Relative frequency of species given sampling effort

Proportion of visits in which a species was detected (n_occupied / n_visits). Empty visits stay in the denominator. This is naive occupancy, not a detection-corrected model.

Usage

obs_frequency(
  x,
  by = "species",
  period = "month",
  location = NULL,
  user = NULL,
  species = NULL,
  group = NULL,
  protocol = NULL,
  date = NULL,
  date_start = NULL,
  date_end = NULL
)

Arguments

x: Path to a project SQLite export, a project obs_df, or a visit tibble from obs_visits().
by: Grouping besides species: "species" (default, overall), "location", "period", or a combination.
period: When by includes "period": "month" (default), "year", "week" (ISO) or "day".
location: Location id or name (partial match). Restricts effort.
user: Observer id or name. Restricts effort.
species: Scientific or common name (partial match). Restricts the reported taxa, not the visits.
group: Species group name. Restricts the reported taxa.
protocol: Protocol id or name. Restricts effort.
date: Length-2 vector c(start, end) as "YYYY-MM-DD", or a single date.
date_start, date_end: Bounds on visit.start_date.

Value

A tibble with n_visits, n_occupied and frequency.

Details

location, user, protocol and dates restrict the visit set (the effort). species and group restrict which taxa are reported; they do not drop visits without those taxa.

A visit counts as occupied when the species has at least one record with number missing or greater than zero. Records with number = 0 are absences.

When visit.counted is in the export, visits whose completeness does not allow a frequency analysis (counted other than s or i) emit a warning. They are still included. If the column is absent, nothing is warned.

Examples

if (FALSE) { # \dontrun{
obs_frequency("project-export.sqlite")
obs_frequency(db, by = "location")
obs_frequency(db, species = "Bufo bufo", by = "period")
} # }