Updated stats

wafo/misc.py

@@ -19,6 +19,8 @@ from time import strftime, gmtime
 from numdifftools.extrapolation import dea3  # @UnusedImport
 from wafo.plotbackend import plotbackend
 from collections import Callable
+import numbers
+
 try:
     from wafo import c_library as clib  # @UnresolvedImport
 except ImportError:
@@ -37,8 +39,28 @@ __all__ = ['now', 'spaceline', 'narg_smallest', 'args_flat', 'is_numlike',
            'betaloge', 'gravity', 'nextpow2', 'discretize', 'polar2cart',
            'cart2polar', 'meshgrid', 'ndgrid', 'trangood', 'tranproc',
            'plot_histgrm', 'num2pistr', 'test_docstrings', 'lazywhere',
+           'lazyselect'
            'piecewise',
-           'valarray']
+           'valarray', 'check_random_state']
+
+
+def check_random_state(seed):
+    """Turn seed into a np.random.RandomState instance
+
+    If seed is None (or np.random), return the RandomState singleton used
+    by np.random.
+    If seed is an int, return a new RandomState instance seeded with seed.
+    If seed is already a RandomState instance, return it.
+    Otherwise raise ValueError.
+    """
+    if seed is None or seed is np.random:
+        return np.random.mtrand._rand
+    if isinstance(seed, (numbers.Integral, np.integer)):
+        return np.random.RandomState(seed)
+    if isinstance(seed, np.random.RandomState):
+        return seed
+    raise ValueError('%r cannot be used to seed a numpy.random.RandomState'
+                     ' instance' % seed)
 
 
 def valarray(shape, value=np.NaN, typecode=None):
@@ -217,6 +239,46 @@ def lazywhere(cond, arrays, f, fillvalue=None, f2=None):
     return out
 
 
+def lazyselect(condlist, choicelist, arrays, default=0):
+    """
+    Mimic `np.select(condlist, choicelist)`.
+
+    Notice it assumes that all `arrays` are of the same shape, or can be
+    broadcasted together.
+
+    All functions in `choicelist` must accept array arguments in the order
+    given in `arrays` and must return an array of the same shape as broadcasted
+    `arrays`.
+
+    Examples
+    --------
+    >>> x = np.arange(6)
+    >>> np.select([x <3, x > 3], [x**2, x**3], default=0)
+    array([  0,   1,   4,   0,  64, 125])
+
+    >>> lazyselect([x < 3, x > 3], [lambda x: x**2, lambda x: x**3], (x,))
+    array([   0.,    1.,    4.,    0.,   64.,  125.])
+
+    >>> a = -np.ones_like(x)
+    >>> lazyselect([x < 3, x > 3],
+    ...             [lambda x, a: x**2, lambda x, a: a * x**3],
+    ...             (x, a))
+    array([   0.,    1.,    4.,    0.,  -64., -125.])
+
+    """
+    arrays = np.broadcast_arrays(*arrays)
+    tcode = np.mintypecode([a.dtype.char for a in arrays])
+    out = valarray(np.shape(arrays[0]), value=default, typecode=tcode)
+    for index in range(len(condlist)):
+        func, cond = choicelist[index], condlist[index]
+        if np.all(cond is False):
+            continue
+        cond, _ = np.broadcast_arrays(cond, arrays[0])
+        temp = tuple(np.extract(cond, arr) for arr in arrays)
+        np.place(out, cond, func(*temp))
+    return out
+
+
 def rotation_matrix(heading, pitch, roll):
     '''
 

wafo/stats/_continuous_distns.py

@@ -15,12 +15,13 @@ from scipy.special import (gammaln as gamln, gamma as gam, boxcox, boxcox1p,
                            inv_boxcox, inv_boxcox1p, erfc, chndtr, chndtrix,
                            log1p, expm1,
                            i0, i1, ndtr as _norm_cdf, log_ndtr as _norm_logcdf)
+# from scipy._lib._numpy_compat import broadcast_to
 
 from numpy import (where, arange, putmask, ravel, shape,
                    log, sqrt, exp, arctanh, tan, sin, arcsin, arctan,
                    tanh, cos, cosh, sinh)
 
-from numpy import polyval, place, extract, asarray, nan, inf, pi
+from numpy import polyval, place, extract, asarray, nan, inf, pi, broadcast_to
 
 import numpy as np
 from scipy.stats.mstats_basic import mode
@@ -35,9 +36,10 @@ from scipy.stats._tukeylambda_stats import (tukeylambda_variance as _tlvar,
 from wafo.stats._distn_infrastructure import (
         rv_continuous, valarray, _skew, _kurtosis, _lazywhere,
         _ncx2_log_pdf, _ncx2_pdf, _ncx2_cdf, get_distribution_names,
+        _lazyselect
         )
 
-from wafo.stats._constants import _XMIN, _EULER, _ZETA3, _XMAX, _LOGXMAX, _EPS
+from wafo.stats._constants import _XMIN, _EULER, _ZETA3, _XMAX, _LOGXMAX
 
 
 ## Kolmogorov-Smirnov one-sided and two-sided test statistics
@@ -215,6 +217,8 @@ class alpha_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _pdf(self, x, a):
         return 1.0/(x**2)/_norm_cdf(a)*_norm_pdf(a-1.0/x)
 
@@ -285,6 +289,8 @@ class arcsine_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _pdf(self, x):
         return 1.0/pi/sqrt(x*(1-x))
 
@@ -535,6 +541,8 @@ class betaprime_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _rvs(self, a, b):
         sz, rndm = self._size, self._random_state
         u1 = gamma.rvs(a, size=sz, random_state=rndm)
@@ -604,10 +612,10 @@ class bradford_gen(rv_continuous):
         return c * exp(-log1p(c * x)) / log1p(c)
 
     def _cdf(self, x, c):
-        return log1p(c * x) / log1p(c)
+        return special.log1p(c * x) / special.log1p(c)
 
     def _ppf(self, q, c):
-        return expm1(q * log1p(c))/c  # ((1.0+c)**q-1)/c
+        return special.expm1(q * special.log1p(c)) / c
 
     def _stats(self, c, moments='mv'):
         k = log1p(c)
@@ -672,6 +680,8 @@ class burr_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _pdf(self, x, c, d):
         return c * d * (x**(-c - 1.0)) * ((1 + x**(-c))**(-d - 1.0))
 
@@ -725,6 +735,8 @@ class burr12_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _pdf(self, x, c, d):
         return np.exp(self._logpdf(x, c, d))
 
@@ -732,7 +744,7 @@ class burr12_gen(rv_continuous):
         return log(c) + log(d) + special.xlogy(c-1, x) + special.xlog1py(-d-1, x**c)
 
     def _cdf(self, x, c, d):
-        return 1 - self._sf(x, c, d)
+        return -special.expm1(self._logsf(x, c, d))
 
     def _logcdf(self, x, c, d):
         return special.log1p(-(1 + x**c)**(-d))
@@ -869,6 +881,7 @@ class chi_gen(rv_continuous):
     %(example)s
 
     """
+
     def _rvs(self, df):
         sz, rndm = self._size, self._random_state
         return sqrt(chi2.rvs(df, size=sz, random_state=rndm))
@@ -1338,6 +1351,8 @@ class fatiguelife_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _rvs(self, c):
         z = self._random_state.standard_normal(self._size)
         x = 0.5*c*z
@@ -1584,6 +1599,7 @@ class frechet_r_gen(rv_continuous):
     %(example)s
 
     """
+
     def _pdf(self, x, c):
         return c*pow(x, c-1)*exp(-pow(x, c))
 
@@ -1900,11 +1916,15 @@ class genextreme_gen(rv_continuous):
         self.a = where(c < 0, 1.0 / min(c, -_XMIN), -inf)
         return where(abs(c) == inf, 0, 1)
 
