R Strategies for Managing Missing Data in ESM, EMA, and Ambulatory Assessments: A Beginner Guide

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Beginner Guide to Managing Missing Data in R for EMA, ESM, and Ambulatory Assessments

When conducting Experience Sampling Method (ESM), Ecological Momentary Assessment (EMA), or any form of Ambulatory Assessment, ensuring data integrity is paramount. Missing data can lead to biased results and reduce the statistical power of your study. R, a statistical programming language, offers a range of tools for handling missing data. Here’s a step-by-step guide with examples to help you navigate this process.

Step 1: Detection of Missing Data

Basic Detection with Base R:

# Summarize missing data for each variable
missing_summary <- sapply(your_dataset, function(x) sum(

Advanced Detection with the naniar package:

# Install and load the naniar package

# Visualize missing data

Step 2: Visualizing Missing Data Patterns

Visual Patterns with VIM package:

# Install and load the VIM package

# Visualizing patterns of missing data
aggr_plot <- aggr(your_dataset, col=c('navyblue', 'red'), numbers=TRUE)

Step 3: Analyzing the Impact of Missing Data

Missing Data Patterns with mice package:

# Install and load the mice package

# Analyzing patterns

Step 4: Handling Missing Data

Imputation Techniques with mice:

# Multiple imputation
imputed_data <- mice(your_dataset, m=5, method='pmm', maxit=50)
complete_data <- complete(imputed_data, action=1)

Using Predictive Mean Matching (PMM):

# PMM for numerical data
imputed_data <- mice(your_dataset, method='pmm')

Step 5: Validation of Imputed Data

Comparing Original and Imputed Distributions:

# Plotting distributions
hist(your_dataset$variable, main="Original Data")
hist(complete_data$variable, main="Imputed Data")

Step 6: Documentation and Reporting

Creating a Missing Data Report:

# Generate a report
n_miss <- sum(
n_obs <- nrow(your_dataset)
report <- data.frame(Total_Observations=n_obs, Total_Missing=n_miss)

Tips for Ensuring Data Integrity:

  • Understand the Pattern: Before imputing, determine if the missingness is random or systematic.
  • Choose the Right Method: Select an imputation method that fits your data type and missingness pattern.
  • Check Consistency: Ensure that the imputed values are within a plausible range.
  • Document Your Process: Keep a record of all steps taken to handle missing data for reproducibility and transparency.

By meticulously following these steps and applying the provided code examples, researchers can effectively manage missing data in their ambulatory assessments, leading to more reliable and valid results. Remember that the goal is not just to fill in gaps but to preserve the study's integrity and maintain the data's original structure and meaning as much as possible.


This is a basic guide to implementing some missing data checks for ESM, EMA, and Ambulatory assessments. We encourage you to look at specific resources to ensure that you are correctly handling missing data to obtain accurate insights.

  • van Buuren, S., & Groothuis-Oudshoorn, K. (2011). mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software, 45(3), 1-67. doi:10.18637/jss.v045.i03
  • Templ, M., Kowarik, A., & Filzmoser, P. (2011). Iterative stepwise regression imputation using standard and robust methods. Computational Statistics & Data Analysis, 55(10), 2793-2806. doi:10.1016/j.csda.2011.04.012
  • Little, R. J. A., & Rubin, D. B. (2002). Statistical analysis with missing data (2nd ed.). Hoboken, NJ: John Wiley & Sons.
  • Enders, C. K. (2010). Applied missing data analysis. New York, NY: Guilford Press.
  • Graham, J. W. (2009). Missing data analysis: Making it work in the real world. Annual Review of Psychology, 60, 549-576. doi:10.1146/annurev.psych.58.110405.085530
  • Allison, P. D. (2002). Missing data. Thousand Oaks, CA: Sage Publications.
  • Schafer, J. L., & Graham, J. W. (2002). Missing data: Our view of the state of the art. Psychological Methods, 7(2), 147-177. doi:10.1037//1082-989X.7.2.147

Readers can use these references to deepen their understanding of various techniques for handling missing data in statistical analysis, particularly within the R programming environment.

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