Missing Data Analysis
Using Stata

Understanding, diagnosing and handling missing data in Data Analytics and Research. Move from complete-case analysis to Multiple Imputation by Chained Equations (MICE), with practical application on real NHANES data.

40Detailed Modules
7Learning Units
4Weeks
$120Course Fee
Missing Data Analysis Using Stata
Stata · NHANES Beginner to Intermediate
This Course Covers: Stata NHANES Multiple Imputation MICE MCAR/MAR/MNAR Complex Survey Design Sensitivity Analysis Course Fee: $120

Handling Missing Data Is a Statistical Decision, Not a Cleanup Task

A dataset may contain thousands of observations, but participants may still have missing laboratory measurements, income information, questionnaire responses, clinical measurements or other important variables.

How these missing values are handled can affect sample size, statistical power, standard errors, confidence intervals, precision, representativeness, statistical estimates and research conclusions. Handling missing data is therefore not simply about deleting incomplete observations or filling empty cells.

Missing Data Analysis Using Stata is a 4-week applied course that takes participants from the foundations of missing data through complete-case analysis and Multiple Imputation by Chained Equations (MICE), using NHANES data and Stata throughout.

Course Structure

  • Duration: 4 Weeks
  • Curriculum: 40 Modules across 7 Learning Units
  • Level: Beginner to Intermediate
  • Software: Stata
  • Applied Dataset: NHANES 2017 – March 2020 Pre-Pandemic
  • $120

Before Deleting or Filling a Single Missing Value

What is missing?
How much information is missing?
Why might the information be missing?
Who is more likely to have missing information?
Could the missing data introduce bias?
What assumptions am I making about the missing-data process?
Should I use complete-case analysis or multiple imputation?
Would my conclusions change if I used another reasonable approach?
How should I report missing data in my research?

40 Detailed Modules, Organized Into 7 Learning Units

For clarity and easier navigation, the 40 modules have been organized into 7 major learning units on this page. These units are not individual modules, each brings together several related modules taught progressively during the 4-week course. Participants receive training across the full 40-module curriculum.

Begin by understanding what missing data is, why it occurs and why it matters for Data Analytics and Research.

1
What Is Missing Data?
  • What missing data means
  • Why values become missing
2
Why Missing Data Matters
  • How missing data affect sample size
  • Missing data, statistical power and bias
3
Missing Data Terminology
  • Missing values vs missingness
  • Complete and incomplete observations
4
How Stata Represents Missing Data
  • How Stata represents missing values
  • Safe handling of missing numeric values in Stata
5
First Step: Identify Missing Data
  • How to identify missing observations
6
Counting Missing Values in Stata
  • Counting missing values in Stata
7
Calculating Percentage Missing
  • How to quantify missingness
8
Missing Data Is Analysis-Specific
  • How to examine patterns of missing data
  • Why missingness should be evaluated per analysis
Stata Skills Introduced describe codebook count missing() misstable summarize misstable patterns

Develop a clear understanding of the assumptions behind missing-data analysis, and move beyond simply saying "my data have missing values" to asking what process may have produced them.

9
The Three Classical Missing-Data Mechanisms
  • How the three mechanisms differ
10
Missing Completely at Random (MCAR)
  • What MCAR means
  • Practical examples
11
Missing at Random (MAR)
  • What MAR means
  • Why MAR does not mean "randomly missing"
12
Missing Not at Random (MNAR)
  • What MNAR means
  • Why MNAR is particularly challenging
13
MCAR, MAR and MNAR Compared
  • Why the mechanism cannot be determined from percentage missing alone
14
Can We Prove MCAR, MAR or MNAR from the Data?
  • The role of study design, subject-matter knowledge and sensitivity analysis

Learn how to investigate who has missing information and whether observed participant characteristics are related to missingness. Finding predictors of missingness does not prove that the data are MAR.

15
Investigating Who Has Missing Data
  • Creating missingness indicators
  • Examining missingness by age, sex, race and ethnicity, education and clinical characteristics
16
Modeling Missingness
  • Modeling missingness using logistic regression
  • Identifying observed predictors of missingness
17
Methods for Handling Missing Data
  • Using diagnostic evidence to inform strategy
  • Overview of available missing-data methods

Understand what happens when incomplete observations are excluded, and why apparently simple missing-data solutions can create new statistical problems. Complete-case analysis should be a deliberate analytical decision, not an automatic response to missing data.

