# Introducing cricpy:A python package to analyze performances of cricketers

Full many a gem of purest ray serene,
The dark unfathomed caves of ocean bear;
Full many a flower is born to blush unseen,
And waste its sweetness on the desert air.

            Thomas Gray, An Elegy Written In A Country Churchyard


# Introduction

It is finally here! cricpy, the python avatar , of my R package cricketr is now ready to rock-n-roll! My R package cricketr had its genesis about 3 and some years ago and went through a couple of enhancements. During this time I have always thought about creating an equivalent python package like cricketr. Now I have finally done it.

So here it is. My python package ‘cricpy!!!’

This package uses the statistics info available in ESPN Cricinfo Statsguru. The current version of this package supports only Test cricket

You should be able to install the package using pip install cricpy and use the many functions available in the package. Please mindful of the ESPN Cricinfo Terms of Use

Cricpy can now analyze performances of teams in Test, ODI and T20 cricket see Cricpy adds team analytics to its arsenal!!

Do check out my post on R package cricketr at Re-introducing cricketr! : An R package to analyze performances of cricketers

If you are passionate about cricket, and love analyzing cricket performances, then check out my racy book on cricket ‘Cricket analytics with cricketr and cricpy – Analytics harmony with R & Python’! This book discusses and shows how to use my R package ‘cricketr’ and my Python package ‘cricpy’ to analyze batsmen and bowlers in all formats of the game (Test, ODI and T20). The paperback is available on Amazon at $21.99 and the kindle version at$9.99/Rs 449/-. A must read for any cricket lover! Check it out!!

This package uses the statistics info available in ESPN Cricinfo Statsguru.

Note: If you would like to do a similar analysis for a different set of batsman and bowlers, you can clone/download my skeleton cricpy-template from Github (which is the R Markdown file I have used for the analysis below). You will only need to make appropriate changes for the players you are interested in. The functions can be executed in RStudio or in a IPython notebook.

# The cricpy package

The cricpy package has several functions that perform several different analyses on both batsman and bowlers. The package has functions that plot percentage frequency runs or wickets, runs likelihood for a batsman, relative run/strike rates of batsman and relative performance/economy rate for bowlers are available.

Other interesting functions include batting performance moving average, forecasting, performance of a player against different oppositions, contribution to wins and losses etc.

The data for a particular player can be obtained with the getPlayerData() function. To do this you will need to go to ESPN CricInfo Player and type in the name of the player for e.g Rahul Dravid, Virat Kohli, Alastair Cook etc. This will bring up a page which have the profile number for the player e.g. for Rahul Dravid this would be http://www.espncricinfo.com/india/content/player/28114.html. Hence, Dravid’s profile is 28114. This can be used to get the data for Rahul Dravid as shown below

The cricpy package is almost a clone of my R package cricketr. The signature of all the python functions are identical with that of its R avatar namely  ‘cricketr’, with only the necessary variations between Python and R. It may be useful to look at my post R vs Python: Different similarities and similar differences. In fact if you are familiar with one of the languages you can look up the package in the other and you will notice the parallel constructs.

You can fork/clone the cricpy package at Github cricpy

The following 2 examples show the similarity between cricketr and cricpy packages

## 1a.Importing cricketr – R

Importing cricketr in R

#install.packages("cricketr")
library(cricketr)

## 2a. Importing cricpy – Python

# Install the package
# Do a pip install cricpy
# Import cricpy
import cricpy
# You could either do
#1.
import cricpy.analytics as ca
#ca.batsman4s("../dravid.csv","Rahul Dravid")
# Or
#2.
from cricpy.analytics import *
#batsman4s("../dravid.csv","Rahul Dravid")


I would recommend using option 1 namely ca.batsman4s() as I may add an advanced analytics module in the future to cricpy.

## 2 Invoking functions

You can seen how the 2 calls are identical for both the R package cricketr and the Python package cricpy

## 2a. Invoking functions with R package ‘cricketr’

library(cricketr)
batsman4s("../dravid.csv","Rahul Dravid")

## 2b. Invoking functions with Python package ‘cricpy’

import cricpy.analytics as ca
ca.batsman4s("../dravid.csv","Rahul Dravid")

# 3a. Getting help from cricketr – R

#help("getPlayerData")

# 3b. Getting help from cricpy – Python

help(ca.getPlayerData)
## Help on function getPlayerData in module cricpy.analytics:
##
## getPlayerData(profile, opposition='', host='', dir='./data', file='player001.csv', type='batting', homeOrAway=[1, 2], result=[1, 2, 4], create=True)
##     Get the player data from ESPN Cricinfo based on specific inputs and store in a file in a given directory
##
##     Description
##
##     Get the player data given the profile of the batsman. The allowed inputs are home,away or both and won,lost or draw of matches. The data is stored in a .csv file in a directory specified. This function also returns a data frame of the player
##
##     Usage
##
##     getPlayerData(profile,opposition="",host="",dir="./data",file="player001.csv",
##     type="batting", homeOrAway=c(1,2),result=c(1,2,4))
##     Arguments
##
##     profile
##     This is the profile number of the player to get data. This can be obtained from http://www.espncricinfo.com/ci/content/player/index.html. Type the name of the player and click search. This will display the details of the player. Make a note of the profile ID. For e.g For Sachin Tendulkar this turns out to be http://www.espncricinfo.com/india/content/player/35320.html. Hence the profile for Sachin is 35320
##     opposition
##     The numerical value of the opposition country e.g.Australia,India, England etc. The values are Australia:2,Bangladesh:25,England:1,India:6,New Zealand:5,Pakistan:7,South Africa:3,Sri Lanka:8, West Indies:4, Zimbabwe:9
##     host
##     The numerical value of the host country e.g.Australia,India, England etc. The values are Australia:2,Bangladesh:25,England:1,India:6,New Zealand:5,Pakistan:7,South Africa:3,Sri Lanka:8, West Indies:4, Zimbabwe:9
##     dir
##     Name of the directory to store the player data into. If not specified the data is stored in a default directory "./data". Default="./data"
##     file
##     Name of the file to store the data into for e.g. tendulkar.csv. This can be used for subsequent functions. Default="player001.csv"
##     type
##     type of data required. This can be "batting" or "bowling"
##     homeOrAway
##     This is a list with either 1,2 or both. 1 is for home 2 is for away
##     result
##     This is a list that can take values 1,2,4. 1 - won match 2- lost match 4- draw
##     Details
##
##     More details can be found in my short video tutorial in Youtube https://www.youtube.com/watch?v=q9uMPFVsXsI
##
##     Value
##
##     Returns the player's dataframe
##
##     Note
##
##     Maintainer: Tinniam V Ganesh
##
##     Author(s)
##
##     Tinniam V Ganesh
##
##     References
##
##     http://www.espncricinfo.com/ci/content/stats/index.html
##
##
##     getPlayerDataSp
##
##     Examples
##
##     ## Not run:
##     # Both home and away. Result = won,lost and drawn
##     tendulkar = getPlayerData(35320,dir=".", file="tendulkar1.csv",
##     type="batting", homeOrAway=[1,2],result=[1,2,4])
##
##     # Only away. Get data only for won and lost innings
##     tendulkar = getPlayerData(35320,dir=".", file="tendulkar2.csv",
##     type="batting",homeOrAway=[2],result=[1,2])
##
##     # Get bowling data and store in file for future
##     kumble = getPlayerData(30176,dir=".",file="kumble1.csv",
##     type="bowling",homeOrAway=[1],result=[1,2])
##
##     #Get the Tendulkar's Performance against Australia in Australia
##     tendulkar = getPlayerData(35320, opposition = 2,host=2,dir=".",
##     file="tendulkarVsAusInAus.csv",type="batting")

The details below will introduce the different functions that are available in cricpy.

## 3. Get the player data for a player using the function getPlayerData()

Important Note This needs to be done only once for a player. This function stores the player’s data in the specified CSV file (for e.g. dravid.csv as above) which can then be reused for all other functions). Once we have the data for the players many analyses can be done. This post will use the stored CSV file obtained with a prior getPlayerData for all subsequent analyses

import cricpy.analytics as ca
#dravid =ca.getPlayerData(28114,dir="..",file="dravid.csv",type="batting",homeOrAway=[1,2], result=[1,2,4])
#acook =ca.getPlayerData(11728,dir="..",file="acook.csv",type="batting",homeOrAway=[1,2], result=[1,2,4])
import cricpy.analytics as ca
#lara =ca.getPlayerData(52337,dir="..",file="lara.csv",type="batting",homeOrAway=[1,2], result=[1,2,4])253802
#kohli =ca.getPlayerData(253802,dir="..",file="kohli.csv",type="batting",homeOrAway=[1,2], result=[1,2,4])

## 4 Rahul Dravid’s performance – Basic Analyses

The 3 plots below provide the following for Rahul Dravid

1. Frequency percentage of runs in each run range over the whole career
2. Mean Strike Rate for runs scored in the given range
3. A histogram of runs frequency percentages in runs ranges
import cricpy.analytics as ca
import matplotlib.pyplot as plt
ca.batsmanRunsFreqPerf("../dravid.csv","Rahul Dravid")

ca.batsmanMeanStrikeRate("../dravid.csv","Rahul Dravid")

ca.batsmanRunsRanges("../dravid.csv","Rahul Dravid") 

## 5. More analyses

import cricpy.analytics as ca
ca.batsman4s("../dravid.csv","Rahul Dravid")

ca.batsman6s("../dravid.csv","Rahul Dravid") 

ca.batsmanDismissals("../dravid.csv","Rahul Dravid")

## 6. 3D scatter plot and prediction plane

The plots below show the 3D scatter plot of Dravid Runs versus Balls Faced and Minutes at crease. A linear regression plane is then fitted between Runs and Balls Faced + Minutes at crease

import cricpy.analytics as ca
ca.battingPerf3d("../dravid.csv","Rahul Dravid")

## 7. Average runs at different venues

The plot below gives the average runs scored by Dravid at different grounds. The plot also the number of innings at each ground as a label at x-axis. It can be seen Dravid did great in Rawalpindi, Leeds, Georgetown overseas and , Mohali and Bangalore at home

import cricpy.analytics as ca
ca.batsmanAvgRunsGround("../dravid.csv","Rahul Dravid")

## 8. Average runs against different opposing teams

This plot computes the average runs scored by Dravid against different countries. Dravid has an average of 50+ in England, New Zealand, West Indies and Zimbabwe.

import cricpy.analytics as ca
ca.batsmanAvgRunsOpposition("../dravid.csv","Rahul Dravid")

## 9 . Highest Runs Likelihood

The plot below shows the Runs Likelihood for a batsman. For this the performance of Sachin is plotted as a 3D scatter plot with Runs versus Balls Faced + Minutes at crease. K-Means. The centroids of 3 clusters are computed and plotted. In this plot Dravid’s  highest tendencies are computed and plotted using K-Means

import cricpy.analytics as ca
ca.batsmanRunsLikelihood("../dravid.csv","Rahul Dravid")

## 10. A look at the Top 4 batsman – Rahul Dravid, Alastair Cook, Brian Lara and Virat Kohli

The following batsmen have been very prolific in test cricket and will be used for teh analyses

1. Rahul Dravid :Average:52.31,100’s – 36, 50’s – 63
2. Alastair Cook : Average: 45.35, 100’s – 33, 50’s – 57
3. Brian Lara : Average: 52.88, 100’s – 34 , 50’s – 48
4. Virat Kohli: Average: 54.57 ,100’s – 24 , 50’s – 19

The following plots take a closer at their performances. The box plots show the median the 1st and 3rd quartile of the runs

## 11. Box Histogram Plot

This plot shows a combined boxplot of the Runs ranges and a histogram of the Runs Frequency

import cricpy.analytics as ca
ca.batsmanPerfBoxHist("../dravid.csv","Rahul Dravid")

ca.batsmanPerfBoxHist("../acook.csv","Alastair Cook")

ca.batsmanPerfBoxHist("../lara.csv","Brian Lara")

ca.batsmanPerfBoxHist("../kohli.csv","Virat Kohli")

## 12. Contribution to won and lost matches

The plot below shows the contribution of Dravid, Cook, Lara and Kohli in matches won and lost. It can be seen that in matches where India has won Dravid and Kohli have scored more and must have been instrumental in the win

For the 2 functions below you will have to use the getPlayerDataSp() function as shown below. I have commented this as I already have these files

import cricpy.analytics as ca
#dravidsp = ca.getPlayerDataSp(28114,tdir=".",tfile="dravidsp.csv",ttype="batting")
#acooksp = ca.getPlayerDataSp(11728,tdir=".",tfile="acooksp.csv",ttype="batting")
#larasp = ca.getPlayerDataSp(52337,tdir=".",tfile="larasp.csv",ttype="batting")
#kohlisp = ca.getPlayerDataSp(253802,tdir=".",tfile="kohlisp.csv",ttype="batting")
import cricpy.analytics as ca
ca.batsmanContributionWonLost("../dravidsp.csv","Rahul Dravid")

ca.batsmanContributionWonLost("../acooksp.csv","Alastair Cook")

ca.batsmanContributionWonLost("../larasp.csv","Brian Lara")

ca.batsmanContributionWonLost("../kohlisp.csv","Virat Kohli")

## 13. Performance at home and overseas

From the plot below it can be seen

Dravid has a higher median overseas than at home.Cook, Lara and Kohli have a lower median of runs overseas than at home.

