Introduction to Statistical

Computing in Clinical Research

Biostatistics 212
Lecture 1

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

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

Course details
Introduction to Statistical Computing - 1 unit
Schedule 7 lectures, 7 lab sessions, on 7 Tuesdays in a row
Dates: August 4 September 15
Lectures 1:15-2:45
Labs 3:00-4:00
All in China Basin, CBL 6702 (6704 for lab)
Final Project Due 9/22/09

Course details
Introduction to Statistical Computing
Grading: Satisfactory/Unsatisfactory
Requirements:
-Hand in all six Labs (even if late)
-Satisfactory Final Project
-80% of total points
Reading: Optional

Course details, cont

Course Director
Mark Pletcher
Teaching Assistants
Justin Parekh Section 1
Elena Flowers Section 2 (Mac)
Tamara Castillo
Maurice Garcia

Lecturers
Andy Choi
Jennifer Cocohoba
Lab Instructor
Mandana Khalili

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 a figure with STATA
7- Organizing a project, making a table

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

Overview of labs, cont

Official Lab time is 3:00-4:00, but we will start right after
lecture, and you can leave when you are done.

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 leaders course email address:
biostat212_section1@yahoo.com (Justin) or
biostat212_section2@yahoo.com (Elena)

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.

Course Materials

Course Overview
Final Project
Lectures and Labs (just in time)
Other handouts
Books

Getting started with STATA

Session 1

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)

Software packages for analyzing

data

STATA
SAS
S-plus, and R
SPS-S
SUDAAN
Epi-Info
JMP
MatLab
StatExact

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

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 (free) is even easier than STATA?

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

Demo #1

Open the program

Load some data
Look at it
Run a command

STATA - Windows
Two basic windows
Command
Results

Optional windows
Variable list
History of commands

Other functions
Data browser/editor
Do file editor
Viewer (for log, help
files, etc)

STATA - Buttons

The usual open, save, print

Log-file open/suspend/close
Do-file editor
Browse and Edit
Break

STATA - Menus
Almost every command can be accessed via
menu

Demo #2
Enter in some data
Look at it
Run a couple of commands

Menu vs. Command line

Menu advantages
Look for commands you dont know about
See the options for each command
Complex commands easier learn syntax

Command line advantages

Faster (if you know the command!)
Closer to the program
Only way to write do files
Document and repeat analyses

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

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.

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

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

STATA commands
Analytic statistics 2 categorical variables

STATA commands
Analytic statistics 2 categorical variables
tabulate [var1] [var2]
Cross-tab
Descriptive options
, row
, col

(row percentages)
(column percentages)

Statistics options
, chi2
, exact

(chi2 test)
(fishers exact test)

Getting help
Try to find the command on the pull-down menus
Help menu
If you dont know the command - Search...
If you know the command - Stata command...

Try the manuals

more detail, theoretical underpinnings, etc

STATA commands
Analytic statistics 1 categorical, 1 continuous

STATA commands
Analytic statistics 1 categorical, 1 continuous
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

STATA commands
Analytic statistics 2 continuous

STATA commands
Analytic statistics 2 continuous
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)]

Demo #3

Load a STATA dataset

Explore the data
Describe the data
Answer some simple research questions
Gender and HTN, age and HTN

In Lab Today
Familiarize yourself with Stata
Load a dataset
Use Stata commands to analyze data and fill
in the blanks

Next week
Do files, log files, and workflow in Stata
Find a dataset!

Website addresses
Course website
http://www.epibiostat.ucsf.edu/courses/schedule/biostat212.html

Computing information
http://www.epibiostat.ucsf.edu/courses/ChinaBasinLocation.html
#computing

Download RDP for Macs (for Stata 10 Server)

http://www.microsoft.com/mac/otherproducts/otherproducts.aspx?
pid
=remotedesktopclient

Citrix Web Server

http://apps.epi-ucsf.org/