cc/cirrus_work: bin/spearman.py annotate

annotate bin/spearman.py @ 69:0d2701901fed

for timing analysis

author	Henry S. Thompson <ht@inf.ed.ac.uk>
date	Wed, 26 Jul 2023 18:42:19 +0100
parents	da1cbcd8acee
children

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
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	15 Usage: python3 -i spearman.py name id
27 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
34 2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	26 import sys, math
25 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')
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	31 plt.gca().set_title('Rank correlation per segment wrt whole archive %s'%id)
27 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
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	48 def plot_x(sort=False,block=True,all_only=True,title=None):
34 2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	49 # Make these two subplots, w. and w/o sorting
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	50 # See https://stackoverflow.com/questions/4700614/how-to-put-the-legend-outside-the-plot
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	51 # for legend hacking
32 91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	52 if sort:
91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	53 aso=np.argsort(-all)
91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	54 plot_all=all[aso]
91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	55 plot_x=np.array([xd[i].mean for i in range(N)])[aso]
91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	56 else:
91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	57 plot_all=all
91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	58 plot_x=[xd[i].mean for i in range(N)]
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	59 if title is None:
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	60 l1='Rank correlation of segment x whole crawl'
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	61 l2='Mean of segment x whole crawl'
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	62 plt.legend(loc='best',fontsize='small')
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	63 else:
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	64 l1=l2=None
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	65 plt.plot(plot_all,'rx',label=l1)
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	66 plt.plot([0,N-1],[all_m,all_m],'r',label=l2)
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	67 if not(all_only):
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	68 plt.plot(plot_x,'bx',label='Mean of rank correlation of each segment x all other segments')
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	69 plt.plot([0,N-1],[xm,xm],'b',label='Mean of segment x segment means')
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	70 plt.axis([0,N-1,0.85 if all_only else 0.8,1.0])
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	71 plt.grid(True)
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	72 if title is not None:
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	73 plt.title(title)
31 e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	74 plt.show(block=block)
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	75
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	76 def hist_x(align='mid'):
33 317bf47b506c generalise hist Henry S. Thompson <ht@inf.ed.ac.uk> parents: 32 diff changeset	77 hist(xm,xsd,[xd[i].mean for i in range(N)],
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	78 'Mean of rank correlation of each segment x all other segments',
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	79 align)
33 317bf47b506c generalise hist Henry S. Thompson <ht@inf.ed.ac.uk> parents: 32 diff changeset	80
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	81 def hist_all(align='mid'):
33 317bf47b506c generalise hist Henry S. Thompson <ht@inf.ed.ac.uk> parents: 32 diff changeset	82 hist(all_m,np.sqrt(all_s.variance),all,
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	83 'Rank correlation of each segment x whole crawl %s'%id,
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	84 align)
33 317bf47b506c generalise hist Henry S. Thompson <ht@inf.ed.ac.uk> parents: 32 diff changeset	85
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	86 def hist(m,sd,hh,title,align):
33 317bf47b506c generalise hist Henry S. Thompson <ht@inf.ed.ac.uk> parents: 32 diff changeset	87 sdd=[(i,m-(i*sd)) for i in range(-2,3)]
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	88 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	89 sdax=hax.twiny()
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	90 hax.hist(hh,color='lightblue',align=align)
33 317bf47b506c generalise hist Henry S. Thompson <ht@inf.ed.ac.uk> parents: 32 diff changeset	91 hax.set_title(title)
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	92 for s,v in sdd:
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	93 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	94 sdax.set_xlim(hax.get_xlim())
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	95 sdax.set_ylim(hax.get_ylim())
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	96 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	97 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	98 plt.show()
21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	99
34 2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	100 def ci(rho,n,conf=0.95):
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	101 # Courtesy of https://stats.stackexchange.com/a/18904
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	102 # rho is (rank) correlation, n is sample size
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	103 stderr=1.0/math.sqrt(n-3)
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	104 z=stats.norm.ppf(1.0-((1.0-conf)/2))
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	105 delta=z*stderr
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	106 lower=math.tanh(math.atanh(rho)-delta)
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	107 upper=math.tanh(math.atanh(rho)+delta)
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	108 return (lower,upper)
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	109
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	110 def plot_ci(rhos,n,trim=None,conf=0.95):
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	111 # rhos are (rank) correlation values
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	112 rhos_s=rhos[(-rhos).argsort()]
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	113 if trim is None:
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	114 l=len(rhos)
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	115 else:
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	116 rhos_s=rhos_s[:trim]
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	117 l=trim