This function also requires the use of getPlayerDataSp() as shown above

import cricpy.analytics as ca
ca.batsmanPerfHomeAway("../dravidsp.csv","Rahul Dravid")

ca.batsmanPerfHomeAway("../acooksp.csv","Alastair Cook")

ca.batsmanPerfHomeAway("../larasp.csv","Brian Lara")

ca.batsmanPerfHomeAway("../kohlisp.csv","Virat Kohli")

## 14 Moving Average of runs in career

Take a look at the Moving Average across the career of the Top 4 (ignore the dip at the end of all plots. Need to check why this is so!). Lara’s performance seems to have been quite good before his retirement(wonder why retired so early!). Kohli’s performance has been steadily improving over the years

import cricpy.analytics as ca
ca.batsmanMovingAverage("../dravid.csv","Rahul Dravid")

ca.batsmanMovingAverage("../acook.csv","Alastair Cook")

ca.batsmanMovingAverage("../lara.csv","Brian Lara")

ca.batsmanMovingAverage("../kohli.csv","Virat Kohli")

## 15 Cumulative Average runs of batsman in career

This function provides the cumulative average runs of the batsman over the career. Dravid averages around 48, Cook around 44, Lara around 50 and Kohli shows a steady improvement in his cumulative average. Kohli seems to be getting better with time.

import cricpy.analytics as ca
ca.batsmanCumulativeAverageRuns("../dravid.csv","Rahul Dravid")

ca.batsmanCumulativeAverageRuns("../acook.csv","Alastair Cook")

ca.batsmanCumulativeAverageRuns("../lara.csv","Brian Lara")

ca.batsmanCumulativeAverageRuns("../kohli.csv","Virat Kohli")

## 16 Cumulative Average strike rate of batsman in career

Lara has a terrific strike rate of 52+. Cook has a better strike rate over Dravid. Kohli’s strike rate has improved over the years.

import cricpy.analytics as ca
ca.batsmanCumulativeStrikeRate("../dravid.csv","Rahul Dravid")

ca.batsmanCumulativeStrikeRate("../acook.csv","Alastair Cook")

ca.batsmanCumulativeStrikeRate("../lara.csv","Brian Lara")

ca.batsmanCumulativeStrikeRate("../kohli.csv","Virat Kohli")

## 17 Future Runs forecast

Here are plots that forecast how the batsman will perform in future. Currently ARIMA has been used for the forecast. (To do:  Perform Holt-Winters forecast!)

import cricpy.analytics as ca
ca.batsmanPerfForecast("../dravid.csv","Rahul Dravid")
##                              ARIMA Model Results
## ==============================================================================
## Dep. Variable:                 D.runs   No. Observations:                  284
## Model:                 ARIMA(5, 1, 0)   Log Likelihood               -1522.837
## Method:                       css-mle   S.D. of innovations             51.488
## Date:                Sun, 28 Oct 2018   AIC                           3059.673
## Time:                        09:47:39   BIC                           3085.216
## Sample:                    07-04-1996   HQIC                          3069.914
##                          - 01-24-2012
## ================================================================================
##                    coef    std err          z      P>|z|      [0.025      0.975]
## --------------------------------------------------------------------------------
## const           -0.1336      0.884     -0.151      0.880      -1.867       1.599
## ar.L1.D.runs    -0.7729      0.058    -13.322      0.000      -0.887      -0.659
## ar.L2.D.runs    -0.6234      0.071     -8.753      0.000      -0.763      -0.484
## ar.L3.D.runs    -0.5199      0.074     -7.038      0.000      -0.665      -0.375
## ar.L4.D.runs    -0.3490      0.071     -4.927      0.000      -0.488      -0.210
## ar.L5.D.runs    -0.2116      0.058     -3.665      0.000      -0.325      -0.098
##                                     Roots
## =============================================================================
##                  Real           Imaginary           Modulus         Frequency
## -----------------------------------------------------------------------------
## AR.1            0.5789           -1.1743j            1.3093           -0.1771
## AR.2            0.5789           +1.1743j            1.3093            0.1771
## AR.3           -1.3617           -0.0000j            1.3617           -0.5000
## AR.4           -0.7227           -1.2257j            1.4230           -0.3348
## AR.5           -0.7227           +1.2257j            1.4230            0.3348
## -----------------------------------------------------------------------------
##                 0
## count  284.000000
## mean    -0.306769
## std     51.632947
## min   -106.653589
## 25%    -33.835148
## 50%     -8.954253
## 75%     21.024763
## max    223.152901
##
## C:\Users\Ganesh\ANACON~1\lib\site-packages\statsmodels\tsa\kalmanf\kalmanfilter.py:646: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
##   if issubdtype(paramsdtype, float):
## C:\Users\Ganesh\ANACON~1\lib\site-packages\statsmodels\tsa\kalmanf\kalmanfilter.py:650: FutureWarning: Conversion of the second argument of issubdtype from complex to np.complexfloating is deprecated. In future, it will be treated as np.complex128 == np.dtype(complex).type.
##   elif issubdtype(paramsdtype, complex):
## C:\Users\Ganesh\ANACON~1\lib\site-packages\statsmodels\tsa\kalmanf\kalmanfilter.py:577: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
##   if issubdtype(paramsdtype, float):

## 18 Relative Batsman Cumulative Average Runs

The plot below compares the Relative cumulative average runs of the batsman for each of the runs ranges of 10 and plots them. The plot indicate the following Range 30 – 100 innings – Lara leads followed by Dravid Range 100+ innings – Kohli races ahead of the rest

import cricpy.analytics as ca
frames = ["../dravid.csv","../acook.csv","../lara.csv","../kohli.csv"]
names = ["Dravid","A Cook","Brian Lara","V Kohli"]
ca.relativeBatsmanCumulativeAvgRuns(frames,names)

## 19. Relative Batsman Strike Rate

The plot below gives the relative Runs Frequency Percetages for each 10 run bucket. The plot below show

Brian Lara towers over the Dravid, Cook and Kohli. However you will notice that Kohli’s strike rate is going up

import cricpy.analytics as ca
frames = ["../dravid.csv","../acook.csv","../lara.csv","../kohli.csv"]
names = ["Dravid","A Cook","Brian Lara","V Kohli"]
ca.relativeBatsmanCumulativeStrikeRate(frames,names)

## 20. 3D plot of Runs vs Balls Faced and Minutes at Crease

The plot is a scatter plot of Runs vs Balls faced and Minutes at Crease. A prediction plane is fitted

import cricpy.analytics as ca
ca.battingPerf3d("../dravid.csv","Rahul Dravid")

ca.battingPerf3d("../acook.csv","Alastair Cook")

ca.battingPerf3d("../lara.csv","Brian Lara")

ca.battingPerf3d("../kohli.csv","Virat Kohli")

## 21. Predicting Runs given Balls Faced and Minutes at Crease

A multi-variate regression plane is fitted between Runs and Balls faced +Minutes at crease.

import cricpy.analytics as ca
import numpy as np
import pandas as pd
BF = np.linspace( 10, 400,15)
Mins = np.linspace( 30,600,15)
newDF= pd.DataFrame({'BF':BF,'Mins':Mins})
dravid = ca.batsmanRunsPredict("../dravid.csv",newDF,"Dravid")
print(dravid)
##             BF        Mins        Runs
## 0    10.000000   30.000000    0.519667
## 1    37.857143   70.714286   13.821794
## 2    65.714286  111.428571   27.123920
## 3    93.571429  152.142857   40.426046
## 4   121.428571  192.857143   53.728173
## 5   149.285714  233.571429   67.030299
## 6   177.142857  274.285714   80.332425
## 7   205.000000  315.000000   93.634552
## 8   232.857143  355.714286  106.936678
## 9   260.714286  396.428571  120.238805
## 10  288.571429  437.142857  133.540931
## 11  316.428571  477.857143  146.843057
## 12  344.285714  518.571429  160.145184
## 13  372.142857  559.285714  173.447310
## 14  400.000000  600.000000  186.749436

The fitted model is then used to predict the runs that the batsmen will score for a given Balls faced and Minutes at crease.

## 22 Analysis of Top 3 wicket takers

The following 3 bowlers have had an excellent career and will be used for the analysis

1. Glenn McGrath:Wickets: 563, Average = 21.64, Economy Rate – 2.49
2. Kapil Dev : Wickets: 434, Average = 29.64, Economy Rate – 2.78
3. James Anderson: Wickets: 564, Average = 28.64, Economy Rate – 2.88

How do Glenn McGrath, Kapil Dev and James Anderson compare with one another with respect to wickets taken and the Economy Rate. The next set of plots compute and plot precisely these analyses.

## 23. Get the bowler’s data

This plot below computes the percentage frequency of number of wickets taken for e.g 1 wicket x%, 2 wickets y% etc and plots them as a continuous line

import cricpy.analytics as ca
#mcgrath =ca.getPlayerData(6565,dir=".",file="mcgrath.csv",type="bowling",homeOrAway=[1,2], result=[1,2,4])
#kapil =ca.getPlayerData(30028,dir=".",file="kapil.csv",type="bowling",homeOrAway=[1,2], result=[1,2,4])
#anderson =ca.getPlayerData(8608,dir=".",file="anderson.csv",type="bowling",homeOrAway=[1,2], result=[1,2,4])

## 24. Wicket Frequency Plot

This plot below plots the frequency of wickets taken for each of the bowlers

import cricpy.analytics as ca
ca.bowlerWktsFreqPercent("../mcgrath.csv","Glenn McGrath")

ca.bowlerWktsFreqPercent("../kapil.csv","Kapil Dev")

ca.bowlerWktsFreqPercent("../anderson.csv","James Anderson")

## 25. Wickets Runs plot

The plot below create a box plot showing the 1st and 3rd quartile of runs conceded versus the number of wickets taken

import cricpy.analytics as ca
ca.bowlerWktsRunsPlot("../mcgrath.csv","Glenn McGrath")

ca.bowlerWktsRunsPlot("../kapil.csv","Kapil Dev")

ca.bowlerWktsRunsPlot("../anderson.csv","James Anderson")

## 26 Average wickets at different venues

The plot gives the average wickets taken by Muralitharan at different venues. McGrath best performances are at Centurion, Lord’s and Port of Spain averaging about 4 wickets. Kapil Dev’s does good at Kingston and Wellington. Anderson averages 4 wickets at Dunedin and Nagpur

import cricpy.analytics as ca
ca.bowlerAvgWktsGround("../mcgrath.csv","Glenn McGrath")

ca.bowlerAvgWktsGround("../kapil.csv","Kapil Dev")

ca.bowlerAvgWktsGround("../anderson.csv","James Anderson")

## 27 Average wickets against different opposition

The plot gives the average wickets taken by Muralitharan against different countries. The x-axis also includes the number of innings against each team

import cricpy.analytics as ca
ca.bowlerAvgWktsOpposition("../mcgrath.csv","Glenn McGrath")

ca.bowlerAvgWktsOpposition("../kapil.csv","Kapil Dev")

ca.bowlerAvgWktsOpposition("../anderson.csv","James Anderson")

## 28 Wickets taken moving average

From the plot below it can be see James Anderson has had a solid performance over the years averaging about wickets

import cricpy.analytics as ca
ca.bowlerMovingAverage("../mcgrath.csv","Glenn McGrath")

ca.bowlerMovingAverage("../kapil.csv","Kapil Dev")

ca.bowlerMovingAverage("../anderson.csv","James Anderson")

## 29 Cumulative average wickets taken

The plots below give the cumulative average wickets taken by the bowlers. mcGrath plateaus around 2.4 wickets, Kapil Dev’s performance deteriorates over the years. Anderson holds on rock steady around 2 wickets

import cricpy.analytics as ca
ca.bowlerCumulativeAvgWickets("../mcgrath.csv","Glenn McGrath")

ca.bowlerCumulativeAvgWickets("../kapil.csv","Kapil Dev")

ca.bowlerCumulativeAvgWickets("../anderson.csv","James Anderson")

## 30 Cumulative average economy rate

The plots below give the cumulative average economy rate of the bowlers. McGrath’s was very expensive early in his career conceding about 2.8 runs per over which drops to around 2.5 runs towards the end. Kapil Dev’s economy rate drops from 3.6 to 2.8. Anderson is probably more expensive than the other 2.

import cricpy.analytics as ca
ca.bowlerCumulativeAvgEconRate("../mcgrath.csv","Glenn McGrath")

ca.bowlerCumulativeAvgEconRate("../kapil.csv","Kapil Dev")

ca.bowlerCumulativeAvgEconRate("../anderson.csv","James Anderson")

## 31 Future Wickets forecast

import cricpy.analytics as ca
ca.bowlerPerfForecast("../mcgrath.csv","Glenn McGrath")
##                              ARIMA Model Results
## ==============================================================================
## Dep. Variable:              D.Wickets   No. Observations:                  236
## Model:                 ARIMA(5, 1, 0)   Log Likelihood                -480.815
## Method:                       css-mle   S.D. of innovations              1.851
## Date:                Sun, 28 Oct 2018   AIC                            975.630
## Time:                        09:28:32   BIC                            999.877
## Sample:                    11-12-1993   HQIC                           985.404
##                          - 01-02-2007
## ===================================================================================
##                       coef    std err          z      P>|z|      [0.025      0.975]
## -----------------------------------------------------------------------------------
## const               0.0037      0.033      0.113      0.910      -0.061       0.068
## ar.L1.D.Wickets    -0.9432      0.064    -14.708      0.000      -1.069      -0.818
## ar.L2.D.Wickets    -0.7254      0.086     -8.469      0.000      -0.893      -0.558
## ar.L3.D.Wickets    -0.4827      0.093     -5.217      0.000      -0.664      -0.301
## ar.L4.D.Wickets    -0.3690      0.085     -4.324      0.000      -0.536      -0.202
## ar.L5.D.Wickets    -0.1709      0.064     -2.678      0.008      -0.296      -0.046
##                                     Roots
## =============================================================================
##                  Real           Imaginary           Modulus         Frequency
## -----------------------------------------------------------------------------
## AR.1            0.5630           -1.2761j            1.3948           -0.1839
## AR.2            0.5630           +1.2761j            1.3948            0.1839
## AR.3           -0.8433           -1.0820j            1.3718           -0.3554
## AR.4           -0.8433           +1.0820j            1.3718            0.3554
## AR.5           -1.5981           -0.0000j            1.5981           -0.5000
## -----------------------------------------------------------------------------
##                 0
## count  236.000000
## mean    -0.005142
## std      1.856961
## min     -3.457002
## 25%     -1.433391
## 50%     -0.080237
## 75%      1.446149
## max      5.840050

