labdsv (version 1.8-0)

abuocc: Abundance/Occurrence Graphical Analysis

Description

Calculates and plots summary statistics about species occurrences in a data frame

Usage

abuocc(taxa,minabu=0,panel='all')

Arguments

taxa

a taxon data.frame with samples as rows and species as columns

minabu

a minimum abundance threshold species must exceed to be included in the calculations (default=0)

panel

controls which of three graphs is drawn, and can be 'all' or integers 1-4

Value

Returns an (invisible) list composed of:

spc.plt

number of species/sample

plt.spc

number of samples each species occurs in

mean

mean abundance of each species when present (excluding values smaller than minabu)

Details

This functions calculates and plots four data summaries about the occurrence of species:

Plots:

1) the number of samples each species occurs in on a log scale, sorted from maximum to minimum

2) the number of species in each sample plot (species richness) from highest to lowest

3) the mean abundance of non-zero values (on a log scale) as a function of the number of plots a species occurs in

4) the total abundance/sample as a function of the plot-level species richness

The third plot allows you to identify individual species with the mouse; the fourth plot allows you to identify individual samples with the mouse.

References

http://ecology.msu.montana.edu/labdsv/R/labs/lab1/lab1.html

See Also

fisherfit, prestonfit, radfit

Examples

# NOT RUN {
    data(bryceveg) # produces a data.frame called bryceveg
    abuocc(bryceveg)
# }