Compute dissimilarity estimates between two samples based on Expected Species Shared (ESS)-measures, using abundance data for the species contained in each samples

Calculate rarefaction-based alpha- and beta-diversity. Offer parametric extrapolation to estimate the total expected species in a single community and the total expected shared species between two communities. Visualize the curve-fitting for these estimators.

Peng Zhao

rarestR

Rarefaction-Based Species Richness Estimator

Yi Zou

ess function

<dl><dt>x</dt>
<dd>a community data matrix (sample x species); sample name is the row name of the matrix</dd>
<dt>m</dt>
<dd>the sample size parameter that represents the number of individuals randomly drawn from each sample, which by default is set to m=1, but can be changed according to the users' requirements. Rows with a total sample size &lt;m will be excluded automatically from the analysis.</dd>
<dt>index</dt>
<dd>the distance measure used in the calculation, as one of the four options "CNESSa", "CNESS","NESS" and "ESS", with the default set as "CNESSa"</dd></dl>

Arguments

Compute dissimilarity estimates between two samples based on Expected Species Shared (ESS)-measures, using abundance data for the species contained in each samples — ess

<dl>

<dt>x</dt>
<dd>a community data matrix (sample x species); sample name is the row name of the matrix</dd>


<dt>m</dt>
<dd>the sample size parameter that represents the number of individuals randomly drawn from each sample, which by default is set to m=1, but can be changed according to the users' requirements. Rows with a total sample size &lt;m will be excluded automatically from the analysis.</dd>


<dt>index</dt>
<dd>the distance measure used in the calculation, as one of the four options "CNESSa", "CNESS","NESS" and "ESS", with the default set as "CNESSa"</dd>

</dl>

Compute dissimilarity estimates between two samples based on Expected Species Shared (ESS)-measures, using abundance data for the species contained in each samples

ess: Compute dissimilarity estimates between two samples based on Expected Species Shared (ESS)-measures, using abundance data for the species contained in each samples

Description

Usage

Value

Arguments

References

Examples