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April 19, 2013 19:03
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Python: Calculate Adjusted Wallace, Wallace and Rand coefficients, and Simpson's index of diversity
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import sys | |
import math | |
def getContTable(ar1, ar2): | |
cont = {} | |
for i in xrange(0, len(ar1)): | |
keyAr1 = ar1[i] | |
keyAr2 = ar2[i] | |
if keyAr1 in cont: | |
if keyAr2 in cont[keyAr1]: | |
cont[keyAr1][keyAr2] += 1 | |
else: | |
cont[keyAr1][keyAr2] = 1 | |
else: | |
cont[keyAr1] = {keyAr2: 1} | |
return cont | |
def getContTableTotals(cont, ar1, ar2): | |
sumRow = {} | |
sumCol = {} | |
h1 = set(ar1) | |
h2 = set(ar2) | |
for x in h2: | |
sumRow[x] = 0 | |
for y in h1: | |
if y in cont: | |
if x in cont[y]: | |
val = cont[y][x] | |
sumRow[x] += val | |
if y in sumCol: | |
sumCol[y] += val | |
else: | |
sumCol[y] = val | |
total = 0 | |
for x in h1: | |
total += sumCol[x] | |
return (sumRow, sumCol, total) | |
def getMismatchMatrix(cont, ar1, ar2): | |
totals = getContTableTotals(cont, ar1, ar2) | |
# print totals | |
n = totals[2] | |
h1 = set(ar1) | |
h2 = set(ar2) | |
a = 0 | |
for x in h1: | |
for y in h2: | |
if x in cont: | |
if y in cont[x]: | |
val = cont[x][y] | |
a += (val * (val - 1)) / 2 | |
a1 = 0 | |
sumCol = totals[1] | |
for x in sumCol: | |
val = sumCol[x] | |
a1 += (val * (val - 1)) / 2 | |
b = a1 - a | |
a2 = 0 | |
sumRow = totals[0] | |
for x in sumRow: | |
val = sumRow[x] | |
a2 += (val * (val - 1)) / 2 | |
c = a2 - a | |
d = float((n * (n - 1)) / 2) - a1 - c | |
return (a, b, c, d, n) | |
def getRand(a, b, c, d): | |
rand = (a + d) / float(a + b + c + d) | |
return rand | |
def getWallace(a, b, c): | |
w1 = float(0) | |
w2 = float(0) | |
if (a + b) > 0: | |
w1 = a / float(a + b) | |
if (a + c) > 0: | |
w2 = a / float(a + c) | |
return (w1, w2) | |
def getSimpsons(ar): | |
n = len(ar) | |
d = {} | |
for x in ar: | |
if x in d: | |
d[x] += 1 | |
else: | |
d[x] = 1 | |
sumTotal = 0 | |
sumFc2 = 0 | |
sumFc3 = 0 | |
for x in d: | |
val = d[x] | |
sumTotal += val * (val - 1) | |
sumFc2 += (val / float(n)) ** 2.0 | |
sumFc3 += (val / float(n)) ** 3.0 | |
sid = 1.0 | |
if n * (n - 1) > 0: | |
sid = 1.0 - (sumTotal / float(n * (n - 1))) | |
sqSumFc2 = sumFc2 ** 2.0 | |
s2 = (4.0 / float(n)) * float(sumFc3 - sqSumFc2) | |
sidLow = sid - 2 * math.sqrt(s2) | |
sidHigh = sid + 2 * math.sqrt(s2) | |
return (sid, sidLow, sidHigh, len(d)) | |
def getAdjustedWallace(cont, ar1, ar2): | |
sumCol, sumRow, totals = getContTableTotals(cont, ar1, ar2) | |
rSumW1 = 0 | |
rSumW2 = 0 | |
csumFc2 = {} | |
csumFc3 = {} | |
for i in cont: | |
rSum = sumRow[i] | |
rsumFc2 = 0 | |
rsumFc3 = 0 | |
for j in cont[i]: | |
val = cont[i][j] | |
cSum = sumCol[j] | |
rsumFc2 += (val / float(rSum)) ** 2.0 | |
rsumFc3 += (val / float(rSum)) ** 3.0 | |
if j in csumFc2: | |
csumFc2[j] += (val / float(cSum)) ** 2.0 | |
else: | |
