BIOSTAT 212: Introduction to Statistical Computing in Clinical Research (Summer 2018)

Section outline

• Select section General

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  General

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    Home Overall Schedule Courses Programs Rosters

    Introduction to Statistical Computing
    in Clinical Research (BIOSTAT 212)

    BIOSTAT 212 Summer 2018 (1 unit) 
    Department of Epidemiology and Biostatistics
     Course Director: Kristen Aiemjoy, MSc PhD(c)
    Teaching Assistants: Ekland Abdiwahab, Rashed Alrasheed, Atul Kumar, Eduardo Rodriguez, Andrew Wang
    
    

  • Select activity Announcements

    

    Announcements Forum
  • Select activity BIOSTAT 212 Forum

    

    BIOSTAT 212 Forum
  • Select activity Stata commands used in each lecture:

    Stata commands used in each lecture:

  • Select activity Biostat 212 commands.do

    

    Biostat 212 commands.do File

    Uploaded 07/23/18, 15:44
  • Select activity Events:

    Events:

  • Select activity Missing Data and Multiple Imputation in Stata: August 20 12-1 in MH-1407

    

    Missing Data and Multiple Imputation in Stata: August 20 12-1 in MH-1407 File
  • Select activity Multilevel/Longitudinal Modeling in Stata: August 21st 12-1 in MH-1407

    

    Multilevel/Longitudinal Modeling in Stata: August 21st 12-1 in MH-1407 File
  • Select activity External resources:

    External resources:

  • Select activity Stata 15 Users Guide

    

    Stata 15 Users Guide URL
  • Select activity STATA Cheatsheets

    

    STATA Cheatsheets File
  • Select activity Princeton: Getting started in Stata

    

    Princeton: Getting started in Stata URL
  • Select activity UCLA: Data analysis examples

    

    UCLA: Data analysis examples URL
  • Select activity Seeing Theory: A visual introduction to probability and statistics

    

    Seeing Theory: A visual introduction to probability and statistics URL
  • Select activity Markdown Syntax

    

    Markdown Syntax URL
• Select section Tuesday, July 31, 2018, 1:15 PM - 2:45 PM

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  Tuesday, July 31, 2018, 1:15 PM - 2:45 PM

  Lecture 1: Introduction to Stata  
  

  What is Stata? Stata compared to other statistical software packages. Tour of Stata windows and features. Command syntax. Working Directories. Opening data sets. Stats built-in data sets. Exploring data (basics). using .do files. log files. Commenting in .do files

  Location: MH-1400 

  • Select activity Session Slides:

    Session Slides:
    

  • Select activity Lecture 1 slides

    

    Lecture 1 slides File

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  • Select activity Recommended readings:

    Recommended readings:

  • Select activity [Book] An Introduction to Stata for Health researc...

    [Book] An Introduction to Stata for Health researchers

    • Ch. 1. Getting started
    • Ch. 4. Command Syntax
    • Ch. 6. Getting data in and out of Stata
      
  • Select activity Stata User's guide 15

    Stata User's guide 15
    

  • Select activity Ch. 15. Saving and printing output – log files

    

    Ch. 15. Saving and printing output – log files
  • Select activity Ch. 16.1 .do file description

    

    Ch. 16.1 .do file description
  • Select activity The Stata user interface (Window...

    The Stata user interface (Windows)

  • Select activity The Stata user interface (Mac) ...

    The Stata user interface (Mac)

    
    

  • Select activity MarcDoc: Literate Programming in StataMarcDoc&nbsp...

    MarcDoc: Literate Programming in Stata
    

    MarcDoc Quick Tips

• Select section Tuesday, July 31, 2018, 3:00 - 4:00 PM

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  Tuesday, July 31, 2018, 3:00 - 4:00 PM

  Computer Lab  

  Location: MH-1400
  

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  • Select activity Introducing MarkDoc MarkDoc is a add-on package t...

    Introducing MarkDoc

    MarkDoc is a add-on package to generate dynamic documents (PDF, docX, TeX, html) from a Stata html file. 

    The help file is terrific and gives throrough instructions on syntax, adding graphs, tables, etc https://github.com/haghish/MarkDoc/wiki

  • Select activity Lab 1 slides: Introducing MarkDoc

    

    Lab 1 slides: Introducing MarkDoc File

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  • Select activity MarkDoc_Installation.do

    

    MarkDoc_Installation.do File

    Uploaded 07/20/18, 12:16
  • Select activity MarkDoc: Literate Programming in Stata

    

    MarkDoc: Literate Programming in Stata File PDF
  • Select activity Live coding demo: MarkDocYou do not need to turn t...

