Data Science for Agriculture

How to manage and manipulate data for agricultural research

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Scientific

Mammal Body Size 1


There were a relatively large number of extinctions of mammalian species roughly 10,000 years ago. To help understand why these extinctions happened scientists are interested in understanding whether there were differences in the body size of those species that went extinct and those that did not.

To address this question we can use the largest dataset on mammalian body size in the world, which has data on the mass of recently extinct mammals as well as extant mammals (i.e., those that are still alive today). Take a look at the metadata to understand the structure of the data. One key thing to remember is that species can occur on more than one continent, and if they do then they will occur more than once in this dataset. Also let’s ignore species that went extinct in the very recent past (designated by the word "historical" in the status column).

Import the data into R. If you’ve looked at a lot of data you’ll realize that this dataset is tab delimited. Use the argument sep = "\t" in read.csv() to properly format the data. There is no header row, so use head = FALSE.

Add column names to help identify columns.

colnames(mammal_sizes) <- c("continent", "status", "order", 
"family", "genus", "species", "log_mass", "combined_mass", 
"reference")

To start let’s explore the data a little and then start looking at the major question.

  1. The following dplyr code will determine how many genera (plural of genus) are in the dataset: 
    nrow(distinct(select(mammal_sizes, genus)))

    Modify this code into a function to determine the number of species. Remember that a species is uniquely defined by the combination of its genus name and its species name. Print the result to the screen. The number should be between 4000 and 5000.

  2. Find out how many of the species are extinct and how many are extant, print the result to the screen. HINT: first separate the data into the extinct and extant components and then count the number of species.
  3. Print out how many families are present in the dataset.
  4. Now print the genus name, the species name, and the mass of the largest and smallest species (note, it is not possible for a mammal to have negative mass.)
  5. Calculate the average (i.e., mean) mass of an extinct species and the average mass of an extant species. The function mean() should help you here. Don’t worry about species that occur more than once. We’ll consider the values on different continents to represent independent data points.
    Print out the results for extinct then extant.
[click here for output]