## 32 Get player data special

As discussed above the next 2 charts require the use of getPlayerDataSp()

import cricpy.analytics as ca
#mcgrathsp =ca.getPlayerDataSp(6565,tdir=".",tfile="mcgrathsp.csv",ttype="bowling")
#kapilsp =ca.getPlayerDataSp(30028,tdir=".",tfile="kapilsp.csv",ttype="bowling")
#andersonsp =ca.getPlayerDataSp(8608,tdir=".",tfile="andersonsp.csv",ttype="bowling")

## 33 Contribution to matches won and lost

The plot below is extremely interesting Glenn McGrath has been more instrumental in Australia winning than Kapil and Anderson as seems to have taken more wickets when Australia won.

import cricpy.analytics as ca
ca.bowlerContributionWonLost("../mcgrathsp.csv","Glenn McGrath")

ca.bowlerContributionWonLost("../kapilsp.csv","Kapil Dev")

ca.bowlerContributionWonLost("../andersonsp.csv","James Anderson")

## 34 Performance home and overseas

McGrath and Kapil Dev have performed better overseas than at home. Anderson has performed about the same home and overseas

import cricpy.analytics as ca
ca.bowlerPerfHomeAway("../mcgrathsp.csv","Glenn McGrath")

ca.bowlerPerfHomeAway("../kapilsp.csv","Kapil Dev")

ca.bowlerPerfHomeAway("../andersonsp.csv","James Anderson")

## 35 Relative cumulative average economy rate of bowlers

The Relative cumulative economy rate shows that McGrath has the best economy rate followed by Kapil Dev and then Anderson.

import cricpy.analytics as ca
frames = ["../mcgrath.csv","../kapil.csv","../anderson.csv"]
names = ["Glenn McGrath","Kapil Dev","James Anderson"]
ca.relativeBowlerCumulativeAvgEconRate(frames,names)

## 36 Relative Economy Rate against wickets taken

McGrath has been economical regardless of the number of wickets taken. Kapil Dev has been slightly more expensive when he takes more wickets

import cricpy.analytics as ca
frames = ["../mcgrath.csv","../kapil.csv","../anderson.csv"]
names = ["Glenn McGrath","Kapil Dev","James Anderson"]
ca.relativeBowlingER(frames,names)

## 37 Relative cumulative average wickets of bowlers in career

The plot below shows that McGrath has the best overall cumulative average wickets. Kapil’s leads Anderson till about 150 innings after which Anderson takes over

import cricpy.analytics as ca
frames = ["../mcgrath.csv","../kapil.csv","../anderson.csv"]
names = ["Glenn McGrath","Kapil Dev","James Anderson"]
ca.relativeBowlerCumulativeAvgWickets(frames,names)

# Key Findings

The plots above capture some of the capabilities and features of my cricpy package. Feel free to install the package and try it out. Please do keep in mind ESPN Cricinfo’s Terms of Use.

Here are the main findings from the analysis above

## Key insights

1. Brian Lara is head and shoulders above the rest in the overall strike rate
2. Kohli performance has been steadily improving over the years and with the way he is going he will shatter all records.
3. Kohli and Dravid have scored more in matches where India has won than the other two.
4. Dravid has performed very well overseas
5. The cumulative average runs has Kohli just edging out the other 3. Kohli is probably midway in his career but considering that his moving average is improving strongly, we can expect great things of him with the way he is going.
6. McGrath has had some great performances overseas
7. Mcgrath has the best economy rate and has contributed significantly to Australia’s wins.
8.In the cumulative average wickets race McGrath leads the pack. Kapil leads Anderson till about 150 matches after which Anderson takes over.

The code for cricpy can be accessed at Github at cricpy

Do let me know if you run into issues.

## Conclusion

I have long wanted to make a python equivalent of cricketr and I have been able to make it. cricpy is still work in progress. I have add the necessary functions for ODI and Twenty20.  Go ahead give ‘cricpy’ a spin!!

Stay tuned!

Important note: Do check out my other posts using cricpy at cricpy-posts

# Big Data-1: Move into the big league:Graduate from Python to Pyspark

This post discusses similar constructs in Python and Pyspark. As in my earlier post R vs Python: Different similarities and similar differences the focus is on the key and common constructs to highlight the similarities.

Important Note:You can also access this notebook at databricks public site  Big Data-1: Move into the big league:Graduate from Python to Pyspark (the formatting here is much better!!).

For this notebook I have used Databricks community edition

Hope you found this useful!

Note: There are still a few more important constructs which I will be adding to this post.

# My book ‘Practical Machine Learning in R and Python: Second edition’ on Amazon

Note: The 3rd edition of this book is now available My book ‘Practical Machine Learning in R and Python: Third edition’ on Amazon

The third edition of my book ‘Practical Machine Learning with R and Python – Machine Learning in stereo’ is now available in both paperback ($12.99) and kindle ($9.99/Rs449) versions.  This second edition includes more content,  extensive comments and formatting for better readability.

In this book I implement some of the most common, but important Machine Learning algorithms in R and equivalent Python code.
1. Practical machine with R and Python: Third Edition – Machine Learning in Stereo(Paperback-$12.99) 2. Practical machine with R and Third Edition – Machine Learning in Stereo(Kindle-$9.99/Rs449)

This book is ideal both for beginners and the experts in R and/or Python. Those starting their journey into datascience and ML will find the first 3 chapters useful, as they touch upon the most important programming constructs in R and Python and also deal with equivalent statements in R and Python. Those who are expert in either of the languages, R or Python, will find the equivalent code ideal for brushing up on the other language. And finally,those who are proficient in both languages, can use the R and Python implementations to internalize the ML algorithms better.

Here is a look at the topics covered

Preface …………………………………………………………………………….4
Introduction ………………………………………………………………………6
1. Essential R ………………………………………………………………… 8
2. Essential Python for Datascience ……………………………………………57
3. R vs Python …………………………………………………………………81
4. Regression of a continuous variable ……………………………………….101
5. Classification and Cross Validation ………………………………………..121
6. Regression techniques and regularization ………………………………….146
7. SVMs, Decision Trees and Validation curves ………………………………191
8. Splines, GAMs, Random Forests and Boosting ……………………………222
9. PCA, K-Means and Hierarchical Clustering ………………………………258
References ……………………………………………………………………..269

Hope you have a great time learning as I did while implementing these algorithms!

# My book ‘Practical Machine Learning with R and Python’ on Amazon

Note: The 3rd edition of this book is now available My book ‘Practical Machine Learning in R and Python: Third edition’ on Amazon

My book ‘Practical Machine Learning with R and Python: Second Edition – Machine Learning in stereo’ is now available in both paperback ($10.99) and kindle ($7.99/Rs449) versions. In this book I implement some of the most common, but important Machine Learning algorithms in R and equivalent Python code. This is almost like listening to parallel channels of music in stereo!
1. Practical machine with R and Python: Third Edition – Machine Learning in Stereo(Paperback-$12.99) 2. Practical machine with R and Python Third Edition – Machine Learning in Stereo(Kindle-$8.99/Rs449)
This book is ideal both for beginners and the experts in R and/or Python. Those starting their journey into datascience and ML will find the first 3 chapters useful, as they touch upon the most important programming constructs in R and Python and also deal with equivalent statements in R and Python. Those who are expert in either of the languages, R or Python, will find the equivalent code ideal for brushing up on the other language. And finally,those who are proficient in both languages, can use the R and Python implementations to internalize the ML algorithms better.

Here is a look at the topics covered

Essential R …………………………………….. 7
Essential Python for Datascience ………………..   54
R vs Python ……………………………………. 77
Regression of a continuous variable ………………. 96
Classification and Cross Validation ……………….113
Regression techniques and regularization …………. 134
SVMs, Decision Trees and Validation curves …………175
Splines, GAMs, Random Forests and Boosting …………202
PCA, K-Means and Hierarchical Clustering …………. 234

Hope you have a great time learning as I did while implementing these algorithms!

# Introduction

This is the final and concluding part of my series on ‘Practical Machine Learning with R and Python’. In this series I included the implementations of the most common Machine Learning algorithms in R and Python. The algorithms implemented were

1. Practical Machine Learning with R and Python – Part 1 In this initial post, I touch upon regression of a continuous target variable. Specifically I touch upon Univariate, Multivariate, Polynomial regression and KNN regression in both R and Python
2. Practical Machine Learning with R and Python – Part 2 In this post, I discuss Logistic Regression, KNN classification and Cross Validation error for both LOOCV and K-Fold in both R and Python
3. Practical Machine Learning with R and Python – Part 3 This 3rd part included feature selection in Machine Learning. Specifically I touch best fit, forward fit, backward fit, ridge(L2 regularization) & lasso (L1 regularization). The post includes equivalent code in R and Python.
4. Practical Machine Learning with R and Python – Part 4 In this part I discussed SVMs, Decision Trees, Validation, Precision-Recall, AUC and ROC curves
5. Practical Machine Learning with R and Python – Part 5  In this penultimate part, I touch upon B-splines, natural splines, smoothing spline, Generalized Additive Models(GAMs), Decision Trees, Random Forests and Gradient Boosted Treess.

In this last part I cover Unsupervised Learning. Specifically I cover the implementations of Principal Component Analysis (PCA). K-Means and Heirarchical Clustering. You can download this R Markdown file from Github at MachineLearning-RandPython-Part6

1. Machine Learning in plain English-Part 1
2. Machine Learning in plain English-Part 2
3. Machine Learning in plain English-Part 3

Check out my compact and minimal book  “Practical Machine Learning with R and Python:Third edition- Machine Learning in stereo”  available in Amazon in paperback($12.99) and kindle($8.99) versions. My book includes implementations of key ML algorithms and associated measures and metrics. The book is ideal for anybody who is familiar with the concepts and would like a quick reference to the different ML algorithms that can be applied to problems and how to select the best model. Pick your copy today!!

1.1a Principal Component Analysis (PCA) – R code

Principal Component Analysis is used to reduce the dimensionality of the input. In the code below 8 x 8 pixel of handwritten digits is reduced into its principal components. Then a scatter plot of the first 2 principal components give a very good visial representation of the data

library(dplyr)
library(ggplot2)
#Note: This example is adapted from an the example in the book Python Datascience handbook by
# Jake VanderPlas (https://jakevdp.github.io/PythonDataScienceHandbook/05.09-principal-component-analysis.html)

# Read the digits data (From sklearn datasets)
# Create a digits classes target variable
digitClasses <- factor(digits$X0.000000000000000000e.00.29) #Invoke the Principal Componsent analysis on columns 1-64 digitsPCA=prcomp(digits[,1:64]) # Create a dataframe of PCA df <- data.frame(digitsPCA$x)
# Bind the digit classes
df1 <- cbind(df,digitClasses)
# Plot only the first 2 Principal components as a scatter plot. This plot uses only the
# first 2 principal components
ggplot(df1,aes(x=PC1,y=PC2,col=digitClasses)) + geom_point() +
ggtitle("Top 2 Principal Components")

## 1.1 b Variance explained vs no principal components – R code

In the code below the variance explained vs the number of principal components is plotted. It can be seen that with 20 Principal components almost 90% of the variance is explained by this reduced dimensional model.

# Read the digits data (from sklearn datasets)
# Digits target
digitClasses <- factor(digits$X0.000000000000000000e.00.29) digitsPCA=prcomp(digits[,1:64]) # Get the Standard Deviation sd=digitsPCA$sdev
# Compute the variance
digitsVar=digitsPCA$sdev^2 #Compute the percent variance explained percentVarExp=digitsVar/sum(digitsVar) # Plot the percent variance exlained as a function of the number of principal components #plot(cumsum(percentVarExp), xlab="Principal Component", # ylab="Cumulative Proportion of Variance Explained", # main="Principal Components vs % Variance explained",ylim=c(0,1),type='l',lwd=2, # col="blue") ## 1.1c Principal Component Analysis (PCA) – Python code import numpy as np from sklearn.decomposition import PCA from sklearn import decomposition from sklearn import datasets import matplotlib.pyplot as plt from sklearn.datasets import load_digits # Load the digits data digits = load_digits() # Select only the first 2 principal components pca = PCA(2) # project from 64 to 2 dimensions #Compute the first 2 PCA projected = pca.fit_transform(digits.data) # Plot a scatter plot of the first 2 principal components plt.scatter(projected[:, 0], projected[:, 1], c=digits.target, edgecolor='none', alpha=0.5, cmap=plt.cm.get_cmap('spectral', 10)) plt.xlabel('PCA 1') plt.ylabel('PCA 2') plt.colorbar(); plt.title("Top 2 Principal Components") plt.savefig('fig1.png', bbox_inches='tight') ## 1.1 b Variance vs no principal components ## – Python code import numpy as np from sklearn.decomposition import PCA from sklearn import decomposition from sklearn import datasets import matplotlib.pyplot as plt from sklearn.datasets import load_digits digits = load_digits() # Select all 64 principal components pca = PCA(64) # project from 64 to 2 dimensions projected = pca.fit_transform(digits.data) # Obtain the explained variance for each principal component varianceExp= pca.explained_variance_ratio_ # Compute the total sum of variance totVarExp=np.cumsum(np.round(pca.explained_variance_ratio_, decimals=4)*100) # Plot the variance explained as a function of the number of principal components plt.plot(totVarExp) plt.xlabel('No of principal components') plt.ylabel('% variance explained') plt.title('No of Principal Components vs Total Variance explained') plt.savefig('fig2.png', bbox_inches='tight') ## 1.2a K-Means – R code In the code first the scatter plot of the first 2 Principal Components of the handwritten digits is plotted as a scatter plot. Over this plot 10 centroids of the 10 different clusters corresponding the 10 diferent digits is plotted over the original scatter plot. library(ggplot2) # Read the digits data digits= read.csv("digits.csv") # Create digit classes target variable digitClasses <- factor(digits$X0.000000000000000000e.00.29)

