Skip to contents

Summarise niche breadth results and their diagnostics

Source: R/niche_breadth.R
summary.niche_breadth.Rd

Summarises a niche_breadth() result: how many species have estimates, the range of niche breadth values, and for each diagnostic flag how many species raised it, what it means and what to do about it.

Usage

# S3 method for class 'niche_breadth'
summary(object, ...)

# S3 method for class 'summary.niche_breadth'
print(x, ...)

Arguments

object

The output of niche_breadth().

...

Ignored.

x

The output of summary().

Value

An object of class summary.niche_breadth: a list with n_species, n_estimated (species with DI and DD niche breadth), n_clean (estimated species with no warning flags), clean (their names, or row numbers without a species column), estimates (quartiles of nb_di, spillover_abundance and nb_dd), flags (a data frame with flag, type, n, meaning and advice, for the flags raised) and settings. Flags of type "info" (abandoned habitats, preference reversals) describe the species and are not warnings.

See also

niche_breadth(), vignette("diagnostics")

Examples

three <- moorea_fish[moorea_fish$species %in% c("Acanthurus nigrofuscus",
  "Scarus schlegeli", "Siganus argenteus"), ]
nb <- niche_breadth(three, species = "species", site = "site",
                    habitat = "habitat", abundance = "abundance",
                    n_boot = 0, seed = 1)
summary(nb)
#> Niche breadth for 3 species
#>   DD niche breadth at: asymptote; bootstrap replicates: 0
#>   with DI and DD estimates: 3
#>   without warning flags:    1
#> 
#> Estimates (quartiles):
#>                        min    q25 median    q75     max
#> nb_di                0.143  0.151  0.159  0.314   0.468
#> spillover_abundance 30.000 36.000 42.000 87.500 133.000
#> nb_dd                0.010  0.188  0.365  0.382   0.399
#> 
#> Flags raised (species):
#>   poor_fit               2  a line does not describe the data well, or the pairwise isodars disagree
#>                             -> check the isodars (fit_isodars()); try the other method
#>   reversal               3  habitats change rank along the niche breadth curve
#>                             -> informational: compare species at a stated abundance (see iai_curve())
#>   abandoned              2  a used habitat is abandoned at high density
#>                             -> informational: the habitat counts for DI but not for DD niche breadth
#> 
#> See vignette("diagnostics") for details. Thresholds are set with niche_breadth(diagnostics = ).