+    def _loglogcdf(self, x, c):
+        return _lazywhere((x == x) & (c != 0), (x, c),
+                          lambda x, c: special.log1p(-c*x)/c, -x)
+
     def _pdf(self, x, c):
         return exp(self._logpdf(x, c))
 
     def _logpdf(self, x, c):
-        cx = _lazywhere((c != 0)*(x == x), (x, c), lambda x, c: c*x,  0.0)
+        cx = _lazywhere((x == x) & (c != 0), (x, c), lambda x, c: c*x,  0.0)
         logex2 = special.log1p(-cx)
         logpex2 = self._loglogcdf(x, c)
         pex2 = exp(logpex2)
@@ -1914,16 +1934,12 @@ class genextreme_gen(rv_continuous):
         putmask(logpdf, (c == 1) & (x == 1), 0.0)
         return logpdf
 
-    def _cdf(self, x, c):
-        return exp(self._logcdf(x, c))
-
-    def _loglogcdf(self, x, c):
-        return _lazywhere((c != 0) & (x == x), (x, c),
-                          lambda x, c: special.log1p(-c * x)/c, -x)
-
     def _logcdf(self, x, c):
         return -exp(self._loglogcdf(x, c))
 
+    def _cdf(self, x, c):
+        return exp(self._logcdf(x, c))
+
     def _sf(self, x, c):
         return - expm1(self._logcdf(x, c))
 
@@ -2233,7 +2249,7 @@ class gengamma_gen(rv_continuous):
 
         gengamma.pdf(x, a, c) = abs(c) * x**(c*a-1) * exp(-x**c) / gamma(a)
 
-    for ``x > 0``, ``a > 0``, and ``c != 0``.
+    for ``x >= 0``, ``a > 0``, and ``c != 0``.
 
     `gengamma` takes ``a`` and ``c`` as shape parameters.
 
@@ -2443,17 +2459,20 @@ class gumbel_l_gen(rv_continuous):
     def _logpdf(self, x):
         return x - exp(x)
 
+    def _cdf(self, x):
+        return -special.expm1(-exp(x))
+
+    def _ppf(self, q):
+        return log(-special.log1p(-q))
+
     def _logsf(self, x):
         return -exp(x)
 
     def _sf(self, x):
         return exp(-exp(x))
 
-    def _cdf(self, x):
+    def _isf(self, x):
-        return -expm1(-exp(x))
+        return log(-log(x))
-
-    def _ppf(self, q):
-        return log(-log1p(-q))
 
     def _stats(self):
         return -_EULER, pi*pi/6.0, \
@@ -2684,6 +2703,8 @@ class invgamma_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _pdf(self, x, a):
         return exp(self._logpdf(x, a))
 
@@ -2691,10 +2712,16 @@ class invgamma_gen(rv_continuous):
         return (-(a+1) * log(x) - gamln(a) - 1.0/x)
 
     def _cdf(self, x, a):
-        return 1.0 - special.gammainc(a, 1.0/x)
+        return special.gammaincc(a, 1.0 / x)
 
     def _ppf(self, q, a):
-        return 1.0 / special.gammaincinv(a, 1.-q)
+        return 1.0 / special.gammainccinv(a, q)
+
+    def _sf(self, x, a):
+        return special.gammainc(a, 1.0 / x)
+
+    def _isf(self, q, a):
+        return 1.0 / special.gammaincinv(a, q)
 
     def _stats(self, a, moments='mvsk'):
         m1 = _lazywhere(a > 1, (a,), lambda x: 1. / (x - 1.), np.inf)
@@ -2742,6 +2769,8 @@ class invgauss_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _rvs(self, mu):
         return self._random_state.wald(mu, 1.0, size=self._size)
 
@@ -2788,6 +2817,8 @@ class invweibull_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _pdf(self, x, c):
         xc1 = np.power(x, -c - 1.0)
         xc2 = np.power(x, -c)
@@ -2833,6 +2864,8 @@ class johnsonsb_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _argcheck(self, a, b):
         return (b > 0) & (a == a)
 
@@ -2915,7 +2948,10 @@ class laplace_gen(rv_continuous):
         return where(x > 0, 1.0-0.5*exp(-x), 0.5*exp(x))
 
     def _ppf(self, q):
-        return where(q > 0.5, -log(2) - log1p(-q), log(2 * q))
+        return where(q > 0.5, -log(2*(1-q)), log(2*q))
+
+    def _isf(self, q):
+        return where(q < 0.5, -log(2*q), log(2*(1-q)))
 
     def _stats(self):
         return 0, 2, 0, 3
@@ -2949,6 +2985,8 @@ class levy_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _pdf(self, x):
         return 1 / sqrt(2*pi*x) / x * exp(-1/(2*x))
 
@@ -2990,6 +3028,8 @@ class levy_l_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _pdf(self, x):
         ax = abs(x)
         return 1/sqrt(2*pi*ax)/ax*exp(-1/(2*ax))
@@ -3026,29 +3066,47 @@ class levy_stable_gen(rv_continuous):
     %(example)s
 
     """
+
     def _rvs(self, alpha, beta):
-        sz = self._size
-        TH = uniform.rvs(loc=-pi/2.0, scale=pi, size=sz)
-        W = expon.rvs(size=sz)
-        if alpha == 1:
-            return 2/pi*(pi/2+beta*TH)*tan(TH)-beta*log((pi/2*W*cos(TH))/(pi/2+beta*TH))
 
-        ialpha = 1.0/alpha
+        def alpha1func(alpha, beta, TH, aTH, bTH, cosTH, tanTH, W):
-        aTH = alpha*TH
+            return (2/pi*(pi/2 + bTH)*tanTH -
-        if beta == 0:
+                    beta*log((pi/2*W*cosTH)/(pi/2 + bTH)))
-            return W/(cos(TH)/tan(aTH)+sin(TH))*((cos(aTH)+sin(aTH)*tan(TH))/W)**ialpha
+
+        def beta0func(alpha, beta, TH, aTH, bTH, cosTH, tanTH, W):
+            return (W/(cosTH/tan(aTH) + sin(TH)) *
+                    ((cos(aTH) + sin(aTH)*tanTH)/W)**(1.0/alpha))
 
+        def otherwise(alpha, beta, TH, aTH, bTH, cosTH, tanTH, W):
+            # alpha is not 1 and beta is not 0
             val0 = beta*tan(pi*alpha/2)
             th0 = arctan(val0)/alpha
-        val3 = W/(cos(TH)/tan(alpha*(th0+TH))+sin(TH))
+            val3 = W/(cosTH/tan(alpha*(th0 + TH)) + sin(TH))
-        res3 = val3*((cos(aTH)+sin(aTH)*tan(TH)-val0*(sin(aTH)-cos(aTH)*tan(TH)))/W)**ialpha
+            res3 = val3*((cos(aTH) + sin(aTH)*tanTH - val0*(sin(aTH) -
+                         cos(aTH)*tanTH))/W)**(1.0/alpha)
             return res3
 
+        def alphanot1func(alpha, beta, TH, aTH, bTH, cosTH, tanTH, W):
+            res = _lazywhere(beta == 0,
+                             (alpha, beta, TH, aTH, bTH, cosTH, tanTH, W),
+                             beta0func, f2=otherwise)
+            return res
+
+        sz = self._size
+        alpha = broadcast_to(alpha, sz)
+        beta = broadcast_to(beta, sz)
+        TH = uniform.rvs(loc=-pi/2.0, scale=pi, size=sz,
+                         random_state=self._random_state)
+        W = expon.rvs(size=sz, random_state=self._random_state)
+        aTH = alpha*TH
+        bTH = beta*TH
+        cosTH = cos(TH)
+        tanTH = tan(TH)
+        res = _lazywhere(alpha == 1, (alpha, beta, TH, aTH, bTH, cosTH, tanTH, W),
+                         alpha1func, f2=alphanot1func)
+        return res
+
     def _argcheck(self, alpha, beta):
-        if beta == -1:
-            self.b = 0.0
-        elif beta == 1:
-            self.a = 0.0
         return (alpha > 0) & (alpha <= 2) & (beta <= 1) & (beta >= -1)
 
     def _pdf(self, x, alpha, beta):
@@ -3087,10 +3145,13 @@ class logistic_gen(rv_continuous):
         return special.expit(x)
 
     def _ppf(self, q):
-        return -log1p(-q) + log(q)
+        return special.logit(q)
+
+    def _sf(self, x):
+        return special.expit(-x)
 
     def _isf(self, q):
-        return log1p(-q) - log(q)
+        return -special.logit(q)
 
     def _stats(self):
         return 0, pi*pi/3.0, 0, 6.0/5.0
@@ -3222,6 +3283,8 @@ class lognorm_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _rvs(self, s):
         return exp(s * self._random_state.standard_normal(self._size))
 
