createRegions: Use hierarchical clustering to group sites into...

In nicholasjclark/BBS.occurrences: BBS community composition and co-occurrence analysis

Description

Use hierarchical clustering to group sites into biogeographical regions based on similarity in avian species composition

Usage

createRegions(dist_weights, n_cores)

Arguments

dist_weights	Optional list giving relative weights (as integers) for the six different distance matrices when creating the final weighted matrix. The six matrices are: species composition, latitude, longitude, mean annual precipitation, mean minimum temperature and mean maximum temperature. Default is to only use species composition, latitude, longitude with equal weights
n_cores	Positive integer stating the number of processing cores to split the job across. Default is parallel::detect_cores() - 1

Details

Distance matrices are created for each of the six site-level parameters. Species composition is calculated by considering the presence-absence of species at each site, where a presence is recorded only if that species has been observed in that site on at least five of the seven total BBS surveys. A mean distance is then calculated from the six different matrices using the specified weights in dist_weights. Hierachical clustering is then performed and the resulting dendrogram is cut to group sites into broader biogeographical regions. Separate grouping is performed for each flyway in Site.descriptors

Value

A dataframe that contains the Site.descriptors along with a new column describing the bioregions

nicholasjclark/BBS.occurrences documentation built on July 19, 2020, 8:31 p.m.