calc_beta_div: Calculate beta diversity from sites by species table.

In mobr: Measurement of Biodiversity

Calculate beta diversity from sites by species table.

Description

A wrapper for the function calc_comm_div that only returns scales = 'beta'

Usage

calc_beta_div(abund_mat, index, effort = NA, C_target_gamma = NA, ...)

Arguments

abund_mat	Abundance based site-by-species table. Species as columns
index	The calculated biodiversity indices. The options are N ... Number of individuals (total abundance) S ... Number of species S_n ... Rarefied or extrapolated number of species for n individuals S_C ... Estimate species richness of a given level of coverage by C_target_gamma S_asymp ... Estimated asymptotic species richness f_0 ... Estimated number of undetected species pct_rare ... The percent of rare species as defined by rare_thres PIE ... Hurlbert's PIE (Probability of Interspecific Encounter) S_PIE ... Effective number of species based on PIE See Details for additional information on the biodiversity statistics.
effort	The standardized number of individuals used for the calculation of rarefied species richness. This can a be single integer or a vector of integers.
C_target_gamma	When computing coverage based richness (S_C) then this argument can be used to specify the coverage to be used for the gamma scale richness estimate. This defaults to NA in which case the target cover is computed by calc_C_target (i.e., the largest allowable sample size).
...	other arguments to pass to calc_comm_div

See Also

calc_comm_div

Examples

data(inv_comm)
beta_metrics = calc_beta_div(inv_comm, 'S_n', effort = c(5, 10))
beta_metrics

mobr documentation built on Sept. 11, 2024, 7:36 p.m.