Side-by-Side Box Plots with Patterns From Data Sets Stacked by reshape2 and melt() in R

Introduction

A while ago, one of my co-workers asked me to group box plots by plotting them side-by-side within each group, and he wanted to use patterns rather than colours to distinguish between the box plots within a group; the publication that will display his plots prints in black-and-white only.  I gladly investigated how to do this in R, and I want to share my method and an example of what the final result looks like with you.

In generating a fictitious data set for this example, I will also demonstrate how to use the melt() function from the “reshape2” package in R to stack a data set while keeping categorical labels for the individual observations.  For now, here is a sneak peek at what we will produce at the end; the stripes are the harder pattern to produce.

triple box plots with patterns

Read the rest of this post to learn how to generate side-by-side box plots with patterns like the ones above!

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Detecting Unfair Dice in Casinos with Bayes’ Theorem

Introduction

I saw an interesting problem that requires Bayes’ Theorem and some simple R programming while reading a bioinformatics textbook.  I will discuss the math behind solving this problem in detail, and I will illustrate some very useful plotting functions to generate a plot from R that visualizes the solution effectively.

The Problem

The following question is a slightly modified version of Exercise #1.2 on Page 8 in “Biological Sequence Analysis” by Durbin, Eddy, Krogh and Mitchison.

An occasionally dishonest casino uses 2 types of dice.  Of its dice, 97% are fair but 3% are unfair, and a “five” comes up 35% of the time for these unfair dice.  If you pick a die randomly and roll it, how many “fives”  in a row would you need to see before it was most likely that you had picked an unfair die?”

Read more to learn how to create the following plot and how it invokes Bayes’ Theorem to solve the above problem!

unfair die plot

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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?

histogram and kernel density plot

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

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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

histogram

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

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How do Dew and Fog Form? Nature at Work with Temperature, Vapour Pressure, and Partial Pressure

In the early morning, especially here in Canada, I often see dew – water droplets formed by the condensation of water vapour on outside surfaces, like windows, car roofs, and leaves of trees.  I also sometimes see fog – water droplets or ice crystals that are suspended in air and often blocking visibility at great distances.  Have you ever wondered how they form?  It turns out that partial pressure, vapour pressure and temperature are the key phenomena at work.

dew fog

Dew (by Staffan Enbom) and Fog (by Jon Zander)

Source: Wikimedia

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Estimating the Decay Rate and the Half-Life of DDT in Trout – Applying Simple Linear Regression with Logarithmic Transformation

This blog post uses a function and a script written in R that were displayed in an earlier blog post.

Introduction

This is the second of a series of blog posts about simple linear regression; the first was written recently on some conceptual nuances and subtleties about this model.  In this blog post, I will use simple linear regression to analyze a data set with a logarithmic transformation and discuss how to make inferences on the regression coefficients and the means of the target on the original scale.  The data document the decay of dichlorodiphenyltrichloroethane (DDT) in trout in Lake Michigan; I found it on Page 49 in the book “Elements of Environmental Chemistry” by Ronald A. Hites.  Future posts will also be written on the chemical aspects of this topic, including the environmental chemistry of DDT and exponential decay in chemistry and, in particular, radiochemistry.

DDT

Dichlorodiphenyltrichloroethane (DDT)

Source: Wikimedia Commons

 

A serious student of statistics or a statistician re-learning the fundamentals like myself should always try to understand the math and the statistics behind a software’s built-in function rather than treating it like a black box.  This is especially worthwhile for a basic yet powerful tool like simple linear regression.  Thus, instead of simply using the lm() function in R, I will reproduce the calculations done by lm() with my own function and script (posted earlier on my blog) to obtain inferential statistics on the regression coefficients.  However, I will not write or explain the math behind the calculations; they are shown in my own function with very self-evident variable names, in case you are interested.  The calculations are arguably the most straightforward aspects of linear regression, and you can easily find the derivations and formulas on the web, in introductory or applied statistics textbooks, and in regression textbooks.

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Discovering Argon with the 2-Sample t-Test

I learned about Lord Rayleigh’s discovery of argon in my 2nd-year analytical chemistry class while reading “Quantitative Chemical Analysis” by Daniel Harris.  (William Ramsay was also responsible for this discovery.)  This is one of my favourite stories in chemistry; it illustrates how diligence in measurement can lead to an elegant and surprising discovery.  I find no evidence that Rayleigh and Ramsay used statistics to confirm their findings; their paper was published 13 years before Gosset published about the t-test.  Thus, I will use a 2-sample t-test in R to confirm their result.

Lord Rayleigh                                    William Ramsay

Photos of Lord Rayleigh and William Ramsay

Source: Wikimedia Commons

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Adding Labels to Points in a Scatter Plot in R

What’s the Scatter?

A scatter plot displays the values of 2 variables for a set of data, and it is a very useful way to visualize data during exploratory data analysis, especially (though not exclusively) when you are interested in the relationship between a predictor variable and a target variable.  Sometimes, such data come with categorical labels that have important meanings, and the visualization of the relationship can be enhanced when these labels are attached to the data.

It is common practice to use a legend to label data that belong to a group, as I illustrated in a previous post on bar charts and pie charts.  However, what if every datum has a unique label, and there are many data in the scatter plot?  A legend would add unnecessary clutter in such situations.  Instead, it would be useful to write the label of each datum near its point in the scatter plot. I will show how to do this in R, illustrating the code with a built-in data set called LifeCycleSavings.

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Displaying Isotopic Abundance Percentages with Bar Charts and Pie Charts

The Structure of an Atom

An atom consists of a nucleus at the centre and electrons moving around it.  The nucleus contains a mixture of protons and neutrons.  For most purposes in chemistry, the two most important properties about these 3 types of particles are their masses and charges.  In terms of charge, protons are positive, electrons are negative, and neutrons are neutral.  A proton’s mass is roughly the same as a neutron’s mass, but a proton is almost 2,000 times heavier than an electron.

lithium atom

This image shows a lithium atom, which has 3 electrons, 3 protons, and 4 neutrons.  

Source: Wikimedia Commons

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