def bigXSquaredSubM(self, verbose=False):
"""Calculate the X^2_m stat
This can handle gaps and ambiguities.
Column zeros in the observed is not a problem with this stat,
as we are dividing by the expected composition, and that comes
from the model, which does not allow compositions with values
of zero. """
if not self.cTree:
self._commonCStuff(resetEmpiricalComps=True)
l = []
for pNum in range(self.data.nParts):
if verbose:
print "Part %i" % pNum
print "======"
obs = []
nSites = [] # no gaps or ?
for taxNum in range(self.nTax):
thisNSites = pf.partSequenceSitesCount(self.data.parts[pNum].cPart, taxNum)
comp = self.data.parts[pNum].composition([taxNum])
for symbNum in range(self.data.parts[pNum].dim):
comp[symbNum] *= thisNSites
nSites.append(thisNSites)
obs.append(comp)
if verbose:
print "\n Observed"
print " " * 10,
for symbNum in range(self.data.parts[pNum].dim):
print "%8s" % self.data.parts[pNum].symbols[symbNum],
print
for taxNum in range(self.nTax):
print "%10s" % self.taxNames[taxNum],
for symbNum in range(self.data.parts[pNum].dim):
print "%8.4f" % obs[taxNum][symbNum],
print " n=%i" % nSites[taxNum]
# pf.p4_expectedCompositionCounts returns a tuple of tuples
# representing the counts of the nodes in proper alignment order.
exp = list(pf.p4_expectedCompositionCounts(self.cTree, pNum))
if verbose:
print "\n Expected"
print " " * 10,
for symbNum in range(self.data.parts[pNum].dim):
print "%8s" % self.data.parts[pNum].symbols[symbNum],
print
for taxNum in range(self.nTax):
print "%10s" % self.taxNames[taxNum],
for symbNum in range(self.data.parts[pNum].dim):
print "%8.4f" % exp[taxNum][symbNum],
print " n=%i" % nSites[taxNum]
# do the summation
theSum = 0.0
for taxNum in range(self.nTax):
for symbNum in range(self.data.parts[pNum].dim):
x = obs[taxNum][symbNum] - exp[taxNum][symbNum]
theSum += (x * x) / exp[taxNum][symbNum]
l.append(theSum)
if verbose:
print "The bigXSquaredSubM stat for this part is %.5f" % theSum
return l
def simsForModelFitTests(self, reps=10, seed=None):
"""Do simulations for model fit tests.
The model fit tests are the Goldman-Cox test, and the tree- and
model-based composition fit test. Both of those tests require
simulations, optimization of the tree and model parameters on the
simulated data, and extraction of statistics for use in the null
distribution. So might as well do them together. The Goldman-Cox
test is not possible if there are any gaps or ambiguities, and in
that case Goldman-Cox simulation stats are not collected.
Doing the simulations is therefore the time-consuming part, and so
this method facilitates doing that job in sections. If you do
that, set the random number seed to different numbers. If the
seed is not set, the process id is used. (So obviously you should
explicitly set the seed if you are doing several runs in the same
process.) Perhaps you may want to do the simulations on different
machines in a cluster. The stats are saved to files. The output
files have the seed number attached to the end, so that different
runs of this method will have different output file names.
Hopefully.
When your model uses empirical comps, simulation uses the
empirical comp of the original data for simulation (good), then
the optimization part uses the empirical comp of the
newly-simulated data (also good, I think). In that case, if it is
tree-homogeneous, the X^2_m statistic would be identical to the
X^2 statistic.
You would follow this method with the modelFitTests() method,
which uses all the stats files to make null distributions to
assess significance of the same stats from self."""
#gm = ['Tree.simsForModelFitTests()']
# Make a new data object in which to do the sims, so we do not over-write self
#print "a self.data = %s" % self.data
#self.data.dump()
savedData = self.data
self.data = None # This triggers self.deleteCStuff()
self.data = savedData.dupe()
# We need 2 trees, one for sims, and one for evaluations. We can
# use self for sims. Make a copy for evaluations.
evalTree = self.dupe()
evalTree.data = self.data
# make sure all the memory works ...
self.calcLogLike(verbose=0)
evalTree.calcLogLike(verbose=0)
# We can't do the Goldman-Cox test if there are any gaps or
# ambiguities.
doGoldmanCox = True
for a in self.data.alignments:
if a.hasGapsOrAmbiguities():
doGoldmanCox = False
break
#print "sims doGoldmanCox = %s" % doGoldmanCox
# Collect info about the observed data
statsHashList = [] # one for each data part
for pNum in range(self.data.nParts):
h = {}
statsHashList.append(h)
h['individualNSites'] = []
h['observedIndividualCounts'] = []
for j in range(self.data.nTax):
h['individualNSites'].append(pf.partSequenceSitesCount(self.data.parts[pNum].cPart, j)) # no gaps or qmarks
h['observedIndividualCounts'].append(self.data.parts[pNum].composition([j]))
# (In the line above, its temporarily composition, not counts)
#print "got seq %i comp = %s' % (j, h['observedIndividualCounts"][-1])
# At the moment, h['observedIndividualCounts'] has composition,
# not counts. So multiply by h['individualNSites']
for i in range(self.data.nTax):
for j in range(self.data.parts[pNum].dim):
h['observedIndividualCounts'][i][j] *= h['individualNSites'][i]
# We will want to skip any sequences composed of all gaps
skipTaxNums = []
for pNum in range(self.data.nParts):
stn = []
for tNum in range(self.data.nTax):
if not statsHashList[pNum]['individualNSites'][tNum]:
stn.append(tNum)
skipTaxNums.append(stn)
#print "skipTaxNums = %s" % skipTaxNums
if seed == None:
seed = os.getpid()
pf.reseedCRandomizer(int(seed))
# Open up some output files in which to put the sim data
outfileBaseName = 'sims' # Could be an argument, user-assignable.
if doGoldmanCox:
f2Name = outfileBaseName + '_GoldmanStats_%s' % seed
f2 = open(f2Name, 'w')
f2.write('# part\tunconstr L\t log like \tGoldman-Cox stat\n')
f3Name = outfileBaseName + '_CompStats_%s' % seed
f3 = open(f3Name, 'w')