@@ -3285,6 +3348,8 @@ class gilbrat_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _rvs(self):
         return exp(self._random_state.standard_normal(self._size))
 
@@ -3397,6 +3462,306 @@ class mielke_gen(rv_continuous):
 mielke = mielke_gen(a=0.0, name='mielke')
 
 
+class kappa4_gen(rv_continuous):
+    """Kappa 4 parameter distribution.
+
+    %(before_notes)s
+
+    Notes
+    -----
+    The probability density function for kappa4 is::
+
+        kappa4.pdf(x, h, k) = (1.0 - k*x)**(1.0/k - 1.0)*
+                              (1.0 - h*(1.0 - k*x)**(1.0/k))**(1.0/h-1)
+
+    if ``h`` and ``k`` are not equal to 0.
+
+    If ``h`` or ``k`` are zero then the pdf can be simplified:
+
+    h = 0 and k != 0::
+
+        kappa4.pdf(x, h, k) = (1.0 - k*x)**(1.0/k - 1.0)*
+                              exp(-(1.0 - k*x)**(1.0/k))
+
+    h != 0 and k = 0::
+
+        kappa4.pdf(x, h, k) = exp(-x)*(1.0 - h*exp(-x))**(1.0/h - 1.0)
+
+    h = 0 and k = 0::
+
+        kappa4.pdf(x, h, k) = exp(-x)*exp(-exp(-x))
+
+    kappa4 takes ``h`` and ``k`` as shape parameters.
+
+    The kappa4 distribution returns other distributions when certain
+    ``h`` and ``k`` values are used.
+
+    +------+-------------+----------------+------------------+
+    | h    | k=0.0       | k=1.0          | -inf<=k<=inf     |
+    +======+=============+================+==================+
+    | -1.0 | Logistic    |                | Generalized      |
+    |      |             |                | Logistic(1)      |
+    |      |             |                |                  |
+    |      | logistic(x) |                |                  |
+    +------+-------------+----------------+------------------+
+    |  0.0 | Gumbel      | Reverse        | Generalized      |
+    |      |             | Exponential(2) | Extreme Value    |
+    |      |             |                |                  |
+    |      | gumbel_r(x) |                | genextreme(x, k) |
+    +------+-------------+----------------+------------------+
+    |  1.0 | Exponential | Uniform        | Generalized      |
+    |      |             |                | Pareto           |
+    |      |             |                |                  |
+    |      | expon(x)    | uniform(x)     | genpareto(x, -k) |
+    +------+-------------+----------------+------------------+
+
+    (1) There are at least five generalized logistic distributions.
+        Four are described here:
+        https://en.wikipedia.org/wiki/Generalized_logistic_distribution
+        The "fifth" one is the one kappa4 should match which currently
+        isn't implemented in scipy:
+        https://en.wikipedia.org/wiki/Talk:Generalized_logistic_distribution
+        http://www.mathwave.com/help/easyfit/html/analyses/distributions/gen_logistic.html
+    (2) This distribution is currently not in scipy.
+
+    References
+    ----------
+    J.C. Finney, "Optimization of a Skewed Logistic Distribution With Respect
+    to the Kolmogorov-Smirnov Test", A Dissertation Submitted to the Graduate
+    Faculty of the Louisiana State University and Agricultural and Mechanical
+    College, (August, 2004),
+    http://etd.lsu.edu/docs/available/etd-05182004-144851/unrestricted/Finney_dis.pdf
+
+    J.R.M. Hosking, "The four-parameter kappa distribution". IBM J. Res.
+    Develop. 38 (3), 25 1-258 (1994).
+
+    B. Kumphon, A. Kaew-Man, P. Seenoi, "A Rainfall Distribution for the Lampao
+    Site in the Chi River Basin, Thailand", Journal of Water Resource and
+    Protection, vol. 4, 866-869, (2012).
+    http://file.scirp.org/pdf/JWARP20121000009_14676002.pdf
+
+    C. Winchester, "On Estimation of the Four-Parameter Kappa Distribution", A
+    Thesis Submitted to Dalhousie University, Halifax, Nova Scotia, (March
+    2000).
+    http://www.nlc-bnc.ca/obj/s4/f2/dsk2/ftp01/MQ57336.pdf
+
+    %(after_notes)s
+
+    %(example)s
+
+    """
+    def _argcheck(self, h, k):
+        condlist = [np.logical_and(h > 0, k > 0),
+                    np.logical_and(h > 0, k == 0),
+                    np.logical_and(h > 0, k < 0),
+                    np.logical_and(h <= 0, k > 0),
+                    np.logical_and(h <= 0, k == 0),
+                    np.logical_and(h <= 0, k < 0)]
+
+        def f0(h, k):
+            return (1.0 - h**(-k))/k
+
+        def f1(h, k):
+            return log(h)
+
+        def f3(h, k):
+            a = np.empty(shape(h))
+            a[:] = -inf
+            return a
+
+        def f5(h, k):
+            return 1.0/k
+
+        self.a = _lazyselect(condlist,
+                             [f0, f1, f0, f3, f3, f5],
+                             [h, k],
+                             default=nan)
+
+        def f00(h, k):
+            return 1.0/k
+
+        def f11(h, k):
+            a = np.empty(shape(h))
+            a[:] = inf
+            return a
+
+        self.b = _lazyselect(condlist,
+                             [f00, f11, f11, f00, f11, f11],
+                             [h, k],
+                             default=nan)
+        return (h == h)
+
+    def _pdf(self, x, h, k):
+        return exp(self._logpdf(x, h, k))
+
+    def _logpdf(self, x, h, k):
+        condlist = [np.logical_and(h != 0, k != 0),
+                    np.logical_and(h == 0, k != 0),
+                    np.logical_and(h != 0, k == 0),
+                    np.logical_and(h == 0, k == 0)]
+
+        def f0(x, h, k):
+            '''pdf = (1.0 - k*x)**(1.0/k - 1.0)*(
+                      1.0 - h*(1.0 - k*x)**(1.0/k))**(1.0/h-1.0)
+               logpdf = ...
+            '''
+            return special.xlog1py(1.0/k-1.0,
+                                   -k*x
+                                   ) + special.xlog1py(1.0/h-1.0,
+                                                       -h*(1.0-k*x)**(1.0/k))
+
+        def f1(x, h, k):
+            '''pdf = (1.0 - k*x)**(1.0/k - 1.0)*exp(-(
+                      1.0 - k*x)**(1.0/k))
+               logpdf = ...
+            '''
+            return special.xlog1py(1.0/k-1.0,-k*x)-(1.0-k*x)**(1.0/k)
+
+        def f2(x, h, k):
+            '''pdf = exp(-x)*(1.0 - h*exp(-x))**(1.0/h - 1.0)
+               logpdf = ...
+            '''
+            return -x + special.xlog1py(1.0/h-1.0, -h*exp(-x))
+
+        def f3(x, h, k):
+            '''pdf = exp(-x-exp(-x))
+               logpdf = ...
+            '''
+            return -x-exp(-x)
+
+        return _lazyselect(condlist,
+                           [f0, f1, f2, f3],
+                           [x, h, k],
+                           default=nan)
+
+    def _cdf(self, x, h, k):
+        return exp(self._logcdf(x, h, k))
+
+    def _logcdf(self, x, h, k):
+        condlist = [np.logical_and(h != 0, k != 0),
+                    np.logical_and(h == 0, k != 0),
+                    np.logical_and(h != 0, k == 0),
+                    np.logical_and(h == 0, k == 0)]
+
+        def f0(x, h, k):
+            '''cdf = (1.0 - h*(1.0 - k*x)**(1.0/k))**(1.0/h)
+               logcdf = ...
+            '''
+            return (1.0/h)*special.log1p(-h*(1.0-k*x)**(1.0/k))
+
+        def f1(x, h, k):
+            '''cdf = exp(-(1.0 - k*x)**(1.0/k))
+               logcdf = ...
+            '''
+            return -(1.0 - k*x)**(1.0/k)
+
+        def f2(x, h, k):
+            '''cdf = (1.0 - h*exp(-x))**(1.0/h)
+               logcdf = ...
+            '''
+            return (1.0/h)*special.log1p(-h*exp(-x))
+
+        def f3(x, h, k):
+            '''cdf = exp(-exp(-x))
+               logcdf = ...
+            '''
+            return -exp(-x)
+
+        return _lazyselect(condlist,
+                           [f0, f1, f2, f3],
+                           [x, h, k],
+                           default=nan)
+
+    def _ppf(self, q, h, k):
+        condlist = [np.logical_and(h != 0, k != 0),
+                    np.logical_and(h == 0, k != 0),
+                    np.logical_and(h != 0, k == 0),
+                    np.logical_and(h == 0, k == 0)]
+
+        def f0(q, h, k):
+            return 1.0/k*(1.0 - ((1.0 - (q**h))/h)**k)
+
+        def f1(q, h, k):
+            return 1.0/k*(1.0 - (-log(q))**k)
+
+        def f2(q, h, k):
+            '''ppf = -log((1.0 - (q**h))/h)
+            '''
+            return -special.log1p(-(q**h)) + log(h)
+
+        def f3(q, h, k):
+            return -log(-log(q))
+
+        return _lazyselect(condlist,
+                           [f0, f1, f2, f3],
+                           [q, h, k],
+                           default=nan)
+
+    def _stats(self, h, k):
+        if h >= 0 and k >= 0:
+            maxr = 5
+        elif h < 0 and k >= 0:
+            maxr = int(-1.0/h*k)
+        elif k < 0:
+            maxr = int(-1.0/k)
+        else:
+            maxr = 5
+
+        outputs = [None if r < maxr else nan for r in range(1, 5)]
+        return outputs[:]
+kappa4 = kappa4_gen(name='kappa4')
+
+
+class kappa3_gen(rv_continuous):
+    """Kappa 3 parameter distribution.
+
+    %(before_notes)s
+
+    Notes
+    -----
+    The probability density function for `kappa` is::
+
+        kappa3.pdf(x, a) =
+            a*[a + x**a]**(-(a + 1)/a),     for ``x > 0``
+            0.0,                            for ``x <= 0``
+
+    `kappa3` takes ``a`` as a shape parameter and ``a > 0``.
+
+    References
+    ----------
+    P.W. Mielke and E.S. Johnson, "Three-Parameter Kappa Distribution Maximum
+    Likelihood and Likelihood Ratio Tests", Methods in Weather Research,
+    701-707, (September, 1973),
+    http://docs.lib.noaa.gov/rescue/mwr/101/mwr-101-09-0701.pdf
+
+    B. Kumphon, "Maximum Entropy and Maximum Likelihood Estimation for the
+    Three-Parameter Kappa Distribution", Open Journal of Statistics, vol 2,
+    415-419 (2012)
+    http://file.scirp.org/pdf/OJS20120400011_95789012.pdf
+
+    %(after_notes)s
+
+    %(example)s
+
+    """
+    def _argcheck(self, a):
+        return a > 0
+
+    def _pdf(self, x, a):
+        return a*(a + x**a)**(-1.0/a-1)
+
+    def _cdf(self, x, a):
+        return x*(a + x**a)**(-1.0/a)
+
+    def _ppf(self, q, a):
+        return (a/(q**-a - 1.0))**(1.0/a)
+
+    def _stats(self, a):
+        outputs = [None if i < a else nan for i in range(1, 5)]
+        return outputs[:]
+kappa3 = kappa3_gen(a=0.0, name='kappa3')
+
+
 class nakagami_gen(rv_continuous):
     """A Nakagami continuous random variable.
 
