Re: [Matplotlib-users] incorrect boxplot?

2009-12-20 Thread Andrew Straw 
Robert Kern wrote:
 On 2009-09-14 13:49 PM, Gökhan Sever wrote:
   
 On Mon, Sep 14, 2009 at 12:30 PM, jason-s...@creativetrax.com
 mailto:jason-s...@creativetrax.com wrote:

 I tried the following (most output text is deleted):

 In [1]: ob1=[1,1,2,2,1,2,4,3,2,2,2,3,4,5,6,7,8,9,7,6,4,5,5]
 In [2]: import matplotlib.pyplot as
 plt
 In [3]:
 plt.figure()
 In [4]:
 plt.boxplot(ob1)
 In [5]:
 plt.savefig('test.png')
 In [6]: import
 scipy.stats
 In [7]:
 scipy.stats.scoreatpercentile(ob1,75)
 Out[7]: 5.5


 Note that the 75th percentile is 5.5.  R agrees with this calculation.
 However, in the boxplot, the top of the box is around 6, not 5.5.  Isn't
 the top of the box supposed to be at the 75th percentile?

 Thanks,

 Jason

 --
 Jason Grout


 From  matplotlib/lib/matplotlib/axes.py

 You can see how matplotlib calculating percentiles. And yes it doesn't
 conform with scipy's scoreatpercentile()


  # get median and quartiles
  q1, med, q3 = mlab.prctile(d,[25,50,75])

 I[36]: q1
 O[36]: 2.0

 I[37]: med
 O[37]: 4.0

 I[38]: q3
 O[38]: 6.0


 Could this be due to a rounding? I don't know, but I am curious to hear
 the explanations for this discrepancy.
 

 prctile does not handle the case where the exact percentile lies between two 
 items. scoreatpercentile does.
   
Fixed in r8039.


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[Matplotlib-users] incorrect boxplot?

2009-09-14 Thread jason-sage 
I tried the following (most output text is deleted):

In [1]: ob1=[1,1,2,2,1,2,4,3,2,2,2,3,4,5,6,7,8,9,7,6,4,5,5]
In [2]: import matplotlib.pyplot as 
plt   
In [3]: 
plt.figure()  
In [4]: 
plt.boxplot(ob1)  
In [5]: 
plt.savefig('test.png')   
In [6]: import 
scipy.stats
In [7]: 
scipy.stats.scoreatpercentile(ob1,75) 
Out[7]: 5.5


Note that the 75th percentile is 5.5.  R agrees with this calculation.  
However, in the boxplot, the top of the box is around 6, not 5.5.  Isn't 
the top of the box supposed to be at the 75th percentile?

Thanks,

Jason

--
Jason Grout


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Re: [Matplotlib-users] incorrect boxplot?

2009-09-14 Thread Gökhan Sever 
On Mon, Sep 14, 2009 at 12:30 PM, jason-s...@creativetrax.com wrote:

 I tried the following (most output text is deleted):

 In [1]: ob1=[1,1,2,2,1,2,4,3,2,2,2,3,4,5,6,7,8,9,7,6,4,5,5]
 In [2]: import matplotlib.pyplot as
 plt
 In [3]:
 plt.figure()
 In [4]:
 plt.boxplot(ob1)
 In [5]:
 plt.savefig('test.png')
 In [6]: import
 scipy.stats
 In [7]:
 scipy.stats.scoreatpercentile(ob1,75)
 Out[7]: 5.5


 Note that the 75th percentile is 5.5.  R agrees with this calculation.
 However, in the boxplot, the top of the box is around 6, not 5.5.  Isn't
 the top of the box supposed to be at the 75th percentile?

 Thanks,

 Jason

 --
 Jason Grout


From  matplotlib/lib/matplotlib/axes.py

You can see how matplotlib calculating percentiles. And yes it doesn't
conform with scipy's scoreatpercentile()


# get median and quartiles
q1, med, q3 = mlab.prctile(d,[25,50,75])

I[36]: q1
O[36]: 2.0

I[37]: med
O[37]: 4.0

I[38]: q3
O[38]: 6.0


Could this be due to a rounding? I don't know, but I am curious to hear the
explanations for this discrepancy.




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Re: [Matplotlib-users] incorrect boxplot?

2009-09-14 Thread Robert Kern 
On 2009-09-14 13:49 PM, Gökhan Sever wrote:


 On Mon, Sep 14, 2009 at 12:30 PM, jason-s...@creativetrax.com
 mailto:jason-s...@creativetrax.com wrote:

 I tried the following (most output text is deleted):

 In [1]: ob1=[1,1,2,2,1,2,4,3,2,2,2,3,4,5,6,7,8,9,7,6,4,5,5]
 In [2]: import matplotlib.pyplot as
 plt
 In [3]:
 plt.figure()
 In [4]:
 plt.boxplot(ob1)
 In [5]:
 plt.savefig('test.png')
 In [6]: import
 scipy.stats
 In [7]:
 scipy.stats.scoreatpercentile(ob1,75)
 Out[7]: 5.5


 Note that the 75th percentile is 5.5.  R agrees with this calculation.
 However, in the boxplot, the top of the box is around 6, not 5.5.  Isn't
 the top of the box supposed to be at the 75th percentile?

 Thanks,

 Jason

 --
 Jason Grout


 From  matplotlib/lib/matplotlib/axes.py

 You can see how matplotlib calculating percentiles. And yes it doesn't
 conform with scipy's scoreatpercentile()


  # get median and quartiles
  q1, med, q3 = mlab.prctile(d,[25,50,75])

 I[36]: q1
 O[36]: 2.0

 I[37]: med
 O[37]: 4.0

 I[38]: q3
 O[38]: 6.0


 Could this be due to a rounding? I don't know, but I am curious to hear
 the explanations for this discrepancy.

prctile does not handle the case where the exact percentile lies between two 
items. scoreatpercentile does.

-- 
Robert Kern

I have come to believe that the whole world is an enigma, a harmless enigma
  that is made terrible by our own mad attempt to interpret it as though it had
  an underlying truth.
   -- Umberto Eco


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Re: [Matplotlib-users] incorrect boxplot?

2009-09-14 Thread jason-sage 
Robert Kern wrote:
 prctile does not handle the case where the exact percentile lies between two 
 items. scoreatpercentile does.

   

If mlab is supposed to be compatible with matlab, then isn't this a problem?

 From matlab, version 7.2.0.283 (R2006a)

  prctile([1 1 2 2 1 2 4 3 2 2 2 3 4 5 6 7 8 9 7 6 4 5 5],[0 25 50 75 
100])

ans =

1.2.4.5.75009.


Of course, the 75th percentile is different here too (5.75 instead of 
scipy's 5.5).  I don't know how to explain that discrepancy.

Jason


--
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