# Compute the Principal COmponents
digitsPCA=prcomp(digits[,1:64])

# Create a data frame of Principal components and the digit classes
df <- data.frame(digitsPCA$x) df1 <- cbind(df,digitClasses) # Pick only the first 2 principal components a<- df[,1:2] # Compute K Means of 10 clusters and allow for 1000 iterations k<-kmeans(a,10,1000) # Create a dataframe of the centroids of the clusters df2<-data.frame(k$centers)

#Plot the first 2 principal components with the K Means centroids
ggplot(df1,aes(x=PC1,y=PC2,col=digitClasses)) + geom_point() +
geom_point(data=df2,aes(x=PC1,y=PC2),col="black",size = 4) +
ggtitle("Top 2 Principal Components with KMeans clustering") 

## 1.2b K-Means – Python code

The centroids of the 10 different handwritten digits is plotted over the scatter plot of the first 2 principal components.

import numpy as np
from sklearn.decomposition import PCA
from sklearn import decomposition
from sklearn import datasets
import matplotlib.pyplot as plt
from sklearn.cluster import KMeans

# Select only the 1st 2 principal components
pca = PCA(2)  # project from 64 to 2 dimensions
projected = pca.fit_transform(digits.data)

# Create 10 different clusters
kmeans = KMeans(n_clusters=10)

# Compute  the clusters
kmeans.fit(projected)
y_kmeans = kmeans.predict(projected)
# Get the cluster centroids
centers = kmeans.cluster_centers_
centers

#Create a scatter plot of the first 2 principal components
plt.scatter(projected[:, 0], projected[:, 1],
c=digits.target, edgecolor='none', alpha=0.5,
cmap=plt.cm.get_cmap('spectral', 10))
plt.xlabel('PCA 1')
plt.ylabel('PCA 2')
plt.colorbar();
# Overlay the centroids on the scatter plot
plt.scatter(centers[:, 0], centers[:, 1], c='darkblue', s=100)
plt.savefig('fig3.png', bbox_inches='tight')

## 1.3a Heirarchical clusters – R code

Herirachical clusters is another type of unsupervised learning. It successively joins the closest pair of objects (points or clusters) in succession based on some ‘distance’ metric. In this type of clustering we do not have choose the number of centroids. We can cut the created dendrogram mat an appropriate height to get a desired and reasonable number of clusters These are the following ‘distance’ metrics used while combining successive objects

• Ward
• Complete
• Single
• Average
• Centroid
# Read the IRIS dataset
iris <- datasets::iris
iris2 <- iris[,-5]
species <- iris[,5]

#Compute the distance matrix
d_iris <- dist(iris2)

# Use the 'average' method to for the clsuters
hc_iris <- hclust(d_iris, method = "average")

# Plot the clusters
plot(hc_iris)

# Cut tree into 3 groups
sub_grp <- cutree(hc_iris, k = 3)

# Number of members in each cluster
table(sub_grp)
## sub_grp
##  1  2  3
## 50 64 36
# Draw rectangles around the clusters
rect.hclust(hc_iris, k = 3, border = 2:5)

## 1.3a Heirarchical clusters – Python code

from sklearn.datasets import load_iris
import matplotlib.pyplot as plt
# Load the IRIS data set

# Generate the linkage matrix using the average method

#Plot the dendrogram
#dendrogram(Z)
#plt.xlabel('Data')
#plt.ylabel('Distance')
#plt.suptitle('Samples clustering', fontweight='bold', fontsize=14);
#plt.savefig('fig4.png', bbox_inches='tight')

# Conclusion

This is the last and concluding part of my series on Practical Machine Learning with R and Python. These parallel implementations of R and Python can be used as a quick reference while working on a large project. A person who is adept in one of the languages R or Python, can quickly absorb code in the other language.

Hope you find this series useful!

More interesting things to come. Watch this space!

References

1. Statistical Learning, Prof Trevor Hastie & Prof Robert Tibesherani, Online Stanford
2. Applied Machine Learning in Python Prof Kevyn-Collin Thomson, University Of Michigan, Coursera

To see all posts see ‘Index of posts

# Practical Machine Learning with R and Python – Part 5

This is the 5th and probably penultimate part of my series on ‘Practical Machine Learning with R and Python’. The earlier parts of this series included

1. Practical Machine Learning with R and Python – Part 1 In this initial post, I touch upon univariate, multivariate, polynomial regression and KNN regression in R and Python
2.Practical Machine Learning with R and Python – Part 2 In this post, I discuss Logistic Regression, KNN classification and cross validation error for both LOOCV and K-Fold in both R and Python
3.Practical Machine Learning with R and Python – Part 3 This post covered ‘feature selection’ in Machine Learning. Specifically I touch best fit, forward fit, backward fit, ridge(L2 regularization) & lasso (L1 regularization). The post includes equivalent code in R and Python.
4.Practical Machine Learning with R and Python – Part 4 In this part I discussed SVMs, Decision Trees, validation, precision recall, and roc curves

This post ‘Practical Machine Learning with R and Python – Part 5’ discusses regression with B-splines, natural splines, smoothing splines, generalized additive models (GAMS), bagging, random forest and boosting

As with my previous posts in this series, this post is largely based on the following 2 MOOC courses

1. Statistical Learning, Prof Trevor Hastie & Prof Robert Tibesherani, Online Stanford
2. Applied Machine Learning in Python Prof Kevyn-Collin Thomson, University Of Michigan, Coursera

You can download this R Markdown file and associated data files from Github at MachineLearning-RandPython-Part5

1. Machine Learning in plain English-Part 1
2. Machine Learning in plain English-Part 2
3. Machine Learning in plain English-Part 3

Check out my compact and minimal book  “Practical Machine Learning with R and Python:Third edition- Machine Learning in stereo”  available in Amazon in paperback($12.99) and kindle($8.99) versions. My book includes implementations of key ML algorithms and associated measures and metrics. The book is ideal for anybody who is familiar with the concepts and would like a quick reference to the different ML algorithms that can be applied to problems and how to select the best model. Pick your copy today!!

For this part I have used the data sets from UCI Machine Learning repository(Communities and Crime and Auto MPG)

## 1. Splines

When performing regression (continuous or logistic) between a target variable and a feature (or a set of features), a single polynomial for the entire range of the data set usually does not perform a good fit.Rather we would need to provide we could fit
regression curves for different section of the data set.

There are several techniques which do this for e.g. piecewise-constant functions, piecewise-linear functions, piecewise-quadratic/cubic/4th order polynomial functions etc. One such set of functions are the cubic splines which fit cubic polynomials to successive sections of the dataset. The points where the cubic splines join, are called ‘knots’.

Since each section has a different cubic spline, there could be discontinuities (or breaks) at these knots. To prevent these discontinuities ‘natural splines’ and ‘smoothing splines’ ensure that the seperate cubic functions have 2nd order continuity at these knots with the adjacent splines. 2nd order continuity implies that the value, 1st order derivative and 2nd order derivative at these knots are equal.

A cubic spline with knots $\alpha_{k}$ , k=1,2,3,..K is a piece-wise cubic polynomial with continuous derivative up to order 2 at each knot. We can write $y_{i} = \beta_{0} +\beta_{1}b_{1}(x_{i}) +\beta_{2}b_{2}(x_{i}) + .. + \beta_{K+3}b_{K+3}(x_{i}) + \epsilon_{i}$.
For each ($x{i},y{i}$), $b_{i}$ are called ‘basis’ functions, where  $b_{1}(x_{i})=x_{i}$$b_{2}(x_{i})=x_{i}^2$, $b_{3}(x_{i})=x_{i}^3$, $b_{k+3}(x_{i})=(x_{i} -\alpha_{k})^3$ where k=1,2,3… K The 1st and 2nd derivatives of cubic splines are continuous at the knots. Hence splines provide a smooth continuous fit to the data by fitting different splines to different sections of the data

## 1.1a Fit a 4th degree polynomial – R code

In the code below a non-linear function (a 4th order polynomial) is used to fit the data. Usually when we fit a single polynomial to the entire data set the tails of the fit tend to vary a lot particularly if there are fewer points at the ends. Splines help in reducing this variation at the extremities

library(dplyr)
library(ggplot2)
source('RFunctions-1.R')
df=read.csv("auto_mpg.csv",stringsAsFactors = FALSE) # Data from UCI
df1 <- as.data.frame(sapply(df,as.numeric))
#Select specific columns
df2 <- df1 %>% dplyr::select(cylinder,displacement, horsepower,weight, acceleration, year,mpg)
auto <- df2[complete.cases(df2),]
# Fit a 4th degree polynomial
fit=lm(mpg~poly(horsepower,4),data=auto)
#Display a summary of fit
summary(fit)
##
## Call:
## lm(formula = mpg ~ poly(horsepower, 4), data = auto)
##
## Residuals:
##      Min       1Q   Median       3Q      Max
## -14.8820  -2.5802  -0.1682   2.2100  16.1434
##
## Coefficients:
##                       Estimate Std. Error t value Pr(>|t|)
## (Intercept)            23.4459     0.2209 106.161   <2e-16 ***
## poly(horsepower, 4)1 -120.1377     4.3727 -27.475   <2e-16 ***
## poly(horsepower, 4)2   44.0895     4.3727  10.083   <2e-16 ***
## poly(horsepower, 4)3   -3.9488     4.3727  -0.903    0.367
## poly(horsepower, 4)4   -5.1878     4.3727  -1.186    0.236
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 4.373 on 387 degrees of freedom
## Multiple R-squared:  0.6893, Adjusted R-squared:  0.6861
## F-statistic: 214.7 on 4 and 387 DF,  p-value: < 2.2e-16
#Get the range of horsepower
hp <- range(auto$horsepower) #Create a sequence to be used for plotting hpGrid <- seq(hp[1],hp[2],by=10) #Predict for these values of horsepower. Set Standard error as TRUE pred=predict(fit,newdata=list(horsepower=hpGrid),se=TRUE) #Compute bands on either side that is 2xSE seBands=cbind(pred$fit+2*pred$se.fit,pred$fit-2*pred$se.fit) #Plot the fit with Standard Error bands plot(auto$horsepower,auto$mpg,xlim=hp,cex=.5,col="black",xlab="Horsepower", ylab="MPG", main="Polynomial of degree 4") lines(hpGrid,pred$fit,lwd=2,col="blue")
matlines(hpGrid,seBands,lwd=2,col="blue",lty=3)

## 1.1b Fit a 4th degree polynomial – Python code

import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import PolynomialFeatures
from sklearn.linear_model import LinearRegression
# Select columns
autoDF1=autoDF[['mpg','cylinder','displacement','horsepower','weight','acceleration','year']]
# Convert all columns to numeric
autoDF2 = autoDF1.apply(pd.to_numeric, errors='coerce')

#Drop NAs
autoDF3=autoDF2.dropna()
autoDF3.shape
X=autoDF3[['horsepower']]
y=autoDF3['mpg']
#Create a polynomial of degree 4
poly = PolynomialFeatures(degree=4)
X_poly = poly.fit_transform(X)

# Fit a polynomial regression line
linreg = LinearRegression().fit(X_poly, y)
# Create a range of values
hpGrid = np.arange(np.min(X),np.max(X),10)
hp=hpGrid.reshape(-1,1)
# Transform to 4th degree
poly = PolynomialFeatures(degree=4)
hp_poly = poly.fit_transform(hp)

#Create a scatter plot
plt.scatter(X,y)
# Fit the prediction
ypred=linreg.predict(hp_poly)
plt.title("Poylnomial of degree 4")
fig2=plt.xlabel("Horsepower")
fig2=plt.ylabel("MPG")
# Draw the regression curve
plt.plot(hp,ypred,c="red")
plt.savefig('fig1.png', bbox_inches='tight')

## 1.1c Fit a B-Spline – R Code

In the code below a B- Spline is fit to data. The B-spline requires the manual selection of knots

#Splines
library(splines)
# Fit a B-spline to the data. Select knots at 60,75,100,150
fit=lm(mpg~bs(horsepower,df=6,knots=c(60,75,100,150)),data=auto)
# Use the fitted regresion to predict
pred=predict(fit,newdata=list(horsepower=hpGrid),se=T)
# Create a scatter plot
plot(auto$horsepower,auto$mpg,xlim=hp,cex=.5,col="black",xlab="Horsepower",
ylab="MPG", main="B-Spline with 4 knots")
#Draw lines with 2 Standard Errors on either side
lines(hpGrid,pred$fit,lwd=2) lines(hpGrid,pred$fit+2*pred$se,lty="dashed") lines(hpGrid,pred$fit-2*pred$se,lty="dashed") abline(v=c(60,75,100,150),lty=2,col="darkgreen") ## 1.1d Fit a Natural Spline – R Code Here a ‘Natural Spline’ is used to fit .The Natural Spline extrapolates beyond the boundary knots and the ends of the function are much more constrained than a regular spline or a global polynomoial where the ends can wag a lot more. Natural splines do not require the explicit selection of knots # There is no need to select the knots here. There is a smoothing parameter which # can be specified by the degrees of freedom 'df' parameter. The natural spline fit2=lm(mpg~ns(horsepower,df=4),data=auto) pred=predict(fit2,newdata=list(horsepower=hpGrid),se=T) plot(auto$horsepower,auto$mpg,xlim=hp,cex=.5,col="black",xlab="Horsepower", ylab="MPG", main="Natural Splines") lines(hpGrid,pred$fit,lwd=2)
lines(hpGrid,pred$fit+2*pred$se,lty="dashed")
lines(hpGrid,pred$fit-2*pred$se,lty="dashed")

## 1.1.e Fit a Smoothing Spline – R code

Here a smoothing spline is used. Smoothing splines also do not require the explicit setting of knots. We can change the ‘degrees of freedom(df)’ paramater to get the best fit

# Smoothing spline has a smoothing parameter, the degrees of freedom
# This is too wiggly
plot(auto$horsepower,auto$mpg,xlim=hp,cex=.5,col="black",xlab="Horsepower",
ylab="MPG", main="Smoothing Splines")

# Here df is set to 16. This has a lot of variance
fit=smooth.spline(auto$horsepower,auto$mpg,df=16)
lines(fit,col="red",lwd=2)

# We can use Cross Validation to allow the spline to pick the value of this smpopothing paramter. We do not need to set the degrees of freedom 'df'
fit=smooth.spline(auto$horsepower,auto$mpg,cv=TRUE)
lines(fit,col="blue",lwd=2)

## 1.1e Splines – Python

There isn’t as much treatment of splines in Python and SKLearn. I did find the LSQUnivariate, UnivariateSpline spline. The LSQUnivariate spline requires the explcit setting of knots

import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from scipy.interpolate import LSQUnivariateSpline
autoDF.shape
autoDF.columns
autoDF1=autoDF[['mpg','cylinder','displacement','horsepower','weight','acceleration','year']]
autoDF2 = autoDF1.apply(pd.to_numeric, errors='coerce')
auto=autoDF2.dropna()
auto=auto[['horsepower','mpg']].sort_values('horsepower')

# Set the knots manually
knots=[65,75,100,150]
# Create an array for X & y
X=np.array(auto['horsepower'])
y=np.array(auto['mpg'])
# Fit a LSQunivariate spline
s = LSQUnivariateSpline(X,y,knots)

#Plot the spline
xs = np.linspace(40,230,1000)
ys = s(xs)
plt.scatter(X, y)
plt.plot(xs, ys)
plt.savefig('fig2.png', bbox_inches='tight')


## 1.2 Generalized Additiive models (GAMs)

Generalized Additive Models (GAMs) is a really powerful ML tool.