    Live coding demo: MarkDoc

    You do not need to turn this in

  • Select activity lab 1 demo

    

    lab 1 demo File

    Uploaded 08/1/18, 13:04
  • Select activity Lab 1 Download the .do file and open in Stata. Yo...

    Lab 1

    Download the .do file and open in Stata. You should be able to run the entire .do file to generate a PDF using the "markdoc" command. 

    This lab is for your own practice. You do not need to turn it in. 

  • Select activity Lab 1

    

    Lab 1 File

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• Select section Thursday, August 2, 2018, 11:00 AM - 12:30 PM

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  Thursday, August 2, 2018, 11:00 AM - 12:30 PM

  Office Hours
  

  Course faculty are available to address questions on course content including prior problem sets.
  

  Location:  MH-2800 and online or +1 646 558 8656 (Meeting ID: 125 284 468)

    

   
  
• Select section Tuesday, August 7, 2018, 1:15 - 2:45 PM

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  Tuesday, August 7, 2018, 1:15 - 2:45 PM

  Lecture 2: Exploring and describing data  
  

  Variable types. Finding help. Importing/Exporting data. Exploring data. Summarizing data. Add-on packages.  Immediate commands. File types. 

  Location: MH-1400
  

  • Select activity Lecture slides and data:

    Lecture slides and data:
    

  • Select activity Lecture 2 slides

    

    Lecture 2 slides File

    Uploaded 08/9/18, 15:42
  • Select activity accupuncture_baseline.dta

    

    accupuncture_baseline.dta File
  • Select activity Lecture audio/video recording (Access restricted t...

    Lecture audio/video recording (Access restricted to registered students):

  • Select activity Watch

    

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  • Select activity Recommended readings:

    Recommended readings:

  • Select activity [Book] An Introduction to Stata for Health re...

    [Book] An Introduction to Stata for Health researchers

    • Ch. 4. Command Syntax
    • Ch. 5. Variables
  • Select activity [eBook] Biostatistics in Public Health Using STATA

    [eBook] Biostatistics in Public Health Using STATA
    

  • Select activity Ch. 2. Data description

    

    Ch. 2. Data description File
• Select section Tuesday, August 7, 2018, 3:00 - 4:00 PM

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  Tuesday, August 7, 2018, 3:00 - 4:00 PM

  Computer Lab  

  Location: MH-1400 
  

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  • Select activity Assignment 1 Assignment 1 due: Tuesday, August 14...

    Assignment 1

    Assignment 1 due: Tuesday, August 14 at 1:00 PM

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    Assignment 1 File

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    Upload Assignment 1 here
• Select section Thursday, August 9, 2018, 11:00 AM - 12:30 PM

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  Thursday, August 9, 2018, 11:00 AM - 12:30 PM

  Office Hours
  

  Course faculty are available to address questions on course content including prior problem sets.
  

  Location:  MH-2800 and online or +1 646 558 8656 (Meeting ID: 125 284 468)

    

   
  
• Select section Tuesday, August 14, 2018, 1:15 - 2:45 PM

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  Tuesday, August 14, 2018, 1:15 - 2:45 PM

  Lecture 3: Data management and cleaning  

  Duplicate values. Missing data. Transforming variables. Sorting data. Variable names and labels. Tips for data management. Merging datasets. Reshaping data. Workflow. MarkDoc for creating dynamic documents

  Location: MH-1400 

  • Select activity Session Slides and Data:

    Session Slides and Data:

  • Select activity Lecture 3 material

    

    Lecture 3 material Folder
  • Select activity Lecture 3 notes .do file

    

    Lecture 3 notes .do file

    Uploaded 08/14/18, 15:30
  • Select activity Lecture audio/video recording (Access restricted t...

    Lecture audio/video recording (Access restricted to registered students):

  • Select activity Watch

    

    Watch URL

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  • Select activity Recommended readings:

    Recommended readings:
    

  • Select activity [Book] An Introduction to Stata for Health re...

    [Book] An Introduction to Stata for Health researchers

    • Ch. 8. Calculations
    • Ch. 9. Commands affecting data structure

    • Ch. 10 Taking good care of your data

    Stata data management manual

• Select section Tuesday, August 14, 2018, 3:00 - 4:00 PM

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  Tuesday, August 14, 2018, 3:00 - 4:00 PM

  Computer Lab  

  Location: MH-1400
  

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  • Select activity Assignment 2 Assignment 2 due: Tuesday, August 21...

    Assignment 2

    Assignment 2 due: Tuesday, August 21 at 1:00 PM

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    Assignment 2 Folder
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    Upload Assignment 2 here
• Select section Thursday, August 16, 2018, 11:00 AM - 12:30 PM

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  Thursday, August 16, 2018, 11:00 AM - 12:30 PM

  Office Hours
  

  Course faculty are available to address questions on course content including prior problem sets.
  