@@ -3881,6 +4246,7 @@ class pearson3_gen(rv_continuous):
         ans, x, skew = np.broadcast_arrays([1.0], x, skew)
         ans = ans.copy()
 
+        # mask is True where skew is small enough to use the normal approx.
         mask = np.absolute(skew) < norm2pearson_transition
         invmask = ~mask
 
@@ -3940,13 +4306,18 @@ class pearson3_gen(rv_continuous):
         return ans
 
     def _rvs(self, skew):
+        skew = broadcast_to(skew, self._size)
         ans, x, transx, skew, mask, invmask, beta, alpha, zeta = (
             self._preprocess([0], skew))
-        if mask[0]:
+
-            return self._random_state.standard_normal(self._size)
+        nsmall = mask.sum()
-        ans = self._random_state.standard_gamma(alpha, self._size)/beta + zeta
+        nbig = mask.size - nsmall
-        if ans.size == 1:
+        ans[mask] = self._random_state.standard_normal(nsmall)
-            return ans[0]
+        ans[invmask] = (self._random_state.standard_gamma(alpha, nbig)/beta +
+                        zeta)
+
+        if self._size == ():
+            ans = ans[0]
         return ans
 
     def _ppf(self, q, skew):
@@ -4028,6 +4399,8 @@ class powerlognorm_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _pdf(self, x, c, s):
         return (c/(x*s) * _norm_pdf(log(x)/s) *
                 pow(_norm_cdf(-log(x)/s), c*1.0-1.0))
@@ -4134,6 +4507,8 @@ class rayleigh_gen(rv_continuous):
     %(example)s
 
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _rvs(self):
         return chi.rvs(2, size=self._size, random_state=self._random_state)
 
@@ -4141,9 +4516,7 @@ class rayleigh_gen(rv_continuous):
         return exp(self._logpdf(r))
 
     def _logpdf(self, r):
-        rr2 = r * r / 2.0
+        return log(r) - 0.5 * r * r
-        return _lazywhere(rr2 != inf, (r, rr2), lambda r, rr2: log(r) - rr2,
-                          -rr2)
 
     def _cdf(self, r):
         return -special.expm1(-0.5 * r**2)
@@ -4152,10 +4525,10 @@ class rayleigh_gen(rv_continuous):
         return sqrt(-2 * special.log1p(-q))
 
     def _sf(self, r):
-        return exp(-0.5 * r**2)
+        return exp(self._logsf(r))
 
     def _logsf(self, r):
-        return -0.5 * r**2
+        return -0.5 * r * r
 
     def _isf(self, q):
         return sqrt(-2 * log(q))
@@ -4290,6 +4663,7 @@ class reciprocal_gen(rv_continuous):
         return 0.5*log(a*b)+log(log(b/a))
 reciprocal = reciprocal_gen(name="reciprocal")
 
+
 class rice_gen(rv_continuous):
     """A Rice continuous random variable.
 
@@ -4321,8 +4695,8 @@ class rice_gen(rv_continuous):
 
     def _rvs(self, b):
         # http://en.wikipedia.org/wiki/Rice_distribution
-        sz = self._size if self._size else 1
+        t = b/np.sqrt(2) + self._random_state.standard_normal(size=(2,) +
-        t = b/np.sqrt(2) + self._random_state.standard_normal(size=(2, sz))
+                                                              self._size)
         return np.sqrt((t*t).sum(axis=0))
 
     def _cdf(self, x, b):
@@ -4653,10 +5027,9 @@ class truncnorm_gen(rv_continuous):
         self._na = _norm_cdf(a)
         self._sb = _norm_sf(b)
         self._sa = _norm_sf(a)
-        if self.a > 0:
+        self._delta = np.where(self.a > 0,
-            self._delta = -(self._sb - self._sa)
+                               -(self._sb - self._sa),
-        else:
+                               self._nb - self._na)
-            self._delta = self._nb - self._na
         self._logdelta = log(self._delta)
         return (a != b)
 
@@ -4670,10 +5043,11 @@ class truncnorm_gen(rv_continuous):
         return (_norm_cdf(x) - self._na) / self._delta
 
     def _ppf(self, q, a, b):
-        if self.a > 0:
+        # XXX Use _lazywhere...
-            return _norm_isf(q*self._sb + self._sa*(1.0-q))
+        ppf = np.where(self.a > 0,
-        else:
+                       _norm_isf(q*self._sb + self._sa*(1.0-q)),
-            return _norm_ppf(q*self._nb + self._na*(1.0-q))
+                       _norm_ppf(q*self._nb + self._na*(1.0-q)))
+        return ppf
 
     def _stats(self, a, b):
         nA, nB = self._na, self._nb
@@ -4830,6 +5204,8 @@ class wald_gen(invgauss_gen):
 