$y_{i} = \beta_{0} + f_{1}(x_{i1}) + f_{2}(x_{i2}) + .. +f_{p}(x_{ip}) + \epsilon_{i}$

In GAMs we use a different functions for each of the variables. GAMs give a much better fit since we can choose any function for the different sections

## 1.2a Generalized Additive Models (GAMs) – R Code

The plot below show the smooth spline that is fit for each of the features horsepower, cylinder, displacement, year and acceleration. We can use any function for example loess, 4rd order polynomial etc.

library(gam)
# Fit a smoothing spline for horsepower, cyliner, displacement and acceleration
gam=gam(mpg~s(horsepower,4)+s(cylinder,5)+s(displacement,4)+s(year,4)+s(acceleration,5),data=auto)
# Display the summary of the fit. This give the significance of each of the paramwetr
# Also an ANOVA is given for each combination of the features
summary(gam)
##
## Call: gam(formula = mpg ~ s(horsepower, 4) + s(cylinder, 5) + s(displacement,
##     4) + s(year, 4) + s(acceleration, 5), data = auto)
## Deviance Residuals:
##     Min      1Q  Median      3Q     Max
## -8.3190 -1.4436 -0.0261  1.2279 12.0873
##
## (Dispersion Parameter for gaussian family taken to be 6.9943)
##
##     Null Deviance: 23818.99 on 391 degrees of freedom
## Residual Deviance: 2587.881 on 370 degrees of freedom
## AIC: 1898.282
##
## Number of Local Scoring Iterations: 3
##
## Anova for Parametric Effects
##                     Df  Sum Sq Mean Sq  F value    Pr(>F)
## s(horsepower, 4)     1 15632.8 15632.8 2235.085 < 2.2e-16 ***
## s(cylinder, 5)       1   508.2   508.2   72.666 3.958e-16 ***
## s(displacement, 4)   1   374.3   374.3   53.514 1.606e-12 ***
## s(year, 4)           1  2263.2  2263.2  323.583 < 2.2e-16 ***
## s(acceleration, 5)   1   372.4   372.4   53.246 1.809e-12 ***
## Residuals          370  2587.9     7.0
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Anova for Nonparametric Effects
##                    Npar Df Npar F     Pr(F)
## (Intercept)
## s(horsepower, 4)         3 13.825 1.453e-08 ***
## s(cylinder, 5)           3 17.668 9.712e-11 ***
## s(displacement, 4)       3 44.573 < 2.2e-16 ***
## s(year, 4)               3 23.364 7.183e-14 ***
## s(acceleration, 5)       4  3.848  0.004453 **
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
par(mfrow=c(2,3))
plot(gam,se=TRUE)

## 1.2b Generalized Additive Models (GAMs) – Python Code

I did not find the equivalent of GAMs in SKlearn in Python. There was an early prototype (2012) in Github. Looks like it is still work in progress or has probably been abandoned.

## 1.3 Tree based Machine Learning Models

Tree based Machine Learning are all based on the ‘bootstrapping’ technique. In bootstrapping given a sample of size N, we create datasets of size N by sampling this original dataset with replacement. Machine Learning models are built on the different bootstrapped samples and then averaged.

Decision Trees as seen above have the tendency to overfit. There are several techniques that help to avoid this namely a) Bagging b) Random Forests c) Boosting

### Bagging, Random Forest and Gradient Boosting

Bagging: Bagging, or Bootstrap Aggregation decreases the variance of predictions, by creating separate Decisiion Tree based ML models on the different samples and then averaging these ML models

Random Forests: Bagging is a greedy algorithm and tries to produce splits based on all variables which try to minimize the error. However the different ML models have a high correlation. Random Forests remove this shortcoming, by using a variable and random set of features to split on. Hence the features chosen and the resulting trees are uncorrelated. When these ML models are averaged the performance is much better.

Boosting: Gradient Boosted Decision Trees also use an ensemble of trees but they don’t build Machine Learning models with random set of features at each step. Rather small and simple trees are built. Successive trees try to minimize the error from the earlier trees.

Out of Bag (OOB) Error: In Random Forest and Gradient Boosting for each bootstrap sample taken from the dataset, there will be samples left out. These are known as Out of Bag samples.Classification accuracy carried out on these OOB samples is known as OOB error

## 1.31a Decision Trees – R Code

The code below creates a Decision tree with the cancer training data. The summary of the fit is output. Based on the ML model, the predict function is used on test data and a confusion matrix is output.

# Read the cancer data
library(tree)
library(caret)
library(e1071)
cancer <- cancer[,2:32]
cancer$target <- as.factor(cancer$target)
train_idx <- trainTestSplit(cancer,trainPercent=75,seed=5)
train <- cancer[train_idx, ]
test <- cancer[-train_idx, ]

# Create Decision Tree
cancerStatus=tree(target~.,train)
summary(cancerStatus)
##
## Classification tree:
## tree(formula = target ~ ., data = train)
## Variables actually used in tree construction:
## [1] "worst.perimeter"      "worst.concave.points" "area.error"
## [4] "worst.texture"        "mean.texture"         "mean.concave.points"
## Number of terminal nodes:  9
## Residual mean deviance:  0.1218 = 50.8 / 417
## Misclassification error rate: 0.02347 = 10 / 426
pred <- predict(cancerStatus,newdata=test,type="class")
confusionMatrix(pred,test$target) ## Confusion Matrix and Statistics ## ## Reference ## Prediction 0 1 ## 0 49 7 ## 1 8 78 ## ## Accuracy : 0.8944 ## 95% CI : (0.8318, 0.9397) ## No Information Rate : 0.5986 ## P-Value [Acc > NIR] : 4.641e-15 ## ## Kappa : 0.7795 ## Mcnemar's Test P-Value : 1 ## ## Sensitivity : 0.8596 ## Specificity : 0.9176 ## Pos Pred Value : 0.8750 ## Neg Pred Value : 0.9070 ## Prevalence : 0.4014 ## Detection Rate : 0.3451 ## Detection Prevalence : 0.3944 ## Balanced Accuracy : 0.8886 ## ## 'Positive' Class : 0 ##  # Plot decision tree with labels plot(cancerStatus) text(cancerStatus,pretty=0) ## 1.31b Decision Trees – Cross Validation – R Code We can also perform a Cross Validation on the data to identify the Decision Tree which will give the minimum deviance. library(tree) cancer <- read.csv("cancer.csv",stringsAsFactors = FALSE) cancer <- cancer[,2:32] cancer$target <- as.factor(cancer$target) train_idx <- trainTestSplit(cancer,trainPercent=75,seed=5) train <- cancer[train_idx, ] test <- cancer[-train_idx, ] # Create Decision Tree cancerStatus=tree(target~.,train) # Execute 10 fold cross validation cvCancer=cv.tree(cancerStatus) plot(cvCancer) # Plot the plot(cvCancer$size,cvCancer$dev,type='b') prunedCancer=prune.tree(cancerStatus,best=4) plot(prunedCancer) text(prunedCancer,pretty=0) pred <- predict(prunedCancer,newdata=test,type="class") confusionMatrix(pred,test$target)
## Confusion Matrix and Statistics
##
##           Reference
## Prediction  0  1
##          0 50  7
##          1  7 78
##
##                Accuracy : 0.9014
##                  95% CI : (0.8401, 0.945)
##     No Information Rate : 0.5986
##     P-Value [Acc > NIR] : 7.988e-16
##
##                   Kappa : 0.7948
##  Mcnemar's Test P-Value : 1
##
##             Sensitivity : 0.8772
##             Specificity : 0.9176
##          Pos Pred Value : 0.8772
##          Neg Pred Value : 0.9176
##              Prevalence : 0.4014
##          Detection Rate : 0.3521
##    Detection Prevalence : 0.4014
##       Balanced Accuracy : 0.8974
##
##        'Positive' Class : 0
## 

## 1.31c Decision Trees – Python Code

Below is the Python code for creating Decision Trees. The accuracy, precision, recall and F1 score is computed on the test data set.

import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from sklearn.metrics import confusion_matrix
from sklearn import tree
from sklearn.model_selection import train_test_split
from sklearn.tree import DecisionTreeClassifier
from sklearn.datasets import make_classification, make_blobs
from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score
import graphviz

(X_cancer, y_cancer) = load_breast_cancer(return_X_y = True)

X_train, X_test, y_train, y_test = train_test_split(X_cancer, y_cancer,
random_state = 0)
clf = DecisionTreeClassifier().fit(X_train, y_train)

print('Accuracy of Decision Tree classifier on training set: {:.2f}'
.format(clf.score(X_train, y_train)))
print('Accuracy of Decision Tree classifier on test set: {:.2f}'
.format(clf.score(X_test, y_test)))

y_predicted=clf.predict(X_test)
confusion = confusion_matrix(y_test, y_predicted)
print('Accuracy: {:.2f}'.format(accuracy_score(y_test, y_predicted)))
print('Precision: {:.2f}'.format(precision_score(y_test, y_predicted)))
print('Recall: {:.2f}'.format(recall_score(y_test, y_predicted)))
print('F1: {:.2f}'.format(f1_score(y_test, y_predicted)))

# Plot the Decision Tree
clf = DecisionTreeClassifier(max_depth=2).fit(X_train, y_train)
dot_data = tree.export_graphviz(clf, out_file=None,
feature_names=cancer.feature_names,
class_names=cancer.target_names,
filled=True, rounded=True,
special_characters=True)
graph = graphviz.Source(dot_data)
graph
## Accuracy of Decision Tree classifier on training set: 1.00
## Accuracy of Decision Tree classifier on test set: 0.87
## Accuracy: 0.87
## Precision: 0.97
## Recall: 0.82
## F1: 0.89

## 1.31d Decision Trees – Cross Validation – Python Code

In the code below 5-fold cross validation is performed for different depths of the tree and the accuracy is computed. The accuracy on the test set seems to plateau when the depth is 8. But it is seen to increase again from 10 to 12. More analysis needs to be done here


import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from sklearn.tree import DecisionTreeClassifier
(X_cancer, y_cancer) = load_breast_cancer(return_X_y = True)
from sklearn.cross_validation import train_test_split, KFold
def computeCVAccuracy(X,y,folds):
accuracy=[]
foldAcc=[]
depth=[1,2,3,4,5,6,7,8,9,10,11,12]
nK=len(X)/float(folds)
xval_err=0
for i in depth:
kf = KFold(len(X),n_folds=folds)
for train_index, test_index in kf:
X_train, X_test = X.iloc[train_index], X.iloc[test_index]
y_train, y_test = y.iloc[train_index], y.iloc[test_index]
clf = DecisionTreeClassifier(max_depth = i).fit(X_train, y_train)
score=clf.score(X_test, y_test)
accuracy.append(score)

foldAcc.append(np.mean(accuracy))

return(foldAcc)

cvAccuracy=computeCVAccuracy(pd.DataFrame(X_cancer),pd.DataFrame(y_cancer),folds=10)

df1=pd.DataFrame(cvAccuracy)
df1.columns=['cvAccuracy']
df=df1.reindex([1,2,3,4,5,6,7,8,9,10,11,12])
df.plot()
plt.title("Decision Tree - 10-fold Cross Validation Accuracy vs Depth of tree")
plt.xlabel("Depth of tree")
plt.ylabel("Accuracy")
plt.savefig('fig3.png', bbox_inches='tight')

## 1.4a Random Forest – R code

A Random Forest is fit using the Boston data. The summary shows that 4 variables were randomly chosen at each split and the resulting ML model explains 88.72% of the test data. Also the variable importance is plotted. It can be seen that ‘rooms’ and ‘status’ are the most influential features in the model

library(randomForest)
df=read.csv("Boston.csv",stringsAsFactors = FALSE) # Data from MASS - SL

# Select specific columns
Boston <- df %>% dplyr::select("crimeRate","zone","indus","charles","nox","rooms","age",                          "distances","highways","tax","teacherRatio","color",
"status","medianValue")

