Exploratory Data Analysis – All Blog Posts on The Chemical Statistician

This series of posts introduced various methods of exploratory data analysis, providing theoretical backgrounds and practical examples.  Fully commented and readily usable R scripts are available for all topics for you to copy and paste for your own analysis!  Most of these posts involve data visualization and plotting, and I include a lot of detail and comments on how to invoke specific plotting commands in R in these examples.

I will return to this blog post to add new links as I write more tutorials.

Useful R Functions for Exploring a Data Frame

The 5-Number Summary – Two Different Methods in R

Combining Histograms and Density Plots to Examine the Distribution of the Ozone Pollution Data from New York in R

Conceptual Foundations of Histograms – Illustrated with New York’s Ozone Pollution Data

Quantile-Quantile Plots for New York’s Ozone Pollution Data

Kernel Density Estimation and Rug Plots in R on Ozone Data in New York and Ozonopolis

2 Ways of Plotting Empirical Cumulative Distribution Functions in R

Conceptual Foundations of Empirical Cumulative Distribution Functions

Combining Box Plots and Kernel Density Plots into Violin Plots for Ozone Pollution Data

Kernel Density Estimation – Conceptual Foundations

Variations of Box Plots in R for Ozone Concentrations in New York City and Ozonopolis

Computing Descriptive Statistics in R for Data on Ozone Pollution in New York City

How to Get the Frequency Table of a Categorical Variable as a Data Frame in R

The advantages of using count() to get N-way frequency tables as data frames in R

Exploratory Data Analysis: Quantile-Quantile Plots for New York’s Ozone Pollution Data

Introduction

Continuing my recent series on exploratory data analysis, today’s post focuses on quantile-quantile (Q-Q) plots, which are very useful plots for assessing how closely a data set fits a particular distribution.  I will discuss how Q-Q plots are constructed and use Q-Q plots to assess the distribution of the “Ozone” data from the built-in “airquality” data set in R.

Previous posts in this series on EDA include

• Descriptive statistics
• Box plots
• The conceptual foundations of kernel density estimation
• How to construct kernel density plots and rug plots in R
• Violin plots
• The conceptual foundations of empirical cumulative distribution functions (CDFs)
• 2 ways of plotting empirical CDFs in R
• Conceptual foundations of histograms and how to plot them in R
• Combining histograms and density plots in R
• The 5-number summary: Differences between fivenum() and summary() in R
• Useful R Functions for Exploring a Data Frame

Learn how to create a quantile-quantile plot like this one with R code in the rest of this blog!

Exploratory Data Analysis: The 5-Number Summary – Two Different Methods in R

Introduction

Continuing my recent series on exploratory data analysis (EDA), today’s post focuses on 5-number summaries, which were previously mentioned in the post on descriptive statistics in this series.  I will define and calculate the 5-number summary in 2 different ways that are commonly used in R.  (It turns out that different methods arise from the lack of universal agreement among statisticians on how to calculate quantiles.)  I will show that the fivenum() function uses a simpler and more interpretable method to calculate the 5-number summary than the summary() function.  This post expands on a recent comment that I made to correct an error in the post on box plots.

> y = seq(1, 11, by = 2)
> y
[1]  1  3  5  7  9 11
> fivenum(y)
[1]  1  3  6  9 11
> summary(y)
     Min.   1st Qu.   Median    Mean     3rd Qu.    Max. 
     1.0     3.5       6.0       6.0      8.5       11.0

Why do these 2 methods of calculating the 5–number summary in R give different results?  Read the rest of this post to find out the answer!

Previous posts in this series on EDA include

• Descriptive statistics
• Box plots
• The conceptual foundations of kernel density estimation
• How to construct kernel density plots and rug plots in R
• Violin plots
• The conceptual foundations of empirical cumulative distribution functions (CDFs)
• 2 ways of plotting empirical CDFs in R
• Conceptual foundations of histograms and how to plot them in R
• Combining histograms and density plots in R

Exploratory Data Analysis: Combining Histograms and Density Plots to Examine the Distribution of the Ozone Pollution Data from New York in R

Introduction

This is a follow-up post to my recent introduction of histograms.  Previously, I presented the conceptual foundations of histograms and used a histogram to approximate the distribution of the “Ozone” data from the built-in data set “airquality” in R.  Today, I will examine this distribution in more detail by overlaying the histogram with parametric and non-parametric kernel density plots.  I will finally answer the question that I have asked (and hinted to answer) several times: Are the “Ozone” data normally distributed, or is another distribution more suitable?

