Nodesig: Compare the distributions of a pair of sister clades

In nodiv: Compares the Distribution of Sister Clades Through a Phylogeny

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 nodiv_data
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

Node_analysis

Examples

data(coquettes)
res <- Nodesig(coquettes, repeats = 50)
hist(res$rval, xlim = 0:1)

nodiv documentation built on Aug. 21, 2023, 9:10 a.m.