# Fit a Random Forest on the Boston training data
rfBoston=randomForest(medianValue~.,data=Boston)
# Display the summatu of the fit. It can be seen that the MSE is 10.88
# and the percentage variance explained is 86.14%. About 4 variables were tried at each # #split for a maximum tree of 500.
# The MSE and percent variance is on Out of Bag trees
rfBoston
##
## Call:
##  randomForest(formula = medianValue ~ ., data = Boston)
##                Type of random forest: regression
##                      Number of trees: 500
## No. of variables tried at each split: 4
##
##           Mean of squared residuals: 9.521672
##                     % Var explained: 88.72
#List and plot the variable importances
importance(rfBoston)
##              IncNodePurity
## crimeRate        2602.1550
## zone              258.8057
## indus            2599.6635
## charles           240.2879
## nox              2748.8485
## rooms           12011.6178
## age              1083.3242
## distances        2432.8962
## highways          393.5599
## tax              1348.6987
## teacherRatio     2841.5151
## color             731.4387
## status          12735.4046
varImpPlot(rfBoston)

## 1.4b Random Forest-OOB and Cross Validation Error – R code

The figure below shows the OOB error and the Cross Validation error vs the ‘mtry’. Here mtry indicates the number of random features that are chosen at each split. The lowest test error occurs when mtry = 8

library(randomForest)
df=read.csv("Boston.csv",stringsAsFactors = FALSE) # Data from MASS - SL

# Select specific columns
Boston <- df %>% dplyr::select("crimeRate","zone","indus","charles","nox","rooms","age",                          "distances","highways","tax","teacherRatio","color",
"status","medianValue")
# Split as training and tst sets
train_idx <- trainTestSplit(Boston,trainPercent=75,seed=5)
train <- Boston[train_idx, ]
test <- Boston[-train_idx, ]

#Initialize OOD and testError
oobError <- NULL
testError <- NULL
# In the code below the number of variables to consider at each split is increased
# from 1 - 13(max features) and the OOB error and the MSE is computed
for(i in 1:13){
fitRF=randomForest(medianValue~.,data=train,mtry=i,ntree=400)
oobError[i] <-fitRF$mse[400] pred <- predict(fitRF,newdata=test) testError[i] <- mean((pred-test$medianValue)^2)
}

# We can see the OOB and Test Error. It can be seen that the Random Forest performs
# best with the lowers MSE at mtry=6
matplot(1:13,cbind(testError,oobError),pch=19,col=c("red","blue"),
type="b",xlab="mtry(no of varaibles at each split)", ylab="Mean Squared Error",
main="Random Forest - OOB and Test Error")
legend("topright",legend=c("OOB","Test"),pch=19,col=c("red","blue"))

## 1.4c Random Forest – Python code

The python code for Random Forest Regression is shown below. The training and test score is computed. The variable importance shows that ‘rooms’ and ‘status’ are the most influential of the variables

import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor

X=df[['crimeRate','zone', 'indus','charles','nox','rooms', 'age','distances','highways','tax',
'teacherRatio','color','status']]
y=df['medianValue']

X_train, X_test, y_train, y_test = train_test_split(X, y, random_state = 0)

regr = RandomForestRegressor(max_depth=4, random_state=0)
regr.fit(X_train, y_train)

print('R-squared score (training): {:.3f}'
.format(regr.score(X_train, y_train)))
print('R-squared score (test): {:.3f}'
.format(regr.score(X_test, y_test)))

feature_names=['crimeRate','zone', 'indus','charles','nox','rooms', 'age','distances','highways','tax',
'teacherRatio','color','status']
print(regr.feature_importances_)
plt.figure(figsize=(10,6),dpi=80)
c_features=X_train.shape[1]
plt.barh(np.arange(c_features),regr.feature_importances_)
plt.xlabel("Feature importance")
plt.ylabel("Feature name")

plt.yticks(np.arange(c_features), feature_names)
plt.tight_layout()

plt.savefig('fig4.png', bbox_inches='tight')

## R-squared score (training): 0.917
## R-squared score (test): 0.734
## [ 0.03437382  0.          0.00580335  0.          0.00731004  0.36461548
##   0.00638577  0.03432173  0.0041244   0.01732328  0.01074148  0.0012638
##   0.51373683]

## 1.4d Random Forest – Cross Validation and OOB Error – Python code

As with R the ‘max_features’ determines the random number of features the random forest will use at each split. The plot shows that when max_features=8 the MSE is lowest

import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.model_selection import cross_val_score

X=df[['crimeRate','zone', 'indus','charles','nox','rooms', 'age','distances','highways','tax',
'teacherRatio','color','status']]
y=df['medianValue']

cvError=[]
oobError=[]
oobMSE=[]
for i in range(1,13):
regr = RandomForestRegressor(max_depth=4, n_estimators=400,max_features=i,oob_score=True,random_state=0)
mse= np.mean(cross_val_score(regr, X, y, cv=5,scoring = 'neg_mean_squared_error'))
# Since this is neg_mean_squared_error I have inverted the sign to get MSE
cvError.append(-mse)
# Fit on all data to compute OOB error
regr.fit(X, y)
# Record the OOB error for each max_features=i setting
oob = 1 - regr.oob_score_
oobError.append(oob)
# Get the Out of Bag prediction
oobPred=regr.oob_prediction_
# Compute the Mean Squared Error between OOB Prediction and target
mseOOB=np.mean(np.square(oobPred-y))
oobMSE.append(mseOOB)

# Plot the CV Error and OOB Error
# Set max_features
maxFeatures=np.arange(1,13)
cvError=pd.DataFrame(cvError,index=maxFeatures)
oobMSE=pd.DataFrame(oobMSE,index=maxFeatures)
#Plot
fig8=df.plot()
fig8=plt.title('Random forest - CV Error and OOB Error vs max_features')
fig8.figure.savefig('fig8.png', bbox_inches='tight')

#Plot the OOB Error vs max_features
plt.plot(range(1,13),oobError)
fig2=plt.title("Random Forest - OOB Error vs max_features (variable no of features)")
fig2=plt.xlabel("max_features (variable no of features)")
fig2=plt.ylabel("OOB Error")
fig2.figure.savefig('fig7.png', bbox_inches='tight')


## 1.5a Boosting – R code

Here a Gradient Boosted ML Model is built with a n.trees=5000, with a learning rate of 0.01 and depth of 4. The feature importance plot also shows that rooms and status are the 2 most important features. The MSE vs the number of trees plateaus around 2000 trees

library(gbm)
# Perform gradient boosting on the Boston data set. The distribution is gaussian since we
# doing MSE. The interaction depth specifies the number of splits
boostBoston=gbm(medianValue~.,data=train,distribution="gaussian",n.trees=5000,
shrinkage=0.01,interaction.depth=4)
#The summary gives the variable importance. The 2 most significant variables are
# number of rooms and lower status
summary(boostBoston)

##                       var    rel.inf
## rooms               rooms 42.2267200
## status             status 27.3024671
## distances       distances  7.9447972
## crimeRate       crimeRate  5.0238827
## nox                   nox  4.0616548
## teacherRatio teacherRatio  3.1991999
## age                   age  2.7909772
## color               color  2.3436295
## tax                   tax  2.1386213
## charles           charles  1.3799109
## highways         highways  0.7644026
## indus               indus  0.7236082
## zone                 zone  0.1001287
# The plots below show how each variable relates to the median value of the home. As
# the number of roomd increase the median value increases and with increase in lower status
# the median value decreases
par(mfrow=c(1,2))
#Plot the relation between the top 2 features and the target
plot(boostBoston,i="rooms")
plot(boostBoston,i="status")

# Create a sequence of trees between 100-5000 incremented by 50
nTrees=seq(100,5000,by=50)
# Predict the values for the test data
pred <- predict(boostBoston,newdata=test,n.trees=nTrees)
# Compute the mean for each of the MSE for each of the number of trees
boostError <- apply((pred-test$medianValue)^2,2,mean) #Plot the MSE vs the number of trees plot(nTrees,boostError,pch=19,col="blue",ylab="Mean Squared Error", main="Boosting Test Error") ## 1.5b Cross Validation Boosting – R code Included below is a cross validation error vs the learning rate. The lowest error is when learning rate = 0.09 cvError <- NULL s <- c(.001,0.01,0.03,0.05,0.07,0.09,0.1) for(i in seq_along(s)){ cvBoost=gbm(medianValue~.,data=train,distribution="gaussian",n.trees=5000, shrinkage=s[i],interaction.depth=4,cv.folds=5) cvError[i] <- mean(cvBoost$cv.error)
}

# Create a data frame for plotting
a <- rbind(s,cvError)
b <- as.data.frame(t(a))
# It can be seen that a shrinkage parameter of 0,05 gives the lowes CV Error
ggplot(b,aes(s,cvError)) + geom_point() + geom_line(color="blue") +
xlab("Shrinkage") + ylab("Cross Validation Error") +
ggtitle("Gradient boosted trees - Cross Validation error vs Shrinkage")

## 1.5c Boosting – Python code

A gradient boost ML model in Python is created below. The Rsquared score is computed on the training and test data.

import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split

X=df[['crimeRate','zone', 'indus','charles','nox','rooms', 'age','distances','highways','tax',
'teacherRatio','color','status']]
y=df['medianValue']

X_train, X_test, y_train, y_test = train_test_split(X, y, random_state = 0)

regr.fit(X_train, y_train)

print('R-squared score (training): {:.3f}'
.format(regr.score(X_train, y_train)))
print('R-squared score (test): {:.3f}'
.format(regr.score(X_test, y_test)))
## R-squared score (training): 0.983
## R-squared score (test): 0.821

## 1.5c Cross Validation Boosting – Python code

the cross validation error is computed as the learning rate is varied. The minimum CV eror occurs when lr = 0.04

import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.ensemble import RandomForestRegressor
from sklearn.model_selection import cross_val_score

X=df[['crimeRate','zone', 'indus','charles','nox','rooms', 'age','distances','highways','tax',
'teacherRatio','color','status']]
y=df['medianValue']

cvError=[]
learning_rate =[.001,0.01,0.03,0.05,0.07,0.09,0.1]
for lr in learning_rate:
mse= np.mean(cross_val_score(regr, X, y, cv=10,scoring = 'neg_mean_squared_error'))
# Since this is neg_mean_squared_error I have inverted the sign to get MSE
cvError.append(-mse)
learning_rate =[.001,0.01,0.03,0.05,0.07,0.09,0.1]
plt.plot(learning_rate,cvError)
plt.title("Gradient Boosting - 5-fold CV- Mean Squared Error vs max_features (variable no of features)")
plt.xlabel("max_features (variable no of features)")
plt.ylabel("Mean Squared Error")
plt.savefig('fig6.png', bbox_inches='tight')

Conclusion This post covered Splines and Tree based ML models like Bagging, Random Forest and Boosting. Stay tuned for further updates.

You may also like

To see all posts see Index of posts

# Practical Machine Learning with R and Python – Part 4

This is the 4th installment of my ‘Practical Machine Learning with R and Python’ series. In this part I discuss classification with Support Vector Machines (SVMs), using both a Linear and a Radial basis kernel, and Decision Trees. Further, a closer look is taken at some of the metrics associated with binary classification, namely accuracy vs precision and recall. I also touch upon Validation curves, Precision-Recall, ROC curves and AUC with equivalent code in R and Python

This post is a continuation of my 3 earlier posts on Practical Machine Learning in R and Python
1. Practical Machine Learning with R and Python – Part 1
2. Practical Machine Learning with R and Python – Part 2
3. Practical Machine Learning with R and Python – Part 3

The RMarkdown file with the code and the associated data files can be downloaded from Github at MachineLearning-RandPython-Part4

1. Machine Learning in plain English-Part 1
2. Machine Learning in plain English-Part 2
3. Machine Learning in plain English-Part 3

Check out my compact and minimal book  “Practical Machine Learning with R and Python:Third edition- Machine Learning in stereo”  available in Amazon in paperback($12.99) and kindle($8.99) versions. My book includes implementations of key ML algorithms and associated measures and metrics. The book is ideal for anybody who is familiar with the concepts and would like a quick reference to the different ML algorithms that can be applied to problems and how to select the best model. Pick your copy today!!

Support Vector Machines (SVM) are another useful Machine Learning model that can be used for both regression and classification problems. SVMs used in classification, compute the hyperplane, that separates the 2 classes with the maximum margin. To do this the features may be transformed into a larger multi-dimensional feature space. SVMs can be used with different kernels namely linear, polynomial or radial basis to determine the best fitting model for a given classification problem.

In the 2nd part of this series Practical Machine Learning with R and Python – Part 2, I had mentioned the various metrics that are used in classification ML problems namely Accuracy, Precision, Recall and F1 score. Accuracy gives the fraction of data that were correctly classified as belonging to the +ve or -ve class. However ‘accuracy’ in itself is not a good enough measure because it does not take into account the fraction of the data that were incorrectly classified. This issue becomes even more critical in different domains. For e.g a surgeon who would like to detect cancer, would like to err on the side of caution, and classify even a possibly non-cancerous patient as possibly having cancer, rather than mis-classifying a malignancy as benign. Here we would like to increase recall or sensitivity which is  given by Recall= TP/(TP+FN) or we try reduce mis-classification by either increasing the (true positives) TP or reducing (false negatives) FN

On the other hand, search algorithms would like to increase precision which tries to reduce the number of irrelevant results in the search result. Precision= TP/(TP+FP). In other words we do not want ‘false positives’ or irrelevant results to come in the search results and there is a need to reduce the false positives.

