optimal.params.gst
From untb v1.6-5
by Robin K S Hankin
Estimation of local immigration using GST(k) statistics
Functions optimal.params.gst()
, GST.k()
and I.k()
apply to count data collected over a network of community samples k
(species by sample matrix). A theoretical relationship between
GST(k)
statistics and local immigration numbers I(k)
, in
the context of a spatially-implicit neutral community model (Munoz et
al 2008), is used to provide GST(k)
and I(k)
statistics
any sample k.
If requested, optimal.params.gst()
further provides the user with
confidence bounds.
- Keywords
- optimize
Usage
optimal.params.gst(D, exact = TRUE, ci = FALSE, cint = c(0.025, 0.975), nbres = 100)
GST.k(D, exact = TRUE)
I.k(D, exact = TRUE)
Arguments
- D
- A data table including species counts in a network of community samples (columns)
- exact
- If
TRUE
, exact similarity statistics are calculated (sampling without replacement) while, if false, approximate statistics (sampling with replacement) are considered (see Munoz et al 2008 for further statistical discussion) - ci
- Specifies whether bootstraps confidence intervals of immigration estimates are to be calculated
- cint
- Bounds of the confidence interval, if
ci = TRUE
- nbres
- Number of rounds of the bootstrap procedure for confidence interval calculation, if ci = T
Value
GST A vector of 0 to 1 GST(k)
numbers (specific output ofGST.k
)nk Number of individuals within samples (length = number of samples) distrib Species counts of the merged dataset (output of GST.k
andI.k
)I Immigration estimates (output of I.k
andoptimal.params.gst
)m Corresponding immigration rates (output of I.k
andoptimal.params.gst
). Specific outputs ofoptimal.params.gst
when ci = T (bootstrap procedure)Ici Confidence interval of I(k)
mci Confidence interval of m(k)
Iboot Table of bootstrapped values of I(k)
mboot Table of bootstrapped values of i m(k)
References
Francois Munoz, Pierre Couteron and B.R. Ramesh
(2008).
See Also
Examples
data(ghats)
optimal.params.gst(ghats)
Community examples
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