vegan (version 1.6-0)

specaccum: Species Accumulation Curves

Description

Function specaccum finds species accumulation curves or the number of species for a certain number of sampled sites or individuals.

Usage

specaccum(comm, method = "exact", permutations = 100, ...)
## S3 method for class 'specaccum':
plot(x, add = FALSE, ci = 2, ci.type = c("bar", "line", "polygon"), 
    col = par("fg"), ci.col = col, ci.lty = 1, xlab = "Sites", 
    ylab = x$method, ...)
## S3 method for class 'specaccum':
boxplot(x, add = FALSE, ...)

Arguments

comm

Community data set.

method

Species accumulation method (partial match). Method "collector" adds sites in the order they happen to be in the data, "random" adds sites in random order, "exact" finds the expected (mean) species ri

permutations

Number of permutations with method = "random".

x

A specaccum result object

add

Add to an existing graph.

ci

Multiplier used to get confidence intervals from standard deviation (standard error of the estimate). Value ci = 0 suppresses drawing confidence intervals.

ci.type

Type of confidence intervals in the graph: "bar" draws vertical bars, "line" draws lines, and "polygon" draws a shaded area.

col

Colour for drawing lines.

ci.col

Colour for drawing lines or filling the "polygon".

ci.lty

Line type for confidence intervals or border of the "polygon".

xlab,ylab

Labels for x and y axis.

...

Other parameters to functions.

Value

• The function returns an object of class "specaccum" with items:
• call
  Function call.
• method
  Accumulator method.
• sites
  Number of sites. For method = "rarefaction" this is the average number of sites corresponding to a certain number of individuals.
• richness
  The number of species corresponding to number of sites. With method = "collector" this is the observed richness, for other methods the average or expected richness.
• sd
  The standard deviation of SAC (or its standard error). This is NULL in method = "collector", and it is estimated from permutations in method = "random", and from analytic equations in other methods.
• perm
  Permutation results with method = "random" and NULL in other cases. Each column in perm holds one permutation.

Details

Species accumulation curves (SAC) are used to compare diversity properties of community data sets using different accumulator functions. The classic method is "random" which finds the mean SAC and its standard deviation from random permutations of the data, or subsampling without replacement (Gotelli & Colwell 2001). The "exact" method finds the expected SAC using the method of Kindt (2003), and its standard deviation. Method "coleman" finds the expected SAC and its standard deviation following Coleman et al. (1982). All these methods are based on sampling sites without replacement. In contrast, the method = "rarefaction" finds the expected species richness and its standard deviation by sampling individuals instead of sites. It achieves this by applying function rarefy with number of individuals corresponding to average number of individuals per site.

The function has a plot method. In addition, method = "random" has summary and boxplot methods.

References

Coleman, B.D, Mares, M.A., Willis, M.R. & Hsieh, Y. (1982). Randomness, area and species richness. Ecology 63: 1121--1133. Gotellli, N.J. & Colwell, R.K. (2001). Quantifying biodiversity: procedures and pitfalls in measurement and comparison of species richness. Ecol. Lett. 4, 379--391.

Kindt, R. (2003). Exact species richness for sample-based accumulation curves. Manuscript.

See Also

rarefy. Underlying graphical functions are boxplot, matlines, segments and polygon.

Examples

data(BCI)
sp1 <- specaccum(BCI)
sp2 <- specaccum(BCI, "random")
sp2
summary(sp2)
plot(sp1, ci.type="poly", col="blue", lwd=2, ci.lty=0, ci.col="lightblue")
boxplot(sp2, col="yellow", add=TRUE, pch="+")