Summarises, for each species and habitat, how many of the species' sites
sampled the habitat, how often the species was found there, and whether
fit_isodars() would treat the habitat as used, absent or undersampled.
Run it before fitting, to decide which species and habitats can be
analysed and whether sites should be grouped (group_sites()).
Usage
check_coverage(
data,
species = NULL,
site,
habitat,
abundance,
effort = NULL,
absent_max_count = 0,
absent_min_sites = 5
)Arguments
- data
Long-format data: one row per species x site x habitat.
- species, site, habitat, abundance, effort
Long format: names of the columns holding species (optional; without it the data are one species), site (or other replicate), habitat, abundance (counts) and sampling effort (optional; without it every row has effort 1).
- absent_max_count, absent_min_sites
Thresholds for
absent = "auto"; see Details.
Value
A tibble with one row per species x habitat: species (if given),
habitat, n_sites (sites where the species was recorded in any
habitat), n_complete (of those, sites where every habitat was sampled),
n_sampled (sites where this habitat was sampled), n_occupied (sites
where the species was recorded in this habitat), total_count and
status ("used", "absent" or "undersampled").
Examples
cov <- check_coverage(moorea_fish, species = "species", site = "site",
habitat = "habitat", abundance = "abundance")
cov[cov$status != "used", ]
#> # A tibble: 325 × 8
#> species habitat n_sites n_complete n_sampled n_occupied total_count status
#> <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <chr>
#> 1 Abudefduf… outer_… 10 10 10 0 0 absent
#> 2 Abudefduf… outer_… 9 9 9 0 0 absent
#> 3 Acanthuru… barrie… 7 7 7 0 0 absent
#> 4 Acanthuru… fringi… 7 7 7 0 0 absent
#> 5 Acanthuru… barrie… 1 1 1 0 0 under…
#> 6 Acanthuru… outer_… 1 1 1 0 0 under…
#> 7 Acanthuru… barrie… 3 3 3 0 0 under…
#> 8 Acanthuru… barrie… 1 1 1 0 0 under…
#> 9 Acanthuru… fringi… 1 1 1 0 0 under…
#> 10 Acanthuru… barrie… 1 1 1 0 0 under…
#> # ℹ 315 more rows