In [7]:

    

from biom import load_table
from skbio import TreeNode
from io import StringIO
import numpy as np
from skbio.diversity.alpha._base import alpha_diversity, observed_otus, faith_pd


    

In [13]:

    

t = load_table('/Users/caporaso/code/q2d2/example-data/keyboard/q191/otu-table.tsv')
d = t.matrix_data.toarray().astype('int').T
tree = TreeNode.read('/Users/caporaso/code/q2d2/example-data/keyboard/q191/rep-set.tre')


    

In [14]:

    

%%timeit
alpha_diversity('faith_pd', d, ids=t.ids('sample'), otu_ids=t.ids('observation'), tree=tree)


    

    




100 loops, best of 3: 9.44 ms per loop

In [15]:

    

%%timeit
alpha_diversity(faith_pd, d, ids=t.ids('sample'), otu_ids=t.ids('observation'), tree=tree)


    

    




1 loops, best of 3: 840 ms per loop

In [16]:

    

840./9.44


    

    
Out[16]:





88.98305084745763

In [ ]: