Scientific Python 5

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. Since we’re starting to get pretty good at this whole programming thing let’s stop messing around with made up datasets and do some serious analysis.

• Download the largest dataset on mammalian body size in the world. Fortunately this dataset 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 Python. If you’ve looked at a lot of data you’ll realize that this dataset is tab delimited. The special character to indicate tab in Python is “\t”
• To start let’s explore the data a little
  • Find out how many species are in this massive dataset and print the result to the screen
    • If the value you see is over 5000, remember that species can occur more than once in the dataset. You might want to look at a function in numpy called unique.
    • If the value you see is less than 4000, remember that species names can be repeated in different genera, so we actually want the unique list of latin binomials (i.e., genus and species combined). numpy.unique can work on a data table with multiple columns simultaneously to accomplish this.
  • Find out how many of the species are extinct and how many are extant, print the result to the screen
  • Find out how many genera are present in the dataset
  • Now print the names and mass of the largest and smallest species (note, it is not possible for a mammal to have negative mass ;)
• Now let’s get to work. Calculate the average (i.e., mean) mass of an extinct species and the average mass of an extant species and print them to the screen. There is a numpy function (mean()) that should help you here as well. 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 in the following sentence: “The average mass of extant species is X and the average mass of extinct species is Y.” with the appropriate values filled in for X and Y.