Nichesort

[mortonjt]

Depends on #12.

Used to generate band tables when the gradient is known.

[coveralls]

Coverage increased (+0.5%) to 99.371% when pulling 3d9ded6 on mortonjt:nichesort into f79d9a6 on biocore:master.

[josenavas]

@mortonjt can you pull from upstream/master?

[coveralls]

Coverage increased (+0.1%) to 99.342% when pulling 42221f5 on mortonjt:nichesort into ff3df22 on biocore:master.

[josenavas]

Missing license notice.

[josenavas]

Some comments. Thanks @mortonjt

[antgonza]

I don't feel strongly about this but normally we do something like this to minimize how many times you calculate the lenght of the iterables:

len_abundances = len(abundances)
len_gradient = len(gradient)
if len_abundances != len_gradient:
    ....

[mortonjt]

Done

[antgonza]

some more comments.

[coveralls]

Coverage increased (+0.1%) to 99.338% when pulling 23acedf on mortonjt:nichesort into ff3df22 on biocore:master.

[mortonjt]

Thanks for taking the time to review this! All comments have been addressed.

[antgonza]

Is this line really doing this:
E[g | x] = \frac{1}{\sum\limits_{j=1}^N x_j} \sum\limits_{i=1}^N x_i g_i

[mortonjt]

Yup

On Jul 27, 2016 11:56 AM, "Antonio Gonzalez" notifications@github.com
wrote:

In gneiss/sort.py
#16 (comment):

• ValueError:

•    If the length of `gradient` contains nans.
  

• """
• len_abundances = len(abundances)
• len_gradient = len(gradient)
• if len_abundances != len_gradient:

•    raise ValueError("Length of `abundances` (%d) doesn't match the length"
  

•                     " of the `gradient` (%d)" % (len_abundances,
  

•                                                  len_gradient))
  

• if np.any(pd.isnull(gradient)):

•    raise ValueError("`gradient` cannot have any nans.")
  

• normalizes the proportions of the organism across all of the

• samples to add to 1.

• v = abundances / abundances.sum()
• m = np.dot(gradient, v)

Is this line really doing this:
E[g | x] = \frac{1}{\sum\limits_{j=1}^N x_j} \sum\limits_{i=1}^N x_i g_i

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[antgonza]

@mortonjt and I discussed offline and realized that the code and the formula are similar but not the same, one was a simplification of the other. @mortonjt fixed it.

[coveralls]

Coverage increased (+0.1%) to 99.346% when pulling 940d7e8 on mortonjt:nichesort into ff3df22 on biocore:master.

[josenavas]

missing raises section

[mortonjt]

Doh. Added

[josenavas]

Thanks @mortonjt ! The comments really help to fully understand what is going on in the code! Just a minor comment about missing a section in the docs and I think this is good to go!

[coveralls]

Coverage increased (+0.1%) to 99.346% when pulling 7ee169c on mortonjt:nichesort into ff3df22 on biocore:master.

[josenavas]

Good to merge - I just realized that I don't have merge privileges here

[coveralls]

Coverage increased (+0.1%) to 99.346% when pulling 0168b42 on mortonjt:nichesort into ff3df22 on biocore:master.

[coveralls]

Coverage increased (+0.1%) to 99.346% when pulling c9e2373 on mortonjt:nichesort into ff3df22 on biocore:master.

[mortonjt]

Thanks for your insights on this! This feedback is seriously improving the usability of this module.