Calculation of statistics at plot levelSource:
Calculation of diversity statistics at the plot level allowing for customized
functions defined as
foo(x, ...), where
x is the vector of abundance
dominance() calculate the
diversity index of Shannon, the evenness, and the dominance
(1 - evenness), respectively.
Dominance is the complementary value to evenness (i.e.
1 - evenness).
simpson() calculates the Simpson's index using the alternative
for vegetation plot observations.
richness() counts the number of taxa per plot and can be used
as alternative to vegtable::count_taxa.
shannon(x, na.rm = TRUE, ...) evenness(x, ...) dominance(x, ...) simpson(x, na.rm = TRUE, ...) richness(x, na.rm = TRUE, ...) veg_diversity(object, ...) # S3 method for vegtable veg_diversity( object, weight, FUN = shannon, aggr_fun = mean, arg_fun = list(), var_name, in_header = TRUE, ... )
A numeric vector containing the abundance of single species.
A logical value indicating whether NA values should be removed from the abundance vector or not.
Further arguments passed among methods. In
'dominance()', these arguments are passed to
'veg_diversity()', these arguments are passed to
A vegtable object.
A character value indicating the name of the column at slot samples which will be used as species abundance.
A function used to calculate the diversity index.
A function used to aggregate abundance values for multiple records of a taxon in a plot observation. Average value is used by default.
A named list with parameters and arguments passed to
taxa2samples(), which will retrieve the respective taxon concept for each taxon usage name and can be used to merge taxa at a determined taxonomic rank, for instance to merge all sub-specific taxa into their respective species (i.e.
'merge_to = "species"').
A character value used as name for the calculated index. If missing, the name of the function will be used.
A logical value indicating whether the results should be included as variables in the slot header of the input object. If
'in_header = TRUE', you may assign the result of the function to the input object.
richness() return a numeric value (the calculated index).
veg_diversity() produce either a data frame with calculated values
per plot observation (option
'in_header = FALSE') or a vegtable
object with the calculated values inserted in the slot header
'in_header = TRUE').