cc/cirrus_work: bin/spearman.py annotate

annotate bin/spearman.py @ 30:c73ec9deabbe

comments and more care about rows vs. columns

author	Henry S. Thompson <ht@inf.ed.ac.uk>
date	Thu, 17 Nov 2022 11:27:07 +0000
parents	669a0b120d34
children	e7c8e64c2fdd

rev	line source
25 50337cd1d16f framework for stats over results of rank correlations Henry S. Thompson <ht@inf.ed.ac.uk> parents: diff changeset	1 #!/usr/bin/env python3
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	2 '''Rank correlation processing for a csv tabulation of counts by segment
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	3 First column is for whole crawl, then 100 columns for segs 0-99
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	4 Each row is counts for some property, e.g. mime-detected or tld
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	5
30 c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	6 For example, assuming all.tsv has the whole-crawl warc-only counts
c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	7 and s...tsv have the segment counts, all with counts in column 1,
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	8
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	9 tr -d ',' <all.tsv \|head -100 \| while read n m; do printf "%s%s\n" $n $(for i in {0..99}; do printf ",%s" $({ grep -w "w $m\$" s${i}.tsv \|\| echo NaN ;} \| cut -f 1 ) ; done ) ; done > all_100.csv
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	10
30 c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	11 will produce such a file with
c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	12 * 100 rows, one for each of the top 100 counts
c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	13 * 101 columns, 0 for all and 1--100 for segs 0--99
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	14
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	15 Usage: python3 -i spearman.py name
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	16 where name.csv has the input
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	17 '''
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	18
25 50337cd1d16f framework for stats over results of rank correlations Henry S. Thompson <ht@inf.ed.ac.uk> parents: diff changeset	19 import numpy as np
50337cd1d16f framework for stats over results of rank correlations Henry S. Thompson <ht@inf.ed.ac.uk> parents: diff changeset	20 from numpy import loadtxt
50337cd1d16f framework for stats over results of rank correlations Henry S. Thompson <ht@inf.ed.ac.uk> parents: diff changeset	21 from scipy import stats
50337cd1d16f framework for stats over results of rank correlations Henry S. Thompson <ht@inf.ed.ac.uk> parents: diff changeset	22 import statsmodels.api as sm
26 5c5440e7854a a bit more Henry S. Thompson <ht@inf.ed.ac.uk> parents: 25 diff changeset	23 import matplotlib.pyplot as plt
25 50337cd1d16f framework for stats over results of rank correlations Henry S. Thompson <ht@inf.ed.ac.uk> parents: diff changeset	24 import pylab
50337cd1d16f framework for stats over results of rank correlations Henry S. Thompson <ht@inf.ed.ac.uk> parents: diff changeset	25
50337cd1d16f framework for stats over results of rank correlations Henry S. Thompson <ht@inf.ed.ac.uk> parents: diff changeset	26 import sys
50337cd1d16f framework for stats over results of rank correlations Henry S. Thompson <ht@inf.ed.ac.uk> parents: diff changeset	27
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	28 def qqa():
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	29 # q-q plot for the whole crawl
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	30 sm.qqplot(all, line='s')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	31 plt.gca().set_title('Rank correlation per segment wrt whole crawl (warc results only)')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	32 plt.show()
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	33
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	34 def qqs():
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	35 # q-q plots for the best and worst (by variance) segments
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	36 global xv, xworst, xbest
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	37 xv=[d.variance for d in xd]
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	38 xworst=xv.index(max(xv))
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	39 xbest=xv.index(min(xv))
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	40 print(xbest,xworst)
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	41 sm.qqplot(x[xbest], line='s')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	42 plt.gca().set_title('Best segment (least variance): %s'%xbest)
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	43 plt.show()
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	44 sm.qqplot(x[xworst], line='s')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	45 plt.gca().set_title('Worst segment (most variance): %s'%xworst)
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	46 plt.show()
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	47
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	48 def plot_x():
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	49 plt.plot([xd[i].mean for i in range(100)],'bx',label='Mean of rank correlation of each segment x all other segments')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	50 plt.plot([0,99],[xm,xm],'b',label='Mean of segment x segment means')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	51 plt.plot(all,'rx',label='Rank correlation of segment x whole crawl')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	52 plt.plot([0,99],[all_m,all_m],'r',label='Mean of segment x whole crawl')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	53 plt.axis([0,99,0.8,1.0])
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	54 plt.legend(loc='best')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	55 plt.grid(True)
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	56 plt.show()
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	57
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	58 def hist():
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	59 sdd=[(i,xm-(i*xsd)) for i in range(-2,3)]
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	60 fig,hax=plt.subplots() # Thanks to https://stackoverflow.com/a/7769497
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	61 sdax=hax.twiny()
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	62 hax.hist([xd[i].mean for i in range(100)],color='lightblue')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	63 hax.set_title('Mean of rank correlation of each segment x all other segments')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	64 for s,v in sdd:
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	65 sdax.plot([v,v],[0,18],'b')
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	66 sdax.set_xlim(hax.get_xlim())
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	67 sdax.set_ylim(hax.get_ylim())
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	68 sdax.set_xticks([v for s,v in sdd])
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	69 sdax.set_xticklabels([str(s) for s,v in sdd])
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	70 plt.show()
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	71
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	72 def first_diff(ranks):
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	73 # first disagreement with baseline == {1,2,...}
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	74 for i in range(len(ranks)):
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	75 if ranks[i]!=i+1.0:
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	76 return i
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	77 return i+1
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	78
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	79 def ranks():
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	80 # Combine segment measures:
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	81 # segID,rank corr. wrt all,inverse variance, mean cross rank corr.,first disagreement
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	82 return np.array([i,all[i],1.0/xd[i].variance,xd[i].mean,first_diff(ranks[i])])
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	83
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	84 counts=loadtxt(sys.argv[1]+".csv",delimiter=',')
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	85 # "If axis=0 (default), then each column represents a variable, with
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	86 # observations in the rows"
30 c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	87 # So each column is a sequence of counts, for whole crawl in column 0
c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	88 # and for segments 0--99 in columns 1--100
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	89 corr=stats.spearmanr(counts,nan_policy='omit').correlation
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	90
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	91 all=corr[0][1:]
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	92 all_s=stats.describe(all)
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	93 all_m=all_s.mean
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	94
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	95 x=np.array([np.concatenate((corr[i][1:i],
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	96 corr[i][i+1:])) for i in range(1,101)])
30 c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	97 # The above, although transposed, works because the correlation matrix
c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	98 # is symmetric
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	99 xd=[stats.describe(x[i]) for i in range(100)]
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	100 xs=stats.describe(np.array([xd[i].mean for i in range(100)]))
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	101 xm=xs.mean
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	102 xsd=np.sqrt(xs.variance)
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	103
30 c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	104 ranks=[stats.rankdata(-counts[:,i],method='average') for for i in range(1,100)]
c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	105
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	106 ### I need to review rows, e.g. counts[0] is an array of 101 counts
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	107 ### for the most common label in the complete crawl,
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	108 ### from the complete crawl and all the segments
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	109 ### versus columns, e.g. counts[:,0] is an array of 100 decreasing counts
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	110 ### for all the labels in the complete crawl

Mercurial > hg > cc > cirrus_work

annotate bin/spearman.py @ 30:c73ec9deabbe