When we try to increase ‘precision’, we do so at the cost of ‘recall’, and vice-versa. I found this diagram and explanation in Wikipedia very useful Source: Wikipedia

“Consider a brain surgeon tasked with removing a cancerous tumor from a patient’s brain. The surgeon needs to remove all of the tumor cells since any remaining cancer cells will regenerate the tumor. Conversely, the surgeon must not remove healthy brain cells since that would leave the patient with impaired brain function. The surgeon may be more liberal in the area of the brain she removes to ensure she has extracted all the cancer cells. This decision increases recall but reduces precision. On the other hand, the surgeon may be more conservative in the brain she removes to ensure she extracts only cancer cells. This decision increases precision but reduces recall. That is to say, greater recall increases the chances of removing healthy cells (negative outcome) and increases the chances of removing all cancer cells (positive outcome). Greater precision decreases the chances of removing healthy cells (positive outcome) but also decreases the chances of removing all cancer cells (negative outcome).”

## 1.1a. Linear SVM – R code

In R code below I use SVM with linear kernel

source('RFunctions-1.R')
library(dplyr)
library(e1071)
library(caret)
library(reshape2)
library(ggplot2)
# Read data. Data from SKLearn
cancer$target <- as.factor(cancer$target)

# Split into training and test sets
train_idx <- trainTestSplit(cancer,trainPercent=75,seed=5)
train <- cancer[train_idx, ]
test <- cancer[-train_idx, ]

# Fit a linear basis kernel. DO not scale the data
svmfit=svm(target~., data=train, kernel="linear",scale=FALSE)
ypred=predict(svmfit,test)
#Print a confusion matrix
confusionMatrix(ypred,test$target) ## Confusion Matrix and Statistics ## ## Reference ## Prediction 0 1 ## 0 54 3 ## 1 3 82 ## ## Accuracy : 0.9577 ## 95% CI : (0.9103, 0.9843) ## No Information Rate : 0.5986 ## P-Value [Acc > NIR] : <2e-16 ## ## Kappa : 0.9121 ## Mcnemar's Test P-Value : 1 ## ## Sensitivity : 0.9474 ## Specificity : 0.9647 ## Pos Pred Value : 0.9474 ## Neg Pred Value : 0.9647 ## Prevalence : 0.4014 ## Detection Rate : 0.3803 ## Detection Prevalence : 0.4014 ## Balanced Accuracy : 0.9560 ## ## 'Positive' Class : 0 ##  ## 1.1b Linear SVM – Python code The code below creates a SVM with linear basis in Python and also dumps the corresponding classification metrics import numpy as np import pandas as pd import os import matplotlib.pyplot as plt from sklearn.model_selection import train_test_split from sklearn.svm import LinearSVC from sklearn.datasets import make_classification, make_blobs from sklearn.metrics import confusion_matrix from matplotlib.colors import ListedColormap from sklearn.datasets import load_breast_cancer # Load the cancer data (X_cancer, y_cancer) = load_breast_cancer(return_X_y = True) X_train, X_test, y_train, y_test = train_test_split(X_cancer, y_cancer, random_state = 0) clf = LinearSVC().fit(X_train, y_train) print('Breast cancer dataset') print('Accuracy of Linear SVC classifier on training set: {:.2f}' .format(clf.score(X_train, y_train))) print('Accuracy of Linear SVC classifier on test set: {:.2f}' .format(clf.score(X_test, y_test))) ## Breast cancer dataset ## Accuracy of Linear SVC classifier on training set: 0.92 ## Accuracy of Linear SVC classifier on test set: 0.94 ## 1.2 Dummy classifier Often when we perform classification tasks using any ML model namely logistic regression, SVM, neural networks etc. it is very useful to determine how well the ML model performs agains at dummy classifier. A dummy classifier uses some simple computation like frequency of majority class, instead of fitting and ML model. It is essential that our ML model does much better that the dummy classifier. This problem is even more important in imbalanced classes where we have only about 10% of +ve samples. If any ML model we create has a accuracy of about 0.90 then it is evident that our classifier is not doing any better than a dummy classsfier which can just take a majority count of this imbalanced class and also come up with 0.90. We need to be able to do better than that. In the examples below (1.3a & 1.3b) it can be seen that SVMs with ‘radial basis’ kernel with unnormalized data, for both R and Python, do not perform any better than the dummy classifier. ## 1.2a Dummy classifier – R code R does not seem to have an explicit dummy classifier. I created a simple dummy classifier that predicts the majority class. SKlearn in Python also includes other strategies like uniform, stratified etc. but this should be possible to create in R also. # Create a simple dummy classifier that computes the ratio of the majority class to the totla DummyClassifierAccuracy <- function(train,test,type="majority"){ if(type=="majority"){ count <- sum(train$target==1)/dim(train)[1]
}
count
}

cancer$target <- as.factor(cancer$target)

# Create training and test sets
train_idx <- trainTestSplit(cancer,trainPercent=75,seed=5)
train <- cancer[train_idx, ]
test <- cancer[-train_idx, ]

#Dummy classifier majority class
acc=DummyClassifierAccuracy(train,test)
sprintf("Accuracy is %f",acc)
## [1] "Accuracy is 0.638498"

## 1.2b Dummy classifier – Python code

This dummy classifier uses the majority class.

import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.dummy import DummyClassifier
from sklearn.metrics import confusion_matrix
(X_cancer, y_cancer) = load_breast_cancer(return_X_y = True)
X_train, X_test, y_train, y_test = train_test_split(X_cancer, y_cancer,
random_state = 0)

# Negative class (0) is most frequent
dummy_majority = DummyClassifier(strategy = 'most_frequent').fit(X_train, y_train)
y_dummy_predictions = dummy_majority.predict(X_test)

print('Dummy classifier accuracy on test set: {:.2f}'
.format(dummy_majority.score(X_test, y_test)))

## Dummy classifier accuracy on test set: 0.63

## 1.3a – Radial SVM (un-normalized) – R code

SVMs perform better when the data is normalized or scaled. The 2 examples below show that SVM with radial basis kernel does not perform any better than the dummy classifier

library(dplyr)
library(e1071)
library(caret)
library(reshape2)
library(ggplot2)