     %(example)s
     """
+    _support_mask = rv_continuous._open_support_mask
+
     def _rvs(self):
         return self._random_state.wald(1.0, 1.0, size=self._size)
 

wafo/stats/_distn_infrastructure.py

@@ -1,11 +1,12 @@
 from __future__ import absolute_import
 from scipy.stats._distn_infrastructure import *  # @UnusedWildImport
 from scipy.stats._distn_infrastructure import (_skew,  # @UnusedImport
-    _kurtosis, _lazywhere, _ncx2_log_pdf,  # @IgnorePep8 @UnusedImport
+    _kurtosis,  _ncx2_log_pdf,  # @IgnorePep8 @UnusedImport
     _ncx2_pdf,  _ncx2_cdf)  # @UnusedImport @IgnorePep8
 from .estimation import FitDistribution
 from ._constants import _XMAX
-
+from wafo.misc import lazyselect as _lazyselect
+from wafo.misc import lazywhere as _lazywhere
 
 _doc_default_example = """\
 Examples
@@ -328,7 +329,7 @@ def nlogps(self, theta, x):
     return T
 
 
-def _penalized_nnlf(self, theta, x):
+def _penalized_nnlf(self, theta, x, penalty=None):
     ''' Return negative loglikelihood function,
     i.e., - sum (log pdf(x, theta), axis=0)
        where theta are the parameters (including loc and scale)
@@ -352,6 +353,7 @@ def _penalized_nnlf(self, theta, x):
     Nbad += np.sum(~finite_logpdf, axis=0)
     logscale = N * log(scale)
     if Nbad > 0:
+        if penalty is None:
             penalty = Nbad * log(_XMAX) * 100
         return -np.sum(logpdf[finite_logpdf], axis=0) + penalty + logscale
     return -np.sum(logpdf, axis=0) + logscale
@@ -597,6 +599,14 @@ def fit2(self, data, *args, **kwds):
     return FitDistribution(self, data, args, **kwds)
 
 
+def _support_mask(self, x):
+    return (self.a <= x) & (x <= self.b)
+
+
+def _open_support_mask(self, x):
+    return (self.a < x) & (x < self.b)
+
+
 rv_generic.freeze = freeze
 rv_discrete.freeze = freeze
 rv_continuous.freeze = freeze
@@ -607,3 +617,5 @@ rv_continuous._penalized_nnlf = _penalized_nnlf
 rv_continuous._reduce_func = _reduce_func
 rv_continuous.fit = fit
 rv_continuous.fit2 = fit2
+rv_continuous._support_mask = _support_mask
+rv_continuous._open_support_mask = _open_support_mask

wafo/stats/estimation.py

@@ -188,8 +188,355 @@ def norm_ppf(q):
     return special.ndtri(q)
 