csumFc2[j] = (val / float(cSum)) ** 2.0 | |
if j in csumFc3: | |
csumFc3[j] += (val / float(cSum)) ** 3.0 | |
else: | |
csumFc3[j] = (val / float(cSum)) ** 3.0 | |
rsqrsumFc2 = rsumFc2 ** 2.0 | |
rvarSID = 0.0 | |
if rSum > 1: | |
rvarSID = float(4.0 * rSum * (rSum - 1.0) * (rSum - 2.0) * rsumFc3 + 2.0 * rSum * (rSum - 1.0) * rsumFc2 - 2.0 * rSum * (rSum - 1.0) * (2.0 * rSum - 3.0) * rsqrsumFc2) / float((rSum * (rSum - 1.0)) ** 2.0) | |
rSumW1 += float((rSum * (rSum - 1.0)) ** 2.0) * rvarSID | |
rSumW2 += rSum * (rSum - 1.0) | |
csumw1 = 0 | |
csumW2 = 0 | |
for j in sumCol: | |
cSum = sumCol[j] | |
fc2 = csumFc2[j] | |
fc3 = csumFc3[j] | |
csqrsumFc2 = fc2 ** 2.0 | |
cvarSID = 0.0 | |
if cSum > 1: | |
# (4*sumcol[j]*(sumcol[j]-1)*(sumcol[j]-2)*csumFc3[j]+2*sumcol[j]*(sumcol[j]-1)*csumFc2[j]-2*sumcol[j]*(sumcol[j]-1)*(2*sumcol[j]-3)*csqrsumFc2[j])/sqr(sumcol[j]*(sumcol[j]-1)); | |
cvarSID = float(4.0 * cSum * (cSum - 1.0) * (cSum - 2.0) * fc3 + 2.0 * cSum * (cSum - 1.0) * fc2 - 2.0 * cSum * (cSum - 1.0) * (2.0 * cSum - 3.0) * csqrsumFc2) / float((cSum * (cSum - 1.0)) ** 2.0) | |
print cvarSID | |
csumw1 += (cSum * (cSum - 1.0) * cvarSID) ** 2.0 | |
csumW2 += cSum * (cSum - 1.0) | |
print "csumW2=%f" % csumW2 | |
varW1 = 0.0 | |
varW2 = 0.0 | |
if rSumW2 > 0: | |
varW1 = float(rSumW1 / float(float(rSumW2) ** 2.0)) | |
if csumW2 > 0: | |
varW2 = float(csumw1 / float(float(csumW2) ** 2.0)) | |
print "varW1=%f" % varW1 | |
print "varW2=%f" % varW2 | |
a, b, c, d, n = getMismatchMatrix(cont, ar1, ar2) | |
w1, w2 = getWallace(a, b, c) | |
sid1 = getSimpsons(ar1) | |
sid2 = getSimpsons(ar2) | |
wi1 = 1 - sid1[0] | |
wi2 = 1 - sid2[0] | |
aw1 = float(w1 - wi2) / float(1 - wi2) | |
aw2 = float(w2 - wi1) / float(1 - wi1) | |
aw1CI = 2.0 * (1.0 / float(1.0 - wi2)) * math.sqrt(varW1) | |
aw1Low = aw1 - aw1CI | |
aw1High = aw1 + aw1CI | |
aw2CI = 2.0 * (1.0 / float(1.0 - wi1)) * math.sqrt(varW2) | |
print "wi1=%f" % wi1 | |
print "aw2CI=%f" % aw2CI | |
aw2Low = aw2 - aw2CI | |
aw2High = aw2 + aw2CI | |
return (aw1, aw1Low, aw1High, aw2, aw2Low, aw2High) | |
if len(sys.argv) == 3: | |
array1 = sys.argv[1] | |
array2 = sys.argv[2] | |
x = array1.split(",") | |
# print x | |
y = array2.split(",") | |
# print y | |
cont = getContTable(x, y) | |
abcdn = getMismatchMatrix(cont, x, y) | |
print "Rand\t%f" % getRand(abcdn[0], abcdn[1], abcdn[2], abcdn[3]) | |
wallace = getWallace(abcdn[0], abcdn[1], abcdn[2]) | |
print "Wallace 1vs2\t%f" % wallace[0] | |
print "Wallace 2vs1\t%f" % wallace[1] | |
sid1 = getSimpsons(x) | |
sid2 = getSimpsons(y) | |
print "Simpsons 1\t%f\t%f\t%f\t%d" % sid1 | |
print "Simpsons 2\t%f\t%f\t%f\t%d" % sid2 | |
print getAdjustedWallace(cont, x, y) | |
else: | |
print """ | |
Please specify 2 lists of clusters delimited by commas ',' | |
Output: | |
Rand coefficient | |
Wallace coefficient 1vs2 | |
Wallace coefficient 2vs1 | |
Simpson's index of diversity | |
""" |
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