  Location:  MH-2800 and online or +1 646 558 8656 (Meeting ID: 125 284 468)

    

   
  
• Select section Tuesday, August 21, 2018, 1:15 - 2:45 PM

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  Tuesday, August 21, 2018, 1:15 - 2:45 PM

  Lecture 4: Data Visualization
  
  Anatomy of a graph. Graph commands. Schemes. Graph options. Saving and exporting. Plotting competition.

  Location: MH-1400
  

  • Select activity Session Slides and Data:

    Session Slides and Data:

  • Select activity Lecture 4 materials

    

    Lecture 4 materials Folder
  • Select activity Biostat212_2018_Lecture4_notes.do

    

    Biostat212_2018_Lecture4_notes.do File

    Uploaded 08/22/18, 13:04
  • Select activity GraphCombine_ChuckHuber.do

    

    GraphCombine_ChuckHuber.do File

    Uploaded 08/22/18, 13:05
  • Select activity Lecture audio/video recording (Access restricted t...

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  • Select activity Watch

    

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  • Select activity Recommended readings:

    Recommended readings:
    

  • Select activity [Book] An Introduction to Stata for Health re...

    [Book] An Introduction to Stata for Health researchers

    • Ch. 16. Graphs
      
  • Select activity Stata graphics manual

    

    Stata graphics manual File
  • Select activity Visual overview for creating graphs in stata

    

    Visual overview for creating graphs in stata URL
  • Select activity [ebook] A Picture is Worth a Thousand Tables

    

    [ebook] A Picture is Worth a Thousand Tables File
• Select section Tuesday, August 21, 2018, 3:00 - 4:00 PM

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  Tuesday, August 21, 2018, 3:00 - 4:00 PM

  Computer Lab  

  Location: MH-1400 
  

  • Select activity Guest lecture by Chuck Huber of Stata on marginspl...

    Guest lecture by Chuck Huber of Stata on marginsplot
    

  • Select activity In the spotlight: Visualizing continuous-by-continuous interactions with margins and twoway contour

    

    In the spotlight: Visualizing continuous-by-continuous interactions with margins and twoway contour URL
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  • Select activity Assignment 3 Assignment 3 Due: Tuesday, August 28...

    Assignment 3

    Assignment 3 Due: Tuesday, August 28 at 1:00 PM

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    Assignment 3 File

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  • Select activity Data visualization challenge (extra credit)

    Data visualization challenge (extra credit)

  • Select activity Data visualization extra credit

    

    Data visualization extra credit Assignment
• Select section Thursday, August 23, 2018, 11:00 AM - 12:30 PM

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  Thursday, August 23, 2018, 11:00 AM - 12:30 PM

  Office Hours
  

  Course faculty are available to address questions on course content including prior problem sets.
  

  Location:  MH-2800 and online or +1 646 558 8656 (Meeting ID: 125 284 468)

    

   
  
• Select section Tuesday, August 28, 2018, 1:15 - 2:45 PM

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  Tuesday, August 28, 2018, 1:15 - 2:45 PM

  Lecture 5: Commands for Statistical analyses

  Descriptive statistics (mean, SD, SE, confidence intervals). Introduction to statistical hypothesis tests in Stata: t-test, ANOVA, chi squared tests. Linear regression. Immediate commands
  

  Location: MH-1400 
  

  • Select activity Session Slides and Data:

    Session Slides and Data:

  • Select activity Lecture5_slides.pdf

    

    Lecture5_slides.pdf File

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    acupuncture.dta File
  • Select activity Lecture 5 slides with answers.pdf

    

    Lecture 5 slides with answers.pdf File

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  • Select activity Recommended readings:[Book] An Introduction t...

    Recommended readings:
    

    [Book] An Introduction to Stata for Health researchers

    • Ch. 11. Description and simple analysis 
    • Ch. 12. Regression analysis 

  • Select activity Choosing the correct statistical test

    

    Choosing the correct statistical test URL
• Select section Tuesday, August 28, 2018, 3:00 - 4:00 PM

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  Tuesday, August 28, 2018, 3:00 - 4:00 PM

  Computer Lab  

  Location: MH-1400
  

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  • Select activity Assignment 4 Assignment 4 due: Tuesday,&nbsp...

    Assignment 4

    Assignment 4 due: Tuesday, September 4 at 1:00 PM

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    Assignment 4 File

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    Upload Assignment 4 here
• Select section Thursday, August 30, 2018, 11:00 AM - 12:30 PM

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  Thursday, August 30, 2018, 11:00 AM - 12:30 PM

  Office Hours
  

  Course faculty are available to address questions on course content including prior problem sets.
  

