logkda

0th

Percentile

Etienne's K(D,A)

Calculates Etienne's $K(D,A)$ using a variety of different methods

Keywords
math
Usage
logkda.R(a, use.brob=TRUE)
logkda.a11(a)
logkda.pari(a, numerical=TRUE)
logkda(a, method="pari", ...)
Arguments
a
Count object
use.brob
In function logkda.R(), Boolean, with default TRUE meaning to use Brobdingnagian numbers for the calculation. This is slower but allows one to analyze larger datasets
numerical
In function logkda.pari(), Boolean, with default TRUE meaning to return a numerical vector and FALSE meaning to return the string produced by pari/gp
method
In function logkda(), a string specifying which method to use. Takes R, a11, or pari
...
In function logkda(), further arguments which are passed to the other functions
Details

The user should use function logkda(), which is a wrapper for the other functions. Note that the default method, pari, requires the pari/gp system to be installed. This is the preferred option because it is much faster than the other methods. Functions logkda.R() and logkda.pari() calculate $K(D,A)$ using the method appearing in Etienne (2005), supplementary online material; they use R and pari/gp respectively. Function logkda.a11 is a direct implementation of formula A11 in Etienne (2005). The formula is

$$K(D,A)= \sum_{\left{a_1,\ldots,a_S|\sum a_i=A\right}} \prod_{i=1}^S\frac{ \overline{s}\left(n_i, a_i\right) \overline{s}\left(a_i, 1\right) }{ \overline{s}\left(n_i,1\right)}$$ where $\overline{s}\left(n_i,a_i\right)$ are Stirling numbers of the first kind (see logS1).

Note

If method takes its default value of pari, and pari/gp is not installed (the test is gp --version), then the method is changed to R and a warning given. Function logkda.a11() is included because the computational method is a direct transcription of formula A11; it is very slow.

It would be nice to use gp2c (rather than gp) but I can't make the -g flag work properly; and I had to hack gp2c-run to make it call gp with the -q flag

References

R. S. Etienne 2005. A New Sampling Formula for Neutral Biodiversity. Ecology Letters, volume 8, pp253--260. doi: 10.111/j.1461-0248.2004.00717.x

C. Batut and K. Belabas and D. Bernardi and H. Cohen and M. Olivier 2000. User's guide to PARI/GP. http://www.parigp-home.de/

See Also

etienne,logS1

Aliases
  • logkda
  • logkda.a11
  • logkda.R
  • logkda.pari
Examples
a <- count(c(dogs=7,pigs=3,crabs=1,hogs=1,slugs=1))

logkda(a)

logkda.R(a)
logkda.R(a, use.brob=FALSE)
logkda.a11(a)
# All four should be the same up to numerical errors
Documentation reproduced from package untb, version 1.3-3, License: GPL

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