def pointbiserialr(x:List(float),y:List(float))->(float,float):
"""
Calculates a point-biserial correlation coefficient and the associated
probability value. Taken from Heiman's Basic Statistics for the Behav.
Sci (1st), p.194.
Usage: lpointbiserialr(x,y) where x,y are equal-length lists
Returns: Point-biserial r, two-tailed p-value
"""
TINY = 1e-30
if len(x) != len(y):
raise ValueError('INPUT VALUES NOT PAIRED IN pointbiserialr. ABORTING.')
data = pstat.abut(x,y)
categories = pstat.unique(x)
if len(categories) != 2:
raise ValueError("Exactly 2 categories required for pointbiserialr().")
else: # there are 2 categories, continue
codemap = pstat.abut(categories,list(range(2)))
recoded = pstat.recode(data,codemap,0)
_x = pstat.linexand(data,0,categories[0])
_y = pstat.linexand(data,0,categories[1])
xmean = central_tendency.mean(pstat.colex(_x,1))
ymean = central_tendency.mean(pstat.colex(_y,1))
n = len(data)
adjust = sqrt((len(_x)/float(n))*(len(_y)/float(n)))
rpb = (ymean - xmean)/variability.samplestdev(pstat.colex(data,1))*adjust
df = n-2
t = rpb*sqrt(df/((1.0-rpb+TINY)*(1.0+rpb+TINY)))
prob = probability.betai(0.5*df,0.5,df/(df+t*t)) # t already a float
return rpb, prob
def linregress(x:List(float),y:List(float))->(float,float,float,float,float):
"""
Calculates a regression line on x,y pairs.
Usage: llinregress(x,y) x,y are equal-length lists of x-y coordinates
Returns: slope, intercept, r, two-tailed prob, sterr-of-estimate
"""
TINY = 1.0e-20
if len(x) != len(y):
raise ValueError('Input values not paired in linregress. Aborting.')
n = len(x)
x = list(map(float,x))
y = list(map(float,y))
xmean = central_tendency.mean(x)
ymean = central_tendency.mean(y)
r_num = float(n*(support.summult(x,y)) - sum(x)*sum(y))
r_den = sqrt((n*support.ss(x) - support.square_of_sums(x))*(n*support.ss(y)-support.square_of_sums(y)))
r = r_num / r_den
z = 0.5*log((1.0+r+TINY)/(1.0-r+TINY))
df = n-2
t = r*sqrt(df/((1.0-r+TINY)*(1.0+r+TINY)))
prob = probability.betai(0.5*df,0.5,df/(df+t*t))
slope = r_num / float(n*support.ss(x) - support.square_of_sums(x))
intercept = ymean - slope*xmean
sterrest = sqrt(1-r*r)*variability.samplestdev(y)
return slope, intercept, r, prob, sterrest
def obrientransform(args: List(List(float))) -> List(List(float)):
"""
Computes a transform on input data (any number of columns). Used to
test for homogeneity of variance prior to running one-way stats. From
Maxwell and Delaney, p.112.
Usage: lobrientransform(*args)
Returns: transformed data for use in an ANOVA
"""
TINY = 1e-10
k = len(args)
n = [0] * k
v = [0.0] * k
m = [0.0] * k
nargs = []
for i in range(k):
nargs.append(copy.deepcopy(args[i]))
n[i] = len(nargs[i])
v[i] = var([float(na) for na in nargs[i]])
m[i] = central_tendency.mean([float(na) for na in nargs[i]])
for j in range(k):
for i in range(n[j]):
t1 = (n[j] - 1.5) * n[j] * (nargs[j][i] - m[j])**2
t2 = 0.5 * v[j] * (n[j] - 1.0)
t3 = (n[j] - 1.0) * (n[j] - 2.0)
nargs[j][i] = (t1 - t2) / float(t3)
check = 1
for j in range(k):
if v[j] - central_tendency.mean(nargs[j]) > TINY:
check = 0
if check != 1:
raise ValueError('Problem in obrientransform.')
else:
return nargs
def ttest_ind(a: List(float), b: List(float)) -> (float, float):
"""
Calculates the t-obtained T-test on TWO INDEPENDENT samples of
scores a, and b. From Numerical Recipies, p.483. If printit=1, results
are printed to the screen. If printit='filename', the results are output
to 'filename' using the given writemode (default=append). Returns t-value,
and prob.
