Introduction to Python for Econometrics,
Statistics and Data Analysis Kevin Sheppard
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3rdEdition,1stRevision
KevinSheppard UniversityofOxford
Monday9th September,2019
Chapter1 Introduction
1.1 Background
ThesenotesaredesignedforsomeonenewtostatisticalcomputingwishingtodevelopasetofskillsnecessarytoperformoriginalresearchusingPython.Theyshouldalsobeusefulforstudents,researchersor practitionerswhorequireaversatileplatformforeconometrics,statisticsorgeneralnumericalanalysis (e.g.numericsolutionstoeconomicmodelsormodelsimulation).
Pythonisapopulargeneral–purposeprogramminglanguagethatiswellsuitedtoawiderangeofproblems.1 RecentdevelopmentshaveextendedPython’srangeofapplicabilitytoeconometrics,statistics,and generalnumericalanalysis.Python–withtherightsetofadd-ons–iscomparabletodomain-specific languagessuchasR,MATLABorJulia.IfyouarewonderingwhetheryoushouldbotherwithPython(or anotherlanguage),anincompletelistofconsiderationsincludes:
YoumightwanttoconsiderRif:
• Youwanttoapplystatisticalmethods.ThestatisticslibraryofRissecondtonone,andRisclearly attheforefrontofnewstatisticalalgorithmdevelopment–meaningyouaremostlikelytofindthat new(ish)procedureinR.
• Performanceisofsecondaryimportance.
• Freeisimportant.
YoumightwanttoconsiderMATLABif:
• Commercialsupportandaclearchanneltoreportissuesisimportant.
• Documentationandorganizationofmodulesaremoreimportantthanthebreadthofalgorithms available.
• Performanceisanimportantconcern.MATLABhasoptimizations,suchasJust-in-Time(JIT)compilationofloops,whichisnotautomaticallyavailableinmostotherpackages.
YoumightwanttoconsiderJuliaif:
1Accordingtotherankingon http://www.tiobe.com/tiobe-index/,Pythonisthe5th mostpopularlanguage. http:// langpop.corger.nl/ ranksPythonas4th or5th .
• Performanceinaninteractivebasedlanguageisyourmostimportantconcern.
• Youdon’tmindlearningenoughPythontointerfacewithPythonpackages.TheJuliaecosystemis initsinfancyandabridgetoPythonisusedtoprovideimportantmissingfeatures.
• Youlikelivingonthebleedingedgeandaren’tworriedaboutcodebreakingacrossnewversionsof Julia.
• Youliketodomostthingsyourself.
Havingreadthereasonstochooseanotherpackage,youmaywonderwhyyoushouldconsiderPython.
• Youneedalanguagewhichcanactasanend-to-endsolutionthatallowsaccesstoweb-basedservices,databaseservers,datamanagementandprocessingandstatisticalcomputation.Pythoncan evenbeusedtowriteserver-sideappssuchasadynamicwebsite(seee.g. http://stackoverflow. com),appsfordesktop-classoperatingsystemswithgraphicaluserinterfaces,orappsfortabletsand phonesapps(iOSandAndroid).
• Datahandlingandmanipulation–especiallycleaningandreformatting–isanimportantconcern. PythonissubstantiallymorecapableatdatasetconstructionthaneitherRorMATLAB.
• Performanceisaconcern,butnotatthetopofthelist.2
• Freeisanimportantconsideration–Pythoncanbefreelydeployed,evento100sofserversinona cloud-basedcluster(e.g.AmazonWebServices,GoogleComputeorAzure).
• KnowledgeofPython,asageneralpurposelanguage,iscomplementarytoR/MATLAB/Julia/Ox/GAUSS/Stata.
1.2 Conventions
Thesenoteswillfollowtwoconventions.
