qiime/qiime — pull request #914 by jrrideout (2013-05-08 07:10:59+00:00)
Title: New richness estimates script

Added a new script ```estimate_observation_richness.py``` that implements interpolation/rarefaction and extrapolation of richness estimates using the multinomial model and Chao1. Based on [Colwell et al. (2012)](http://jpe.oxfordjournals.org/content/5/1/3.short).

In a nutshell, an estimate for the number of observations (like ```observed_species```) is computed along a range of varying sampling depths defined by the user. Both interpolation and extrapolation are supported. The primary input is a BIOM table, and estimates are provided for each sample in the table.

Currently, the only output format is a table with sampling depths, estimates, stderr, and confidence intervals. Later improvements will include plots.

This script is necessary for the stable OTUs paper; in the ChangeLog I've noted that this is experimental.