# When sims are done when the comp is empirical (whether or not
# free) we need to re-set the comps based on the newly-simulated
# data. So first find out if any comps are empirical.
hasEmpiricalComps = 0
for mp in self.model.parts:
for c in mp.comps:
if c.spec == 'empirical':
hasEmpiricalComps = 1
break
#print "hasEmpiricalComps=%s" % hasEmpiricalComps
# Do the sims
for i in range(reps):
self.simulate()
if hasEmpiricalComps:
evalTree.setEmpiricalComps() # Set empirical comps based on newly-simulated data
evalTree.optLogLike(verbose=0) # The time-consuming part
if doGoldmanCox:
if self.data.nParts > 1:
self.data.calcUnconstrainedLogLikelihood2()
diff = self.data.unconstrainedLogLikelihood - evalTree.logLike
f2.write('-1\t%f\t%f\t%f\n' % (self.data.unconstrainedLogLikelihood, evalTree.logLike, diff))
for pNum in range(self.data.nParts):
unc = pf.getUnconstrainedLogLike(self.data.parts[pNum].cPart)
like = pf.p4_partLogLike(evalTree.cTree, self.data.parts[pNum].cPart, pNum, 0) # 0 for getSiteLikes
diff = unc - like
f2.write('%i\t%f\t%f\t%f\n' % (pNum, unc, like, diff))
for pNum in range(self.data.nParts):
h = statsHashList[pNum]
# pf.p4_expectedCompositionCounts returns a tuple of tuples
# representing the counts of the nodes in proper alignment order.
ret = pf.p4_expectedCompositionCounts(evalTree.cTree, pNum)
h['expectedIndividualCounts'] = list(ret) # alignment order
#print h['expectedIndividualCounts']
h['overallSimStat'] = 0.0
h['individualSimStats'] = [0.0] * self.data.nTax
for seqNum in range(self.data.nTax):
if seqNum in skipTaxNums[pNum]:
pass
else:
obsCounts = list(pf.singleSequenceBaseCounts(self.data.parts[pNum].cPart, seqNum))
# obsCounts is the counts observed in the simulation.
# It assumes that there are no gaps. If there are gaps, adjust the counts.
if h['individualNSites'][seqNum] != self.data.parts[pNum].nChar:
factor = float(h['individualNSites'][seqNum]) / self.data.parts[pNum].nChar
#print "factor = %s" % factor
for j in range(self.data.parts[pNum].dim):
obsCounts[j] = float(obsCounts[j]) * factor
#print obsCounts
for j in range(self.data.parts[pNum].dim):
# Avoid dividing by Zero.
if h['expectedIndividualCounts'][seqNum][j]:
dif = obsCounts[j] - h['expectedIndividualCounts'][seqNum][j]
h['individualSimStats'][seqNum] += ((dif * dif) / h['expectedIndividualCounts'][seqNum][j])
h['overallSimStat'] += h['individualSimStats'][seqNum]
f3.write('%i\t' % pNum)
for seqNum in range(self.data.nTax):
f3.write('%f\t' % h['individualSimStats'][seqNum])
f3.write('%f\n' % h['overallSimStat'])
#print h['overallSimStat']
if doGoldmanCox:
f2.close()
f3.close()
# Replace the saved data
self.data = savedData # Since we are replacing an exisiting data, this triggers self.deleteCStuff()
def modelFitTests(self, fName = 'model_fit_tests_out', writeRawStats=0):
"""Do model fit tests on the data.
The two tests are the Goldman-Cox test, and the tree- and model-
based composition fit test. Both require simulations with
optimizations in order to get a null distribution, and those
simulations need to be done before this method. The simulations
should be done with the simsForModelFitTests() method.
Self should have a data and a model attached, and be optimized.
The Goldman-Cox test (Goldman 1993. Statistical tests of models
of DNA substitution. J Mol Evol 36: 182-198.) is a test for
overall fit of the model to the data. It does not work if the
data have gaps or ambiguities.
The tree- and model-based composition test asks the question:
'Does the composition implied by the model fit the data?' If the
model is homogeneous and empirical comp is used, then this is the
same as the chi-square test except that the null distribution
comes from simulations, not from the chi-square distribution. In
that case only the question is, additionally, 'Are the data
homogeneous in composition?', ie the same question asked by the
chi-square test. However, the data might be heterogeneous, and
the model might be heterogeneous over the tree; the tree- and
model-based composition fit test can ask whether the heterogeneous
model fits the heterogeneous data. The composition is tested in
each data partition, separately. The test is done both overall,
ie for all the sequences together, and for individual sequences.
If you just want a compo homogeneity test with empirical
homogeneous comp, try the compoTestUsingSimulations() method-- its
way faster, because there are not optimizations in the sims part.
Output is verbose, to a file."""
gm = ['Tree.modelFitTests()']
self.calcLogLike(verbose=0)
doOut = True # Usually True. Set to False for debugging, experimentation, getting individual stats, etc
# We can't do the Goldman-Cox test if there are any gaps or
# ambiguities.
doGoldmanCox = True
for a in self.data.alignments:
if a.hasGapsOrAmbiguities():
doGoldmanCox = False
break
#print "test doGoldmanCox = %s" % doGoldmanCox
rawFName = '%s_raw.py' % fName
#flob = sys.stderr
#fRaw = sys.stderr
if doOut:
flob = file(fName, 'w')
else:
flob = None
if writeRawStats:
fRaw = file(rawFName, 'w')
else:
