Bare-Bones R.ppt

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1、Bare-Bones R,A Brief Introductory GuideThomas P. Hogan University of Scranton 2010 All Rights Reserved,Citation and Usage,This set of PowerPoint slides is keyed to Bare-Bones R: A Brief Introductory Guide, by Thomas P. Hogan, SAGE Publications, 2010.All are welcome to use and/or adapt the slides wit

2、hout seeking further permission but with the usual professional acknowledgment of source.,Part 1: Base R,1-1 What is RA computer language, with orientation toward statistical applicationsRelatively newGrowing rapidly in use,1-2 Rs Ups and Downs,Plusses Completely free, just download from Internet Ma

3、ny add-on packages for specialized uses Open sourceMinuses Obscure terms, intimidating manuals, odd symbols, inelegant output (except graphics),1-3 Getting Started: Loading R,Have Internet connection Go to http:/cran.r-project/ R for Windows screen, click “base” Find, click on download R Click Run,

4、OK, or Next for all screens End up with R icon on desktop,At http:/cran.r-project.org/,Downloading Base R Figs 1.1 1.4,Click on WindowsThen in next screen, click on “base”Then screens for Run, OK, or NextAnd finally “Finish” will put R icon on desktop,What You Should Have when clicking on R icon: Rg

5、ui and R Console ending with R prompt () Fig 1.5,The R prompt (), This is the “R prompt.” It says R is ready to take your command.,1-4 Using R as Calculator,Enter these after the prompt,observe output 2+3 23+(5) 6/2+(8+5) 2 3 + (5),More as Calculator,You can copy and paste, but dont include the Use

6、# at end of command for notes, e.g. (22+ 34+ 18+ 29+ 36)/5 #Calculating the average, aka meanR as calculator: Not very useful,1-5 Creating a Data Set, Scores = c(22, 34, 18, 29, 36)c means “concatenate” in R in plain English “treat as data set”Now do:ScoresR will print the data set,Important Rules,W

7、e created a variable Variable names are case sensitive No blanks in name (can use _ or . to join words, but not -) Start with a letter (cap or lc) Can use - instead of =,Another variable,Create SCORES, using SCORESSCORES Scores,Non-numeric Data,Enclose in quotes, single or double Separate entries wi

8、th comma Example: names = c(“Mary”, “Tom”, “Ed”, “Dan”, “Meg”),Saving Stuff,To exit: either X or quit ( ) Brings up this screen:Do what you want: Yes or No Do Yes, then re-open R, get Scores & names,Special Note on Saving,Previous slide assumes you control computer If not, use File, Save Workspace,

9、name file, click Save Works much like saving a file in Microsoft To retrieve, do File, Load Workspace, find file, click Open,1-6 Using R Functions: Simple Stuff,Commands for mean, sd, summary (NB: function names case sensitive)mean(Scores) sd(Scores) summary(Scores)Command for correlation cor(Scores

10、,SCORES),R functions,A zillion of em Rs big strength, most common use For examples: Help R functions(text) Enter name of a function (e.g., sd) Yields lots (!) of information,1-7 Reading in Larger Data Sets,In Excel, enter (or download) the SATGPA20 fileSave as .xlsThen save as Text (tab delimited) f

11、ile Will have .txt extension, Larger Data Sets The read.table command,Now read into R like this:SATGPA20R=read.table(“E:/R/SATGPA20.txt“, header =T)Need exact path, in quotesheader = T T or TRUE, F or FALSE Depends on opening line of file,The file.choose ( ) command,At enter file.choose ( ) Accesses

12、 your systems files, much like Open in Microsoft Find the file, click on it R prints the exact path in R Console Can copy and paste into read.table,Checking what youve got:,Enter SATGPA20R Then mean (SATGPA20R) Try mean (GPA),The attach Command,To access individual variables, do this: attach(SATGPA2

