1. Introduction to Statistical Computing in Clinical Research Biostatistics 212 Lecture 1

2. Today... Course overview –Course objectives –Course details: grading, homework, etc –Schedule, lecture overview Where does Stata fit in? Basic data analysis with Stata Stata demos Lab

3. Course Objectives Introduce you to using STATA and Excel for –Data management –Basic statistical and epidemiologic analysis –Turning raw data into presentable tables, figures and other research products Prepare you for Fall courses Start analyzing your own data

4. Course Objectives NOT Statistical theory –You’ll get a bit today and later in the course, but we don’t focus on this. –I’m a clinical epidemiologist, not a statistician

5. Course details Biostats 212 –1 Unit Course –Satisfactory/Unsatisfactory vs. Grades –7 Sessions – Lecture + Lab –Online Office Hours –Online Forum

6. Course details Course Teaching Staff –Brief introductions Mark Pletcher, MD MPH Jen Cocohoba, PharmD, MAS Mohammad Al Komser, MD Sanoj Punnen, MD Elizabeth Rogers, MD Melissa Rosenstein, MD Mandana Khalili, Barbara Grimes, Nancy Hills

7. Course details Lectures –Tuesdays 1:15-2:45, but most will be shorter –Simulcast to 6704! (new this year) Rationale (why not move to a lecture hall?) 30 second delay “Pop over” to 6702 to ask a question? –Both didactic and “demo’s”, time for questions –Jen gives last lecture – special format?

8. Course details Recorded Lectures –Audio + video of lecturer + video of screen –Available same day for viewing –Links posted on website syllabus

9. Course details Labs –Tuesdays 3:00-4:00 officially, but usually starts earlier –6702 and 6704 –TA’s staff from start to 4:00 –Lab instructors staff from 3:00-4:00 –Most important part of the course!

10. Course details Online Office Hours: –Thursdays, 8:00-9:30AM –Jennifer Cocohoba (Asst Course Director) will lead –Serves as the lab session for off-site (online only) students –Will use GoToMeeting See instructions posted on the Syllabus –Drop in if you need help with lab!

11. Course details Forum –Demo –Post all questions here! TA turnaround time –Before you post, see if it’s already there and answered –Consider turning ON all your alerts around lab time? –Quick demo

12. Course details Course Requirements –Hand in all six Labs (even if late) –Satisfactory Final Project Not required –Reading –Attendance

13. Course details Grading (not relevant for all students) –Letter grades: Standard cutoffs 90-100% A 80-89% B 70-79% C 60-69% D <60% or Course Requirements not met: F –Satisfactory/Unsatisfactory >80%Satisfactory

14. Overview of lecture topics 1- Introduction to STATA 2- Do files, log files, and workflow in STATA 3- Generating variables and manipulating data with STATA 4- Using Excel 5- Basic epidemiologic analysis with STATA 6- Making tables and figures with STATA 7- Advanced Programming Topics

15. Overview of labs Lab 1 – Load a dataset and analyze it Lab 2 – Learn how to use do and log files Lab 3* – Import data from excel, generate new variables and manipulate data, document everything with do and log files. Lab 4 – Using and creating Excel spreadsheets Lab 5* – Epidemiologic analysis using Stata Lab 6 – Making a figure with Stata Last lab session will be dedicated to working on the Final Project * - Labs 3 and 5 are significantly longer and harder than the others

16. Overview of labs, cont Official In-Person Lab time is 3:00-4:00 on Tuesday, but we will start right after lecture, and you can leave when you are done.

17. Overview of labs, cont Labs are due the following week prior to lecture. Labs turned in late (less than 1 week) will receive only half credit; after that, no points will be awarded. However, ALL labs must be turned in to pass the class (even if no points are awarded). Lab 1 is paper Labs 2-6 are electronic files, and should be emailed to your section leader’s course email address: biostat212_section1@yahoo.com (Melissa/Sanoj) or biostat212_section2@yahoo.com (Elizabeth/Mohammed)

18. Final Project Create a Table and a Figure using your own data, document analysis using Stata. Due 1 week after last lab session, 20 points docked for each 1 day late. See 1-page description in Syllabus Start looking for data!