fRaw = None
#######################
# Goldman-Cox stats
#######################
# For a two-part data analysis, the first few lines of the
# sims_GoldmanStats_* file will be like the following. Its in
# groups of 3-- the first one for all parts together (part number
# -1), and the next lines for separate parts.
## # part unconstr L log like Goldman-Cox stat
## -1 -921.888705 -1085.696919 163.808215
## 0 -357.089057 -430.941958 73.852901
## 1 -564.799648 -654.754962 89.955314
## -1 -952.063037 -1130.195799 178.132761
## 0 -362.164119 -439.709824 77.545705
## ... and so on.
# For a one-part analysis, it will be the same except that one sim
# gets only one line, starting with zero.
if doGoldmanCox:
goldmanOverallSimStats = []
if self.data.nParts > 1:
goldmanIndividualSimStats = []
for partNum in range(self.data.nParts):
goldmanIndividualSimStats.append([])
import glob
goldmanFNames = glob.glob('sims_GoldmanStats_*')
#print "nParts=%s" % self.data.nParts
#print goldmanFNames
for fName1 in goldmanFNames:
f2 = open(fName1)
aLine = f2.readline()
if not aLine:
gm.append("Empty file %s" % fName1)
raise Glitch, gm
if aLine[0] != '#':
gm.append("Expecting a '#' as the first character in file %s" % fName1)
raise Glitch, gm
aLine = f2.readline()
#print "a got line %s" % aLine,
while aLine:
if self.data.nParts > 1:
splitLine = aLine.split()
if len(splitLine) != 4:
gm.append("Bad line in Goldman stats file %s" % fName1)
gm.append("'%s'" % aLine)
raise Glitch, gm
if int(splitLine[0]) != -1:
gm.append("Bad line in Goldman stats file %s" % fName1)
gm.append("First item should be -1")
gm.append("'%s'" % aLine)
raise Glitch, gm
#print splitLine[-1]
goldmanOverallSimStats.append(float(splitLine[-1]))
aLine = f2.readline()
#print "b got line %s" % aLine,
if not aLine:
gm.append("Premature end to file %s" % fName1)
raise Glitch, gm
for partNum in range(self.data.nParts):
splitLine = aLine.split()
#print "partNum %i, splitLine=%s" % (partNum, splitLine)
if len(splitLine) != 4:
gm.append("Bad line in Goldman stats file %s" % fName1)
gm.append("'%s'" % aLine)
raise Glitch, gm
try:
splitLine[0] = int(splitLine[0])
except ValueError:
gm.append("Bad line in Goldman stats file %s" % fName1)
gm.append("First item should be the partNum %i" % partNum)
gm.append("'%s'" % aLine)
raise Glitch, gm
if splitLine[0] != partNum:
gm.append("Bad line in Goldman stats file %s" % fName1)
gm.append("First item should be the partNum %i" % partNum)
gm.append("'%s'" % aLine)
raise Glitch, gm
#for taxNum in range(self.data.nTax):
# print splitLine[taxNum + 1]
#print splitLine[-1]
if self.data.nParts == 1:
goldmanOverallSimStats.append(float(splitLine[-1]))
else:
goldmanIndividualSimStats[partNum].append(float(splitLine[-1]))
aLine = f2.readline()
#print "c got line %s" % aLine,
f2.close()
#print "goldmanOverallSimStats =", goldmanOverallSimStats
#print "goldmanIndividualSimStats =", goldmanIndividualSimStats
#sys.exit()
if doOut:
flob.write('Model fit tests\n===============\n\n')
flob.write('The data that we are testing have %i taxa,\n' % self.data.nTax)
if len(self.data.alignments) == 1:
flob.write('1 alignment, ')
else:
flob.write('%i alignments, ' % len(self.data.alignments))
if self.data.nParts == 1:
flob.write('and 1 data partition.\n')
else:
flob.write('and %i data partitions.\n' % self.data.nParts)
flob.write('The lengths of those partitions are as follows:\n')
flob.write(' partNum nChar \n')
for i in range(self.data.nParts):
flob.write(' %3i %5i\n' % (i, self.data.parts[i].nChar))
self.data.calcUnconstrainedLogLikelihood2()
if doOut:
flob.write("\nThe unconstrained likelihood is %f\n" % self.data.unconstrainedLogLikelihood)
flob.write('(This is the partition-by-partition unconstrained log likelihood, \n')
flob.write('ie the sum of the unconstrained log likes from each partition separately, \n')
flob.write('and so will not be the same as that given by PAUP, if the data are partitioned.)\n')
flob.write('\n\nGoldman-Cox test for overall model fit\n')
flob.write ('======================================\n')
flob.write('The log likelihood for these data for this tree is %f\n' % self.logLike)
flob.write('The unconstrained log likelihood for these data is %f\n' % self.data.unconstrainedLogLikelihood)
originalGoldmanCoxStat = self.data.unconstrainedLogLikelihood - self.logLike
if doOut:
flob.write('The Goldman-Cox statistic for the original data is the difference, %f\n' % originalGoldmanCoxStat)
if self.data.nParts > 1:
flob.write('(The unconstrained log likelihood for these data is calculated partition by partition.)\n')
flob.write('\n')
if self.data.nParts > 1:
originalGoldmanCoxStatsByPart = []
if doOut:
flob.write('Stats by partition.\n')
flob.write('part\t unconstrLogL\t log like \tGoldman-Cox stat\n')
flob.write('----\t ----------\t -------- \t----------------\n')
for partNum in range(self.data.nParts):
unc = pf.getUnconstrainedLogLike(self.data.parts[partNum].cPart)
like = pf.p4_partLogLike(self.cTree, self.data.parts[partNum].cPart, partNum, 0)
diff = unc - like
if doOut:
flob.write(' %i\t%f\t%f\t %f\n' % (partNum, unc, like, diff))
originalGoldmanCoxStatsByPart.append(diff)
# Do the overall stat
nSims = len(goldmanOverallSimStats)
if doOut: flob.write('\nThere were %i simulations.\n\n' % nSims)
if writeRawStats:
fRaw.write('# Goldman-Cox null distributions.\n')
if self.data.nParts > 1:
fRaw.write('# Simulation stats for overall data, ie for all data partitions combined.\n')
else:
fRaw.write('# Simulation stats.\n')
fRaw.write('goldman_cox_overall = %s\n' % goldmanOverallSimStats)
if self.data.nParts > 1:
for partNum in range(self.data.nParts):
fRaw.write('# Simulation stats for data partition %i\n' % partNum)
fRaw.write('goldman_cox_part%i = %s\n' % (partNum, goldmanIndividualSimStats[partNum]))
prob = func.tailAreaProbability(originalGoldmanCoxStat, goldmanOverallSimStats, verbose=0)
if doOut:
flob.write( '\n Overall Goldman-Cox test: ')
if prob <= 0.05:
flob.write('%13s' % "Doesn't fit.")
else:
flob.write('%13s' % 'Fits.')
flob.write(' P = %5.3f\n' % prob)
if self.data.nParts > 1:
if doOut: flob.write(' Tests for individual data partitions:\n')
for partNum in range(self.data.nParts):
prob = func.tailAreaProbability(originalGoldmanCoxStatsByPart[partNum],
goldmanIndividualSimStats[partNum], verbose=0)
if doOut:
flob.write( ' Part %-2i: ' % partNum)
if prob <= 0.05:
flob.write('%13s' % 'Doesn\'t fit.')
else:
flob.write('%13s' % 'Fits.')
flob.write(' P = %5.3f\n' % prob)
#########################
# COMPOSITION
#########################
statsHashList = []
for pNum in range(self.data.nParts):
h = {}
statsHashList.append(h)
h['individualNSites'] = []
h['observedIndividualCounts'] = []
for j in range(self.data.nTax):
#print pf.partSequenceSitesCount(self.data.parts[pNum].cPart, j)
h['individualNSites'].append(pf.partSequenceSitesCount(self.data.parts[pNum].cPart, j)) # no gaps or qmarks
#print self.data.parts[pNum].composition([j])
h['observedIndividualCounts'].append(self.data.parts[pNum].composition([j]))
# The line above is temporarily composition, not counts
# pf.expectedCompositionCounts returns a tuple of tuples
# representing the counts of the nodes in proper alignment order.
h['expectedIndividualCounts'] = list(pf.p4_expectedCompositionCounts(self.cTree, pNum)) # alignment order
# At the moment, h['observedIndividualCounts'] has composition,
# not counts. So multiply by h['individualNSites']
for i in range(self.data.nTax):
for j in range(self.data.parts[pNum].dim):
h['observedIndividualCounts'][i][j] *= h['individualNSites'][i]
# We will want to skip any sequences composed of all gaps
skipTaxNums = []
for pNum in range(self.data.nParts):
stn = []
for tNum in range(self.data.nTax):
if not statsHashList[pNum]['individualNSites'][tNum]:
stn.append(tNum)
skipTaxNums.append(stn)
#print "skipTaxNums = %s" % skipTaxNums
# Do the boring old compo chi square test.
if doOut: flob.write(longMessage1) # explanation ...