13、0R)Now try: mean(GPA),The data.frame Command,Lets create these 3 variables with c IQ = c(110, 95, 140, 89, 102) CS = c(59, 40, 62, 40, 55) WQ = c(2, 4, 5, 1, 3) Then put them together with: All_Data = data.frame(IQ, CS, WQ) Check with: mean(All_Data),1-8 Getting Help,help(sd) example(sd) On R Consol

14、e:HelpR functions (text)Enter function name, click OK Reminder: function names case sensitive,Rs “function” terms,R language: function(arguments)Plain English: Do this (to this)or Do this (to this, with these conditions),1-9 Dealing with Missing Data,NB: Its a pain in R!Key items In data, enter NA f

15、or a missing value In (most) commands, use na.rm=T,Examples for missing data,Data=c(2,4,6,NA,10) mean(Data, na.rm=T)Add to the SATGPA20 file 21 1 NA NA NA 3.14 23 2 1 NA NA 2.86 Etc. and create new file SATGPA25R Then mean(SATGPA25R, na.rm=T) Note exception for cor function (use=complete),1-10 Using

16、 R Functions: Hypothesis tests,Be sure you have an active data set (SATGPA25R), using attach if neededThen, to test male vs. female on SATM: t.test(SATMSEX) # note tildeExamples of changing defaults: t.test(SATMSEX, var.equal=TRUE, conf.level=0.99),Hypothesis tests: Chi-square,Using SEX and State va

17、riables in SATGPA25Rchisq.test (SEX, State),1-11 R Functions for Commonly Used Statistics,function calculates this mean ( ) mean median ( ) medianmode ( ) mode sd ( ) standard deviation range ( ) range IQR ( ) interquartile rangemin ( ) minimum value max ( ) maximum value cor ( ) correlation quantil

18、e ( ) percentile t.test ( ) t-testchisq.test ( ) chi-sqaure NB1: See notes in text for details NB2: R contains many more functions,1-12 Two Commands for Managing Your Files, ls ( ) Will list your currently saved files rm (file) Insert file name; this will remove the fileNB: R has many such commands,

19、1-13 R Graphics,R graphs: good, simple Lets start with hist and boxplot with the SATGPA25R file hist(SATM) boxplot(SATM) boxplot(SATV, SATM) R Graphics window opens, need to minimize to get R Console,More Graphics: plot,Create these variables RS=c(12,14,16,18,25) MS=c(10,8,16,12,20)Now do this: plot

20、(RS, MS),Line of Best Fit,Do these for the RS and MS variables: lm(MSRS) # lm means linear model res=lm(MSRS) # res means residuals abline(res) # read as a-b line,Controlling Your Graphics: A Brief Look,R has many (often obscure) ways for controlling graphics; well look at a few Basically, well chan

21、ge “defaults”Examples (try each one): Limits (ranges) for X and Y axes plot(RS, MS, xlim = c(5,25), ylim = c(5,25),Controlling Graphs: More Examples,Plot characters: plot(RS, MS, pch=3)Line widths plot(RS, MS, pch=3, lwd=5)Axis labels plot(RS, MS, xlab = “Reading Score”, ylab = “Math Score”)You can

22、put them all together in one command,Part 2: R Commander,2-1 What is R Commander? Point and click version of R Uses (and prints) base R commandsLoading: Easy its just a package See next slide,Loading Rcmdr,On R Gui, top menu bar click Packages, then Install package(s).Pick a CRAN mirror site (nearby

23、), click OK.From the list of packages ,scroll to Rcmdr, highlight it, click OK After it loads, do these: Check with: library ( ) Activate with: library (Rcmdr),Rcmdrs extra packages,Scary message when first activating Rcmdr:Just click Yes and take a break,The R Commander Window,You get, R Commander

24、window withScript windowOutput window (incl Submit button)Message window,2-2 R Commander Windows and Menus,File Edit Data * Statistics * Most important for us Graphs * Models Distributions Tools Help,Our Lesser Used Menus,File Table 2.1 Much like in Microsoft Manage files Edit Table 2.2 Much like in