 
-# internal class to profile parameters of a given distribution
 class Profile(object):
+    ''' Profile Log- likelihood or Product Spacing-function.
+            which can be used for constructing confidence interval for
+            phat[i].
+
+    Parameters
+    ----------
+    fit_dist : FitDistribution object
+        with ML or MPS estimated distribution parameters.
+    i : scalar integer
+        defining which distribution parameter to keep fixed in the
+        profiling process (default first non-fixed parameter)
+    pmin, pmax : real scalars
+        Interval for either the parameter, phat[i] used in the
+        optimization of the profile function (default is based on the
+        100*(1-alpha)% confidence interval computed with the delta method.)
+    n : scalar integer
+        Max number of points used in Lp (default 100)
+    alpha : real scalar
+        confidence coefficent (default 0.05)
+    Returns
+    -------
+    Lp : Profile log-likelihood function with parameters phat given
+        the data and phat[i],  i.e.,
+            Lp = max(log(f(phat|data,phat[i]))),
+
+    Member methods
+    -------------
+    plot() : Plot profile function with 100(1-alpha)% confidence interval
+    get_bounds() : Return 100(1-alpha)% confidence interval
+
+    Member variables
+    ----------------
+    fit_dist : FitDistribution data object.
+    data : profile function values
+    args : profile function arguments
+    alpha : confidence coefficient
+    Lmax : Maximum value of profile function
+    alpha_cross_level :
+
+    PROFILE is a utility function for making inferences either on a particular
+    component of the vector phat or the quantile, x, or the probability, SF.
+    This is usually more accurate than using the delta method assuming
+    asymptotic normality of the ML estimator or the MPS estimator.
+
+    Examples
+    --------
+    # MLE
+    >>> import wafo.stats as ws
+    >>> R = ws.weibull_min.rvs(1,size=100);
+    >>> phat = FitDistribution(ws.weibull_min, R, 1, scale=1, floc=0.0)
+
+    # Better CI for phat.par[i=0]
+    >>> Lp = Profile(phat, i=0)
+    >>> Lp.plot()
+    >>> phat_ci = Lp.get_bounds(alpha=0.1)
+
+    '''
+
+    def __init__(self, fit_dist, i=None, pmin=None, pmax=None, n=100,
+                 alpha=0.05):
+
+        method = fit_dist.method.lower()
+        self.fit_dist = fit_dist
+        self._set_indexes(fit_dist, i)
+
+        self.pmin = pmin
+        self.pmax = pmax
+        self.n = n
+        self.alpha = alpha
+
+        self.data = None
+        self.args = None
+        self.xlabel = 'phat[{}]'.format(np.ravel(self.i_fixed)[0])
+        like_txt = 'likelihood' if method == 'ml' else 'product spacing'
+        self.ylabel = 'Profile log' + like_txt
+        self.title = '{:g}% CI for {:s} params'.format(100*(1.0 - self.alpha),
+                                                       fit_dist.dist.name)
+
+        Lmax = self._loglike_max(fit_dist, method)
+        self.Lmax = Lmax
+        self.alpha_Lrange = 0.5 * chi2isf(self.alpha, 1)
+        self.alpha_cross_level = Lmax - self.alpha_Lrange
+
+        phatv = fit_dist.par.copy()
+        self._set_profile(phatv)
+
+    def _loglike_max(self, fit_dist, method):
+        if method.startswith('ml'):
+            Lmax = fit_dist.LLmax
+        elif method.startswith('mps'):
+            Lmax = fit_dist.LPSmax
+        else:
+            raise ValueError(
+                "PROFILE is only valid for ML- or MPS- estimators")
+        return Lmax
+
+    def _set_indexes(self, fit_dist, i):
+        if i is None:
+            i = self._default_i_fixed(fit_dist)
+        self.i_fixed = np.atleast_1d(i)
+        isnotfixed = self._get_not_fixed_mask(fit_dist)
+        self.i_notfixed = nonzero(isnotfixed)
+        self._check_i_fixed()
+        isfree = isnotfixed
+        isfree[self.i_fixed] = False
+        self.i_free = nonzero(isfree)
+
+    def _default_i_fixed(self, fit_dist):
+        try:
+            i0 = 1 - np.isfinite(fit_dist.par_fix).argmax()
+        except:
+            i0 = 0
+        return i0
+
+    def _get_not_fixed_mask(self, fit_dist):
+        if fit_dist.par_fix is None:
+            isnotfixed = np.ones(fit_dist.par.shape, dtype=bool)
+        else:
+            isnotfixed = 1 - np.isfinite(fit_dist.par_fix)
+        return isnotfixed
+
+    def _check_i_fixed(self):
+        if self.i_fixed not in self.i_notfixed:
+            raise IndexError("Index i must be equal to an index to one of " +
+                             "the free parameters.")
+
+    def _local_link(self, fix_par, par):
+        return fix_par
+
+    def _correct_Lmax(self, Lmax, free_par, fix_par):
+
+        if Lmax > self.Lmax:  # foundNewphat = True
+
+            dL = self.Lmax - Lmax
+            self.alpha_cross_level -= dL
+            self.Lmax = Lmax
+            par = self._par.copy()
+            par[self.i_free] = free_par
+            par[self.i_fixed] = fix_par
+            self.best_par = par
+            self._par = par
+            warnings.warn(
+                'The fitted parameters does not provide the optimum fit. ' +
+                'Something wrong with fit (par = {})'.format(str(par)))
+
+    def _profile_optimum(self, phatfree0, p_opt):
+        phatfree = optimize.fmin(
+            self._profile_fun, phatfree0, args=(p_opt,), disp=0)
+        Lmax = -self._profile_fun(phatfree, p_opt)
+        self._correct_Lmax(Lmax, phatfree, p_opt)
+        return Lmax, phatfree
+
+    def _set_profile(self, phat):
+        self._par = phat.copy()
+
+        # Set up variable to profile and _local_link function
+        p_opt = self._par[self.i_fixed]
+        phatfree = self._par[self.i_free].copy()
+
+        pvec = self._get_pvec(phatfree, p_opt)
+
+        self.data = np.ones_like(pvec) * nan
+        k1 = (pvec >= p_opt).argmax()
+
+        for size, step in ((-1, -1), (pvec.size, 1)):
+            phatfree = self._par[self.i_free].copy()
+            for ix in range(k1, size, step):
+                Lmax, phatfree = self._profile_optimum(phatfree, pvec[ix])
+                self.data[ix] = Lmax
+                if ix != k1 and self.data[ix] < self.alpha_cross_level:
+                    break
+        np.putmask(pvec, np.isnan(self.data), nan)
+        self.args = pvec
+
+        self._prettify_profile()
+
+    def _prettify_profile(self):
+        pvec = self.args
+        ix = nonzero(np.isfinite(pvec))
+        self.data = self.data[ix]
+        self.args = pvec[ix]
+        cond = self.data == -np.inf
+        if any(cond):
+            ind, = cond.nonzero()
+            self.data.put(ind, floatinfo.min / 2.0)
+            ind1 = np.where(ind == 0, ind, ind - 1)
+            cl = self.alpha_cross_level - self.alpha_Lrange / 2.0
+            t0 = ecross(self.args, self.data, ind1, cl)
+            self.data.put(ind, cl)
+            self.args.put(ind, t0)
+
+    def _get_variance(self):
+        return self.fit_dist.par_cov[self.i_fixed, :][:, self.i_fixed]
+
+    def _approx_p_min_max(self, p_opt):
+        pvar = self._get_variance()
+        if pvar <= 1e-5 or np.isnan(pvar):
+            pvar = max(abs(p_opt) * 0.5, 0.2)
+        pvar = max(pvar, 0.1)
+        p_crit = -norm_ppf(self.alpha / 2.0) * sqrt(np.ravel(pvar)) * 1.5
+        return p_opt - p_crit * 5, p_opt + p_crit * 5
+
+    def _p_min_max(self, phatfree0, p_opt):
+        p_low, p_up = self._approx_p_min_max(p_opt)
+        pmin, pmax = self.pmin, self.pmax
+        if pmin is None:
+            pmin = self._search_pmin(phatfree0, p_low, p_opt)
+        if pmax is None:
+            pmax = self._search_pmax(phatfree0, p_up, p_opt)
+        return pmin, pmax
+
+    def _adaptive_pvec(self, p_opt, pmin, pmax):
+        p_crit_low = (p_opt - pmin) / 5
+        p_crit_up = (pmax - p_opt) / 5
+        n4 = np.floor(self.n / 4.0)
+        a, b = p_opt - p_crit_low, p_opt + p_crit_up
+        pvec1 = np.linspace(pmin, a, n4 + 1)
+        pvec2 = np.linspace(a, b, self.n - 2 * n4)
+        pvec3 = np.linspace(b, pmax, n4 + 1)
+        pvec = np.unique(np.hstack((pvec1, p_opt, pvec2, pvec3)))
+        return pvec
+
+    def _get_pvec(self, phatfree0, p_opt):
+        ''' return proper interval for the variable to profile
+        '''
+        if self.pmin is None or self.pmax is None:
+            pmin, pmax = self._p_min_max(phatfree0, p_opt)
+            return self._adaptive_pvec(p_opt, pmin, pmax)
+        return np.linspace(self.pmin, self.pmax, self.n)
+
+    def _search_pmin(self, phatfree0, p_min0, p_opt):
+        phatfree = phatfree0.copy()
+
+        dp = (p_opt - p_min0)/40
+        if dp < 1e-2:
+            dp = 0.1
+        p_min_opt = p_opt - dp
+        Lmax, phatfree = self._profile_optimum(phatfree, p_opt)
+        for _j in range(50):
+            p_min = p_opt - dp
+            Lmax, phatfree = self._profile_optimum(phatfree, p_min)
+            if np.isnan(Lmax):
+                dp *= 0.33
+            elif Lmax < self.alpha_cross_level - self.alpha_Lrange * 5:
+                p_min_opt = p_min
+                dp *= 0.33
+            elif Lmax < self.alpha_cross_level:
+                p_min_opt = p_min
+                break
+            else:
+                dp *= 1.67
+        return p_min_opt
+
+    def _search_pmax(self, phatfree0, p_max0, p_opt):
+        phatfree = phatfree0.copy()
+
+        dp = (p_max0 - p_opt)/40
+        if dp < 1e-2:
+            dp = 0.1
+        p_max_opt = p_opt + dp
+        Lmax, phatfree = self._profile_optimum(phatfree, p_opt)
+        for _j in range(50):
+            p_max = p_opt + dp
+            Lmax, phatfree = self._profile_optimum(phatfree, p_max)
+            if np.isnan(Lmax):
+                dp *= 0.33
+            elif Lmax < self.alpha_cross_level - self.alpha_Lrange * 2:
+                p_max_opt = p_max
+                dp *= 0.33
+            elif Lmax < self.alpha_cross_level:
+                p_max_opt = p_max
+                break
+            else:
+                dp *= 1.67
+        return p_max_opt
+
+    def _profile_fun(self, free_par, fix_par):
+        ''' Return negative of loglike or logps function
+
+           free_par - vector of free parameters
+           fix_par  - fixed parameter, i.e., either quantile (return level),
+                      probability (return period) or distribution parameter
+        '''
+        par = self._par.copy()
+        par[self.i_free] = free_par
+        # _local_link: connects fixed quantile or probability with fixed
+        # distribution parameter
+        par[self.i_fixed] = self._local_link(fix_par, par)
+        return self.fit_dist.fitfun(par)
+
+    def get_bounds(self, alpha=0.05):
+        '''Return confidence interval for profiled parameter
+        '''
+        if alpha < self.alpha:
+            warnings.warn(
+                'Might not be able to return CI with alpha less than %g' %
+                self.alpha)
+        cross_level = self.Lmax - 0.5 * chi2isf(alpha, 1)
+        ind = findcross(self.data, cross_level)
+        N = len(ind)
+        if N == 0:
+            warnings.warn('''Number of crossings is zero, i.e.,
+            upper and lower bound is not found!''')
+            CI = (self.pmin, self.pmax)
+
+        elif N == 1:
+            x0 = ecross(self.args, self.data, ind, cross_level)
+            isUpcrossing = self.data[ind] > self.data[ind + 1]
+            if isUpcrossing:
+                CI = (x0, self.pmax)
+                warnings.warn('Upper bound is larger')
+            else:
+                CI = (self.pmin, x0)
+                warnings.warn('Lower bound is smaller')
+
+        elif N == 2:
+            CI = ecross(self.args, self.data, ind, cross_level)
+        else:
+            warnings.warn('Number of crossings too large! Something is wrong!')
+            CI = ecross(self.args, self.data, ind[[0, -1]], cross_level)
+        return CI
+
+    def plot(self, axis=None):
+        ''' Plot profile function with 100(1-alpha)% CI
+        '''
+        if axis is None:
+            axis = plotbackend.gca()
+
+        p_ci = self.get_bounds(self.alpha)
+        axis.plot(
+            self.args, self.data,
+            p_ci, [self.Lmax, ] * 2, 'r--',
+            p_ci, [self.alpha_cross_level, ] * 2, 'r--')
+        ymax = self.Lmax + self.alpha_Lrange/10
+        ymin = self.alpha_cross_level - self.alpha_Lrange/10
+        axis.vlines(p_ci, ymin=ymin, ymax=self.Lmax,
+                    color='r', linestyles='--')
+        if self.i_fixed is not None:
+            axis.vlines(self.fit_dist.par[self.i_fixed],
+                        ymin=ymin, ymax=self.Lmax,
+                        color='g', linestyles='--')
+        axis.set_title(self.title)
+        axis.set_ylabel(self.ylabel)
+        axis.set_xlabel(self.xlabel)
+        axis.set_ylim(ymin=ymin, ymax=ymax)
+
+
+class ProfileOld(object):
 
