calc_biodiv: Calculate biodiversity statistics from sites by species...

In MoBiodiv/mobr: Measurement of Biodiversity

Calculate biodiversity statistics from sites by species table.

Description

Calculate biodiversity statistics from sites by species table.

Usage

calc_biodiv(
  abund_mat,
  groups,
  index,
  effort,
  extrapolate,
  return_NA,
  rare_thres
)

Arguments

abund_mat	Sites by species table with species abundances in the respective cells
groups	Vector with group labels for the sites. The length of the vector has to correspond to the number of rows of the sites by species table.
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_asymp ... Estimated asymptotic species richness f_0 ... Estimated number of undetected species pct_rare ... The percent of species with abundances below rare_thres PIE ... Hurlbert's PIE (Probability of Interspecific Encounter) S_PIE ... Effective number of species based on PIE See the documentation of get_mob_stats for further details on the biodiversity indices.
effort	The standardized number of individuals used for the calculation of rarefied species richness. This can a be single value or an integer vector.
extrapolate	Boolean which specifies if richness should be extrapolated when effort is larger than the number of individuals using the chao1 method.
return_NA	Boolean in which the rarefaction function returns the observed S when effort is larger than the number of individuals. If set to TRUE then NA is returned. Note that this argument is only relevant when extrapolate = FALSE.
rare_thres	The threshold that determines how pct_rare is computed. It can range from (0, 1] and defaults to 0.05 which specifies that any species with less than or equal to 5 considered rare. It can also be specified as "N/S" which results in using average abundance as the threshold which McGill (2011) found to have the best small sample behavior.

Details

This function is primarily intended as auxiliary function used in get_mob_stats, but can be also used directly for data exploration.

Value

A data.frame with four columns:

• group ... Group label for sites

• index ... Name of the biodiversity index

• effort ... Sampling effort for rarefied richness (NA for the other indices)

• value ... Value of the biodiversity index

Author(s)

Felix May and Dan McGlinn

References

McGill, B. J. 2011. Species abundance distributions. Pages 105-122 Biological Diversity: Frontiers in Measurement and Assessment, eds. A.E. Magurran and B.J. McGill.

MoBiodiv/mobr documentation built on Jan. 31, 2024, 6:15 p.m.