for pNum in range(self.data.nParts):
h = statsHashList[pNum]
# Can't use func.xSquared(), because there might be column
# zeros.
#print "observedIndividualCounts = %s' % h['observedIndividualCounts"]
nRows = len(h['observedIndividualCounts'])
nCols = len(h['observedIndividualCounts'][0])
theSumOfRows = func._sumOfRows(h['observedIndividualCounts']) # I could have just used nSites, above
theSumOfCols = func._sumOfColumns(h['observedIndividualCounts'])
#print theSumOfCols
isOk = 1
columnZeros = []
#for j in range(len(theSumOfRows)):
# if theSumOfRows[j] == 0.0:
# gm.append("Zero in a row sum. Programming error.")
# raise Glitch, gm
for j in range(len(theSumOfCols)):
if theSumOfCols[j] <= 0.0:
columnZeros.append(j)
theExpected = func._expected(theSumOfRows, theSumOfCols)
#print "theExpected = %s" % theExpected
#print "columnZeros = %s" % columnZeros
xSq = 0.0
for rowNum in range(nRows):
if rowNum in skipTaxNums[pNum]:
pass
else:
xSq_row = 0.0
for colNum in range(nCols):
if colNum in columnZeros:
pass
else:
theDiff = h['observedIndividualCounts'][rowNum][colNum] - theExpected[rowNum][colNum]
xSq_row += (theDiff * theDiff) / theExpected[rowNum][colNum]
xSq += xSq_row
dof = (nCols - len(columnZeros) - 1) * (nRows - len(skipTaxNums[pNum]) - 1)
prob = func.chiSquaredProb(xSq, dof)
if doOut: flob.write(' Part %i: Chi-square = %f, (dof=%i) P = %f\n' % (pNum, xSq, dof, prob))
for pNum in range(self.data.nParts):
h = statsHashList[pNum]
h['overallStat'] = 0.0
h['individualStats'] = [0.0] * self.data.nTax
for i in range(self.data.nTax):
if i in skipTaxNums[pNum]:
pass # h['individualStats'] stays at zeros
else:
for j in range(self.data.parts[pNum].dim):
# Avoid dividing by Zero.
if h['expectedIndividualCounts'][i][j]:
dif = h['observedIndividualCounts'][i][j] - h['expectedIndividualCounts'][i][j]
h['individualStats'][i] += ((dif * dif) /h['expectedIndividualCounts'][i][j])
h['overallStat'] += h['individualStats'][i]
h['overallSimStats'] = []
h['individualSimStats'] = []
for i in range(self.data.nTax):
h['individualSimStats'].append([])
if 0:
print "h['individualNSites'] = %s" % h['individualNSites']
print "h['observedIndividualCounts'] = %s" % h['observedIndividualCounts']
print "h['expectedIndividualCounts'] = %s" % h['expectedIndividualCounts']
print "h['overallStat'] = %s" % h['overallStat']
print "h['individualStats'] = %s" % h['individualStats']
raise Glitch, gm
import glob
compoFNames = glob.glob('sims_CompStats_*')
#print compoFNames
for fName1 in compoFNames:
f2 = open(fName1)
aLine = f2.readline()
if not aLine:
gm.append("Empty file %s" % fName1)
raise Glitch, gm
#print "a got line %s" % aLine,
while aLine:
for partNum in range(self.data.nParts):
h = statsHashList[partNum]
splitLine = aLine.split()
if len(splitLine) != (self.data.nTax + 2):
gm.append("Bad line in composition stats file %s" % fName1)
gm.append("'%s'" % aLine)
raise Glitch, gm
if int(splitLine[0]) != partNum:
gm.append("Bad line in composition stats file %s" % fName1)
gm.append("First item should be the partNum %i" % partNum)
gm.append("'%s'" % aLine)
raise Glitch, gm
#for taxNum in range(self.data.nTax):
# print splitLine[taxNum + 1]
#print splitLine[-1]
h['overallSimStats'].append(float(splitLine[-1]))
for i in range(self.data.nTax):
h['individualSimStats'][i].append(float(splitLine[i + 1]))
#raise Glitch, gm
aLine = f2.readline()
if not aLine:
break
#print "b got line %s" % aLine,
f2.close()
nSims = len(statsHashList[0]['overallSimStats'])
if doOut:
flob.write(longMessage2) # Explain tree- and model-based compo fit stat, X^2_m
flob.write( ' %i simulation reps were used.\n\n' % nSims)
spacer1 = ' ' * 10
for partNum in range(self.data.nParts):
h = statsHashList[partNum]
if doOut:
flob.write('Part %-2i:\n-------\n\n' % partNum)
flob.write('Statistics from the original data\n')
flob.write('%s%30s: %f\n' % (spacer1, 'Overall observed stat', h['overallStat']))
flob.write('%s%30s:\n' % (spacer1, 'Stats for individual taxa'))
for taxNum in range(self.data.nTax):
if taxNum not in skipTaxNums[partNum]:
flob.write('%s%30s: %f\n' % (spacer1, self.data.taxNames[taxNum], h['individualStats'][taxNum]))
else:
flob.write('%s%30s: skipped\n' % (spacer1, self.data.taxNames[taxNum]))
flob.write('\nAssessment of fit from null distribution from %i simulations\n' % nSims)
flob.write('%s%30s: ' % (spacer1, 'Overall'))
prob = func.tailAreaProbability(h['overallStat'], h['overallSimStats'], verbose=0)
if doOut:
if prob <= 0.05:
flob.write('%13s' % 'Doesn\'t fit.')
else:
flob.write('%13s' % 'Fits.')
flob.write(' P = %5.3f\n' % prob)
#############
theRet= prob
#############
for taxNum in range(self.data.nTax):
if doOut: flob.write('%s%30s: ' % (spacer1, self.data.taxNames[taxNum]))
if taxNum in skipTaxNums[partNum]:
if doOut: flob.write('%13s\n' % 'skipped.')
else:
prob = func.tailAreaProbability(h['individualStats'][taxNum],
h['individualSimStats'][taxNum], verbose=0)
if doOut:
if prob <= 0.05:
flob.write('%13s' % "Doesn't fit.")
else:
flob.write('%13s' % 'Fits.')
flob.write(' P = %5.3f\n' % prob)
if writeRawStats:
fRaw.write('#\n# Tree and model based composition fit test\n')
fRaw.write('# =========================================\n')
fRaw.write('# Simulation statistics, ie the null distributions\n\n')
fRaw.write('# Part %i:\n' % partNum)
fRaw.write('part%i_overall_compo_null = %s\n' % (partNum, h['overallSimStats']))
for taxNum in range(self.data.nTax):
fRaw.write('part%i_%s_compo_null = %s\n' % (partNum,
_fixFileName(self.data.taxNames[taxNum]),
h['individualSimStats'][taxNum]))
if flob and flob != sys.stdout: # Yes, it is possible to close sys.stdout
flob.close()
if fRaw and fRaw != sys.stdout:
fRaw.close()
return theRet
def bigXSquaredSubM(self, verbose=False):
"""Calculate the X^2_m stat
This can handle gaps and ambiguities.