Read the rest of this post to learn how to combine histograms with density curves like this above plot!

This is another post in my continuing series on exploratory data analysis (EDA).  Previous posts in this series on EDA include

• Descriptive statistics
• Box plots
• The conceptual foundations of kernel density estimation
• How to construct kernel density plots and rug plots in R
• Violin plots
• The conceptual foundations of empirical cumulative distribution functions (CDFs)
• 2 ways of plotting empirical CDFs in R
• The conceptual foundations of histograms

Exploratory Data Analysis: Conceptual Foundations of Histograms – Illustrated with New York’s Ozone Pollution Data

Introduction

Continuing my recent series on exploratory data analysis (EDA), today’s post focuses on histograms, which are very useful plots for visualizing the distribution of a data set.  I will discuss how histograms are constructed and use histograms to assess the distribution of the “Ozone” data from the built-in “airquality” data set in R.  In a later post, I will assess the distribution of the “Ozone” data in greater depth by combining histograms with various types of density plots.

Previous posts in this series on EDA include

• Descriptive statistics
• Box plots
• The conceptual foundations of kernel density estimation
• How to construct kernel density plots and rug plots in R
• Violin plots
• The conceptual foundations of empirical cumulative distribution functions (CDFs)
• 2 ways of plotting empirical CDFs in R

Read the rest of this post to learn how to construct a histogram and get the R code for producing the above plot!

Exploratory Data Analysis: Conceptual Foundations of Empirical Cumulative Distribution Functions

Introduction

Continuing my recent series on exploratory data analysis (EDA), this post focuses on the conceptual foundations of empirical cumulative distribution functions (CDFs); in a separate post, I will show how to plot them in R.  (Previous posts in this series include descriptive statistics, box plots, kernel density estimation, and violin plots.)

To give you a sense of what an empirical CDF looks like, here is an example created from 100 randomly generated numbers from the standard normal distribution.  The ecdf() function in R was used to generate this plot; the entire code is provided at the end of this post, but read my next post for more detail on how to generate plots of empirical CDFs in R.

Read to rest of this post to learn what an empirical CDF is and how to produce the above plot!

Exploratory Data Analysis: Combining Box Plots and Kernel Density Plots into Violin Plots for Ozone Pollution Data

Introduction

Recently, I began a series on exploratory data analysis (EDA), and I have written about descriptive statistics, box plots, and kernel density plots so far.  As previously mentioned in my post on box plots, there is a way to combine box plots and kernel density plots.  This combination results in violin plots, and I will show how to create them in R today.

Continuing from my previous posts on EDA, I will use 2 univariate data sets.  One is the “ozone” data vector that is part of the “airquality” data set that is built into R; this data set contains data on New York’s air pollution.  The other is a simulated data set of ozone pollution in a fictitious city called “Ozonopolis”.  It is important to remember that the ozone data from New York has missing values, and this has created complications that needed to be addressed in previous posts; missing values need to be addressed for violin plots, too, and in a different way than before.  

The vioplot() command in the “vioplot” package creates violin plots; the plotting options in this function are different and less versatile than other plotting functions that I have used in R.  Thus, I needed to be more creative with the plot(), title(), and axis() functions to create the plots that I want.  Read the details carefully to understand and benefit fully from the code.

Read further to learn how to create these violin plots that combine box plots with kernel density plots!  Be careful – the syntax is more complicated than usual!

Exploratory Data Analysis – Computing Descriptive Statistics in R for Data on Ozone Pollution in New York City

Introduction

This is the first of a series of posts on exploratory data analysis (EDA).  This post will calculate the common summary statistics of a univariate continuous data set – the data on ozone pollution in New York City that is part of the built-in “airquality” data set in R.  This is a particularly good data set to work with, since it has missing values – a common problem in many real data sets.  In later posts, I will continue this series by exploring other methods in EDA, including box plots and kernel density plots.