors: Dr. Norhaiza Ahmad . Dr. Noraslinda M. Ismail . Dr. Shariffah Suhaila Syed Jamaludin

Make Predictions from your Data using

PART A: R INTRODr. Norhaiza Ahmad

Department of Mathematical SciencesFaculty of Science

Universiti Teknologi Malaysia

http://people.utm.my/norhaiza/


@haiza

Start your R Session on the PC in this Lab!

1. Go to Desktop2. Click Folder: Mathematics Software or Math

Software 3. Click Folder: R4. There are three R applications:

i. R i386 3.4.0ii. R x64 3.4.0iii. RStudio

2

ChooseRStudio

Otherwise go to the START button and search for R studio


@haiza

Workshop Schedule: Make Predictions from your Data using R

PART ITEM DETAILS

PART A Intro toPredictiveLinearModel

IntroductiontoModelling- theory&terminology. Datastructure.

RQuickie About R.Rbase .BasicRSyntax.RstudioInterface.Packages.Help

PART B PredictiveLinearModelforContinuousData(Response)

(i)Basic RegressionModel,SinglePredictorVariable

(ii)MultipleLinearRegression,ModelAssessment

PARTC PredictiveLinearModelforCountsData(Response)

IntrotoGeneralised LinearModel


@haiza4

DataBigDatavsSmallData

Extract Information From Data

• Classification• Discrimination• Comparison• Relationship

•Prediction

Extractinformation


Example:PredictingBodyMassIndex

5

DatabaseofindividualsVariablesmeasured:height,weight,body fat

HowtouseBMItopredictbodyfatpercentage?


@haiza

Predictive Modelling

Predictive modeling is a technique that uses mathematical and computational methods to predict or forecast an event or outcome.


@haiza

Types of Predictive Models

Parametric

Models

Non-ParametricModels

• modelsuseafixednumberofparameters

• basedonanunderlyingprobabilisticmodel

• modelsdonothaveafixednumberofparameters

• basedonanunderlyingprobabilisticmodel

• eg.DecisionTreesetc.

This workshop focusses on:Regression Modeli.e linear regression model


@haiza8

General modeling framework


@haiza

Wewillbeusingadatacalled

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• House sale prices for King County, Washington USA, which includes Seattle. • It includes homes sold between May 2014 and May 2015. • 21613observations.21variables

id 1 2 3 4 5 6 21613

date 20141013 20141209 20150225 20141209 20150218 20140512 .. .. .. 20141015price 221900 538000 180000 604000 510000 1225000 .. .. .. 325000bedrooms 3 3 2 4 3 4 .. .. .. 2bathrooms 1 2.25 1 3 2 4.5 .. .. .. 0.75sqft_living 1180 2570 770 1960 1680 5420 .. .. .. 1020sqft_lot 5650 7242 10000 5000 8080 101930 .. .. .. 1076floors 1 2 1 1 1 1 .. .. .. 2waterfront 0 0 0 0 0 0 .. .. .. 0view 0 0 0 0 0 0 .. .. .. 0condition 3 3 3 5 3 3 .. .. .. 3grade 7 7 6 7 8 11 .. .. .. 7sqft_above 1180 2170 770 1050 1680 3890 .. .. .. 1020sqft_basement 0 400 0 910 0 1530 .. .. .. 0yr_built 1955 1951 1933 1965 1987 2001 .. .. .. 2008yr_renovated 0 1991 0 0 0 0 .. .. .. 0zipcode 98178 98125 98028 98136 98074 98053 .. .. .. 98144lat 47.5112 47.721 47.7379 47.5208 47.6168 47.6561 .. .. .. 47.5941long -122.257 -122.319 -122.233 -122.393 -122.045 -122.005 .. .. .. -122.299sqft_living15 1340 1690 2720 1360 1800 4760 .. .. .. 1020sqft_lot15 5650 7639 8062 5000 7503 101930 .. .. .. 1357

Consideradatasetcalledhouse_prices

Question: Can we predict the sale price of houses based on their features?


@haiza

Consideronlycertainfeaturesofthehouses:sqft_living, condition, bedrooms, yr_built, waterfront

id 1 2 3 4 5 6 21613

price 221900 538000 180000 604000 510000 1225000 .. .. .. 325000bedrooms 3 3 2 4 3 4 .. .. .. 2sqft_living 1180 2570 770 1960 1680 5420 .. .. .. 1020waterfront 0 0 0 0 0 0 .. .. .. 0condition 3 3 3 5 3 3 .. .. .. 3yr_built 1955 1951 1933 1965 1987 2001 .. .. .. 2008

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𝑦 = 𝑓 𝑥 + 𝜀Housesaleprices(in$)

squarefeet ,condition,bedrooms,yearhousewasbuilt,waterfront

Canwepredictthesalepriceofhousesbasedonthefeaturesofhouses?