25、 Microsoft Can do with right click of mouse,Our Lesser Used Menus (cont),Models Mostly more advanced stats DistributionsTools Load packages Options change output defaults Help Searchable index R Commander manual,2-3 The Data Menu (very important) (Submenus for creating/getting data sets),New data se

26、t create new data setLoad data set only for existing .rda dataImport data import from various file typesData in packages not important for us,Data Menu (cont.) (Submenus for managing data sets),Active data set Do stuff with current data setManage variables in active data set Do stuff with variables

27、in current data set,New data set Fig. 2.3,Click on it, brings up spreadsheetName it SampleData,New data set (cont),Enter these data: var1 var2 var3 2 1 5 5 4 7 3 7 8 6 8 9 9 2 9 Then kill window with X Note: SampleData in Active Data Set,Now Try These,View active data set Edit active data set In Scr

28、ipt window, type* mean(SampleData) sd (SampleData) mean(var1) gives error message Attach(SampleData) mean(var1) * When typing do not include , do hit Submit,Changing “var” names,DataManage variables in active data setRename variables Change names to Rater1, Rater2, Rater3Then check withmean(SampleDa

29、ta)mean(Rater1),Compute new variable,DataManage variables in active data set Compute new variable Give name to new variable, call it Total In Expression to compute, enter Rater1+Rater2+Rater3 Check with View data set mean (SampleData),Import data (very important submenu),Allows importing from .txt f

30、ile SPSS file Excel file Several others Try it with a .txt file (must already exist; try with SATGPA25.txt),Convert Numeric Variables to Factors,Recall types of scales (esp. nominal) Rcmdr assumes numeric To convert to nominal (factor) Data, then Manage variables in active data set, and Convert nume

31、ric variables to factors. Highlight the variable you want to convert, click OK. In the next window, give labels to the levels of the variable. Try with SEX and State in SATGPA25R,2-4 The Statistics Menu,Obviously very important Most pretty clear how to do Some go beyond intro stats Some surprises on

32、 whats where Well just sample some of them Put SATGPA25R in Active data set,Statistics: Summaries (Try each of these with SATGPA25R in Data set, observe output),Active data set (see next slide) Numerical summaries (see next slide) Frequency distributions Summaries Count missing observations Table of

33、 statistics Correlation matrix Correlation test Shapiro-Wilk test of normality,Getting started on Stat menu,Statistics Summaries - Active data setStatistics Summaries Numerical summariesEtc. with others,Numerical Summaries Screen Fig 2.4,Statistics: Means (Try t-test, ANOVA),Single-sample t-test Ind

34、ependent samples t-test (TRY*) Paired t-test One-way ANOVA (TRY*) Multi-way ANOVA * With SATGPA25R,Independent Samples t-test (Do SATM by SEX) Fig 2.7,One-Way ANOVA (Do GPA by State) Fig 2.8,Two-Way Table (chi-square) Fig 2.9,Statistics - Contingency tables - Two-Way table,2-5 The Graphics Menu,All

35、pretty intuitive (if you know the graph) Try with SATGPA25R Pie: State Histogram: SATM Boxplot by group: SATM by SEX Scatterplot: GPA from SATV,Changing Graphs Appearance,Rcmdr Graphs uses defaults Change them in Script window Use commands given earlier Many ways to do; not terribly intuitive See ex

36、ample on next slide,Changing Graphs Defaults: Example,Histogram of GPA (with defaults): Hist(SATGPA25R$GPA, scale=“frequency“, breaks=“Sturges“, col=“darkgray“)copy, paste, change, Submit Hist(SATGPA25R$GPA, scale=“frequency“, breaks=4, col=“black“, lwd=3),2-6 The Distributions Menu: Two Quick Examp

37、les,Distributions Continuous distributions Normal distributionNormal probabilities insert -1.5 DistributionsContinuous distributionst distributiont probabilities insert 1.71, df 28,Part 3: Some Other Stuff,Supplementary, Not Essential, Brief3-1 A Few Other Ways to Enter Data 3-2 Exporting R Results