1. Codeblockswillbeusedthroughout.
"""A docstring
# Comments appear in a different color
# Reserved keywords are highlighted and as assert break class continue def del elif else except exec finally for from global if import in is lambda not or pass print raise return try while with yield
# Common functions and classes are highlighted in a # different color. Note that these are not reserved,
2PythonperformancecanbemadearbitrarilyclosetoCusingavarietyofmethods,includingNumba(purepython),Cython (C/Pythoncreolelanguage)ordirectlycallingCcode.Moreover,recentadvanceshavesubstantiallyclosedthegapwithrespect tootherJust-in-TimecompiledlanguagessuchasMATLAB.
# and can be used although best practice would be # to avoid them if possible arraymatrix range list True False None
# Long lines are indented
some_text= 'This is a very, very, very, very, very, very, very, very, very, very, very, very long line '
2. Whenacodeblockcontains >>>,thisindicatesthatthecommandisrunninganinteractiveIPython session.Outputwilloftenappearaftertheconsolecommand,andwill not beprecededbyacommandindicator.
>>>x=1.0
>>>x+2
3.0
Ifthecodeblockdoesnotcontaintheconsolesessionindicator,thecodecontainedintheblockis intendedtobeexecutedinastandalonePythonfile.
import numpy as np
x=np.array([1,2,3,4])
y=np.sum(x) print(x) print(y)
1.3 ImportantComponentsofthePythonScientificStack
1.3.1 Python
Python3.5(orlater)isrequired.ThisprovidesthecorePythoninterpreter.Mostoftheexamplesshould workwiththelatestversionofPython2.7aswell.
1.3.2 NumPy
NumPyprovidesasetofarrayandmatrixdatatypeswhichareessentialforstatistics,econometricsand dataanalysis.
1.3.3 SciPy
SciPycontainsalargenumberofroutinesneededforanalysisofdata.Themostimportantincludeawide rangeofrandomnumbergenerators,linearalgebraroutines,andoptimizers.SciPydependsonNumPy.
1.3.4 JupyterandIPython
IPythonprovidesaninteractivePythonenvironmentwhichenhancesproductivitywhendevelopingcode orperforminginteractivedataanalysis.JupyterprovidesagenericsetofinfrastructurethatenablesIPython toberuninavarietyofsettingsincludinganimprovedconsole(QtConsole)orinaninteractivewebbrowserbasednotebook.
1.3.5 matplotlibandseaborn
matplotlibprovidesaplottingenvironmentfor2Dplots,withlimitedsupportfor3Dplotting.seabornis aPythonpackagethatimprovesthedefaultappearanceofmatplotlibplotswithoutanyadditionalcode.
1.3.6 pandas pandasprovideshigh-performancedatastructures.
1.3.7 statsmodels
statsmodelsispandas-awareandprovidesmodelsusedinthestatisticalanalysisofdataincludinglinear regression,GeneralizedLinearModels(GLMs),andtime-seriesmodels(e.g.,ARIMA).
1.3.8 PerformanceModules
Anumberofmodulesareavailabletohelpwithperformance.TheseincludeCythonandNumba.Cython isaPythonmodulewhichfacilitatesusingasimplePython-derivedcreoletowritefunctionsthatcanbe compiledtonative(Ccode)Pythonextensions.Numbausesamethodofjust-in-timecompilationto translateasubsetofPythontonativecodeusingLow-LevelVirtualMachine(LLVM).
1.4 Setup
TherecommendedmethodtoinstallthePythonscientificstackistouseContinuumAnalytics’Anaconda. Appendix 1.A.3 describesamorecomplexinstallationprocedurewithinstructionsfordirectlyinstalling PythonandtherequiredmoduleswhenitisnotpossibletoinstallAnaconda.