Response/Outcomevariableofinterest explanatory/predictorvariables


@haiza

Background: General modeling framework formula

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𝑦 = 𝑓 𝑥 + 𝜀

Response/Outcomevariableofinterest

explanatory/predictorvariables

where𝑦:outcomevariableofinterest𝑥 explanatory/predictorvariable(s)𝑓 :functionoftherelationshipbetweenyand𝑥 𝜀:unsystematicerrorcomponenti.e.noise


@haiza

The modelling problem

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𝑦 = 𝑓 𝑥 + 𝜀

Response/Outcomevariableofinterest

explanatory/predictorvariables

consider

functionoftherelationshipbetweenyand▁𝑥

unknown

unknown

known.givenbydata(nobservations)

known.givenbydata(nobservations)

Aim: 1. Fitamodel 𝑓()* that approximates𝑓() whileignoring𝜀.è Separatesignalnoise

2. Generate fitted/predicted values𝑦, = 𝑓()*


@haiza

Fitted (Predicted) Linear Regression Model

𝑦 = 𝑓 𝑥 + 𝜀Generalmodellingi.e theobservedvalueofyis

𝑦, = 𝑓(𝑥)-Fitted (Predicted) Linear Regression Model is given by

ToFitaLinearRegressionModel,weestimate𝑓 . by𝑓(. )*

Thus,


@haiza

Recall: Types of Data

Data

Qualitative

Nominal Ordinal

Quantitative

Discrete Continuous

IntervalCategorical

CountsFrequency

Rank


@haiza

SCOPE OF WORKSHOPData

Prediction

UsingLinearRegressionModel

ContinuousData

SimpleLinearRegression

MultipleLinear

Regression

DiscreteData

CountsData

GeneralizedLinearModel

UsingRSoftware

ResponseVariable

ResponseVariable


@haiza16

About R: a quickie1. About R2. Interfaceoptions forR3. RStudio4. AnatomyofR:Functionsand

Packages5. Saving&Quitting


@haiza

About R?

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WhyR?

FREE

LargeCommunityofRUsers

Growsintandemwith

Development in

Statistics

Economicsustainability

Applicationcodes- latestresearchworkarelikelytobeavailabletouse.

Helpavailable:

Extensivehelpdocumentationinsystem

Justask!OrBrowse inarchiveQ&A

• A computer language, with orientation towards statistical applications

• Open-sourced software -non-commercial- FREE§ open exchange,

publicly accessible Community-oriented software

• Origin in academics:§ solid foundation of core

statistical and numerical algorithms and continues to grow to this end.


@haiza

How to download R?

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http://www.r-project.org/ Rbase


@haiza

PointstoNote

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• WhenyoudownloadandinstallR,youaredownloadingandinstallingbaseRandselectedpackages.

OnceRdownloadiscomplete:§ anRIconwillappearonyourdesktop.


@haiza

Main Interface Options -R Users

20

Rbase

RCommander

RStudio


@haiza21

ProceduretodownloadRStudio onyourownPC(1) MakesureyouhavealreadydownloadedRbase

(2)DownloadthefreeversionofRStudio athttps://www.rstudio.com/products/rstudio/download/

How to download R Studio?


RInterface:RbasevsRStudio

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Rbase RStudio


@haiza

1. GotoDesktop2. ClickFolder:MathematicsSoftwareorMath

Software3. ClickFolder:R4. ChooseRStudio

23

OtherwisegototheSTARTbuttonandsearchforRStudio

ProceduretodownloadRStudio onyourownPC(1)MakesureyouhavealreadydownloadedRbase(2)DownloadthefreeversionofRStudio athttps://www.rstudio.com/products/rstudio/download/

Start your R Studio Session!


