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The paper describes

Species richness is a basic surrogate for the more complex concept of ecological diversity [

However, general agreement among researchers about which index should be used is currently lacking, and this is a major reason for the continued study of species richness in local communities [

Yet, problems with simple species richness estimation exist [

Comparing measures of species richness is an important task and it is not always straightforward. If the cumulative value (

Rarefaction curves traditionally report the average values of randomized species richness derived from resampling without replacement. A consequence of this is that the variance of the species richness estimation among randomizations decreases with sample size and equals 0 at the right-hand of the curve. As a consequence, such estimations cannot be used to compare different data sets. Sampling with replacement, on the contrary, provides meaningful variance of average species richness and thus allows comparison between different data sets. This corresponds to performing bootstrap on species richness and allows useful additional computations (bias, confidence intervals) [

The function

Rarefaction curves are important diagnostic tools that consist of the plot of randomized richness against the sampling intensity.

The comparison of species richness of 2 communities may be biased if the sampling effort strongly differs. For that reason, some authors (e.g., [

A second function,

Comparing cumulative species richnesses is not straightforward because each community is described by only one value and consequently usual statistical tests do not apply. For that reason, published papers often consider average richnesses and this point is discussed below. The test implies evaluating the null hypothesis “there is no difference between observed richnesses but sampling fluctuations” against an alternate hypothesis “richnesses are different”. The nature of the alternate hypothesis will, as usual, determine whether the test is uni or bilateral.

_{1} and
_{2} be the richness of community 1 and 2. The difference between these values,
_{1} − S_{2}_{rand}

The function

The package

The function

There are many indices designed to describe biodiversity but the question of comparing these measures has not received the attention it deserves. The aim in writing

In some cases however, the difference in individuals density is directly reflecting the differences in community structure rather than effects of sampling regimes. In the example of the soil macrofauna richness in the secondary forest and the cultivated plot, strong differences in densities as well as in richness were observed. The first effect of cutting down the forest and settling a cultivated plot is the destruction of many micro-habitats which leads to the decrease of the density of most populations as well as the extinction of numerous species [

Such differences in the rarefaction curves may be explained by very marked differences in species spatial patterning

Stable version is available from CRAN:

Rarefaction curves for species richness of soil macrofauna in two study plots in French Guiana. Upper panel: sample-based rarefaction curves. Lower panel: individual-based rarefaction curve. In this example, the individual density is larger in the forest plot (open circles) which also hosts the higher species richness than the cultivated plot (crosses) (data from [

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