ContinuumAnalytics’Anaconda
Anaconda,afreeproductofContinuumAnalytics(www.continuum.io),isavirtuallycompletescientific stackforPython.ItincludesboththecorePythoninterpreterandstandardlibrariesaswellasmostmodulesrequiredfordataanalysis.Anacondaisfreetouseandmodulesforacceleratingtheperformanceof linearalgebraonIntelprocessorsusingtheMathKernelLibrary(MKL)areprovided.ContinuumAnalyticsalsoprovidesotherhigh-performancemodulesforreadinglargedatafilesorusingtheGPUtofurther accelerateperformanceforanadditional,modestcharge.Mostimportantly,installationisextraordinarily easyonWindows,Linux,andOSX.Anacondaisalsosimpletoupdatetothelatestversionusing
condaupdateconda condaupdateanaconda
Windows
InstallationonWindowsrequiresdownloadingtheinstallerandrunning.AnacondacomesinbothPython 2.7and3.xflavors,andthelatestPython3.xisthepreferredchoice.TheseinstructionsuseANACONDA toindicatetheAnacondainstallationdirectory(e.g.thedefaultisC:\Anaconda).Oncethesetuphas completed,openacommandprompt(cmd.exe)andrun
cd ANACONDA\Scripts condaupdateconda condaupdateanaconda condainstallhtml5libseaborn
whichwillfirstensurethatAnacondaisup-to-date. condainstall canbeusedlatertoinstallotherpackagesthatmaybeofinterest.NotethatifAnacondaisinstalledintoadirectoryotherthanthedefault,the fullpathshouldnotcontainUnicodecharactersorspaces.
Notes
TherecommendedsettingsforinstallingAnacondaonWindowsare:
• Installforallusers,whichrequiresadminprivileges.Ifthesearenotavailable,thenchoosethe“Just forme”option,butbeawareofinstallingonapaththatcontainsnon-ASCIIcharacterswhichcan causeissues.
• AddAnacondatotheSystemPATH-ThisisimportanttoensurethatAnacondacommandscanbe runfromthecommandprompt.
• RegisterAnacondaasthesystemPythonunlessyouhaveaspecificreasonnotto(unlikely).
IfAnacondaisnotaddedtothesystempath,itisnecessarytoaddthe ANACONDA and ANACONDA\Scripts directoriestothePATHusing
set PATH=ANACONDA;ANACONDA\Scripts;%PATH% beforerunningPythonprograms.
LinuxandOSX
InstallationonLinuxrequiresexecuting bashAnaconda3-x.y.z-Linux-ISA.sh where x.y.z willdependontheversionbeinginstalledand ISA willbeeitherx86ormorelikelyx86_64. AnacondacomesinbothPython2.7and3.xflavors,andthelatestPython3.xisthepreferredchoice.The OSXinstallerisavailableeitherinaGUIinstalled(pkgformat)orasabashinstallerwhichisinstalled inanidenticalmannertotheLinuxinstallation.Itisstronglyrecommendedthattheanaconda/binis prependedtothepath.Thiscanbeperformedinasession-by-sessionbasisbyentering export PATH=ANACONDA/bin;$PATH
OnLinuxthischangecanbemadepermanentbyenteringthislinein .bashrc whichisahiddenfilelocated in ~/.OnOSX,thislinecanbeaddedto .bash_profile whichislocatedinthehomedirectory(~/).3 Afterinstallationcompletes,execute condaupdateconda condaupdateanaconda condainstallhtml5libseaborn
3Usetheappropriatesettingsfileifusingadifferentshell(e.g. .zshrc forzsh).
whichwillfirstensurethatAnacondaisup-to-dateandthentoinstalltheIntelMathKernellibrary-linked modules,whichprovidesubstantialperformanceimprovements–thispackagerequiresalicensewhich isfreetoacademicusersandlowcosttoothers.Ifacquiringalicenseisnotpossible,omitthisline. condainstall canbeusedlatertoinstallotherpackagesthatmaybeofinterest.
Notes
AllinstructionsforOSXandLinuxassumethat ANACONDA/bin hasbeenaddedtothepath.Ifthisisnot thecase,itisnecessarytorun
cd ANACONDA cd bin
andthenallcommandsmustbeprependedbya . asin
./condaupdateconda
1.5 UsingPython
PythoncanbeprogrammedusinganinteractivesessionusingIPythonorbydirectlyexecutingPython scripts–textfilesthatendwiththeextension.py–usingthePythoninterpreter.