Column zeros in the observed is not a problem with this stat,
as we are dividing by the expected composition, and that comes
from the model, which does not allow compositions with values
of zero. """
if not self.cTree:
self._commonCStuff(resetEmpiricalComps=True)
l = []
for pNum in range(self.data.nParts):
if verbose:
print "Part %i" % pNum
print "======"
obs = []
nSites = [] # no gaps or ?
for taxNum in range(self.nTax):
thisNSites = pf.partSequenceSitesCount(self.data.parts[pNum].cPart, taxNum)
comp = self.data.parts[pNum].composition([taxNum])
for symbNum in range(self.data.parts[pNum].dim):
comp[symbNum] *= thisNSites
nSites.append(thisNSites)
obs.append(comp)
if verbose:
print "\n Observed"
print " " * 10,
for symbNum in range(self.data.parts[pNum].dim):
print "%8s" % self.data.parts[pNum].symbols[symbNum],
print
for taxNum in range(self.nTax):
print "%10s" % self.taxNames[taxNum],
for symbNum in range(self.data.parts[pNum].dim):
print "%8.4f" % obs[taxNum][symbNum],
print " n=%i" % nSites[taxNum]
# pf.p4_expectedCompositionCounts returns a tuple of tuples
# representing the counts of the nodes in proper alignment order.
exp = list(pf.p4_expectedCompositionCounts(self.cTree, pNum))
if verbose:
print "\n Expected"
print " " * 10,
for symbNum in range(self.data.parts[pNum].dim):
print "%8s" % self.data.parts[pNum].symbols[symbNum],
print
for taxNum in range(self.nTax):
print "%10s" % self.taxNames[taxNum],
for symbNum in range(self.data.parts[pNum].dim):
print "%8.4f" % exp[taxNum][symbNum],
print " n=%i" % nSites[taxNum]
# do the summation
theSum = 0.0
for taxNum in range(self.nTax):
for symbNum in range(self.data.parts[pNum].dim):
x = obs[taxNum][symbNum] - exp[taxNum][symbNum]
theSum += (x * x) / exp[taxNum][symbNum]
l.append(theSum)
if verbose:
print "The bigXSquaredSubM stat for this part is %.5f" % theSum
return l
def simsForModelFitTests(self, reps=10, seed=None):
"""Do simulations for model fit tests.
The model fit tests are the Goldman-Cox test, and the tree- and
model-based composition fit test. Both of those tests require
simulations, optimization of the tree and model parameters on the
simulated data, and extraction of statistics for use in the null
distribution. So might as well do them together. The Goldman-Cox
test is not possible if there are any gaps or ambiguities, and in
that case Goldman-Cox simulation stats are not collected.
Doing the simulations is therefore the time-consuming part, and so
this method facilitates doing that job in sections. If you do
that, set the random number seed to different numbers. If the
seed is not set, the process id is used. (So obviously you should
explicitly set the seed if you are doing several runs in the same
process.) Perhaps you may want to do the simulations on different
machines in a cluster. The stats are saved to files. The output
files have the seed number attached to the end, so that different
runs of this method will have different output file names.
Hopefully.
When your model uses empirical comps, simulation uses the
empirical comp of the original data for simulation (good), then
the optimization part uses the empirical comp of the
newly-simulated data (also good, I think). In that case, if it is
tree-homogeneous, the X^2_m statistic would be identical to the
X^2 statistic.
You would follow this method with the modelFitTests() method,
which uses all the stats files to make null distributions to
assess significance of the same stats from self."""
#gm = ['Tree.simsForModelFitTests()']
# Make a new data object in which to do the sims, so we do not over-write self
#print "a self.data = %s" % self.data
#self.data.dump()
savedData = self.data
self.data = None # This triggers self.deleteCStuff()
self.data = savedData.dupe()
# We need 2 trees, one for sims, and one for evaluations. We can
# use self for sims. Make a copy for evaluations.
evalTree = self.dupe()
evalTree.data = self.data
# make sure all the memory works ...
self.calcLogLike(verbose=0)
evalTree.calcLogLike(verbose=0)
# We can't do the Goldman-Cox test if there are any gaps or
# ambiguities.
doGoldmanCox = True
for a in self.data.alignments:
if a.hasGapsOrAmbiguities():
doGoldmanCox = False
break
#print "sims doGoldmanCox = %s" % doGoldmanCox
# Collect info about the observed data
statsHashList = [] # one for each data part
for pNum in range(self.data.nParts):
h = {}
statsHashList.append(h)
h['individualNSites'] = []
h['observedIndividualCounts'] = []
for j in range(self.data.nTax):
h['individualNSites'].append(pf.partSequenceSitesCount(self.data.parts[pNum].cPart, j)) # no gaps or qmarks
h['observedIndividualCounts'].append(self.data.parts[pNum].composition([j]))
# (In the line above, its temporarily composition, not counts)
#print "got seq %i comp = %s' % (j, h['observedIndividualCounts"][-1])
# At the moment, h['observedIndividualCounts'] has composition,
# not counts. So multiply by h['individualNSites']
for i in range(self.data.nTax):
for j in range(self.data.parts[pNum].dim):
h['observedIndividualCounts'][i][j] *= h['individualNSites'][i]
# We will want to skip any sequences composed of all gaps
skipTaxNums = []
for pNum in range(self.data.nParts):
stn = []
for tNum in range(self.data.nTax):
if not statsHashList[pNum]['individualNSites'][tNum]:
stn.append(tNum)
skipTaxNums.append(stn)
#print "skipTaxNums = %s" % skipTaxNums
if seed == None:
seed = os.getpid()
pf.reseedCRandomizer(int(seed))
# Open up some output files in which to put the sim data
outfileBaseName = 'sims' # Could be an argument, user-assignable.
if doGoldmanCox:
f2Name = outfileBaseName + '_GoldmanStats_%s' % seed
f2 = open(f2Name, 'w')
f2.write('# part\tunconstr L\t log like \tGoldman-Cox stat\n')
f3Name = outfileBaseName + '_CompStats_%s' % seed
f3 = open(f3Name, 'w')