train_idx <- trainTestSplit(cancer,trainPercent=75,seed=5)
train <- cancer[train_idx, ]
test <- cancer[-train_idx, ]
# Unnormalized data
ypred=predict(svmfit,test)
confusionMatrix(ypred,test$target) ## Confusion Matrix and Statistics ## ## Reference ## Prediction 0 1 ## 0 0 0 ## 1 57 85 ## ## Accuracy : 0.5986 ## 95% CI : (0.5131, 0.6799) ## No Information Rate : 0.5986 ## P-Value [Acc > NIR] : 0.5363 ## ## Kappa : 0 ## Mcnemar's Test P-Value : 1.195e-13 ## ## Sensitivity : 0.0000 ## Specificity : 1.0000 ## Pos Pred Value : NaN ## Neg Pred Value : 0.5986 ## Prevalence : 0.4014 ## Detection Rate : 0.0000 ## Detection Prevalence : 0.0000 ## Balanced Accuracy : 0.5000 ## ## 'Positive' Class : 0 ##  ## 1.4b – Radial SVM (un-normalized) – Python code import numpy as np import pandas as pd import os import matplotlib.pyplot as plt from sklearn.datasets import load_breast_cancer from sklearn.model_selection import train_test_split from sklearn.svm import SVC # Load the cancer data (X_cancer, y_cancer) = load_breast_cancer(return_X_y = True) X_train, X_test, y_train, y_test = train_test_split(X_cancer, y_cancer, random_state = 0) clf = SVC(C=10).fit(X_train, y_train) print('Breast cancer dataset (unnormalized features)') print('Accuracy of RBF-kernel SVC on training set: {:.2f}' .format(clf.score(X_train, y_train))) print('Accuracy of RBF-kernel SVC on test set: {:.2f}' .format(clf.score(X_test, y_test))) ## Breast cancer dataset (unnormalized features) ## Accuracy of RBF-kernel SVC on training set: 1.00 ## Accuracy of RBF-kernel SVC on test set: 0.63 ## 1.5a – Radial SVM (Normalized) -R Code The data is scaled (normalized ) before using the SVM model. The SVM model has 2 paramaters a) C – Large C (less regularization), more regularization b) gamma – Small gamma has larger decision boundary with more misclassfication, and larger gamma has tighter decision boundary The R code below computes the accuracy as the regularization paramater is changed trainingAccuracy <- NULL testAccuracy <- NULL C1 <- c(.01,.1, 1, 10, 20) for(i in C1){ svmfit=svm(target~., data=train, kernel="radial",cost=i,scale=TRUE) ypredTrain <-predict(svmfit,train) ypredTest=predict(svmfit,test) a <-confusionMatrix(ypredTrain,train$target)
b <-confusionMatrix(ypredTest,test$target) trainingAccuracy <-c(trainingAccuracy,a$overall[1])
testAccuracy <-c(testAccuracy,b$overall[1]) } print(trainingAccuracy) ## Accuracy Accuracy Accuracy Accuracy Accuracy ## 0.6384977 0.9671362 0.9906103 0.9976526 1.0000000 print(testAccuracy) ## Accuracy Accuracy Accuracy Accuracy Accuracy ## 0.5985915 0.9507042 0.9647887 0.9507042 0.9507042 a <-rbind(C1,as.numeric(trainingAccuracy),as.numeric(testAccuracy)) b <- data.frame(t(a)) names(b) <- c("C1","trainingAccuracy","testAccuracy") df <- melt(b,id="C1") ggplot(df) + geom_line(aes(x=C1, y=value, colour=variable),size=2) + xlab("C (SVC regularization)value") + ylab("Accuracy") + ggtitle("Training and test accuracy vs C(regularization)") ## 1.5b – Radial SVM (normalized) – Python The Radial basis kernel is used on normalized data for a range of ‘C’ values and the result is plotted. import numpy as np import pandas as pd import os import matplotlib.pyplot as plt from sklearn.datasets import load_breast_cancer from sklearn.model_selection import train_test_split from sklearn.svm import SVC from sklearn.preprocessing import MinMaxScaler scaler = MinMaxScaler() # Load the cancer data (X_cancer, y_cancer) = load_breast_cancer(return_X_y = True) X_train, X_test, y_train, y_test = train_test_split(X_cancer, y_cancer, random_state = 0) X_train_scaled = scaler.fit_transform(X_train) X_test_scaled = scaler.transform(X_test) print('Breast cancer dataset (normalized with MinMax scaling)') trainingAccuracy=[] testAccuracy=[] for C1 in [.01,.1, 1, 10, 20]: clf = SVC(C=C1).fit(X_train_scaled, y_train) acctrain=clf.score(X_train_scaled, y_train) accTest=clf.score(X_test_scaled, y_test) trainingAccuracy.append(acctrain) testAccuracy.append(accTest) # Create a dataframe C1=[.01,.1, 1, 10, 20] trainingAccuracy=pd.DataFrame(trainingAccuracy,index=C1) testAccuracy=pd.DataFrame(testAccuracy,index=C1) # Plot training and test R squared as a function of alpha df=pd.concat([trainingAccuracy,testAccuracy],axis=1) df.columns=['trainingAccuracy','trainingAccuracy'] fig1=df.plot() fig1=plt.title('Training and test accuracy vs C (SVC)') fig1.figure.savefig('fig1.png', bbox_inches='tight') ## Breast cancer dataset (normalized with MinMax scaling) Output image: ## 1.6a Validation curve – R code Sklearn includes code creating validation curves by varying paramaters and computing and plotting accuracy as gamma or C or changd. I did not find this R but I think this is a useful function and so I have created the R equivalent of this. # The R equivalent of np.logspace seqLogSpace <- function(start,stop,len){ a=seq(log10(10^start),log10(10^stop),length=len) 10^a } # Read the data. This is taken the SKlearn cancer data cancer <- read.csv("cancer.csv") cancer$target <- as.factor(cancer$target) set.seed(6) # Create the range of C1 in log space param_range = seqLogSpace(-3,2,20) # Initialize the overall training and test accuracy to NULL overallTrainAccuracy <- NULL overallTestAccuracy <- NULL # Loop over the parameter range of Gamma for(i in param_range){ # Set no of folds noFolds=5 # Create the rows which fall into different folds from 1..noFolds folds = sample(1:noFolds, nrow(cancer), replace=TRUE) # Initialize the training and test accuracy of folds to 0 trainingAccuracy <- 0 testAccuracy <- 0 # Loop through the folds for(j in 1:noFolds){ # The training is all rows for which the row is != j (k-1 folds -> training) train <- cancer[folds!=j,] # The rows which have j as the index become the test set test <- cancer[folds==j,] # Create a SVM model for this svmfit=svm(target~., data=train, kernel="radial",gamma=i,scale=TRUE) # Add up all the fold accuracy for training and test separately ypredTrain <-predict(svmfit,train) ypredTest=predict(svmfit,test) # Create confusion matrix a <-confusionMatrix(ypredTrain,train$target)
b <-confusionMatrix(ypredTest,test$target) # Get the accuracy trainingAccuracy <-trainingAccuracy + a$overall[1]
testAccuracy <-testAccuracy+b$overall[1] } # Compute the average of accuracy for K folds for number of features 'i' overallTrainAccuracy=c(overallTrainAccuracy,trainingAccuracy/noFolds) overallTestAccuracy=c(overallTestAccuracy,testAccuracy/noFolds) } #Create a dataframe a <- rbind(param_range,as.numeric(overallTrainAccuracy), as.numeric(overallTestAccuracy)) b <- data.frame(t(a)) names(b) <- c("C1","trainingAccuracy","testAccuracy") df <- melt(b,id="C1") #Plot in log axis ggplot(df) + geom_line(aes(x=C1, y=value, colour=variable),size=2) + xlab("C (SVC regularization)value") + ylab("Accuracy") + ggtitle("Training and test accuracy vs C(regularization)") + scale_x_log10() ## 1.6b Validation curve – Python Compute and plot the validation curve as gamma is varied. import numpy as np import pandas as pd import os import matplotlib.pyplot as plt from sklearn.datasets import load_breast_cancer from sklearn.model_selection import train_test_split from sklearn.preprocessing import MinMaxScaler from sklearn.svm import SVC from sklearn.model_selection import validation_curve # Load the cancer data (X_cancer, y_cancer) = load_breast_cancer(return_X_y = True) scaler = MinMaxScaler() X_scaled = scaler.fit_transform(X_cancer) # Create a gamma values from 10^-3 to 10^2 with 20 equally spaced intervals param_range = np.logspace(-3, 2, 20) # Compute the validation curve train_scores, test_scores = validation_curve(SVC(), X_scaled, y_cancer, param_name='gamma', param_range=param_range, cv=10) #Plot the figure fig2=plt.figure() #Compute the mean train_scores_mean = np.mean(train_scores, axis=1) train_scores_std = np.std(train_scores, axis=1) test_scores_mean = np.mean(test_scores, axis=1) test_scores_std = np.std(test_scores, axis=1) fig2=plt.title('Validation Curve with SVM') fig2=plt.xlabel('$\gamma$(gamma)') fig2=plt.ylabel('Score') fig2=plt.ylim(0.0, 1.1) lw = 2 fig2=plt.semilogx(param_range, train_scores_mean, label='Training score', color='darkorange', lw=lw) fig2=plt.fill_between(param_range, train_scores_mean - train_scores_std, train_scores_mean + train_scores_std, alpha=0.2, color='darkorange', lw=lw) fig2=plt.semilogx(param_range, test_scores_mean, label='Cross-validation score', color='navy', lw=lw) fig2=plt.fill_between(param_range, test_scores_mean - test_scores_std, test_scores_mean + test_scores_std, alpha=0.2, color='navy', lw=lw) fig2.figure.savefig('fig2.png', bbox_inches='tight')  Output image: ## 1.7a Validation Curve (Preventing data leakage) – Python code In this course Applied Machine Learning in Python, the Professor states that when we apply the same data transformation to a entire dataset, it will cause a data leakage. “The proper way to do cross-validation when you need to scale the data is not to scale the entire dataset with a single transform, since this will indirectly leak information into the training data about the whole dataset, including the test data (see the lecture on data leakage later in the course). Instead, scaling/normalizing must be computed and applied for each cross-validation fold separately” So I apply separate scaling to the training and testing folds and plot. In the lecture the Prof states that this can be done using pipelines. import numpy as np import pandas as pd import os import matplotlib.pyplot as plt from sklearn.datasets import load_breast_cancer from sklearn.cross_validation import KFold from sklearn.preprocessing import MinMaxScaler from sklearn.svm import SVC # Read the data (X_cancer, y_cancer) = load_breast_cancer(return_X_y = True) # Set the parameter range param_range = np.logspace(-3, 2, 20) # Set number of folds folds=5 #Initialize overallTrainAccuracy=[] overallTestAccuracy=[] # Loop over the paramater range for c in param_range: trainingAccuracy=0 testAccuracy=0 kf = KFold(len(X_cancer),n_folds=folds) # Partition into training and test folds for train_index, test_index in kf: # Partition the data acccording the fold indices generated X_train, X_test = X_cancer[train_index], X_cancer[test_index] y_train, y_test = y_cancer[train_index], y_cancer[test_index] # Scale the X_train and X_test scaler = MinMaxScaler() X_train_scaled = scaler.fit_transform(X_train) X_test_scaled = scaler.transform(X_test) # Fit a SVC model for each C clf = SVC(C=c).fit(X_train_scaled, y_train) #Compute the training and test score acctrain=clf.score(X_train_scaled, y_train) accTest=clf.score(X_test_scaled, y_test) trainingAccuracy += np.sum(acctrain) testAccuracy += np.sum(accTest) # Compute the mean training and testing accuracy overallTrainAccuracy.append(trainingAccuracy/folds) overallTestAccuracy.append(testAccuracy/folds) overallTrainAccuracy=pd.DataFrame(overallTrainAccuracy,index=param_range) overallTestAccuracy=pd.DataFrame(overallTestAccuracy,index=param_range) # Plot training and test R squared as a function of alpha df=pd.concat([overallTrainAccuracy,overallTestAccuracy],axis=1) df.columns=['trainingAccuracy','testAccuracy'] fig3=plt.title('Validation Curve with SVM') fig3=plt.xlabel('$\gamma$(gamma)') fig3=plt.ylabel('Score') fig3=plt.ylim(0.5, 1.1) lw = 2 fig3=plt.semilogx(param_range, overallTrainAccuracy, label='Training score', color='darkorange', lw=lw) fig3=plt.semilogx(param_range, overallTestAccuracy, label='Cross-validation score', color='navy', lw=lw) fig3=plt.legend(loc='best') fig3.figure.savefig('fig3.png', bbox_inches='tight')  Output image: ## 1.8 a Decision trees – R code Decision trees in R can be plotted using RPart package library(rpart) library(rpart.plot) rpart = NULL # Create a decision tree m <-rpart(Species~.,data=iris) #Plot rpart.plot(m,extra=2,main="Decision Tree - IRIS") ## 1.8 b Decision trees – Python code from sklearn.datasets import load_iris from sklearn.tree import DecisionTreeClassifier from sklearn import tree from sklearn.model_selection import train_test_split import graphviz iris = load_iris() X_train, X_test, y_train, y_test = train_test_split(iris.data, iris.target, random_state = 3) clf = DecisionTreeClassifier().fit(X_train, y_train) print('Accuracy of Decision Tree classifier on training set: {:.2f}' .format(clf.score(X_train, y_train))) print('Accuracy of Decision Tree classifier on test set: {:.2f}' .format(clf.score(X_test, y_test))) dot_data = tree.export_graphviz(clf, out_file=None, feature_names=iris.feature_names, class_names=iris.target_names, filled=True, rounded=True, special_characters=True) graph = graphviz.Source(dot_data) graph ## Accuracy of Decision Tree classifier on training set: 1.00 ## Accuracy of Decision Tree classifier on test set: 0.97 ## 1.9a Feature importance – R code I found the following code which had a snippet for feature importance. Sklean has a nice method for this. For some reason the results in R and Python are different. Any thoughts? set.seed(3) # load the library library(mlbench) library(caret) # load the dataset cancer <- read.csv("cancer.csv") cancer$target <- as.factor(cancer$target) # Split as data data <- cancer[,1:31] target <- cancer[,32] # Train the model model <- train(data, target, method="rf", preProcess="scale", trControl=trainControl(method = "cv")) # Compute variable importance importance <- varImp(model) # summarize importance print(importance) # plot importance plot(importance) ## 1.9b Feature importance – Python code import numpy as np import pandas as pd import os import matplotlib.pyplot as plt from sklearn.tree import DecisionTreeClassifier from sklearn.model_selection import train_test_split from sklearn.datasets import load_breast_cancer import numpy as np # Read the data cancer= load_breast_cancer() (X_cancer, y_cancer) = load_breast_cancer(return_X_y = True) X_train, X_test, y_train, y_test = train_test_split(X_cancer, y_cancer, random_state = 0) # Use the DecisionTreClassifier clf = DecisionTreeClassifier(max_depth = 4, min_samples_leaf = 8, random_state = 0).fit(X_train, y_train) c_features=len(cancer.feature_names) print('Breast cancer dataset: decision tree') print('Accuracy of DT classifier on training set: {:.2f}' .format(clf.score(X_train, y_train))) print('Accuracy of DT classifier on test set: {:.2f}' .format(clf.score(X_test, y_test))) # Plot the feature importances fig4=plt.figure(figsize=(10,6),dpi=80) fig4=plt.barh(range(c_features), clf.feature_importances_) fig4=plt.xlabel("Feature importance") fig4=plt.ylabel("Feature name") fig4=plt.yticks(np.arange(c_features), cancer.feature_names) fig4=plt.tight_layout() plt.savefig('fig4.png', bbox_inches='tight')  ## Breast cancer dataset: decision tree ## Accuracy of DT classifier on training set: 0.96 ## Accuracy of DT classifier on test set: 0.94 Output image: ## 1.10a Precision-Recall, ROC curves & AUC- R code I tried several R packages for plotting the Precision and Recall and AUC curve. PRROC seems to work well. The Precision-Recall curves show the tradeoff between precision and recall. The higher the precision, the lower the recall and vice versa.AUC curves that hug the top left corner indicate a high sensitivity,specificity and an excellent accuracy. source("RFunctions-1.R") library(dplyr) library(caret) library(e1071) library(PRROC) # Read the data (this data is from sklearn!) d <- read.csv("digits.csv") digits <- d[2:66] digits$X64 <- as.factor(digits$X64) # Split as training and test sets train_idx <- trainTestSplit(digits,trainPercent=75,seed=5) train <- digits[train_idx, ] test <- digits[-train_idx, ] # Fit a SVM model with linear basis kernel with probabilities svmfit=svm(X64~., data=train, kernel="linear",scale=FALSE,probability=TRUE) ypred=predict(svmfit,test,probability=TRUE) head(attr(ypred,"probabilities")) ## 0 1 ## 6 7.395947e-01 2.604053e-01 ## 8 9.999998e-01 1.842555e-07 ## 12 1.655178e-05 9.999834e-01 ## 13 9.649997e-01 3.500032e-02 ## 15 9.994849e-01 5.150612e-04 ## 16 9.999987e-01 1.280700e-06 # Store the probability of 0s and 1s m0<-attr(ypred,"probabilities")[,1] m1<-attr(ypred,"probabilities")[,2] # Create a dataframe of scores scores <- data.frame(m1,test$X64)

# Class 0 is data points of +ve class (in this case, digit 1) and -ve class (digit 0)
#Compute Precision Recall
pr <- pr.curve(scores.class0=scores[scores$test.X64=="1",]$m1,
scores.class1=scores[scores$test.X64=="0",]$m1,
curve=T)

# Plot precision-recall curve
plot(pr)

#Plot the ROC curve
roc<-roc.curve(m0, m1,curve=TRUE)
plot(roc)

## 1.10b Precision-Recall, ROC curves & AUC- Python code

For Python Logistic Regression is used to plot Precision Recall, ROC curve and compute AUC

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.linear_model import LogisticRegression
from sklearn.metrics import precision_recall_curve
from sklearn.metrics import roc_curve, auc
X, y = dataset.data, dataset.target
#Create 2 classes -i) Digit 1 (from digit 1) ii) Digit 0 (from all other digits)
# Make a copy of the target
z= y.copy()
# Replace all non 1's as 0
z[z != 1] = 0

X_train, X_test, y_train, y_test = train_test_split(X, z, random_state=0)
# Fit a LR model
lr = LogisticRegression().fit(X_train, y_train)

#Compute the decision scores
y_scores_lr = lr.fit(X_train, y_train).decision_function(X_test)
y_score_list = list(zip(y_test[0:20], y_scores_lr[0:20]))

#Show the decision_function scores for first 20 instances
y_score_list

precision, recall, thresholds = precision_recall_curve(y_test, y_scores_lr)
closest_zero = np.argmin(np.abs(thresholds))
closest_zero_p = precision[closest_zero]
closest_zero_r = recall[closest_zero]
#Plot
plt.figure()
plt.xlim([0.0, 1.01])
plt.ylim([0.0, 1.01])
plt.plot(precision, recall, label='Precision-Recall Curve')
plt.plot(closest_zero_p, closest_zero_r, 'o', markersize = 12, fillstyle = 'none', c='r', mew=3)
plt.xlabel('Precision', fontsize=16)
plt.ylabel('Recall', fontsize=16)
plt.axes().set_aspect('equal')
plt.savefig('fig5.png', bbox_inches='tight')

#Compute and plot the ROC
y_score_lr = lr.fit(X_train, y_train).decision_function(X_test)
fpr_lr, tpr_lr, _ = roc_curve(y_test, y_score_lr)
roc_auc_lr = auc(fpr_lr, tpr_lr)

plt.figure()
plt.xlim([-0.01, 1.00])
plt.ylim([-0.01, 1.01])
plt.plot(fpr_lr, tpr_lr, lw=3, label='LogRegr ROC curve (area = {:0.2f})'.format(roc_auc_lr))
plt.xlabel('False Positive Rate', fontsize=16)
plt.ylabel('True Positive Rate', fontsize=16)
plt.title('ROC curve (1-of-10 digits classifier)', fontsize=16)
plt.legend(loc='lower right', fontsize=13)
plt.plot([0, 1], [0, 1], color='navy', lw=3, linestyle='--')
plt.axes()
plt.savefig('fig6.png', bbox_inches='tight')


output

## 1.10c Precision-Recall, ROC curves & AUC- Python code

In the code below classification probabilities are used to compute and plot precision-recall, roc and AUC

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.svm import LinearSVC
from sklearn.calibration import CalibratedClassifierCV

X, y = dataset.data, dataset.target
# Make a copy of the target
z= y.copy()
# Replace all non 1's as 0
z[z != 1] = 0

X_train, X_test, y_train, y_test = train_test_split(X, z, random_state=0)
svm = LinearSVC()
# Need to use CalibratedClassifierSVC to redict probabilities for lInearSVC
clf = CalibratedClassifierCV(svm)
clf.fit(X_train, y_train)
y_proba_lr = clf.predict_proba(X_test)
from sklearn.metrics import precision_recall_curve

precision, recall, thresholds = precision_recall_curve(y_test, y_proba_lr[:,1])
closest_zero = np.argmin(np.abs(thresholds))
closest_zero_p = precision[closest_zero]
closest_zero_r = recall[closest_zero]
#plt.figure(figsize=(15,15),dpi=80)
plt.figure()
plt.xlim([0.0, 1.01])
plt.ylim([0.0, 1.01])
plt.plot(precision, recall, label='Precision-Recall Curve')
plt.plot(closest_zero_p, closest_zero_r, 'o', markersize = 12, fillstyle = 'none', c='r', mew=3)
plt.xlabel('Precision', fontsize=16)
plt.ylabel('Recall', fontsize=16)
plt.axes().set_aspect('equal')
plt.savefig('fig7.png', bbox_inches='tight')