getBetaMetrics: Beta diversity metrics

In BioTIMEr: Tools to Use and Explore the 'BioTIME' Database

Beta diversity metrics

Description

Calculates a set of standard beta diversity metrics

Usage

getBetaMetrics(x, measure)

Arguments

x	(data.frame) BioTIME data table in the format of the output of the gridding function and/or resampling functions.
measure	(character) chosen currency defined by a single column name.

Details

The function getBetaMetrics computes three beta diversity metrics for a given community data frame, where measure is a character input specifying the abundance or biomass field used for the calculations. getBetaMetrics calls the vegdist function which calculates for each row the following metrics: Jaccard dissimilarity (method = "jaccard"), Morisita-Horn dissimilarity (method = "horn") and Bray-Curtis dissimilarity (method = "bray"). Here, the dissimilarity metrics are calculated against the baseline year of each assemblage time series i.e. the first year of each time series. Note that the input data frame needs to be in the format of the output of the gridding and/or resampling functions, which includes keeping the default BioTIME data column names. If such columns are not found an error is issued and the computations are halted.

Value

Returns a data.frame with results for Jaccard dissimilarity (JaccardDiss), Morisita-Horn dissimilarity (MorisitaHornDiss), and Bray-Curtis dissimilarity (BrayCurtsDiss) for each year and assemblageID.

Examples

x <- data.frame(
  resamp = 1L,
  YEAR = rep(rep(2010:2015, each = 4), times = 4),
  Species = c(replicate(
   n = 8L,
   sample(letters, 24L, replace = FALSE))),
  ABUNDANCE = rpois(24 * 8, 10),
  assemblageID = rep(LETTERS[1L:8L], each = 24)
  )

res <- getBetaMetrics(x, measure = "ABUNDANCE")

BioTIMEr documentation built on Sept. 14, 2024, 9:09 a.m.