# When sims are done when the comp is empirical (whether or not
# free) we need to re-set the comps based on the newly-simulated
# data. So first find out if any comps are empirical.
hasEmpiricalComps = 0
for mp in self.model.parts:
for c in mp.comps:
if c.spec == 'empirical':
hasEmpiricalComps = 1
break
#print "hasEmpiricalComps=%s" % hasEmpiricalComps
# Do the sims
for i in range(reps):
self.simulate()
if hasEmpiricalComps:
evalTree.setEmpiricalComps() # Set empirical comps based on newly-simulated data
evalTree.optLogLike(verbose=0) # The time-consuming part
if doGoldmanCox:
if self.data.nParts > 1:
self.data.calcUnconstrainedLogLikelihood2()
diff = self.data.unconstrainedLogLikelihood - evalTree.logLike
f2.write('-1\t%f\t%f\t%f\n' % (self.data.unconstrainedLogLikelihood, evalTree.logLike, diff))
for pNum in range(self.data.nParts):
unc = pf.getUnconstrainedLogLike(self.data.parts[pNum].cPart)
like = pf.p4_partLogLike(evalTree.cTree, self.data.parts[pNum].cPart, pNum, 0) # 0 for getSiteLikes
diff = unc - like
f2.write('%i\t%f\t%f\t%f\n' % (pNum, unc, like, diff))
for pNum in range(self.data.nParts):
h = statsHashList[pNum]
# pf.p4_expectedCompositionCounts returns a tuple of tuples
# representing the counts of the nodes in proper alignment order.
ret = pf.p4_expectedCompositionCounts(evalTree.cTree, pNum)
h['expectedIndividualCounts'] = list(ret) # alignment order
#print h['expectedIndividualCounts']
h['overallSimStat'] = 0.0
h['individualSimStats'] = [0.0] * self.data.nTax
for seqNum in range(self.data.nTax):
if seqNum in skipTaxNums[pNum]:
pass
else:
obsCounts = list(pf.singleSequenceBaseCounts(self.data.parts[pNum].cPart, seqNum))
# obsCounts is the counts observed in the simulation.
# It assumes that there are no gaps. If there are gaps, adjust the counts.
if h['individualNSites'][seqNum] != self.data.parts[pNum].nChar:
factor = float(h['individualNSites'][seqNum]) / self.data.parts[pNum].nChar
#print "factor = %s" % factor
for j in range(self.data.parts[pNum].dim):
obsCounts[j] = float(obsCounts[j]) * factor
#print obsCounts
for j in range(self.data.parts[pNum].dim):
# Avoid dividing by Zero.
if h['expectedIndividualCounts'][seqNum][j]:
dif = obsCounts[j] - h['expectedIndividualCounts'][seqNum][j]
h['individualSimStats'][seqNum] += ((dif * dif) / h['expectedIndividualCounts'][seqNum][j])
h['overallSimStat'] += h['individualSimStats'][seqNum]
f3.write('%i\t' % pNum)
for seqNum in range(self.data.nTax):
f3.write('%f\t' % h['individualSimStats'][seqNum])
f3.write('%f\n' % h['overallSimStat'])
#print h['overallSimStat']
if doGoldmanCox:
f2.close()
f3.close()
# Replace the saved data
self.data = savedData # Since we are replacing an exisiting data, this triggers self.deleteCStuff()
def modelFitTests(self, fName = 'model_fit_tests_out', writeRawStats=0):
"""Do model fit tests on the data.
The two tests are the Goldman-Cox test, and the tree- and model-
based composition fit test. Both require simulations with
optimizations in order to get a null distribution, and those
simulations need to be done before this method. The simulations
should be done with the simsForModelFitTests() method.
Self should have a data and a model attached, and be optimized.
The Goldman-Cox test (Goldman 1993. Statistical tests of models
of DNA substitution. J Mol Evol 36: 182-198.) is a test for
overall fit of the model to the data. It does not work if the
data have gaps or ambiguities.
The tree- and model-based composition test asks the question:
'Does the composition implied by the model fit the data?' If the
model is homogeneous and empirical comp is used, then this is the
same as the chi-square test except that the null distribution
comes from simulations, not from the chi-square distribution. In
that case only the question is, additionally, 'Are the data
homogeneous in composition?', ie the same question asked by the
chi-square test. However, the data might be heterogeneous, and
the model might be heterogeneous over the tree; the tree- and
model-based composition fit test can ask whether the heterogeneous
model fits the heterogeneous data. The composition is tested in
each data partition, separately. The test is done both overall,
ie for all the sequences together, and for individual sequences.
If you just want a compo homogeneity test with empirical
homogeneous comp, try the compoTestUsingSimulations() method-- its
way faster, because there are not optimizations in the sims part.
Output is verbose, to a file."""
gm = ['Tree.modelFitTests()']
self.calcLogLike(verbose=0)
doOut = True # Usually True. Set to False for debugging, experimentation, getting individual stats, etc
# We can't do the Goldman-Cox test if there are any gaps or
# ambiguities.
doGoldmanCox = True
for a in self.data.alignments:
if a.hasGapsOrAmbiguities():
doGoldmanCox = False
break
#print "test doGoldmanCox = %s" % doGoldmanCox
rawFName = '%s_raw.py' % fName
#flob = sys.stderr
#fRaw = sys.stderr
if doOut:
flob = file(fName, 'w')
else:
flob = None
if writeRawStats:
fRaw = file(rawFName, 'w')
else:
fRaw = None
#######################
# Goldman-Cox stats
#######################
# For a two-part data analysis, the first few lines of the
# sims_GoldmanStats_* file will be like the following. Its in
# groups of 3-- the first one for all parts together (part number
# -1), and the next lines for separate parts.
## # part unconstr L log like Goldman-Cox stat
## -1 -921.888705 -1085.696919 163.808215
## 0 -357.089057 -430.941958 73.852901
## 1 -564.799648 -654.754962 89.955314
## -1 -952.063037 -1130.195799 178.132761
## 0 -362.164119 -439.709824 77.545705
## ... and so on.
# For a one-part analysis, it will be the same except that one sim
# gets only one line, starting with zero.
if doGoldmanCox:
goldmanOverallSimStats = []
if self.data.nParts > 1:
goldmanIndividualSimStats = []
for partNum in range(self.data.nParts):
goldmanIndividualSimStats.append([])
import glob
goldmanFNames = glob.glob('sims_GoldmanStats_*')
#print "nParts=%s" % self.data.nParts
#print goldmanFNames
for fName1 in goldmanFNames:
f2 = open(fName1)
aLine = f2.readline()
if not aLine:
gm.append("Empty file %s" % fName1)
raise Glitch, gm
if aLine[0] != '#':
gm.append("Expecting a '#' as the first character in file %s" % fName1)
raise Glitch, gm
aLine = f2.readline()
#print "a got line %s" % aLine,
while aLine:
if self.data.nParts > 1:
splitLine = aLine.split()
if len(splitLine) != 4:
gm.append("Bad line in Goldman stats file %s" % fName1)
gm.append("'%s'" % aLine)
raise Glitch, gm
if int(splitLine[0]) != -1:
gm.append("Bad line in Goldman stats file %s" % fName1)
gm.append("First item should be -1")
gm.append("'%s'" % aLine)
raise Glitch, gm
#print splitLine[-1]
goldmanOverallSimStats.append(float(splitLine[-1]))
aLine = f2.readline()
#print "b got line %s" % aLine,
if not aLine:
gm.append("Premature end to file %s" % fName1)
raise Glitch, gm
for partNum in range(self.data.nParts):
splitLine = aLine.split()
#print "partNum %i, splitLine=%s" % (partNum, splitLine)
if len(splitLine) != 4:
gm.append("Bad line in Goldman stats file %s" % fName1)
gm.append("'%s'" % aLine)
raise Glitch, gm
try:
splitLine[0] = int(splitLine[0])
except ValueError:
gm.append("Bad line in Goldman stats file %s" % fName1)
gm.append("First item should be the partNum %i" % partNum)
gm.append("'%s'" % aLine)
raise Glitch, gm
if splitLine[0] != partNum:
gm.append("Bad line in Goldman stats file %s" % fName1)
gm.append("First item should be the partNum %i" % partNum)
gm.append("'%s'" % aLine)
raise Glitch, gm
#for taxNum in range(self.data.nTax):
# print splitLine[taxNum + 1]
#print splitLine[-1]
if self.data.nParts == 1:
goldmanOverallSimStats.append(float(splitLine[-1]))
else:
goldmanIndividualSimStats[partNum].append(float(splitLine[-1]))
aLine = f2.readline()
#print "c got line %s" % aLine,
f2.close()
#print "goldmanOverallSimStats =", goldmanOverallSimStats
#print "goldmanIndividualSimStats =", goldmanIndividualSimStats
#sys.exit()
if doOut:
flob.write('Model fit tests\n===============\n\n')
flob.write('The data that we are testing have %i taxa,\n' % self.data.nTax)
if len(self.data.alignments) == 1:
flob.write('1 alignment, ')
else:
flob.write('%i alignments, ' % len(self.data.alignments))
if self.data.nParts == 1:
flob.write('and 1 data partition.\n')
else:
flob.write('and %i data partitions.\n' % self.data.nParts)
flob.write('The lengths of those partitions are as follows:\n')
flob.write(' partNum nChar \n')
for i in range(self.data.nParts):
flob.write(' %3i %5i\n' % (i, self.data.parts[i].nChar))
self.data.calcUnconstrainedLogLikelihood2()
if doOut:
flob.write("\nThe unconstrained likelihood is %f\n" % self.data.unconstrainedLogLikelihood)
flob.write('(This is the partition-by-partition unconstrained log likelihood, \n')
flob.write('ie the sum of the unconstrained log likes from each partition separately, \n')
flob.write('and so will not be the same as that given by PAUP, if the data are partitioned.)\n')
flob.write('\n\nGoldman-Cox test for overall model fit\n')
flob.write ('======================================\n')
flob.write('The log likelihood for these data for this tree is %f\n' % self.logLike)
flob.write('The unconstrained log likelihood for these data is %f\n' % self.data.unconstrainedLogLikelihood)
originalGoldmanCoxStat = self.data.unconstrainedLogLikelihood - self.logLike
if doOut:
flob.write('The Goldman-Cox statistic for the original data is the difference, %f\n' % originalGoldmanCoxStat)
if self.data.nParts > 1:
flob.write('(The unconstrained log likelihood for these data is calculated partition by partition.)\n')
flob.write('\n')
if self.data.nParts > 1:
originalGoldmanCoxStatsByPart = []
if doOut:
flob.write('Stats by partition.\n')
flob.write('part\t unconstrLogL\t log like \tGoldman-Cox stat\n')
flob.write('----\t ----------\t -------- \t----------------\n')
for partNum in range(self.data.nParts):
unc = pf.getUnconstrainedLogLike(self.data.parts[partNum].cPart)
like = pf.p4_partLogLike(self.cTree, self.data.parts[partNum].cPart, partNum, 0)
diff = unc - like
if doOut:
flob.write(' %i\t%f\t%f\t %f\n' % (partNum, unc, like, diff))
originalGoldmanCoxStatsByPart.append(diff)
# Do the overall stat
nSims = len(goldmanOverallSimStats)
if doOut: flob.write('\nThere were %i simulations.\n\n' % nSims)
if writeRawStats:
fRaw.write('# Goldman-Cox null distributions.\n')
if self.data.nParts > 1:
fRaw.write('# Simulation stats for overall data, ie for all data partitions combined.\n')
else:
fRaw.write('# Simulation stats.\n')
fRaw.write('goldman_cox_overall = %s\n' % goldmanOverallSimStats)
if self.data.nParts > 1:
for partNum in range(self.data.nParts):
fRaw.write('# Simulation stats for data partition %i\n' % partNum)
fRaw.write('goldman_cox_part%i = %s\n' % (partNum, goldmanIndividualSimStats[partNum]))
prob = func.tailAreaProbability(originalGoldmanCoxStat, goldmanOverallSimStats, verbose=0)
if doOut:
flob.write( '\n Overall Goldman-Cox test: ')
if prob <= 0.05:
flob.write('%13s' % "Doesn't fit.")
else:
flob.write('%13s' % 'Fits.')
flob.write(' P = %5.3f\n' % prob)
if self.data.nParts > 1:
if doOut: flob.write(' Tests for individual data partitions:\n')
for partNum in range(self.data.nParts):
prob = func.tailAreaProbability(originalGoldmanCoxStatsByPart[partNum],
goldmanIndividualSimStats[partNum], verbose=0)
if doOut:
flob.write( ' Part %-2i: ' % partNum)
if prob <= 0.05:
flob.write('%13s' % 'Doesn\'t fit.')
else:
flob.write('%13s' % 'Fits.')
flob.write(' P = %5.3f\n' % prob)
#########################
# COMPOSITION
#########################
statsHashList = []
for pNum in range(self.data.nParts):
h = {}
statsHashList.append(h)
h['individualNSites'] = []
h['observedIndividualCounts'] = []
for j in range(self.data.nTax):
#print pf.partSequenceSitesCount(self.data.parts[pNum].cPart, j)
h['individualNSites'].append(pf.partSequenceSitesCount(self.data.parts[pNum].cPart, j)) # no gaps or qmarks
#print self.data.parts[pNum].composition([j])
h['observedIndividualCounts'].append(self.data.parts[pNum].composition([j]))
# The line above is temporarily composition, not counts
# pf.expectedCompositionCounts returns a tuple of tuples
# representing the counts of the nodes in proper alignment order.
h['expectedIndividualCounts'] = list(pf.p4_expectedCompositionCounts(self.cTree, pNum)) # alignment order
# At the moment, h['observedIndividualCounts'] has composition,
# not counts. So multiply by h['individualNSites']
for i in range(self.data.nTax):
for j in range(self.data.parts[pNum].dim):
h['observedIndividualCounts'][i][j] *= h['individualNSites'][i]
# We will want to skip any sequences composed of all gaps
skipTaxNums = []
for pNum in range(self.data.nParts):
stn = []
for tNum in range(self.data.nTax):
if not statsHashList[pNum]['individualNSites'][tNum]:
stn.append(tNum)
skipTaxNums.append(stn)
#print "skipTaxNums = %s" % skipTaxNums
# Do the boring old compo chi square test.
if doOut: flob.write(longMessage1) # explanation ...