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	118 cc=(np.array([ci(r,n,conf) for r in rhos_s])).T
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	119 ue=cc[1]-rhos_s
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	120 le=rhos_s-cc[0]
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	121 #for i in range(len(rhos)):
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	122 #print(cc[i][0],rhos_s[i]-cc[i][0],rhos_s[i],cc[i][1],-rhos_s[i]+cc[i][1])
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	123 plt.errorbar(np.arange(l),rhos_s,yerr=[le,ue],fmt='o')
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	124 plt.title("Rank correlation of segments x whole archive %s\nwith confidence bars at %d%%"%(id,conf*100))
34 2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	125 plt.show()
2e8002a64f72 compute and graph confidence intervals Henry S. Thompson <ht@inf.ed.ac.uk> parents: 33 diff changeset	126
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	127 def first_diff(ranks):
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	128 # first disagreement with baseline == {1,2,...}
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	129 for i in range(len(ranks)):
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	130 if ranks[i]!=i+1.0:
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	131 return i
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	132 return i+1
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	133
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	134 def ranks():
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	135 # Combine segment measures:
669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	136 # segID,rank corr. wrt all,inverse variance, mean cross rank corr.,first disagreement
31 e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	137 # convert to ranks, smallest value == highest rank
e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	138 all_ranked=stats.rankdata(-all,method='average') # invert since
e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	139 # large corr is good
32 91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	140 x_variance_ranked=stats.rankdata([xd[i].variance for i in range(N)])
31 e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	141 # small corr variance is good
32 91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	142 x_mean_ranked=stats.rankdata([-(xd[i].mean) for i in range(N)])
31 e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	143 # invert since
e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	144 # large mean corr is good
32 91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	145 fd_ranked=stats.rankdata([-first_diff(x_ranks[i]) for i in range(N)])
31 e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	146 # invert since
e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	147 # large first diff is good
e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	148 return np.array([[i,
e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	149 all_ranked[i],
e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	150 x_variance_ranked[i],
e7c8e64c2fdd get multi-ranking done right Henry S. Thompson <ht@inf.ed.ac.uk> parents: 30 diff changeset	151 x_mean_ranked[i],
32 91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	152 fd_ranked[i]] for i in range(N)])
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	153
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	154 def main():
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	155 global counts, id, corr, all, all_s, all_m, x, xd, xs, xm, xsd, x_ranks, rr
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	156 global aa, aa_by_all, N
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	157 counts=loadtxt(sys.argv[1]+".csv",delimiter=',')
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	158 id=sys.argv[2]
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	159 N=counts.shape[1]-1
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	160 # "If axis=0 (default), then each column represents a variable, with
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	161 # observations in the rows"
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	162 # So each column is a sequence of counts, for whole crawl in column 0
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	163 # and for segments 0--N-1 in columns 1--N
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	164 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	165
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	166 all=corr[0][1:]
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	167 all_s=stats.describe(all)
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	168 all_m=all_s.mean
27 21da4d6521db move all plots into functions Henry S. Thompson <ht@inf.ed.ac.uk> parents: 26 diff changeset	169
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	170 x=np.array([np.concatenate((corr[i][1:i],
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	171 corr[i][i+1:])) for i in range(1,N+1)])
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	172 # The above, although transposed, works because the correlation matrix
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	173 # is symmetric
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	174 xd=[stats.describe(x[i]) for i in range(N)]
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	175 xs=stats.describe(np.array([xd[i].mean for i in range(N)]))
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	176 xm=xs.mean
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	177 xsd=np.sqrt(xs.variance)
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	178
37 da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	179 x_ranks=[stats.rankdata(-counts[:,i],method='average') for i in range(1,N+1)]
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	180
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	181 aa=ranks()
da1cbcd8acee push actions in main fn Henry S. Thompson <ht@inf.ed.ac.uk> parents: 35 diff changeset	182 aa_by_all=aa[aa[:,1].argsort()]
30 c73ec9deabbe comments and more care about rows vs. columns Henry S. Thompson <ht@inf.ed.ac.uk> parents: 29 diff changeset	183
32 91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	184 ### I need to review rows, e.g. counts[0] is an array of N+1 counts
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	185 ### 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	186 ### from the complete crawl and all the segments
32 91741bf3ab51 add sort flag to plot_x Henry S. Thompson <ht@inf.ed.ac.uk> parents: 31 diff changeset	187 ### versus columns, e.g. counts[:,0] is an array of N decreasing counts
29 669a0b120d34 start work on ranking, Henry S. Thompson <ht@inf.ed.ac.uk> parents: 27 diff changeset	188 ### for all the labels in the complete crawl

Mercurial > hg > cc > cirrus_work

annotate bin/spearman.py @ 69:0d2701901fed