## 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!

## Exploratory Data Analysis: 2 Ways of Plotting Empirical Cumulative Distribution Functions in R

#### Introduction

Continuing my recent series on exploratory data analysis (EDA), and following up on the last post on the conceptual foundations of empirical cumulative distribution functions (CDFs), this post shows how to plot them in R.  (Previous posts in this series on EDA include descriptive statistics, box plots, kernel density estimation, and violin plots.)

I will plot empirical CDFs in 2 ways:

1. using the built-in ecdf() and plot() functions in R
2. calculating and plotting the cumulative probabilities against the ordered data

Continuing from the previous posts in this series on EDA, I will use the “Ozone” data from the built-in “airquality” data set in R.  Recall that this data set has missing values, and, just as before, this problem needs to be addressed when constructing plots of the empirical CDFs.

Recall the plot of the empirical CDF of random standard normal numbers in my earlier post on the conceptual foundations of empirical CDFs.  That plot will be compared to the plots of the empirical CDFs of the ozone data to check if they came from a normal distribution.

## When Does the Kinetic Theory of Gases Fail? Examining its Postulates with Assistance from Simple Linear Regression in R

#### Introduction

The Ideal Gas Law, $\text{PV} = \text{nRT}$, is a very simple yet useful relationship that describes the behaviours of many gases pretty well in many situations.  It is “Ideal” because it makes some assumptions about gas particles that make the math and the physics easy to work with; in fact, the simplicity that arises from these assumptions allows the Ideal Gas Law to be easily derived from the kinetic theory of gases.  However, there are situations in which those assumptions are not valid, and, hence, the Ideal Gas Law fails.

Boyle’s law is inherently a part of the Ideal Gas Law.  It states that, at a given temperature, the pressure of an ideal gas is inversely proportional to its volume.  Equivalently, it states the product of the pressure and the volume of an ideal gas is a constant at a given temperature.

$\text{P} \propto \text{V}^{-1}$

#### An Example of The Failure of the Ideal Gas Law

This law is valid for many gases in many situations, but consider the following data on the pressure and volume of 1.000 g of oxygen at 0 degrees Celsius.  I found this data set in Chapter 5.2 of “General Chemistry” by Darrell Ebbing and Steven Gammon.

               Pressure (atm)      Volume (L)              Pressure X Volume (atm*L)
[1,]           0.25                2.8010                  0.700250
[2,]           0.50                1.4000                  0.700000
[3,]           0.75                0.9333                  0.699975
[4,]           1.00                0.6998                  0.699800
[5,]           2.00                0.3495                  0.699000
[6,]           3.00                0.2328                  0.698400
[7,]           4.00                0.1744                  0.697600
[8,]           5.00                0.1394                  0.697000

The right-most column is the product of pressure and temperature, and it is not constant.  However, are the differences between these values significant, or could it be due to some random variation (perhaps round-off error)?

Here is the scatter plot of the pressure-volume product with respect to pressure.

These points don’t look like they are on a horizontal line!  Let’s analyze these data using normal linear least-squares regression in R.