1.5.1 PythonandIPython
Mostofthisintroductionfocusesoninteractiveprogramming,whichhassomedistinctadvantageswhen learningalanguage.ThestandardPythoninteractiveconsoleisverybasicanddoesnotsupportuseful featuressuchastabcompletion.IPython,andespeciallytheQtConsoleversionofIPython,transforms theconsoleintoahighlyproductiveenvironmentwhichsupportsanumberofusefulfeatures:
• Tabcompletion-Afterentering1ormorecharacters,pressingthetabbuttonwillbringupalistof functions,packages,andvariableswhichmatchthetypedtext.Ifthelistofmatchesislarge,pressing tabagainallowsthearrowkeyscanbeusedtobrowseandselectacompletion.
• “Magic”functionwhichmaketaskssuchasnavigatingthelocalfilesystem(using %cd~/directory/ orjust cd~/directory/ assumingthat %automagic ison)orrunningotherPythonprograms(using run program.py)simple.Entering %magic insideandIPythonsessionwillproduceadetaileddescription oftheavailablefunctions.Alternatively, %lsmagic producesasuccinctlistofavailablemagiccommands.Themostusefulmagicfunctionsare
– cd -changedirectory
– edit filename -launchaneditortoedit filename
– ls or ls pattern -listthecontentsofadirectory
– run filename-runthePythonfile filename
– timeit -timetheexecutionofapieceofcodeorfunction
.
• Integratedhelp-WhenusingtheQtConsole,callingafunctionprovidesaviewofthetopofthehelp function.Forexample,entering mean( willproduceaviewofthetop20linesofitshelptext.
• Inlinefigures-BoththeQtConsoleandthenotebookcanalsodisplayfigureinlinewhichproducesa tidy,self-containedenvironment.Thiscanbeenabledbyentering %matplotlibinline inanIPython session.
• Thespecialvariable containsthelastresultintheconsole,andsothemostrecentresultcanbe savedtoanewvariableusingthesyntax x=_
• Supportforprofiles,whichprovidefurthercustomizationofsessions.
1.5.2 LaunchingIPython
OSXandLinux
IPythoncanbestartedbyrunning ipython intheterminal.IPythonusingtheQtConsolecanbestartedusing jupyterqtconsole
AsinglelinelauncheronOSXorLinuxcanbeconstructedusing bash-c "jupyter qtconsole"
Thissinglelinelaunchercanbesavedas filename.commandwhere filename isameaningfulname(e.g. IPython-Terminal)tocreatealauncheronOSXbyenteringthecommand chmod755/FULL/PATH/TO/filename.command
ThesamecommandcantocreateaDesktoplauncheronUbuntubyrunning sudoapt-getinstall--no-install-recommendsgnome-panel gnome-desktop-item-edit~/Desktop/--create-new andthenusingthecommandastheCommandinthedialogthatappears.
Windows(Anaconda)
TorunIPythonopencmdandenter IPython inthestartmenu.StartingIPythonusingtheQtConsoleis similarandissimplycalled QtConsole inthestartmenu.Launching IPython fromthestartmenushould createawindowsimilartothatinfigure 1.1
Next,run
jupyterqtconsole--generate-config intheterminalorcommandprompttogenerateafilenamed jupyter_qtconsole_config.py.Thisfilecontains settingsthatareusefulforcustomizingtheQtConsolewindow.Afewrecommendedmodificationsare
Figure1.1:IPythonrunninginthestandardWindowsconsole(cmd.exe).
c.IPythonWidget.font_size=11
c.IPythonWidget.font_family= "Bitstream Vera Sans Mono"
c.JupyterWidget.syntax_style= 'monokai'
ThesecommandsassumethattheBitstreamVerafontshavebeenlocallyinstalled,whichareavailable from http://ftp.gnome.org/pub/GNOME/sources/ttf-bitstream-vera/1.10/.Opening QtConsole should createawindowsimilartothatinfigure 1.2 (althoughtheappearancemightdiffer)ifyoudidnotusethe recommendationconfiguration.
