What is rarefaction plot?
What is rarefaction plot?
The rarefaction curve is a plot of the number of species against the number of samples. This curve is created by randomly re-sampling the pool of N samples several times and then plotting the average number of species found on each sample.
How do I use iNEXT?
MAIN FUNCTION: iNEXT() Each knot represents a particular sample size for which diversity estimates will be calculated. By default, endpoint is set to be double the reference sample size. For example, if endpoint=10, knot=4, then diversity estimates will be computed for a sequence of samples with sizes (1,4,7,10).
What are hill numbers?
Hill numbers are a mathematically unified family of diversity indices (differing among themselves only by an exponent q) that incorporate relative abundance and species richness and overcome many of these shortcomings.
What is the purpose of a rarefaction curve?
Rarefaction curves are necessary for estimating species richness. Raw species richness counts, which are used to create accumulation curves, can only be compared when the species richness has reached a clear asymptote. Rarefaction curves produce smoother lines that facilitate point-to-point or full dataset comparisons.
What does a species accumulation curve show?
The species accumulation curve, or collector’s curve, of a population gives the expected number of observed species or distinct classes as a function of sampling effort. Species accumulation curves allow researchers to assess and compare diversity across populations or to evaluate the benefits of additional sampling.
What is rarefaction and extrapolation?
Integrated curves based on sampling theory that smoothly link rarefaction (interpolation) and prediction (extrapolation) standardize samples on the basis of sample size or sample completeness and facilitate the comparison of biodiversity data.
What is Shannon’s index?
The Shannon diversity index (a.k.a. the Shannon–Wiener diversity index) is a popular metric used in ecology. It’s based on Claude Shannon’s formula for entropy and estimates species diversity. The index takes into account the number of species living in a habitat (richness) and their relative abundance (evenness).
What is the Berger Parker index?
The Berger-Parker index (Berger and Parker 1970) expresses the proportional importance of the most abundant type. This metric is highly biased by sample size and richness, moreover it does not make use of all the information available from sample. Dominance: D=nmaxN.
What is the Simpson’s index?
Simpson’s Diversity Index is a measure of diversity which takes into account the number of species present, as well as the relative abundance of each species. As species richness and evenness increase, so diversity increases.
What does a species-Area plot show?
The species-area relationship or species-area curve describes the relationship between the area of a habitat, or of part of a habitat, and the number of species found within that area.
What is the rarefaction curve?
The rarefaction curve is a plot of the number of species against the number of samples. This curve is created by randomly re-sampling the pool of N samples several times and then plotting the average number of species found on each sample.
How to plot rarefaction curves using R/R studio?
Once you have the table generated you can plot the rarefaction curves using R/R studio using the library vegan and the rarecurve function in the package. Here is the script to run, or you can find it here (link to the script on GitHub)
Can rarecurve () output custom colours per group of curves?
An attempt at rarefaction curves output with custom colours per groups of curves. We can’t use the approach outlined in this example to vary lwd because of the way rarecurve () draws the individual curves, in a loop.
How do you create a species distribution curve?
This curve is created by randomly re-sampling the pool of N samples several times and then plotting the average number of species found on each sample. Generally, it initially grows rapidly (as the most common species are found) and then slightly flattens (as the rarest species remain to be sampled).