Chao1 formula

[cricket]

Hello Qiime Forum,

What formula is being used to calculate the Chao1 values
(alpha_diversity.py)?

Qiimely,

C

[Antonio González Peña]

Hey C,

QIIME uses the pycogent implementation of chao1 with bias correction,
from the code:

def chao1_bias_corrected(observed, singles, doubles):
"""Calculates bias-corrected chao1 given counts: Eq. 2 in EstimateS manual.

Formula: chao1 = S_obs + N_1(N_1-1)/(2*(N_2+1)) where N_1 and N_2 are
count of singletons and doubletons respectively.

Note: this is the bias-corrected formulat from Chao 1987, Eq. 2 in the
EstimateS manual.
"""
return observed + singles*(singles-1) / (2.0*(doubles+1))

Cheers

--
Antonio González Peña
Research Assistant, Knight Lab
University of Colorado at Boulder
https://chem.colorado.edu/knightgroup/

[Jesse Stombaugh]

Hello,

By default, chao1 used the bias corrected formula for alpha-diversity:

Formula: chao1 = S_obs + N_1(N_1-1)/(2*(N_2+1)) where N_1 and N_2 are count of singletons and doubletons respectively.

Note: this is the bias-corrected formula from Chao 1987, Eq. 2 in the EstimateS manual.

-Jesse

On Thu, Dec 22, 2011 at 12:25 PM, cricket <errcr...@gmail.com> wrote:

--
Jesse Stombaugh, Ph.D.
Research Associate
University of Colorado, Boulder

[cricket]

Thank you both very much. That clears up some discrepancies.

C

2011/12/22 Antonio González Peña <antg...@gmail.com>

--
 - cricket