Your first missing data visualizations

It can be difficult to get a handle on where the missing values are in your data, and here is where visualization can really help.

The function vis_miss() creates an overview visualization of the missingness in the data. It also has options to cluster rows based on missingness, using cluster = TRUE; as well as options for sorting the columns, from most missing to least missing (sort_miss = TRUE).

This exercise is part of the course

Dealing With Missing Data in R

Exercise instructions

Using the riskfactors dataset from naniar:

Use vis_miss() to visualize the missingness in the data.
Use vis_miss() with cluster = TRUE to explore some clusters of missingness.
Use vis_miss() and sort the missings with sort_miss to arrange the columns by missingness.

Hands-on interactive exercise

Have a go at this exercise by completing this sample code.

# Visualize all of the missingness in the `riskfactors`  dataset
vis_miss(___)

# Visualize and cluster all of the missingness in the `riskfactors` dataset
vis_miss(___, ___ = TRUE)

# visualize and sort the columns by missingness in the `riskfactors` dataset
vis_miss(___, ___ = TRUE)

Edit and Run Code

This exercise is part of the course

Dealing With Missing Data in R

BeginnerSkill Level

4.8+

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Chapter 1 introduces you to missing data, explaining what missing values are, their behavior in R, how to detect them, and how to count them. We then introduce missing data summaries and how to summarise missingness across cases, variables, and how to explore across groups within the data. Finally, we discuss missing data visualizations, how to produce overview visualizations for the entire dataset and over variables, cases, and other summaries, and how to explore these across groups.

Exercise 1: Introduction to missing data Exercise 2: Using and finding missing values Exercise 3: How many missing values are there?Exercise 4: Working with missing values Exercise 5: Why care about missing values?Exercise 6: Summarizing missingness Exercise 7: Tabulating Missingness Exercise 8: Other summaries of missingness Exercise 9: How do we visualize missing values?Exercise 10: Your first missing data visualizations

Current Exercise

Exercise 11: Visualizing missing cases and variables Exercise 12: Visualizing missingness patterns

In chapter two, you will learn how to uncover hidden missing values like "missing" or "N/A" and replace them with `NA`. You will learn how to efficiently handle implicit missing values - those values implied to be missing, but not explicitly listed. We also cover how to explore missing data dependence, discussing Missing Completely at Random (MCAR), Missing At Random (MAR), Missing Not At Random (MNAR), and what they mean for your data analysis.

Exercise 1: Searching for and replacing missing values Exercise 2: Using miss_scan_count Exercise 3: Using replace_with_na Exercise 4: Using replace_with_na scoped variants Exercise 5: Filling down missing values Exercise 6: Fix implicit missings using complete()Exercise 7: Fix explicit missings using fill()Exercise 8: Using complete() and fill() together Exercise 9: Missing Data dependence Exercise 10: Differences between MCAR and MAR Exercise 11: Exploring missingness dependence Exercise 12: Further exploring missingness dependence

In this chapter, you will learn about workflows for working with missing data. We introduce special data structures, the shadow matrix, and nabular data, and demonstrate how to use them in workflows for exploring missing data so that you can link summaries of missingness back to values in the data. You will learn how to use ggplot to explore and visualize how values changes as other variables go missing. Finally, you learn how to visualize missingness across two variables, and how and why to visualize missings in a scatterplot.

Exercise 1: Tools to explore missing data dependence Exercise 2: Creating shadow matrix data Exercise 3: Performing grouped summaries of missingness Exercise 4: Further exploring more combinations of missingness Exercise 5: Visualizing missingness across one variable Exercise 6: Nabular data and filling by missingness Exercise 7: Nabular data and summarising by missingness Exercise 8: Explore variation by missingness: box plots Exercise 9: Visualizing missingness across two variables Exercise 10: Exploring missing data with scatter plots Exercise 11: Using facets to explore missingness Exercise 12: Faceting to explore missingness (multiple plots)

In this chapter, you will learn about filling in the missing values in your data, which is called imputation. You will learn how to impute and track missing values, and what the good and bad features of imputations are so that you can explore, visualise, and evaluate the imputed data against the original values. You will learn how to use, evaluate, and compare different imputation models, and explore how different imputation models affect the inferences you can draw from the models.

Exercise 1: Filling in the blanks Exercise 2: Impute data below range with nabular data Exercise 3: Visualize imputed values in a scatter plot Exercise 4: Create histogram of imputed data Exercise 5: What makes a good imputation Exercise 6: Evaluating bad imputations Exercise 7: Evaluating imputations: The scale Exercise 8: Evaluating imputations: Across many variables Exercise 9: Performing imputations Exercise 10: Using simputation to impute data Exercise 11: Evaluating and comparing imputations Exercise 12: Evaluating imputations (many models & variables)Exercise 13: Evaluating imputations and models Exercise 14: Combining and comparing many imputation models Exercise 15: Evaluating the different parameters in the model Exercise 16: Final Lesson