     ''' Profile Log- likelihood or Product Spacing-function.
             which can be used for constructing confidence interval for
@@ -276,6 +623,18 @@ class Profile(object):
     >>> sf_ci = Lsf.get_bounds(alpha=0.2)
     '''
 
+    def _get_not_fixed_mask(self, fit_dist):
+        if fit_dist.par_fix is None:
+            isnotfixed = np.ones(fit_dist.par.shape, dtype=bool)
+        else:
+            isnotfixed = 1 - np.isfinite(fit_dist.par_fix)
+        return isnotfixed
+
+    def _check_i_fixed(self):
+        if self.i_fixed not in self.i_notfixed:
+            raise IndexError("Index i must be equal to an index to one of " +
+                             "the free parameters.")
+
     def __init__(self, fit_dist, method=None, **kwds):
         if method is None:
             method = fit_dist.method.lower()
@@ -307,19 +666,11 @@ class Profile(object):
             raise ValueError(
                 "PROFILE is only valid for ML- or MPS- estimators")
 
-        if fit_dist.par_fix is None:
+        isnotfixed = self._get_not_fixed_mask(fit_dist)
-            isnotfixed = np.ones(fit_dist.par.shape, dtype=bool)
-        else:
-            isnotfixed = 1 - np.isfinite(fit_dist.par_fix)
-
         self.i_notfixed = nonzero(isnotfixed)
 
         self.i_fixed = atleast_1d(self.i_fixed)
-
+        self._check_i_fixed()
-        if 1 - isnotfixed[self.i_fixed]:
-            raise IndexError(
-                "Index i must be equal to an index to one of the free " +
-                "parameters.")
 
         isfree = isnotfixed
         isfree[self.i_fixed] = False
@@ -339,7 +690,7 @@ class Profile(object):
         self.profile_par = not (self.profile_x or self.profile_logSF)
 
         if self.link is None:
-            self.link = LINKS[self.fit_dist.dist.name]
+            self.link = LINKS.get(self.fit_dist.dist.name)
         if self.profile_par:
             self._local_link = self._par_link
             self.xlabel = 'phat(%d)' % self.i_fixed
@@ -373,20 +724,26 @@ class Profile(object):
     def _logSF_link(self, fix_par, par):
         return self.link(self.x, fix_par, par, self.i_fixed)
 
-    def _correct_Lmax(self, Lmax):
+    def _correct_Lmax(self, Lmax, free_par, fix_par):
+
         if Lmax > self.Lmax:  # foundNewphat = True
-            warnings.warn(
+
-                'The fitted parameters does not provide the optimum fit. ' +
-                'Something wrong with fit')
             dL = self.Lmax - Lmax
             self.alpha_cross_level -= dL
             self.Lmax = Lmax
+            par = self._par.copy()
+            par[self.i_free] = free_par
+            par[self.i_fixed] = fix_par
+            self.best_par = par
+            warnings.warn(
+                'The fitted parameters does not provide the optimum fit. ' +
+                'Something wrong with fit (par = {})'.format(str(par)))
 
     def _profile_optimum(self, phatfree0, p_opt):
         phatfree = optimize.fmin(
             self._profile_fun, phatfree0, args=(p_opt,), disp=0)
         Lmax = -self._profile_fun(phatfree, p_opt)
-        self._correct_Lmax(Lmax)
+        self._correct_Lmax(Lmax, phatfree, p_opt)
         return Lmax, phatfree
 
     def _set_profile(self, phatfree0, p_opt):
@@ -400,7 +757,7 @@ class Profile(object):
             for ix in range(k1, size, step):
                 Lmax, phatfree = self._profile_optimum(phatfree, pvec[ix])
                 self.data[ix] = Lmax
-                if self.data[ix] < self.alpha_cross_level:
+                if ix != k1 and self.data[ix] < self.alpha_cross_level:
                     break
         np.putmask(pvec, np.isnan(self.data), nan)
         self.args = pvec
@@ -443,13 +800,14 @@ class Profile(object):
         ''' return proper interval for the variable to profile
         '''
 
-        linspace = np.linspace
         if self.pmin is None or self.pmax is None:
 
             pvar = self._get_variance()
 
             if pvar <= 1e-5 or np.isnan(pvar):
-                pvar = max(abs(p_opt) * 0.5, 0.5)
+                pvar = max(abs(p_opt) * 0.5, 0.2)
+            else:
+                pvar = max(pvar, 0.1)
 
             p_crit = (-norm_ppf(self.alpha / 2.0) *
                       sqrt(np.ravel(pvar)) * 1.5)
@@ -465,14 +823,14 @@ class Profile(object):
 
             N4 = np.floor(self.N / 4.0)
 
-            pvec1 = linspace(self.pmin, p_opt - p_crit_low, N4 + 1)
+            pvec1 = np.linspace(self.pmin, p_opt - p_crit_low, N4 + 1)
-            pvec2 = linspace(
+            pvec2 = np.linspace(p_opt - p_crit_low, p_opt + p_crit_up,
-                p_opt - p_crit_low, p_opt + p_crit_up, self.N - 2 * N4)
+                                self.N - 2 * N4)
-            pvec3 = linspace(p_opt + p_crit_up, self.pmax, N4 + 1)
+            pvec3 = np.linspace(p_opt + p_crit_up, self.pmax, N4 + 1)
             pvec = np.unique(np.hstack((pvec1, p_opt, pvec2, pvec3)))
 
         else:
-            pvec = linspace(self.pmin, self.pmax, self.N)
+            pvec = np.linspace(self.pmin, self.pmax, self.N)
         return pvec
 
     def _search_pmin(self, phatfree0, p_min0, p_opt):
@@ -488,7 +846,7 @@ class Profile(object):
             Lmax, phatfree = self._profile_optimum(phatfree, p_min)
             if np.isnan(Lmax):
                 dp *= 0.33
-            elif Lmax < self.alpha_cross_level - self.alpha_Lrange * 2:
+            elif Lmax < self.alpha_cross_level - self.alpha_Lrange * 5:
                 p_min_opt = p_min
                 dp *= 0.33
             elif Lmax < self.alpha_cross_level:
@@ -588,14 +946,20 @@ class Profile(object):
         p_ci = self.get_bounds(self.alpha)
         axis.plot(
             self.args, self.data,
-            self.args[[0, -1]], [self.Lmax, ] * 2, 'r--',
+            p_ci, [self.Lmax, ] * 2, 'r--',
-            self.args[[0, -1]], [self.alpha_cross_level, ] * 2, 'r--')
+            p_ci, [self.alpha_cross_level, ] * 2, 'r--')
-        axis.vlines(p_ci, ymin=axis.get_ylim()[0],
+        ymax = self.Lmax + self.alpha_Lrange/10
-                    ymax=self.Lmax,  # self.alpha_cross_level,
+        ymin = self.alpha_cross_level - self.alpha_Lrange/10
+        axis.vlines(p_ci, ymin=ymin, ymax=self.Lmax,
                     color='r', linestyles='--')
+        if self.i_fixed is not None:
+            axis.vlines(self.fit_dist.par[self.i_fixed],
+                        ymin=ymin, ymax=self.Lmax,
+                        color='g', linestyles='--')
         axis.set_title(self.title)
         axis.set_ylabel(self.ylabel)
         axis.set_xlabel(self.xlabel)
+        axis.set_ylim(ymin=ymin, ymax=ymax)
 
