Think Stats in Clojure Part III: Exploring Data

This is the third instalment of our Think Stats study group; we are working through Allen Downey’s Think Stats, implementing everything in Clojure. In the previous part we showed how to use functions from the Incanter library to explore and transform a dataset. Now we build on that knowledge to explore the National Survey for Family Growth (NSFG) data and answer the question do first babies arrive late? This takes us to the end of chapter 1 of the book.

If you’d like to follow along, start by cloning our thinkstats repository from Github:

git clone --recursive

Change into the project directory and fire up Gorilla REPL:

cd thinkstats
lein gorilla

Getting Started

Our project includes the namespace thinkstats.incanter that brings together our general Incanter utility functions, and for the functions we developed last time for cleaning and augmenting the female pregnancy data.

Let’s start by importing these and the Incanter namspaces we’re going to need this time:

(ns mysterious-aurora
  (:require [incanter.core :as i
              :refer [$ $map $where $rollup $order $fn $group-by $join]]
            [incanter.stats :as s]
            [thinkstats.incanter :as ie :refer [$! $not-nil]]
            [ :as f]))

(We’ve also included thinkstats.gorilla, which just includes some functionality to render Incanter datasets more nicely in Gorilla REPL.)

The function combines reading the data set with clean-and-augment-fem-preg:

(def ds (f/fem-preg-ds))

This function is parsing and transforming the dataset; depending on the speed of your computer, it could take one or two minutes to run.

Validating Data

There are a couple of things covered in chapter 1 of the book that we haven’t done yet: looking at frequencies of values in particular columns of the NSFG data and validating against the code book, and building a function to index rows by :caseid.

We can use the core Clojure frequencies function in conjunction with Incanter’s $ to select values of a column and return a map of value to frequency:

(frequencies ($ :outcome ds))
;=> {1 9148, 2 1862, 4 1921, 5 190, 3 120, 6 352}

Incanter’s $rollup function can be used to compute a summary function over a column or set of columns, and has built-in support for :min, :max, :mean, :sum, and :count. Rolling up :outcome by :count will compute the freqency for each outcome and return a new dataset:

($rollup :count :total :outcome ds)
:outcome :total
1 9148
2 1862
4 1921
5 190
3 120
6 352

Compare this with the table in the code book (you’ll find the table on page 103).

Exploring and Interpreting Data

We saw previously that we can use $where to select rows matching a predicate. For example, to select rows for a given :caseid:

($where {:caseid "10229"} ds)

This could be quite slow for a large dataset as it has to examine every row. An alternative strategy is to build an index in advance then use that to select the desired rows. Here’s how we might do this:

(defn build-column-ix
  [col-name ds]
  (reduce (fn [accum [row-ix v]]
            (update accum v (fnil conj []) row-ix))
          (map-indexed vector ($ col-name ds))))

(def caseid-ix (build-column-ix :caseid ds))

Now we can quickly select rows for a given :caseid using this index:

(i/sel ds :rows (caseid-ix "10229"))

Recall that we can also select a subset of columns at the same time:

(i/sel ds :rows (caseid-ix "10229") :cols [:pregordr :agepreg :outcome])
:pregordr :agepreg :outcome
1 19.58 4
2 21.75 4
3 23.83 4
4 25.5 4
5 29.08 4
6 32.16 4
7 33.16 1

Recall also the meaning of :outcome; a value of 4 indicates a miscarriage and 1 a live birth. So this respondent suffered 6 miscarriages between the ages of 19 and 32, finally seeing a live birth at age 33.

We can use functions from the incanter.stats namespace to compute basic statistics on our data:

(s/mean ($! :totalwgt-lb ds))
;=> 7.2623018494055485
(s/median ($! :totalwgt-lb ds))
;=> 7.375

(Note the use of $! to exclude nil values, which would otherwise trigger a null pointer exception.)

To compute several statistics at once:

(s/summary ($! [:totalwgt-lb] ds))
;=> ({:col :totalwgt-lb, :min 0.0, :max 15.4375, :mean 7.2623018494055485, :median 7.375, :is-numeric true})

Note that, while mean and median take a sequence of values (argument to $! is just a keyword), the summary function expects a dataset (argument to $! is a vector).

Do First Babies Arrive Late?

We now know enough to have a first attempt at answering this question. The columns we’ll use are:

:outcome Pregnancy outcome (1 == live birth)
:birthord Birth order
:prglngth Duration of completed pregnancy in weeks

Compute the mean pregnancy length for the first birth:

(s/mean ($! :prglngth ($where {:outcome 1 :birthord 1} ds)))
;=> 38.60095173351461

…and for subsequent births:

(s/mean ($! :prglngth ($where {:outcome 1 :birthord {:$ne 1}} ds)))
;=> 38.52291446673706

The diffenence between these two values in just 0.08 weeks, so I’d say that these data do not indicate that first babies arrive late.

Here we’ve computed mean pregnancy length for first baby and others; if we want a table of mean pregnancy length by birth order, we can use $rollup again:

($rollup :mean :prglngth :birthord ($where {:outcome 1 :prglngth $not-nil} ds))
:birthord :prglngth
3 47501/1234
4 16187/421
5 2419/63
10 36
9 75/2
7 763/20
1 56782/1471
8 263/7
6 1903/50
2 55420/1437

The mean has been returned as a rational, but we can use transform-col to convert it to a floating-point number:

(as-> ds x
      ($where {:outcome 1 :prglngth $not-nil} x)
      ($rollup :mean :prglngth :birthord x)
      (i/transform-col x :prglngth float))
:birthord :prglngth
3 38.49352
4 38.448933
5 38.396824
10 36.0
9 37.5
7 38.15
1 38.600952
8 37.57143
6 38.06
2 38.56646

Finally, we can use $order to sort this dataset on birth order:

(as-> ds x
      ($where {:outcome 1 :prglngth $not-nil} x)
      ($rollup :mean :prglngth :birthord x)
      (i/transform-col x :prglngth float)
      ($order :birthord :asc x))
:birthord :prglngth
1 38.600952
2 38.56646
3 38.49352
4 38.448933
5 38.396824
6 38.06
7 38.15
8 37.57143
9 37.5
10 36.0

The Incanter functions $where, $rollup, $order, etc. all take a dataset to act on as their last argument. If this argument is omitted, they use the dynamic $data variable that is usually bound using with-data. So the following two expressions are equivalent:

($where {:outcome 1 :prglngth $not-nil} ds)

(with-data ds
  ($where {:outcome 1 :prglngth $not-nil}))

It’s a bit annoying that we have to use as-> when we add transform-col to the mix, as this function takes the dataset as its first argument. Let’s add the following to our thinkstats.incanter namespace:

(defn $transform
  "Like Incanter's `transform-col`, but takes the dataset as an optional
   last argument and, when not specified, uses the dynamically-bound
  [col f & args]
  (let [[ds args] (if (or (i/matrix? (last args)) (i/dataset? (last args)))
                    [(last args) (butlast args)]
                    [i/$data args])]
    (apply i/transform-col ds col f args)))

Now we can use the ->> threading macro:

(->> ($where {:outcome 1 :prglngth $not-nil} ds)
     ($rollup :mean :prglngth :birthord)
     ($transform :prglngth float)
     ($order :birthord :asc))

We have now met most of the core Incanter functions for manipulating datasets, and a few of the statistics functions. I hope that, as we get further into the book, we’ll learn how to calculate error bounds for computed values, and how to decide when we have a statistically significant result. In the next installment we start to look at statistical distributions and plot our first histograms.

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