@haiza24



RStudio• NavigatePanels• Entering&ExecutingCommands-v Rconsolev Rscript

• functionsinR&Help• Rpackages


@haiza

NavigatingRstudio:ThePanels

ConsolePanel

ViewerPanel

EnvironmentPanelSourcePanel

Panelsonright:maintain

theworkingenvironment

Panelsonleft:RunCodes/Commands

4Panelsshown

writeyourcommandshere(likeanotepad)

writeyourcommands

aftertheprompt>


@haiza26

ASIDE:NavigatingRStudio

AttheRibbon,ChooseTabViewà Panes

Youcanspecifywhichpaneltodisplay

Ordisplayaparticularpane,eg.TodisplayConsoleonly

AttheRibbon,ChooseTabViewà Panesà ZoomConsole

Toreturndisplayofallpanels

AttheRibbon,ChooseTabViewà Panesà ShowAllPanes


@haiza

How to Run & Execute R commands?

27

Method1 Method

2R-CONSOLE R-SCRIPT

Method2

- Commandsareexecuted- Likearoughpaper- Notconvenientforcode

storage


@haiza

> 6+3[1] 9

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• WriteyourRcommandsaftereachRprompt (>)• HitEnter toexecutecommand

• Otheroperators:+,-,*,/

Output

Write6+3

TypethefollowingontheRconsolePanel

How to Run commands in R:Method 1: R Console

28ConsolePanel

ViewerPanel

entryindex1


@haiza

HandyTip

29

• Usetheupanddownarrowkeys-

TorecallpreviousRlinecommandsintheconsole

Handy Tips


@haiza

Making Comments in R

30

• CommentlinesinRaredenotedby“#”• Anylinesthatiswrittenafter“#”willnotbereadasanRcommand

• Comment linesareusefulformakingnotation/notesinyourprogram

> 31 %% 7 #remainder after division of 31 by 7


@haiza

R Object Assignment

31

# use symbol ‘=‘ or ‘<-’ for assignment

• Risanobjectorientedprogram.• #Eachinput/outputcanbeassigned/storedtoanobject#case-sensitive

• OnceanRobjectisassigned,itcanbecalleduponatanytimeaslongasitissaved.Herethenumber2isstoredinanobjectcalled“x”.

> x = 2> x > y <-2> y

# CALL UP the r-object to display results

(if required)


@haiza32

# Use ‘;’ to combine line commands

• Ingeneral,RobjectsarestoredinanRworkspace,alsoknownastheglobalenvironment.

> x = 2; x > len = 2; len> x=2; len=2;x+2

R Object Assignment


@haiza

HandyTip2

33

• Usebracketsaroundassignment– toautomaticallycallupstoredobject

# Use ‘()’ to auto call up assignment

> (x=2)> (len=2)

Handy Tips


@haiza

Important Rules on object assignment

34

• Variablenamesarecasesensitive• Noblanksinname

(canuse_or.tojoinwords,butnot-)• Startwithaletter(capitalorlower-case)


@haiza

How to Run & Execute R commands?

35

Method1 Method

2R-CONSOLE R-SCRIPT

Method2

- Commandsareexecuted- Likearoughpaper- Notconvenientforcode

storage

Ascriptfile:filewhereyoucantypeyourcommandsandrunthemontheconsoleatyourownconvenience.Itis

similartoanotepad/textfile!


@haiza36

How to Run commands in R:Method 2: R Script

Nowopenascriptfile.

AttheRibbon,ChooseTabFileà NewFileà RScript

Thisisanewscript“Untitled1”.Youcannameitandsavelikeanotepad


@haiza

Writing and executing commands from an R Script

37

# This is my first Rscript6+36-3

Step2:Toruncommandsonascriptfile:

Placethecursorononthelineyouwanttoexecute.Presstherunbuttononthetab.èTheresultsofexecutingtheselineswillappearintheConsole.

Step1:TypetheseinyourRscript file.Note:Thereisno“>“promptinascriptfile

Step3:Saveyourscriptfileinyourpreferreddrive/folder.èsimilartosavinganotepad/textfile


@haiza

HandyTip• YoucanalsotypetheRCodesintheScriptfile(Sourcepanel)andexecuteeachlinebypressingCmd + enter.(alternativetopressing RUNicon ontheSourcePanel)

• ItisadvisabletowriteyourcodeintheRScriptfile(sourcepanel),sothatyouwillbeabletosaveyourworkattheendofyourcodingsession.

38


@haiza39



RStudio• NavigatePanels• Entering&ExecutingCommands-v Rconsolev Rscript

• functionsinR&Help• Rpackages


40

\

PackagesinR=BRAINofR.