18
Complete-Case Analysis
  • Complete-case analysis and listwise deletion
19
Identifying the Complete-Case Sample in Stata
  • How Stata excludes incomplete observations
  • Using e(sample)
20
Manually Creating a Complete-Case Indicator
  • Creating complete-case indicators
  • Measuring how many participants are excluded
21
Advantages and Limitations of Complete-Case Analysis
  • Loss of statistical power and precision
  • Potential selection bias
22
Why Simple Single Imputation Can Be Problematic
  • Why mean imputation can be problematic
  • Why single imputation underestimates uncertainty

Progress from deleting incomplete observations to understanding modern multiple-imputation methods, and Stata's mi framework.

23
What Is Multiple Imputation?
  • Why one imputed value is insufficient
  • Imputation uncertainty
24
The Three Stages of Multiple Imputation
  • Imputation, Analysis and Pooling
  • Introduction to Rubin's rules
25
What Variables Should Be in an Imputation Model?
  • Substantive model variables, predictors of missingness and auxiliary variables
26
Different Variables Require Different Imputation Models
  • Continuous, binary, ordered and unordered categorical variables
27
Multiple Imputation in Stata
  • Introduction to Stata's mi framework

The major practical component of the course. Participants apply missing-data methods using NHANES 2017 to March 2020 Pre-Pandemic data and Stata, connecting statistical theory directly to real applied research practice.

28
NHANES Practical: Setting Up the Analysis
  • Examining NHANES missingness
29
Complete-Case NHANES Model
  • Complete-case NHANES analysis
  • Preserving the complex survey design
30
Declaring the Data for Multiple Imputation
  • Preparing data for MI and registering variables
31
Multiple Imputation Using Chained Equations
  • MICE, reproducibility using random-number seeds
32
When Variable Types Differ
  • Continuous, binary and categorical-variable imputation
33
Checking the MI Data
  • Identifying potential imputation problems
34
Analyzing Multiply Imputed Data
  • Obtaining and interpreting pooled estimates
  • How MI interacts with NHANES complex survey analysis
Applied Variables May Include AgeBMIPoverty-Income Ratio SexRace & EthnicityEducation SmokingPhysical ActivityDiabetes Cardiovascular DiseaseGLP-1 RA UseBlood Pressure Control
Stata Skills svysetsvy:mi set mi register imputedmi register regular mi impute chainedmi describe mi misstable summarizemi estimate

Bring the complete missing-data analysis process together and finish the course with the professional missing-data workflow.

35
Complete Case Versus Multiple Imputation
  • Comparing effect estimates, standard errors, confidence intervals and p-values
36
Sensitivity Analysis
  • Investigating differences between analytical approaches
37
Reporting Missing Data in Research
  • Reporting assumptions, imputations and variables used
38
Common Mistakes to Avoid
  • Common missing-data mistakes
39
Practical NHANES Exercise
  • Applied exercise across the full workflow
40
Final Analytical Framework
  • Professional interpretation of missing-data analyses
Identify Quantify Describe Investigate Assume Select Method Analyze Diagnose Compare Report

By the End of This Course

  • Identify, quantify and examine patterns of missing data
  • Explain MCAR, MAR and MNAR and the assumptions behind each
  • Investigate predictors of missingness and perform complete-case analysis
  • Explain the limitations of mean and single imputation
  • Build an appropriate imputation model and perform MICE in Stata
  • Analyze multiply imputed datasets and interpret pooled estimates
  • Understand multiple imputation within an NHANES complex survey context
  • Conduct sensitivity analyses and report missing-data methods professionally

Built for Anyone Working with Incomplete Real-World Data

Data analysts Researchers Research assistants Postgraduate students Master's & PhD students Epidemiologists Public health professionals Clinical researchers Healthcare researchers Monitoring & Evaluation professionals Stata users Anyone working with incomplete real-world datasets

Basic knowledge of datasets and introductory statistics is recommended.

Missing Data Is Not Simply a Data-Cleaning Problem

It is a statistical and research problem. Deleting incomplete observations without understanding why they are missing can alter the analytical sample and potentially affect research conclusions. Filling empty cells without accounting for uncertainty can produce misleading results.

Why are the data missing?

Who has missing information?

What assumptions am I making?

Could missingness bias my results?

Which method is appropriate?

Would another method change my conclusions?

How should I communicate my decisions?

Important NHANES Perspective

Survey weighting and missing-data handling solve different analytical problems. Multiple imputation does not replace NHANES survey weights, strata or Primary Sampling Units (PSUs). Similarly, using survey weights does not automatically solve problems created by missing data. Both issues must be considered when conducting rigorous NHANES analysis.

Learn to Handle Missing Data Professionally

Do not automatically delete incomplete observations. Do not automatically replace missing values with averages. Do not assume missing data are harmless. Learn to identify missingness, investigate the missing-data process, understand MCAR, MAR and MNAR, conduct complete-case analysis, perform multiple imputation using Stata and report your analytical decisions professionally.