19. Course Materials Online Syllabus (http://www.epibiostat.ucsf.edu/courses/schedule/biostat212.html)http://www.epibiostat.ucsf.edu/courses/schedule/biostat212.html –Lectures and Labs/Datasets (“just in time”) –Miscellaneous handouts –Final Project –Short demo

20. Getting started with STATA Session 1

21. Types of software packages used in clinical research Statistical analysis packages Spreadsheets Database programs Custom applications –Cost-effectiveness analysis (TreeAge, etc) –Survey analysis (SUDAAN, etc)

22. Software packages for analyzing data STATA SAS S-plus, and R SPS-S SUDAAN Epi-Info JMP MatLab StatExact

23. Why use STATA? Quick start, user friendly Immediate results, response You can look at the data Menu-driven option Good graphics Log and do files Good manuals, help menu

24. Why NOT use STATA? SAS is used more often? SAS does some things STATA does not? Programming easier with S-plus and R? R is free Complicated data structure and manipulation easier with SAS? Epi-info is free and even easier than STATA?

25. STATA – Basic functionality Holds data for you –Stata holds 1 “flat” file dataset only (.dta file) Listens to what you want –Type a command, press enter Does stuff –Statistics, data manipulation, etc Shows you the results –Results window

26. Demo #1 Open the program Entering vs. loading data Look at data Run a command Orient to windows and buttons

27. STATA - Windows Two basic windows –Command –Results Optional windows –Variable list –Properties –History of commands Other functions –Data browser/editor –Variables Manager –Do file editor –Viewer (for log, help files, etc)

28. STATA - Buttons The usual – open, save, print Log-file open/suspend/close Do-file editor Browse and Edit Break

29. STATA - Menus Almost every command can be accessed via menu  dialog box

30. Menu vs. Command line Menu advantages –Browse for commands you don’t know already –See the options for each command in dialog boxes –Good way to learn syntax for complex commands Command line advantages –MUCH faster –ONLY way to write “do” files Document and repeat analyses

31. Demo #2 Load a STATA dataset –(intro to CARDIA) Explore the data Describe the data Answer some simple research questions –Variables: male sex, smoking, binge drinking, BMI and systolic blood pressure

32. STATA commands Describing your data describe [varlist] –Displays variable names, types, labels list [varlist] –Displays the values of all observations codebook [varlist] –Displays labels and codes for all variables

33. STATA commands Descriptive statistics – continuous data summarize [varlist] [, detail] –# obs, mean, SD, range –“, detail” gets you more detail (median, etc) ci [varlist] –Mean, standard error of mean, and confidence intervals –Actually works for dichotomous variables, too.

34. STATA commands Graphical exploration – continuous data histogram varname –Simple histogram of your variable graph box varlist –Box plot of your variable qnorm varname –Quantile plot of your variable to check normality

35. STATA commands Descriptive statistics – categorical data tabulate [varname] –Counts and percentages –(see also, table - this is very different!)

36. STATA commands Analytic statistics – 2 categorical variables

37. tabulate [var1] [var2] –“Cross-tab” –Descriptive options, row(row percentages), col(column percentages) –Statistics options, chi2(chi2 test), exact(fisher’s exact test)

38. Getting help Try to find the command on the pull-down menus Help menu –If you don’t know the command – “Search...” –If you know the command – “Stata command...” Try the manuals –PDF files with more detail, theoretical underpinnings, etc –Accessed through the help menu

39. STATA commands Analytic statistics – 1 categorical, 1 continuous

40. bysort catvar: summarize [contvar] –mean, SD, range of one in subgroup ttest [contvar], by(catvar) –t-test oneway [contvar] [catvar] –ANOVA table [catvar] [, contents(mean [contvar]…) –Table of statistics

41. STATA commands Analytic statistics – 2 continuous

42. scatter [var1] [var2] –Scatterplot of the two variables pwcorr [varlist] [, sig] –Pairwise correlations between variables –“sig” option gives p-values spearman [varlist] [, stats(rho p)] lowess yvar xvar

43. In Lab Today… Expect some chaos! –IT will be here to help with wireless, logins, etc –All ATCR and MAS students need logins for our network Familiarize yourself with Stata Load a dataset Use Stata commands to analyze data and fill in the blanks

44. Next week Do files, log files, and workflow in Stata Start looking for a dataset

45. Website addresses Course website –http://www.epibiostat.ucsf.edu/courses/schedule/biostat212.htmlhttp://www.epibiostat.ucsf.edu/courses/schedule/biostat212.html Computing information –http://www.epibiostat.ucsf.edu/courses/ChinaBasinLocation.html# computinghttp://www.epibiostat.ucsf.edu/courses/ChinaBasinLocation.html# computing Download RDP for Macs (for Stata Server) –http://www.microsoft.com/mac/remote-desktop-clienthttp://www.microsoft.com/mac/remote-desktop-client Citrix Web Server –http://apps.epi-ucsf.org/http://apps.epi-ucsf.org/ Stata 12 Server –65.175.48.75