WhenyoudownloadandinstallRforthefirsttime,- youwillbeautomatically downloadingandinstalling:base packageandselectedpackages(fromCRAN).

packageBase

SelectedPackages

Add-OnPackages

HowRworks:AnatomyofR

Otherpackagescanbeaddedontoowhenrequired!

• R has many codes for many inbuilt functions, datasets & Help documentations

• These are contained in ‘Packages’ developed by the R-team and the community


Package‘base’

Containsvarious:

• Functions• Datasets• Help

Manymorepackageswithdifferentcapabilities!

Package‘stats’

Containsvarious:


…..

Package‘ggplot2’

Containsvarious:


HowRworks:AnatomyofRExamples of ‘Packages’ in R

BasePackage• Corepackage• AutomaticallyinstalledwhenyoudownloadR

gglot2 Package• FancyDataVisualization

stats Package• Generalstatisticalapplications


42

• R Packages are stored in certain Repositories:

HowRworks:AnatomyofR

Package‘base’

Containsvarious:


CRAN

ROfficial/Default

….. Manyotherpackages

Bioconductor

Rspecifictobioinformatics

GitHubOtherrepositories:NotRbutRepository formanyopensourcedprojects

Package‘…’

Containsvarious:



Rforge

Includedevelopmentversionsofpackages

Package‘…’

Containsvarious:




@haiza

FindingPackagesinRStudio

GoToViewerPanel.PressthetabPackages.ThelistofpackagesalreadyinstalledinyourPCappears.Usethesearchfinder tofindaspecificpackagename

TheseareallthepackagesthatareavailableinyourR

ToseeallthepackagesalreadyinstalledinyourPC

Findpackages


@haiza

InstallingPackagesinRStudio

GoToViewerPanel.PressthetabPackages.

1. ClickInstall2. APop-up

windowappear3. Writethename

ofthepackageinthepop-upboxExample:

abind4. PressInstall

ToinstallthepackagesnotavailableonyourRSession

NoticethatthepackagethatyouhaveinstalledisnowcontainedinthelistofpackagesofyourRsession


@haiza

LoadingPackagesinRStudio

1. Findthepackagethatyouwanttouse

2. Tickontheboxnexttothenameofthepackageeg.abind

Toload(ie.use)apackageinRStudio

(Alternatively:manuallywriteattheRprompt>library(”nameofpackage”)

GoToViewerPanel.PressthetabPackages.

Noticethat:> library(abind) isshownintheRconsole


Task

46

Inthefollowingpartoftheworkshop,wewillusespecificpackagesinRinthisworkshop:

CheckifthesepackagesareavailableintheRstudio ofyourPC:

• moderndive• dplyr• ggplot2• tidyverse• MASS• glm2

Iftheyarenotinthelistofpackagesè Installthepackage(s)Iftheyarealreadyinthelistofpackagesè checkiftheyareloadedinthesystem,otherwiseloadthemup.


@haiza

R functions• Rcommandsareexecuted byrunningafunction• A functionisaname,whichistypedfollowedbyapairof

brackets.Argumentsareaddedinsidethebrackets> sqrt(2)> sin(pi)

• SometimesfunctionsinRhaveextraargument.> sum(2,3,5)> log(10,10)

• Rhasmanyin-builtfunctions.• Thesefunctionsarecontainedinspecificpackages• Thesefunctionscanalsobecombinedand

programmedmanually• Asfunctionsarebeingbuiltandcontributedallthe

timeè useHELPinRto(a)knowwhichpackagetheyarein(b)knowhowtousethem 47


@haiza48

Getting help for R functions: in R StudioGoToViewerPanel.PresstabHelp


@haiza

HelpfunctionsinRStudio

49

Task:Searchforlinear model

Getting help for R functions: in R StudioAttheViewerPanel-HelpTab,usekeywordsearchtofindthefunction&relatedpackage

ggplot2:fortify.lm


@haiza50




@haiza

SavingStuff&Exiting

51

• Bringsuptothisscreen:• makeitapracticetosave

yourworkonascriptfile

• Unlessyouneedtorecallcertainobjectsregularly,wedonotneedtosavetheworkspace.

• Workspaceisyourcurrentworkingenvironment.Thisincludesallthefunctions, objectsetc thatyouhavecreatedinthatsession.

• Toexit:• hitX(top rightcorner)

oratRprompt

>quit ( )

SAVING EXITING


@haiza

NEXT

•PARTB(i):PredictiveLinearModelforContinuousData(Response)- singlepredictorvariable

52

make predictions from your data using

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