estShannonf

Estimation function for Shannon's index. Internal use in
 <code>sbdiv</code> for methods <code>rpht</code>, <code>tsht</code>,
 <code>asht</code>. Sums up species counts in each columns for every
 treatment group and estimates Shannon's index with bias correction on
 the resulting vectors of summed up species counts.
 $$\widehat{HBC}_{i} = \hat{H}_{i} + (S_i -1)/(2N_{i\bullet}) -
 (1-\sum(1/\hat{p}_{i\bullet s}))/(12N_{i\bullet}^2) -
 \sum((1/\hat{p}_{i\bullet s})-(1/(\hat{p}_{i\bullet
	s}^2)))/(12N_{i\bullet}^3);$$
$i=1,...,k;s=1,...,S;p_{i \bullet
 s}=\frac{\sum_{j=1}^{n}x_{sj}}{N_{i\bullet}}$;
$$\hat{H}_i=(-1)\sum_{s=1}^{S}(\hat{p}_{i \bullet s} log(\hat{p}_{i \bullet s}))$$
$N_{i\bullet}= \sum_{j=1}^{n}N_{ij}$ Number of observed individuals in treatment $i$.

 misc 

Provides estimation of simultaneous bootstrap and asymptotic confidence intervals for diversity indices, namely the Shannon and the Simpson index. Several pre--specified multiple comparison types are available to choose. Further user--defined contrast matrices are applicable. In addition, simboot estimates adjusted as well as unadjusted p--values for two of the three proposed bootstrap methods. Further simboot allows for comparing biological diversities of two or more groups while simultaneously testing a user-defined selection of Hill numbers of orders q, which are considered as appropriate and useful indices for measuring diversity.

Ralph Scherer

simboot

Simultaneous Inference for Diversity Indices

Philip Pallmann

estShannonf function

<dl> <dt>X</dt>
<dd>$n$ times $p$ matrix containing species in $p$ columns and replicates in $n$ rows.</dd> <dt>f</dt>
<dd>Factor variable containing treatment groups. Must be of length: replicates
 times treatment groups.</dd></dl>

Arguments

Estimator for Shannon's index odered by a factorial variable f. — estShannonf

<dl>

 <dt>X</dt>
<dd>$n$ times $p$ matrix containing species in $p$ columns and replicates in $n$ rows.</dd>

 <dt>f</dt>
<dd>Factor variable containing treatment groups. Must be of length: replicates
 times treatment groups.</dd>

</dl>

estShannonf: Estimator for Shannon's index odered by a factorial variable f.

Description

Usage

Value

Arguments