1.5.3
GettingHelp
HelpisavailableinIPythonsessionsusing help(function).Somefunctions(andmodules)haveverylong helpfiles.WhenusingIPython,thesecanbepagedusingthecommand ?function or function? sothatthe textcanbescrolledusingpageupanddownandqtoquit. ??function or function?? canbeusedtotype theentirefunctionincludingboththedocstringandthecode.
1.5.4 RunningPythonprograms
Whileinteractiveprogrammingisusefulforlearningalanguageorquicklydevelopingsomesimplecode, complexprojectsrequiretheuseofcompleteprograms.ProgramscanberuneitherusingtheIPython magicwork %runprogram.py orbydirectlylaunchingthePythonprogramusingthestandardinterpreter using pythonprogram.py.TheadvantageofusingtheIPythonenvironmentisthatthevariablesusedin theprogramcanbeinspectedaftertheprogramrunhascompleted.DirectlycallingPythonwillrunthe programandthenterminate,andsoitisnecessarytooutputanyimportantresultstoafilesothatthey canbeviewedlater.4
4ProgramscanalsoberuninthestandardPythoninterpreterusingthecommand: exec(compile(open(’filename.py’).read(),’filename.py’,’exec’))
Figure1.2:IPythonrunninginaQtConsolesession. TotestthatyoucansuccessfullyexecuteaPythonprogram,inputthecodeintheblockbelowintoa textfileandsaveitas firstprogram.py.
# First Python program import time
print('Welcome to your first Python program ') input('Press enter to exit the program ') print('Bye!') time.sleep(2)
Onceyouhavesavedthisfile,opentheconsole,navigatetothedirectoryyousavedthefileandenter pythonfirstprogram.py.Finally,runtheprograminIPythonbyfirstlaunchingIPython,andtheusing %cd tochangetothelocationoftheprogram,andfinallyexecutingtheprogramusing %runfirstprogram.py
1.5.5 %pylab and %matplotlib
WhenwritingPythoncode,onlyasmallsetofcorefunctionsandvariabletypesareavailableintheinterpreter.Thestandardmethodtoaccessadditionalvariabletypesorfunctionsistouse imports,which explicitlyallowaccesstospecificpackagesorfunctions.Whileitisbestpracticetoonly import required functionsorpackages,therearemanyfunctionsinmultiplepackagesthatarecommonlyencountered inthesenotes.PylabisacollectionofcommonNumPy,SciPyandMatplotlibfunctionsthatcanbeeasilyimportedusingasinglecommandinanIPythonsession, %pylab.Thisisnearlyequivalenttocalling from pylab import *,sinceitalsosetsthe backend thatisusedtodrawplots.Thebackendcanbemanuallysetusing %pylab backend where backend isoneoftheavailablebackends(e.g., qt5 or inline).Similarly %matplotlib backend canbeusedtosetjustthebackendwithoutimportingallofthemodulesandfunctionscomewith %pylab
Mostchaptersassumethat %pylab hasbeencalledsothatfunctionsprovidedbyNumPycanbecalled
Figure1.3:Asuccessfultestthatmatplotlib,IPython,NumPyandSciPywereallcorrectlyinstalled. withoutexplicitlyimportingthem.
1.5.6 TestingtheEnvironment
Tomakesurethatyouhavesuccessfullyinstalledtherequiredcomponents,runIPythonusingshortcut orbyrunning ipython or jupyterqtconsole runinaterminalwindow.Enterthefollowingcommands, oneatatime(themeaningofthecommandswillbecoveredlaterinthesenotes).
>>>%pylabqt5
>>>x= randn(100,100)
>>>y= mean(x,0)
>>> import seaborn
>>> plot(y)
>>> import scipy as sp
Ifeverythingwassuccessfullyinstalled,youshouldseesomethingsimilartofigure 1.3.
