By-Group Statistical Summary in Clojure
This article is originally published at https://statcompute.wordpress.com
In the previous post (https://statcompute.wordpress.com/2018/03/16/for-loop-and-map-in-clojure), I did a performance comparison between MAP and FOR loop in Clojure with a small dataset. It is interesting to see that the performance of PMAP, e.g. parallel MAP, is considerably below the performance of MAP and FOR loop, which is quite counter-intuitive.
Today, I employed a relatively large dataset with 0.3 million records to perform a by-group statistical summary. In the example, five different approaches were experimented, including MAP, PMAP, Reducer MAP, FOR loop, and LOOP/RECUR. As shown below, PMAP is at least 30% more efficient than the rest in this particular case.
(require '[clojure.pprint :as p]
'[ultra-csv.core :as u]
'[clj-statistics-fns.core :as s]
'[clojure.core.reducers :as r])
(def ds (u/read-csv "/home/liuwensui/Downloads/nycflights.csv"))
;; SHOW HEADERS OF THE DATA
(prn (keys (first ds)))
; (:day :hour :tailnum :arr_time :month :dep_time :carrier :arr_delay :year :dep_delay :origin :flight :distance :air_time :dest :minute)
;; PRINT A DATA SAMPLE
(p/print-table
(map #(select-keys % [:origin :dep_delay]) (take 3 ds)))
; | :origin | :dep_delay |
; |---------+------------|
; | EWR | 2 |
; | LGA | 4 |
; | JFK | 2 |
;; APPROACH #1: MAP()
(time
(p/print-table
(map
(fn [x] {:origin (first x)
:freq (format "%,8d" (count (second x)))
:nmiss (format "%,8d" (count (filter nil? (map #(get % :dep_delay) (second x)))))
:med_delay (format "%,8d" (s/median (remove nil? (map #(get % :dep_delay) (second x)))))
:75q_delay (format "%,8d" (s/kth-percentile 75 (remove nil? (map #(get % :dep_delay) (second x)))))
:max_delay (format "%,8d" (reduce max (remove nil? (map #(get % :dep_delay) (second x)))))})
(group-by :origin ds))))
; | :origin | :freq | :nmiss | :med_delay | :75q_delay | :max_delay |
; |---------+----------+----------+------------+------------+------------|
; | EWR | 120,835 | 3,239 | -1 | 15 | 1,126 |
; | LGA | 104,662 | 3,153 | -3 | 7 | 911 |
; | JFK | 111,279 | 1,863 | -1 | 10 | 1,301 |
; "Elapsed time: 684.71396 msecs"
;; APPROACH #2: PMAP()
(time
(p/print-table
(pmap
(fn [x] {:origin (first x)
:freq (format "%,8d" (count (second x)))
:nmiss (format "%,8d" (count (filter nil? (map #(get % :dep_delay) (second x)))))
:med_delay (format "%,8d" (s/median (remove nil? (map #(get % :dep_delay) (second x)))))
:75q_delay (format "%,8d" (s/kth-percentile 75 (remove nil? (map #(get % :dep_delay) (second x)))))
:max_delay (format "%,8d" (reduce max (remove nil? (map #(get % :dep_delay) (second x)))))})
(group-by :origin ds))))
; | :origin | :freq | :nmiss | :med_delay | :75q_delay | :max_delay |
; |---------+----------+----------+------------+------------+------------|
; | EWR | 120,835 | 3,239 | -1 | 15 | 1,126 |
; | LGA | 104,662 | 3,153 | -3 | 7 | 911 |
; | JFK | 111,279 | 1,863 | -1 | 10 | 1,301 |
; "Elapsed time: 487.065551 msecs"
;; APPROACH #3: REDUCER MAP()
(time
(p/print-table
(into ()
(r/map
(fn [x] {:origin (first x)
:freq (format "%,8d" (count (second x)))
:nmiss (format "%,8d" (count (filter nil? (pmap #(get % :dep_delay) (second x)))))
:med_delay (format "%,8d" (s/median (remove nil? (pmap #(get % :dep_delay) (second x)))))
:75q_delay (format "%,8d" (s/kth-percentile 75 (remove nil? (pmap #(get % :dep_delay) (second x)))))
:max_delay (format "%,8d" (reduce max (remove nil? (pmap #(get % :dep_delay) (second x)))))})
(group-by :origin ds)))))
; | :origin | :freq | :nmiss | :med_delay | :75q_delay | :max_delay |
; |---------+----------+----------+------------+------------+------------|
; | JFK | 111,279 | 1,863 | -1 | 10 | 1,301 |
; | LGA | 104,662 | 3,153 | -3 | 7 | 911 |
; | EWR | 120,835 | 3,239 | -1 | 15 | 1,126 |
; "Elapsed time: 3734.039994 msecs"
;; APPROACH #4: LIST COMPREHENSION
(time
(p/print-table
(for [g (group-by :origin ds)]
((fn [x] {:origin (first x)
:freq (format "%,8d" (count (second x)))
:nmiss (format "%,8d" (count (filter nil? (map #(get % :dep_delay) (second x)))))
:med_delay (format "%,8d" (s/median (remove nil? (map #(get % :dep_delay) (second x)))))
:75q_delay (format "%,8d" (s/kth-percentile 75 (remove nil? (map #(get % :dep_delay) (second x)))))
:max_delay (format "%,8d" (reduce max (remove nil? (map #(get % :dep_delay) (second x)))))})
g))))
; | :origin | :freq | :nmiss | :med_delay | :75q_delay | :max_delay |
; |---------+----------+----------+------------+------------+------------|
; | EWR | 120,835 | 3,239 | -1 | 15 | 1,126 |
; | LGA | 104,662 | 3,153 | -3 | 7 | 911 |
; | JFK | 111,279 | 1,863 | -1 | 10 | 1,301 |
; "Elapsed time: 692.411023 msecs"
;; APPROACH #5: LOOP/RECUR
(time
(p/print-table
(loop [i (group-by :origin ds) result '()]
(if ((complement empty?) i)
(recur
(rest i)
(conj result {:origin (first (first i))
:freq (format "%,8d" (count (second (first i))))
:nmiss (format "%,8d" (count (filter nil? (map #(get % :dep_delay) (second (first i))))))
:med_delay (format "%,8d" (s/median (remove nil? (map #(get % :dep_delay) (second (first i))))))
:75q_delay (format "%,8d" (s/kth-percentile 75 (remove nil? (map #(get % :dep_delay) (second (first i))))))
:max_delay (format "%,8d" (reduce max (remove nil? (map #(get % :dep_delay) (second (first i))))))}))
result))))
; | :origin | :freq | :nmiss | :med_delay | :75q_delay | :max_delay |
; |---------+----------+----------+------------+------------+------------|
; | JFK | 111,279 | 1,863 | -1 | 10 | 1,301 |
; | LGA | 104,662 | 3,153 | -3 | 7 | 911 |
; | EWR | 120,835 | 3,239 | -1 | 15 | 1,126 |
; "Elapsed time: 692.717104 msecs"
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