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# Copyright (c) 2014, Salesforce.com, Inc. All rights reserved. |
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# Copyright (c) 2015-2016, Gamelan Labs, Inc. |
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# Copyright (c) 2016, Google, Inc. |
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# |
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# Redistribution and use in source and binary forms, with or without |
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# modification, are permitted provided that the following conditions |
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# are met: |
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# |
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# - Redistributions of source code must retain the above copyright |
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# notice, this list of conditions and the following disclaimer. |
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# - Redistributions in binary form must reproduce the above copyright |
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# notice, this list of conditions and the following disclaimer in the |
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# documentation and/or other materials provided with the distribution. |
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# - Neither the name of Salesforce.com nor the names of its contributors |
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# may be used to endorse or promote products derived from this |
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# software without specific prior written permission. |
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# |
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS |
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT |
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS |
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# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE |
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# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, |
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# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, |
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# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS |
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# OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND |
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# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR |
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# TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE |
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# USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
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""" |
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This module computes the chi^2 survival function and the required |
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functions. |
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This was implemented so that we could use the goftests module |
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with pypy. Given that the only scipy dependence inside goftests |
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was from the chi^2 survival function (1 - cdf), and then gamma |
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function. |
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""" |
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from __future__ import division |
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import math |
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import sys |
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from numpy import inf |
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def log(x): |
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if x > sys.float_info.min: |
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value = math.log(x) |
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else: |
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value = -inf |
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return value |
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def incomplete_gamma(x, s): |
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r""" |
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This function computes the incomplete lower gamma function |
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using the series expansion: |
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\gamma(x, s) = x^s \Gamma(s)e^{-x}\sum^\infty_{k=0} |
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\frac{x^k}{\Gamma(s + k + 1)} |
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This series will converge strongly because the Gamma |
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function grows factorially. |
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Because the Gamma function does grow so quickly, we can |
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run into numerical stability issues. I have chosen to carry |
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out as much math as possible in the log domain to reduce |
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numerical error. This function matches the results from |
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scipy to numerical precision. |
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""" |
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value = 0.0 |
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if x < 0.0: |
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return 1.0 |
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if x > 1e3: |
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return math.gamma(s) |
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log_gamma_s = log(math.gamma(s)) |
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log_x = log(x) |
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for k in range(0, 100): |
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log_num = (k + s)*log_x + (-x) + log_gamma_s |
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log_denom = log(math.gamma(k + s + 1)) |
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value += math.exp(log_num - log_denom) |
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return value |
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def chi2sf(x, s): |
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r""" |
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This function returns the survival function of the chi^2 |
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distribution. The survival function is given as: |
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1 - CDF |
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where rhe chi^2 CDF is given as |
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F(x; s) = \frac{ \gamma( x/2, s/2 ) }{ \Gamma(s/2) }, |
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with $\gamma$ is the incomplete gamma function defined above. |
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Therefore, the survival probability is givne by: |
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1 - \frac{ \gamma( x/2, s/2 ) }{ \Gamma(s/2) }. |
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This function matches the results from |
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scipy to numerical precision. |
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""" |
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top = incomplete_gamma(x/2.0, s/2.0) |
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bottom = math.gamma(s/2.0) |
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value = top/bottom |
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return 1.0 - value |
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posterior /
goftests
