Programming with Perl

Analyzing Patient Data

Words are useful, but what's more useful are the sentences and stories we build with them. Similarly, while a lot of powerful tools are built into languages like Perl, even more live in the libraries they are used to build.

In order to load our inflammation data, we need to import a library called PDL (short for Perl Data Language). In general you should use this library if you want to do fancy things with numbers, especially if you have matrices. We can load PDL using:

use strict;    # FIXME: see <https://github.com/zmughal/perl-novice-inflammation/issues/2>
use warnings;
use PDL;

Importing a library is like getting a piece of lab equipment out of a storage locker and setting it up on the bench. Once it's done, we can ask the library to read our data file for us:

PDL->rcols( 'inflammation-01.csv', [], colsep => ',' );

[
 [ 0  0  …  0  0]
 [ ⋮  ⋮  ⋱  ⋮  ⋮]
 [ 0  0  …  2  1]
 [ 0  1  …  0  0]
]

The expression rcols( ... ) is a function call that asks Perl to run the function rcols that belongs to the PDL library. The arrow notation is used in Perl to refer to parts of things thing->component.

The call to to rcols has three parameters: the name of the file we want to read, a list of the columns to read, and the delimiter that separates values on a line. These both need to be character strings (or strings for short), so we put them in quotes.

When we are finished typing and press Enter (or Return), the interpreter runs our command. Since we haven't told it to do anything else with the function's output, the interpreter displays it. In this case, that output is the data we just loaded.

Our call to numpy.loadtxt read our file, but didn't save the data in memory. To do that, we need to assign the array to a variable. A variable is just a name for a value, such as x, current_temperature, or subject_id. Python's variables must begin with a letter. We can create a new variable simply by assigning a value to it using =. As an illustration, let's step back and instead of considering a table of data, consider the simplest "collection" of data, a single value. The line below assigns a value to a variable:

my $weight_kg = 55;

Once a variable has a value, we can print it:

print $weight_kg, "\n"; # FIXME: should this be say()?

55

and do arithmetic with it:

print 'weight in pounds: ', 2.2 * $weight_kg, "\n"; # FIXME: say()?

weight in pounds: 121.0

We can also change a variable's value by assigning it a new one:

$weight_kg = 57.5;
print 'weight in kilograms is now:', $weight_kg;

weight in kilograms is now: 57.5

FIXME note that we don't need to put a my since we aren't declaring it for the first time.

As the example above shows, we can print several things at once by separating them with commas.

If we imagine the variable as a sticky note with a name written on it, assignment is like putting the sticky note on a particular value: