| Nodesig {nodiv} | R Documentation |
Compare the distributions of a pair of sister clades
Description
Compares the overlap of species richness of a pair of sister clades to the expectation from a null model. By default, the function compares the two descendants from the basal node of the phylogeny
Usage
Nodesig(nodiv_data, Node_sp = NULL, repeats = 100, method = c("rdtable", "quasiswap"),
show = T)
Arguments
nodiv_data |
An object of type |
Node_sp |
A character or numeric vector indicating which species that belong to one of the clades. If NULL, the species of a descendant from the basal node of nodiv_data is chosen randomly |
repeats |
The number of repeats to use for the null model |
method |
The null model algorithm used in the calculations |
show |
Should a progress bar be printed during calculations? |
Details
The \"rdtable\" algorithm is efficient, but may underestimate the deviation between nodes. It should primarily be used for exploratory data analysis. Note that the more robust \"quasiswap\" algorithm may take hours to run on data sets with a few hundred species.
Value
The return value is a list with 5 elements:
SR |
A numeric vector of the standardized difference between the empirical and simulated species richness for one node in each site |
rval |
The rank of the empirical species richness of one node in the distribution of simulated values |
nodeemp |
The numerical species richness in each site |
nodemeans |
The mean simulated species richness of one node in each site |
nodesds |
The standard deviation of the simulated species richness of one node in each site |
Author(s)
Michael Krabbe Borregaard
References
Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283
See Also
Examples
data(coquettes)
res <- Nodesig(coquettes, repeats = 50)
hist(res$rval, xlim = 0:1)