38、3-3 Bonus: Build Your Own Functions 3-4 An Example of an Add-on Package 3-5 Keeping Up to Date 3-6 Going Further: Selected References,3-1 A Few Other Ways to Enter Data,From Word, a few rules One space between entries NA for missing data Save as Plain text (.txt) Access with read.table,From Word: Ex

39、ample,Sample data Age Pop Looks 18 5 65 20 1 13 21 6 34 NA 9 60 21 7 98 Save as APL.txt on E drive, folder R Read in as: APL = read.table(“E:/R/APL.txt”, header=T),Checking from Word,Do these: APL mean (APL) mean (Pop) gives error attach (APL) mean (Pop),From SPSS file,Be sure you have foreign libra

40、ry Check with: library ( ) if needed, load Activate with: library (foreign) Have an SPSS file FinalData, which well put into FinalR, using read.spss andto.data.frame like thisFinalR = read.spss(E/Project/FinalData.sav, to.data.frame = T),3-2 Exporting R Results,For most intro applications, youll be

41、content with output on R Console or Rcmdr Output windowYou can copy and paste to Word Hint: Use monospaced font for better alignmentCan also save to a variety of formats from Base R or Rcmdr,Exporting Stats from Base R,Stats to an Excel file R object = function(data set) MYMEANS = mean (SATGPA20R) S

42、ave MYMEANS as a .csv file Then write.csv(MYMEANS, file=“exact path”) write.csv(MYMEANS, file=“E:/R/MYMEANS.csv”) Can access MYMEANS.csv with Excel Can read it, in R, with read.csv(MYMEANS),Exporting Graphs from Base R,Easy in R Graphics window and works same for base R and Rcmdr Right click on the

43、graph Copy as metafile (and paste wherever) Save as metafile (and save wherever),Exporting from R Commander,Easy, works much like in Word After running a stat, Go to File menu, Save output as, give file a name and destination, click Save Note file saved as a .txt file Saving graphs: Same as from Bas

44、e R,3-3 Bonus: Build Your Own Functions,You can custom-make a function and save it for future use Example: function to get mean of a data set + 2 times its SD weirdstat = function(x) mean(x) + (2*sd(x) Now try: weirdstat(GPA) Function names get saved like data sets and they are case sensitive,3-4 An

45、 Example of an Add-on Package,Getting Info about Packages (need Internet) Take it slowly Go to Task Views in http:/cran.r-project.org/ Gives categories of packages (23 now) Click on link for a category Package names: usually cryptic, often obscure To see whats in a package: Click on its link Look at

46、 its Reference Manual,Installing an Add-on Package,Follow usual steps for download Be sure to activate with library(pkg) Download psychometric packageUsing an Add-on Package Basically a collection of functionsExamples with psychometric package r.nil(r, n) rdif.nul(r1, r2, n1, n2),3-5 Keeping Up to D

47、ate,All parts of R (base, Commander, add-on packages) periodically updatedCheck cran-r site for updatesUpdate by downloading new version (need Internet connection for this),3-6 Selected References,Key URLs R home: http:/www.r-project.org/ Download: http:/cran.r-project.org/ For many other introducti

48、ons to R:http:/cran.r-project.org/other-docs.html,References (cont),Some Official books online as pdfs Fox, J. (2005). Getting started with the R Commander R Development Core Team (2009). R Data Import/Export version 2.9.0.Venables, W. N., Smith, D. M., & the R Development Core Team (2009). An intro

49、duction to R. Notes on R: A programming environment for data analysis and graphics version 2.9.0.,References (cont),Some other books Dalgaard, P. (2008). Introductory statistics with R (2nd ed.). New York: Springer.Everitt, B. S., & Hothorn, T. (2006). A handbook of statistical analyses using R. Boc

50、a Raton, FL: Chapman and Hall.Murrell, P. (2005). R graphics. Boca Raton, FL: Chapman and Hall.,To cite use of R,To cite the use of R for statistical work, R documentation recommends the following:R Development Core Team (2009). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http:/www.R-project.org.Get the latest citation by typing citation ( ) at the prompt in the R Console.,