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
Nodesig(nodiv_data, Node_sp = NULL, repeats = 100, method = c("rdtable", "quasiswap"),
show = T)The return value is a list with 5 elements:
A numeric vector of the standardized difference between the empirical and simulated species richness for one node in each site
The rank of the empirical species richness of one node in the distribution of simulated values
The numerical species richness in each site
The mean simulated species richness of one node in each site
The standard deviation of the simulated species richness of one node in each site
An object of type nodiv_data
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
The number of repeats to use for the null model
The null model algorithm used in the calculations
Should a progress bar be printed during calculations?
Michael Krabbe Borregaard
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.
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
Node_analysis
data(coquettes)
res <- Nodesig(coquettes, repeats = 50)
hist(res$rval, xlim = 0:1)
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