Usage: lttest_ind(a,b,printit=0,name1='Samp1',name2='Samp2',writemode='a')
Returns: t-value, two-tailed prob
"""
printit = 0
name1 = 'Samp1'
name2 = 'Samp2'
writemode = 'a'
#bg: optional args
x1 = central_tendency.mean(a)
x2 = central_tendency.mean(b)
v1 = variability.stdev(a)**2
v2 = variability.stdev(b)**2
n1 = len(a)
n2 = len(b)
df = n1 + n2 - 2
svar = ((n1 - 1) * v1 + (n2 - 1) * v2) / float(df)
t = (x1 - x2) / sqrt(svar * (1.0 / n1 + 1.0 / n2))
prob = probability.betai(0.5 * df, 0.5, df / (df + t * t))
if printit != 0:
statname = 'Independent samples T-test.'
outputpairedstats(printit, writemode, name1, n1,
x1, v1, min(a), max(a), name2, n2, x2, v2, min(b),
max(b), statname, t, prob)
return t, prob
def ttest_1samp(a: List(float), popmean: int) -> (float, float):
"""
Calculates the t-obtained for the independent samples T-test on ONE group
of scores a, given a population mean. If printit=1, results are printed
to the screen. If printit='filename', the results are output to 'filename'
using the given writemode (default=append). Returns t-value, and prob.
Usage: lttest_1samp(a,popmean,Name='Sample',printit=0,writemode='a')
Returns: t-value, two-tailed prob
"""
printit = 0 #bg: optional arg
name = 'Sample' #bg: optional arg
writemode = 'a' #bg: optional arg
x = central_tendency.mean(a)
v = variability.var(a)
n = len(a)
df = n - 1
svar = ((n - 1) * v) / float(df)
t = (x - popmean) / sqrt(svar * (1.0 / n))
prob = probability.betai(0.5 * df, 0.5, float(df) / (df + t * t))
if printit != 0:
statname = 'Single-sample T-test.'
outputpairedstats(printit, writemode,
'Population', '--', popmean, 0, 0, 0, name, n, x, v,
min(a), max(a), statname, t, prob)
return t, prob
def variation(inlist: List(float)) -> float:
"""
Returns the coefficient of variation, as defined in CRC Standard
Probability and Statistics, p.6.
Usage: lvariation(inlist)
"""
return 100.0 * variability.samplestdev(inlist) / float(
central_tendency.mean(inlist))
def z(inlist: List(float), score: float) -> float:
"""
Returns the z-score for a given input score, given that score and the
list from which that score came. Not appropriate for population calculations.
Usage: lz(inlist, score)
"""
_z = (score - central_tendency.mean(inlist)) / samplestdev(inlist)
return _z
def samplevar(inlist: List(float)) -> float:
"""
Returns the variance of the values in the passed list using
N for the denominator (i.e., DESCRIBES the sample variance only).
Usage: lsamplevar(inlist)
"""
n = len(inlist)
mn = central_tendency.mean(inlist)
deviations = []
for item in inlist:
deviations.append(item - mn)
return support.ss(deviations) / float(n)
def var(inlist: List(float)) -> float:
"""
Returns the variance of the values in the passed list using N-1
for the denominator (i.e., for estimating population variance).
Usage: lvar(inlist)
"""
n = len(inlist)
mn = central_tendency.mean(inlist)
#bg#deviations = dyn([0]*len(inlist))
deviations = [0] * len(inlist)
for i in range(len(inlist)):
deviations[i] = inlist[i] - mn
return support.ss(deviations) / float(n - 1)
def cov(x: List(float), y: List(float)) -> float:
"""
Returns the estimated covariance of the values in the passed
array (i.e., N-1). Dimension can equal None (ravel array first), an
integer (the dimension over which to operate), or a sequence (operate
over multiple dimensions). Set keepdims=1 to return an array with the
same number of dimensions as inarray.
Usage: lcov(x,y,keepdims=0)
"""
keepdims = 0 #bg: was optional argument
n = len(x)
xmn = central_tendency.mean(x)
ymn = central_tendency.mean(y)
xdeviations = [0] * len(x)
ydeviations = [0] * len(y)
for i in range(len(x)):
xdeviations[i] = x[i] - xmn
ydeviations[i] = y[i] - ymn
ss = 0.0
for i in range(len(xdeviations)):
ss = ss + xdeviations[i] * ydeviations[i]
return ss / float(n - 1)
def describe(inlist: List(float)) -> (int, (float, float), float, float, float,
float):
"""
Returns some descriptive statistics of the passed list (assumed to be 1D).
Usage: ldescribe(inlist)
Returns: n, mean, standard deviation, skew, kurtosis
"""
n = len(inlist)
mm = (min(inlist), max(inlist))
m = central_tendency.mean(inlist)
sd = variability.stdev(inlist)
sk = skew(inlist)
kurt = kurtosis(inlist)
return n, mm, m, sd, sk, kurt
def pearsonr(x:List(float),y:List(float))->(float,float):
"""
Calculates a Pearson correlation coefficient and the associated
probability value. Taken from Heiman's Basic Statistics for the Behav.