 
 class FitDistribution(rv_frozen):
@@ -857,7 +1221,7 @@ class FitDistribution(rv_frozen):
         (including loc and scale)
         '''
         if eps is None:
-            eps = (_EPS) ** 0.4
+            eps = (_EPS) ** 0.25
         num_par = len(theta)
         # pab 07.01.2001: Always choose the stepsize h so that
         # it is an exactly representable number.
@@ -901,7 +1265,7 @@ class FitDistribution(rv_frozen):
         return -H
 
     def _nnlf(self, theta, x):
-        return self.dist._penalized_nnlf(theta, x)
+        return self.dist._penalized_nnlf(theta, x, self._penalty)
 
     def _nlogps(self, theta, x):
         """ Moran's negative log Product Spacings statistic
@@ -974,27 +1338,28 @@ class FitDistribution(rv_frozen):
         nonfiniteD = 1 - finiteD
         Nbad += np.sum(nonfiniteD, axis=0)
         if Nbad > 0:
-            T = -np.sum(logD[finiteD], axis=0) + 100.0 * log(_XMAX) * Nbad
+            if self._penalty is None:
+                penalty = 100.0 * log(_XMAX) * Nbad
             else:
-            T = -np.sum(logD, axis=0)
+                penalty = 0.0
-        return T
+            return -np.sum(logD[finiteD], axis=0) + penalty
+        return -np.sum(logD, axis=0)
 
     def _fit(self, *args, **kwds):
-
+        self._penalty = None
         dist = self.dist
         data = self.data
 
         Narg = len(args)
-        if Narg > dist.numargs:
+        if Narg > dist.numargs + 2:
                 raise ValueError("Too many input arguments.")
-        start = [None] * 2
+        if (Narg < dist.numargs + 2) or not ('loc' in kwds and 'scale' in kwds):
-        if (Narg < dist.numargs) or not ('loc' in kwds and 'scale' in kwds):
             # get distribution specific starting locations
             start = dist._fitstart(data)
-            args += start[Narg:-2]
+            args += start[Narg:]
-        loc = kwds.pop('loc', start[-2])
+        loc = kwds.pop('loc', args[-2])
-        scale = kwds.pop('scale', start[-1])
+        scale = kwds.pop('scale', args[-1])
-        args += (loc, scale)
+        args = args[:-2] + (loc, scale)
         x0, func, restore, args, fixedn = self._reduce_func(args, kwds)
         if self.search:
             optimizer = kwds.pop('optimizer', optimize.fmin)
@@ -1011,8 +1376,24 @@ class FitDistribution(rv_frozen):
             # by now kwds must be empty, since everybody took what they needed
             if kwds:
                 raise TypeError("Unknown arguments: %s." % kwds)
-            vals = optimizer(func, x0, args=(np.ravel(data),), disp=0)
+            output = optimizer(func, x0, args=(data,), full_output=True)
-            vals = tuple(vals)
+
+            # output = optimize.fmin_bfgs(func, vals, args=(data,), full_output=True)
+            # dfunc = nd.Gradient(func)(vals, data)
+            # nd.directionaldiff(f, x0, vec)
+            warnflag = output[-1]
+            if warnflag == 1:
+                output = optimizer(func, output[0], args=(data,), full_output=True)
+                warnflag = output[-1]
+            vals = tuple(output[0])
+            if warnflag == 1:
+                warnings.warn("The maximum number of iterations was exceeded.")
+
+            elif warnflag == 2:
+                warnings.warn("Did not converge")
+            else:
+                vals = tuple(output[0])
+
         else:
             vals = tuple(x0)
         if restore is not None:
@@ -1022,8 +1403,12 @@ class FitDistribution(rv_frozen):
     def _compute_cov(self):
         '''Compute covariance
         '''
+        # self._penalty = 0
         somefixed = (self.par_fix is not None) and any(isfinite(self.par_fix))
+
         H = np.asmatrix(self._hessian(self._fitfun, self.par, self.data))
+        # H = -nd.Hessian(lambda par: self._fitfun(par, self.data),
+        #               method='forward')(self.par)
         self.H = H
         try:
             if somefixed:
@@ -1153,6 +1538,7 @@ class FitDistribution(rv_frozen):
         plotbackend.subplot(2, 2, 4)
         self.plotresprb()
 
+        plotbackend.subplots_adjust(hspace=0.4, wspace=0.4)
         fixstr = ''
         if self.par_fix is not None:
             numfix = len(self.i_fixed)
@@ -1161,12 +1547,16 @@ class FitDistribution(rv_frozen):
                 format1 = ', '.join(['%g'] * numfix)
                 phatistr = format0 % tuple(self.i_fixed)
                 phatvstr = format1 % tuple(self.par[self.i_fixed])
-                fixstr = 'Fixed: phat[%s] = %s ' % (phatistr, phatvstr)
+                fixstr = 'Fixed: phat[{0:s}] = {1:s} '.format(phatistr,
+                                                              phatvstr)
 
-        infostr = 'Fit method: %s, Fit p-value: %2.2f %s' % (
+        infostr = 'Fit method: {0:s}, Fit p-value: {1:2.2f} {2:s}, phat=[{3:s}]'
-            self.method.upper(), self.pvalue, fixstr)
+        par_txt = ('{:1.2g}, '*len(self.par))[:-2].format(*self.par)
         try:
-            plotbackend.figtext(0.05, 0.01, infostr)
+            plotbackend.figtext(0.05, 0.01, infostr.format(self.method.upper(),
+                                                           self.pvalue,
+                                                           fixstr,
+                                                           par_txt))
         except:
             pass
 
@@ -1339,14 +1729,68 @@ def test1():
     import wafo.stats as ws
     dist = ws.weibull_min
     # dist = ws.bradford
-    R = dist.rvs(0.3, size=1000)
+    dist = ws.gengamma
+    R = dist.rvs(2,.5, size=500)
     phat = FitDistribution(dist, R,  method='ml')
+    phats = FitDistribution(dist, R,  method='mps')
+    import matplotlib.pyplot as plt
 
 # Better CI for phat.par[i=0]
-    Lp1 = Profile(phat, i=0)  # @UnusedVariable
+    plt.figure(0)
+    N = dist.numargs + 2
+    for i in range(N-1, -1, -1):
+        plt.subplot(N, 1, i+1)
+
+        pmax = None
+        if i == 0:
+            pmax = None
+        Lp1 = Profile(phats, i=i)
+        j = 0
+        while hasattr(Lp1, 'best_par') and j < 7:
+            phats = FitDistribution(dist, R, args=Lp1.best_par,
+                                    method='mps', search=True)
+            Lp1 = Profile(phats, i=i, pmax=pmax)
+
+            j += 1
         Lp1.plot()
-    import matplotlib.pyplot as plt
+        if i != 0:
-    plt.show()
+            plt.title('')
+        if i != N//2:
+            plt.ylabel('')
+    plt.subplots_adjust(hspace=0.5)
+    par_txt = ('{:1.2g}, '*len(phats.par))[:-2].format(*phats.par)
+    plt.suptitle('phat = [{}]'.format(par_txt))
+
+    plt.figure(1)
+    phats.plotfitsummary()
+
+    plt.figure(2)
+
+    for i in range(N-1, -1, -1):
+        plt.subplot(N, 1, i+1)
+        pmax = None
+        if i == 0:
+            pmax = None
+        Lp1 = Profile(phat, i=i, pmax=pmax)  # @UnusedVariable
+        j = 0
+        while hasattr(Lp1, 'best_par') and j < 7:
+            phats = FitDistribution(dist, R, args=Lp1.best_par,
+                                    method='ml', search=True)
+            Lp1 = Profile(phat, i=i)  # @UnusedVariable
+            j += 1
+        Lp1.plot()
+        if i != 0:
+            plt.title('')
+        if i != N//2:
+            plt.ylabel('')
+    par_txt = ('{:1.2g}, '*len(phat.par))[:-2].format(*phat.par)
+    plt.suptitle('phat = [{}]'.format(par_txt))
+
+    plt.subplots_adjust(hspace=0.5)
+    plt.figure(3)
+    phat.plotfitsummary()
+    plt.show('hold')
+
 #    Lp2 = Profile(phat, i=2)
 #    SF = 1./990
 #    x = phat.isf(SF)