def boxcox_llf(lmb, data):
"""The boxcox log-likelihood function.
"""
N = len(data)
y = boxcox(data,lmb)
my = stats.mean(y)
f = (lmb-1)*sum(log(data))
f -= N/2.0*log(sum((y-my)**2.0/N))
return f
def boxcox(x,lmbda=None,alpha=None):
"""Return a positive dataset tranformed by a Box-Cox power transformation.
If lmbda is not None, do the transformation for that value.
If lmbda is None, find the lambda that maximizes the log-likelihood
function and return it as the second output argument.
If alpha is not None, return the 100(1-alpha)% confidence interval for
lambda as the third output argument.
"""
if any(x < 0):
raise ValueError, "Data must be positive."
if lmbda is not None: # single transformation
lmbda = lmbda*(x==x)
y = where(lmbda == 0, log(x), (x**lmbda - 1)/lmbda)
return y
# Otherwise find the lmbda that maximizes the log-likelihood function.
def tempfunc(lmb, data): # function to minimize
return -boxcox_llf(lmb,data)
lmax = optimize.brent(tempfunc, brack=(-2.0,2.0),args=(x,))
y, lmax = boxcox(x, lmax)
if alpha is None:
return y, lmax
# Otherwise find confidence interval
interval = _boxcox_conf_interval(x, lmax, alpha)
return y, lmax, interval
def bartlett(*args):
"""Perform Bartlett test with the null hypothesis that all input samples
have equal variances.
Inputs are sample vectors: bartlett(x,y,z,...)
Outputs: (T, pval)
T -- the Test statistic
pval -- significance level if null is rejected with this value of T
(prob. that null is true but rejected with this p-value.)
Sensitive to departures from normality. The Levene test is
an alternative that is less sensitive to departures from
normality.
References:
http://www.itl.nist.gov/div898/handbook/eda/section3/eda357.htm
Snedecor, George W. and Cochran, William G. (1989), Statistical
Methods, Eighth Edition, Iowa State University Press.
"""
k = len(args)
if k < 2:
raise ValueError, "Must enter at least two input sample vectors."
Ni = zeros(k)
ssq = zeros(k,'d')
for j in range(k):
Ni[j] = len(args[j])
ssq[j] = stats.var(args[j])
Ntot = sum(Ni)
spsq = sum((Ni-1)*ssq)/(1.0*(Ntot-k))
numer = (Ntot*1.0-k)*log(spsq) - sum((Ni-1.0)*log(ssq))
denom = 1.0 + (1.0/(3*(k-1)))*((sum(1.0/(Ni-1.0)))-1.0/(Ntot-k))
T = numer / denom
pval = distributions.chi2.sf(T,k-1) # 1 - cdf
return T, pval
def anderson(x,dist='norm'):
"""Anderson and Darling test for normal, exponential, or Gumbel
(Extreme Value Type I) distribution.
Given samples x, return A2, the Anderson-Darling statistic,
the significance levels in percentages, and the corresponding
critical values.
Critical values provided are for the following significance levels
norm/expon: 15%, 10%, 5%, 2.5%, 1%
Gumbel: 25%, 10%, 5%, 2.5%, 1%
logistic: 25%, 10%, 5%, 2.5%, 1%, 0.5%
If A2 is larger than these critical values then for that significance
level, the hypothesis that the data come from a normal (exponential)
can be rejected.
"""
if not dist in ['norm','expon','gumbel','extreme1','logistic']:
raise ValueError, "Invalid distribution."
y = sort(x)
xbar = stats.mean(x)
N = len(y)
if dist == 'norm':
s = stats.std(x)
w = (y-xbar)/s
z = distributions.norm.cdf(w)
sig = array([15,10,5,2.5,1])
critical = around(_Avals_norm / (1.0 + 4.0/N - 25.0/N/N),3)
elif dist == 'expon':
w = y / xbar
z = distributions.expon.cdf(w)
sig = array([15,10,5,2.5,1])
critical = around(_Avals_expon / (1.0 + 0.6/N),3)
elif dist == 'logistic':
def rootfunc(ab,xj,N):
a,b = ab
tmp = (xj-a)/b
tmp2 = exp(tmp)
val = [sum(1.0/(1+tmp2))-0.5*N,
sum(tmp*(1.0-tmp2)/(1+tmp2))+N]
return array(val)
sol0=array([xbar,stats.std(x)])
sol = optimize.fsolve(rootfunc,sol0,args=(x,N),xtol=1e-5)
w = (y-sol[0])/sol[1]
z = distributions.logistic.cdf(w)
sig = array([25,10,5,2.5,1,0.5])
critical = around(_Avals_logistic / (1.0+0.25/N),3)
else:
def fixedsolve(th,xj,N):
val = stats.sum(xj)*1.0/N
tmp = exp(-xj/th)
term = sum(xj*tmp)
term /= sum(tmp)
return val - term
s = optimize.fixed_point(fixedsolve, 1.0, args=(x,N),xtol=1e-5)
xbar = -s*log(sum(exp(-x/s))*1.0/N)
w = (y-xbar)/s
z = distributions.gumbel_l.cdf(w)
sig = array([25,10,5,2.5,1])
critical = around(_Avals_gumbel / (1.0 + 0.2/sqrt(N)),3)
i = arange(1,N+1)
S = sum((2*i-1.0)/N*(log(z)+log(1-z[::-1])))
A2 = -N-S
return A2, critical, sig