Sci (2nd), p.195.
Usage: lpearsonr(x,y) where x and y are equal-length lists
Returns: Pearson's r value, two-tailed p-value
"""
TINY = 1.0e-30
if len(x) != len(y):
raise ValueError('Input values not paired in pearsonr. Aborting.',x,y)
n = len(x)
x = list(map(float,x))
y = list(map(float,y))
xmean = central_tendency.mean(x)
ymean = central_tendency.mean(y)
r_num = n*(support.summult(x,y)) - sum(x)*sum(y)
r_den = sqrt((n*support.ss(x) - support.square_of_sums(x))*(n*support.ss(y)-support.square_of_sums(y)))
r = (r_num / r_den) # denominator already a float
df = n-2
t = r*sqrt(df/((1.0-r+TINY)*(1.0+r+TINY)))
prob = probability.betai(0.5*df,0.5,df/float(df+t*t))
return r, prob
def ttest_rel(a: List(float), b: List(float)) -> (float, float):
"""
Calculates the t-obtained T-test on TWO RELATED samples of scores,
a and b. From Numerical Recipies, p.483. If printit=1, results are
printed to the screen. If printit='filename', the results are output to
'filename' using the given writemode (default=append). Returns t-value,
and prob.
Usage: lttest_rel(a,b,printit=0,name1='Sample1',name2='Sample2',writemode='a')
Returns: t-value, two-tailed prob
"""
printit = 0
name1 = 'Sample1'
name2 = 'Sample2'
writemode = 'a' #bg: optional arg
if len(a) != len(b):
raise ValueError('Unequal length lists in ttest_rel.')
x1 = central_tendency.mean(a)
x2 = central_tendency.mean(b)
v1 = variability.var(a)
v2 = variability.var(b)
n = len(a)
cov = 0
for i in range(len(a)):
cov = cov + (a[i] - x1) * (b[i] - x2)
df = n - 1
_cov = cov / float(df)
sd = sqrt((v1 + v2 - 2.0 * _cov) / float(n))
t = (x1 - x2) / sd
prob = probability.betai(0.5 * df, 0.5, df / (df + t * t))
if printit != 0:
statname = 'Related samples T-test.'
outputpairedstats(printit, writemode, name1, n, x1, v1, min(a), max(a),
name2, n, x2, v2, min(b), max(b), statname, t, prob)
return t, prob
def moment(inlist: List(float), moment: int) -> float:
"""
Calculates the nth moment about the mean for a sample (defaults to
the 1st moment). Used to calculate coefficients of skewness and kurtosis.
Usage: lmoment(inlist,moment=1)
Returns: appropriate moment (r) from ... 1/n * SUM((inlist(i)-mean)**r)
"""
if moment == 1:
return 0.0
else:
mn = central_tendency.mean(inlist)
n = len(inlist)
s = 0
for x in inlist:
s = s + (x - mn)**moment
return s / float(n)
with t:
l = list(map(float, range(1, LIST_SIZE)))
lf = list(map(float, range(1, LIST_SIZE)))
lf[2] = 3.0
ll = [l] * 5
print('\nCENTRAL TENDENCY')
print('geometricmean:', central_tendency.geometricmean(l),
central_tendency.geometricmean(lf),
central_tendency.geometricmean(l),
central_tendency.geometricmean(lf))
print('harmonicmean:', central_tendency.harmonicmean(l),
central_tendency.harmonicmean(lf), central_tendency.harmonicmean(l),
central_tendency.harmonicmean(lf))
print('mean:', central_tendency.mean(l), central_tendency.mean(lf),
central_tendency.mean(l), central_tendency.mean(lf))
print('median:', central_tendency.median(l), central_tendency.median(lf),
central_tendency.median(l), central_tendency.median(lf))
print('medianscore:', central_tendency.medianscore(l),
central_tendency.medianscore(lf), central_tendency.medianscore(l),
central_tendency.medianscore(lf))
print('mode:', central_tendency.mode(l), central_tendency.mode(l))
print('\nMOMENTS')
print('moment:', moment.moment(l, 2), moment.moment(lf, 2),
moment.moment(l, 2), moment.moment(lf, 2))
print('variation:', moment.variation(l), moment.variation(l),
moment.variation(lf), moment.variation(lf))
print('skew:', moment.skew(l), moment.skew(lf), moment.skew(l),
moment.skew(lf))
def testMeanResult(self):
self.assertEqual(5.5, central_tendency.mean(sample1))
self.assertTrue((13.78 - central_tendency.mean(sample7)) < 0.01)
def testMeanResult(self):
self.assertEqual(5.5, central_tendency.mean(sample1))
self.assertTrue((13.78 - central_tendency.mean(sample7)) < 0.01)