for pNum in range(self.data.nParts):
h = statsHashList[pNum]
# Can't use func.xSquared(), because there might be column
# zeros.
#print "observedIndividualCounts = %s' % h['observedIndividualCounts"]
nRows = len(h['observedIndividualCounts'])
nCols = len(h['observedIndividualCounts'][0])
theSumOfRows = func._sumOfRows(h['observedIndividualCounts']) # I could have just used nSites, above
theSumOfCols = func._sumOfColumns(h['observedIndividualCounts'])
#print theSumOfCols
isOk = 1
columnZeros = []
#for j in range(len(theSumOfRows)):
# if theSumOfRows[j] == 0.0:
# gm.append("Zero in a row sum. Programming error.")
# raise Glitch, gm
for j in range(len(theSumOfCols)):
if theSumOfCols[j] <= 0.0:
columnZeros.append(j)
theExpected = func._expected(theSumOfRows, theSumOfCols)
#print "theExpected = %s" % theExpected
#print "columnZeros = %s" % columnZeros
xSq = 0.0
for rowNum in range(nRows):
if rowNum in skipTaxNums[pNum]:
pass
else:
xSq_row = 0.0
for colNum in range(nCols):
if colNum in columnZeros:
pass
else:
theDiff = h['observedIndividualCounts'][rowNum][colNum] - theExpected[rowNum][colNum]
xSq_row += (theDiff * theDiff) / theExpected[rowNum][colNum]
xSq += xSq_row
dof = (nCols - len(columnZeros) - 1) * (nRows - len(skipTaxNums[pNum]) - 1)
prob = func.chiSquaredProb(xSq, dof)
if doOut: flob.write(' Part %i: Chi-square = %f, (dof=%i) P = %f\n' % (pNum, xSq, dof, prob))
for pNum in range(self.data.nParts):
h = statsHashList[pNum]
h['overallStat'] = 0.0
h['individualStats'] = [0.0] * self.data.nTax
for i in range(self.data.nTax):
if i in skipTaxNums[pNum]:
pass # h['individualStats'] stays at zeros
else:
for j in range(self.data.parts[pNum].dim):
# Avoid dividing by Zero.
if h['expectedIndividualCounts'][i][j]:
dif = h['observedIndividualCounts'][i][j] - h['expectedIndividualCounts'][i][j]
h['individualStats'][i] += ((dif * dif) /h['expectedIndividualCounts'][i][j])
h['overallStat'] += h['individualStats'][i]
h['overallSimStats'] = []
h['individualSimStats'] = []
for i in range(self.data.nTax):
h['individualSimStats'].append([])
if 0:
print "h['individualNSites'] = %s" % h['individualNSites']
print "h['observedIndividualCounts'] = %s" % h['observedIndividualCounts']
print "h['expectedIndividualCounts'] = %s" % h['expectedIndividualCounts']
print "h['overallStat'] = %s" % h['overallStat']
print "h['individualStats'] = %s" % h['individualStats']
raise Glitch, gm
import glob
compoFNames = glob.glob('sims_CompStats_*')
#print compoFNames
for fName1 in compoFNames:
f2 = open(fName1)
aLine = f2.readline()
if not aLine:
gm.append("Empty file %s" % fName1)
raise Glitch, gm
#print "a got line %s" % aLine,
while aLine:
for partNum in range(self.data.nParts):
h = statsHashList[partNum]
splitLine = aLine.split()
if len(splitLine) != (self.data.nTax + 2):
gm.append("Bad line in composition stats file %s" % fName1)
gm.append("'%s'" % aLine)
raise Glitch, gm
if int(splitLine[0]) != partNum:
gm.append("Bad line in composition stats file %s" % fName1)
gm.append("First item should be the partNum %i" % partNum)
gm.append("'%s'" % aLine)
raise Glitch, gm
#for taxNum in range(self.data.nTax):
# print splitLine[taxNum + 1]
#print splitLine[-1]
h['overallSimStats'].append(float(splitLine[-1]))
for i in range(self.data.nTax):
h['individualSimStats'][i].append(float(splitLine[i + 1]))
#raise Glitch, gm
aLine = f2.readline()
if not aLine:
break
#print "b got line %s" % aLine,
f2.close()
nSims = len(statsHashList[0]['overallSimStats'])
if doOut:
flob.write(longMessage2) # Explain tree- and model-based compo fit stat, X^2_m
flob.write( ' %i simulation reps were used.\n\n' % nSims)
spacer1 = ' ' * 10
for partNum in range(self.data.nParts):
h = statsHashList[partNum]
if doOut:
flob.write('Part %-2i:\n-------\n\n' % partNum)
flob.write('Statistics from the original data\n')
flob.write('%s%30s: %f\n' % (spacer1, 'Overall observed stat', h['overallStat']))
flob.write('%s%30s:\n' % (spacer1, 'Stats for individual taxa'))
for taxNum in range(self.data.nTax):
if taxNum not in skipTaxNums[partNum]:
flob.write('%s%30s: %f\n' % (spacer1, self.data.taxNames[taxNum], h['individualStats'][taxNum]))
else:
flob.write('%s%30s: skipped\n' % (spacer1, self.data.taxNames[taxNum]))
flob.write('\nAssessment of fit from null distribution from %i simulations\n' % nSims)
flob.write('%s%30s: ' % (spacer1, 'Overall'))
prob = func.tailAreaProbability(h['overallStat'], h['overallSimStats'], verbose=0)
if doOut:
if prob <= 0.05:
flob.write('%13s' % 'Doesn\'t fit.')
else:
flob.write('%13s' % 'Fits.')
flob.write(' P = %5.3f\n' % prob)
#############
theRet= prob
#############
for taxNum in range(self.data.nTax):
if doOut: flob.write('%s%30s: ' % (spacer1, self.data.taxNames[taxNum]))
if taxNum in skipTaxNums[partNum]:
if doOut: flob.write('%13s\n' % 'skipped.')
else:
prob = func.tailAreaProbability(h['individualStats'][taxNum],
h['individualSimStats'][taxNum], verbose=0)
if doOut:
if prob <= 0.05:
flob.write('%13s' % "Doesn't fit.")
else:
flob.write('%13s' % 'Fits.')
flob.write(' P = %5.3f\n' % prob)
if writeRawStats:
fRaw.write('#\n# Tree and model based composition fit test\n')
fRaw.write('# =========================================\n')
fRaw.write('# Simulation statistics, ie the null distributions\n\n')
fRaw.write('# Part %i:\n' % partNum)
fRaw.write('part%i_overall_compo_null = %s\n' % (partNum, h['overallSimStats']))
for taxNum in range(self.data.nTax):
fRaw.write('part%i_%s_compo_null = %s\n' % (partNum,
_fixFileName(self.data.taxNames[taxNum]),
h['individualSimStats'][taxNum]))
if flob and flob != sys.stdout: # Yes, it is possible to close sys.stdout
flob.close()
if fRaw and fRaw != sys.stdout:
fRaw.close()
return theRet