  Location:  MH-2800 and online or +1 646 558 8656 (Meeting ID: 125 284 468)

    

   
  
• Select section Tuesday, September 4, 2018, 1:15 - 2:45 PM

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  Tuesday, September 4, 2018, 1:15 - 2:45 PM

  Lecture 6: Epi commands and tables  

  Basic epidemiology concepts. Epi commands in Stata. Interpretation of Stata output. Logistic regression. Packages for exporting tables (outreg2, tabout2)

  Location: MH-1400
  

  • Select activity Session Materials:

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  • Select activity tablePackagesInstall.do

    

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  • Select activity [Book] An Introduction to Stata for Health re...

    [Book] An Introduction to Stata for Health researchers

    • Ch. 11.4 Epidemiologic tables
    • Ch. 14 Measurement and diagnosis 
      
  • Select activity Publication quality tables in Stata: a tutorial for the tabout program

    

    Publication quality tables in Stata: a tutorial for the tabout program URL
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  • Select activity Using outreg2 to report regression output, descriptive statistics, frequencies and basic crosstabulations

    

    Using outreg2 to report regression output, descriptive statistics, frequencies and basic crosstabulations URL
  • Select activity Free & Interactive Online Introduction to LaTeX

    

    Free & Interactive Online Introduction to LaTeX URL
• Select section Tuesday, September 4, 2018, 3:00 - 4:00 PM

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  Tuesday, September 4, 2018, 3:00 - 4:00 PM

  Computer Lab  
  

  Location: MH-1400
  

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  • Select activity Assignment 5 Assignment 5 due: Tuesday, September...

    Assignment 5
    

    Assignment 5 due: Tuesday, September 11 at 1:00 PM

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• Select section Thursday, September 6, 2018, 11:00 AM - 12:30 PM

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  Thursday, September 6, 2018, 11:00 AM - 12:30 PM

  Office Hours
  

  Course faculty are available to address questions on course content including prior problem sets.
  

  Location:  MH-2800 and online or +1 646 558 8656 (Meeting ID: 125 284 468)

    

   
  
• Select section Tuesday, September 11, 2018, 1:15 - 2:45 PM

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  Tuesday, September 11, 2018, 1:15 - 2:45 PM

  Highlighted

  Lecture 7: Stored results, Macros, Matrices, Loops & Programs

  Live coding

  Location: MH-1400
  

  • Select activity Lecture7.do

    

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  • Select activity Lecture audio/video recording (Access restricted t...

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  • Select activity Recommended readings:

    Recommended readings:
    

  • Select activity [Book] An Introduction to Stata for Health re...

    [Book] An Introduction to Stata for Health researchers

    • Ch. 15.1. Random samples, simulations
    • Ch. 17. Advanced topics
  • Select activity [eBook] Biostatistics in Public Health Using STATA. CH 12 Introduction to Advanced Programming in STATA

    

    [eBook] Biostatistics in Public Health Using STATA. CH 12 Introduction to Advanced Programming in STATA File
  • Select activity Stata Programming Essentials

    

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  • Select activity Ch 18: Programming Stata (in Stata V15 Users Manual)

    

    Ch 18: Programming Stata (in Stata V15 Users Manual) URL
• Select section Tuesday, September 11, 2018, 3:00 - 4:00 PM

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  Tuesday, September 11, 2018, 3:00 - 4:00 PM

  Computer Lab  

  Location: MH-1400
  

  • Select activity Generating Synthetic dataLIVE CODINGLed by: Eduard...

    Generating Synthetic data

    LIVE CODING

    Led by: Eduardo Rodriguez

  • Select activity Biostat212_DataGenerationDemo.do

    

    Biostat212_DataGenerationDemo.do File
  • Select activity Time to work on final project and ask questions

    Time to work on final project and ask questions

• Select section Thursday, September 13, 2018, 11:00 AM - 12:30 PM

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  Thursday, September 13, 2018, 11:00 AM - 12:30 PM

  Office Hours
  

  Course faculty are available to address questions on course content including prior problem sets.
  

  Location:  MH-2800 and online or +1 646 558 8656 (Meeting ID: 125 284 468)

    

   
  
• Select section Final Project

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  Final Project

  Final Project

  Due: Tuesday, Sept 18 at 9:00 PM

  • Select activity Biostat 212 2018 Final Project Instructions

    

    Biostat 212 2018 Final Project Instructions File
  • Select activity Example Final Project

    

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  • Select activity Upload your Final Project here

    

    Upload your Final Project here Assignment