Develop tools for summarizing a dataset numerically, and how we can use these summaries to produce interesting new visualizations.
Mid-course survey summary
Thank you all again for filling out the mid-course review forms. They were very helpful for me in planning the notes for the remainder of the semester. Some themes I saw:
- generally happy with the format of the quizzes and the notes 🗒️ I provide
- generally enjoy the short lecture followed by working on labs and projects
- you like using your own computer 💻
- enjoy working on the projects in class
- a desire for more practice problems and labs 🔬
- almost no comments on the pace 🏃 of the course (so I assume its good!)
- some clarity on what is expected on the project drafts
- request for more office hours ⏰ right before the projects are due
It did not seem that there was a pattern of many other concerns (yay!). I’ve tried to add a little bit more practice to the labs, but mostly kept the format of the course consistent with what we have been doing lately. I’ll try to clarify a bit more what is expected on the Project D drafts (there are no drafts for C). Also, I will have and announce extra office hours before the next assignment.
Additionally, I did take other one-off comments that were made under consideration even if not listed here. If you have any other comments or concerns, please still let me know!
Graphics are an excellent way of summarizing and presenting information contained in a dataset. In many cases it can be useful to combine these with purely numeric summaries. These summaries are something colloquially called statistics, though I prefer to avoid this terminology.
In these notes, I will use the
in order to show various numerical summaries. Here is an example of
Each row corresponds to a type of mammal, and gives basic numeric values that describe their sleeping cycles.
The first statistical summary that most people learn about is the mean, also commonly known as an average. It is calculated by adding all of a variables values together and dividing by the total number of values. If we have a dataset of n points with a variable x (denoting x with an underscore 1 as the first value, with a 2 as the second, and so forth), the mean can be formally defined as:
The notation of using x with a line above it to represent the mean is very common
throughout the sciences and social sciences. It is often used in textbooks
and papers without even being defined. To calculate means in R, as we have
already, seen we can use the
mean function. Here is an illustration that
mean behaves as expected using the
nrow functions for
Note, I am showing in the second line a description of what the mean is doing and verifying that it works. Do not coyp and use the second form in your work.
Also here are a number of functions that allow us to compute quantiles,
a generalization of percentiles. For example, the
deciles function splits
the dataset into 10 equally sized buckets:
This shows that about 1/2 of the mammals are awake less than 14.20 hours and about 1/2 are awake more than 14.20. I use the word “about” here due to subtitles regarding ties and repeated values; for all practical purposes this is generally not important. Note that the 50% percentile has a special name that you have probably heard before: the median.
Similarly, we see that roughly 1/10 of the mammals are awake less than 8.12 hours and 1/10 are awake less than 20.8 hours. We also see that the sleepiest mammal is awake for only 4.1 hours and that one mammal is awake 22.1 hours of the day.
We can similarly calculate what are called quartiles, splitting the data into
four equally sized groups using the
Notice that four buckets requires 5 numbers, and that three of these line up with
the deciles above. There are also functions
ventiles (20) and
can be quite useful:
Ventiles are a bit esoteric, but I have found in my work that they can be very useful in practice. Percentiles are often useful when we want to look at the extreme values, such as the 97th, 98th and 99th percentiles.
Once we have defined the mean, we can then define the deviation of a data value as the difference between the value and its mean:
There is not a special R function for deviances because they are very
easy to calculate using the
mean function. As an example, here is how
to create them:
Typically we will not need deviances directly, but they are used in the calculation of quantities measuring the variation about a mean.
We can use deviations to measure the spread of a variable by adding the squared values of deviances. Why squares? For one thing, squaring the value makes negative deviations positive; though, the same effect would come from applying the absolution value function. The specific reason specifically for choosing the square is a bit too technical for our discussion.
The sum of squared deviances are calculated by the following formula:
And can be computed in R as:
The sum of squares cannot be used directly to compare datasets of different sizes as it grows with the number of points. In order to compare sums of squares across datasets, we use a measurement called variance which is basically just the average of the sums of squares:
The notation of using s^2 to represent the variance of a dataset is quite common.
Why do we use (n-1) rather than (n) to take the average? The technical reason is that if we want to measure the variance of a population using a sample from that population, we need to use $n-1$ in order to have an unbiased estimate of the population value… The short answer is not to worry about it, which I strongly suggest at this point.
The variance can be computed manually as follows:
Or, using the
var function as follows:
Note: like the
mean function, you should only use the
in your work. I show the other form simply as a demonstration of the definition.
We often work with a quantity called the standard deviation, defined as simply the square root of the variance.
Why bother taking the square root? For one thing, it is a matter of units. In
our example, the variance is given in “squared people” (a nearly meaningless
quantity), but the standard deviation is given in “people” just like the variable
itself. We can calculate the standard deviation for the awake variable using the
Or, we can take out the
group_summarize function to compute the
standard deviation of the awake variable by the type of mammal:
Where we see that omnivores have more consistent hours spent sleeping and insectivores have the largest variation of sleeping hours per day.
Finally, we can use these measurments of distribution and variation in graphical forms. Typically, this comes up when we have a grouping categorical variable and another numeric variable of interest.
A boxplot shows, for each group on the x-axis, the distribution of the variable on the y-axis. The solid bar indicates the y-axis variable’s median and the height of the box and the “whiskers” indicate measurments of variation (see the link boxplot for more information about the different ways these can be computed).
Similarly, a violin plot is a newer twist on the boxplot that attempts to show more details about the distribution by varying its width with the distribution of the points:
We will work on the next lab for the remainder of the class: lab17.Rmd
Please upload your script to GitHub ahead of the next class.