1.5.7 jupyternotebook
Ajupyternotebookisasimpleandusefulmethodtosharecodewithothers.Notebooksallowforafluid synthesisofformattedtext,typesetmathematics(usingLATEXviaMathJax)andPython.Theprimarymethod forusingnotebooksisthroughawebinterface,whichallowscreation,deletion,exportandinteractive editingofnotebooks.
Figure1.4:ThedefaultIPythonNotebookscreenshowingtwonotebooks. Tolaunchthejupyternotebookserver,openacommandpromptorterminalandenter
jupyternotebook
Thiscommandwillstarttheserverandopenthedefaultbrowserwhichshouldbeamodernversionof Chrome(preferable),ChromiumorFirefox.IfthedefaultbrowserisSafari,InternetExplorerorEdge,the URLcanbecopiedandpastedintoChrome.Thefirstscreenthatappearswilllooksimilartofigure 1.4, exceptthatthelistofnotebookswillbeempty.ClickingonNewNotebookwillcreateanewnotebook, which,afterabitoftyping,canbetransformedtoresemblefigure 1.5.Notebookscanbeimportedby dragginganddroppingandexportedfromthemenuinsideanotebook.
1.5.8 IntegratedDevelopmentEnvironments
AsyouprogressinPythonandbeginwritingmoresophisticatedprograms,youwillfindthatusinganIntegratedDevelopmentEnvironment(IDE)willincreaseyourproductivity.Mostcontainproductivityenhancementssuchasbuilt-inconsoles,codecompletion(orIntelliSense,forcompletingfunctionnames) andintegrateddebugging.DiscussionofIDEsisbeyondthescopeofthesenotes,although Spyder isa reasonablechoice(free,cross-platform). AptanaStudio isanotherfreealternative.MypreferredIDEis PyCharm,whichhasacommunityeditionthatisfreeforuse(theprofessionaleditionislowcostforacademics).
Figure1.5:AnIPythonnotebookshowingformattedmarkdown,LATEXmathandcellscontainingcode.
Spyder
SpyderisanIDEspecializedforuseinscientificapplicationsofPythonratherthanforgeneralpurpose applicationdevelopment.Thisisbothanadvantageandadisadvantagewhencomparedtoafullfeatured IDEsuchasPyCharm,PythonToolsforVisualStudio(PVTS),PyDevorAptanaStudio.Themainadvantage isthatmanypowerfulbutcomplexfeaturesarenotintegratedintoSpyder,andsothelearningcurveis muchshallower.Thedisadvantageissimilar-inmorecomplexprojects,orifdevelopingsomethingthatis notstraightscientificPython,Spyderislesscapable.However,nettingthesetwo,Spyderisalmostcertainly theIDEtousewhenstartingPython,anditisalwaysrelativelysimpletomigratetoasophisticatedIDEif needed.
Spyderisstartedbyentering spyder intheterminalorcommandprompt.Awindowsimilartothatin figure 1.6 shouldappear.Themaincomponentsaretheeditor(1),theobjectinspector(2),whichdynamicallywillshowhelpforfunctionsthatareusedintheeditor,andtheconsole(3).Bydefault,Spyderopens astandardPythonconsole,althoughitalsosupportsusingthemorepowerfulIPythonconsole.Theobject inspectorwindow,bydefault,isgroupedwithavariableexplorer,whichshowsthevariablesthatarein memoryandthefileexplorer,whichcanbeusedtonavigatethefilesystem.Theconsoleisgroupedwith anIPythonconsolewindow(needstobeactivatedfirstusingtheInterpretersmenualongthetopedge), andthehistorylogwhichcontainsalistofcommandsexecuted.Thebuttonsalongthetopedgefacilitate savingcode,runningcodeanddebugging.
1.6 Exercises
1. InstallPython.
2. Testtheinstallationusingthecodeinsection 1.5.6
3. ConfigureIPythonusingthestart-upscriptinsection ??.
