Tally number of species observations based on specified criteria

Wrapper function to filter_observations() which filters species observations from biodiversity surveys, based on specified criteria. Subsequently tallies the number of species per survey/sampling point (similar to function specnumber() in package vegan), and extracts output data. If tallied at the level of sampling points (level = 'point'), removes taxon group-level (genus/family) if all species within group are observed at the point (& period), using the function check_taxongrps(). Data on both the biodiversity surveys and their species observations (and respective abundances) must be provided.

Usage

tally_observations(
  observations,
  survey_ref,
  level = "point",
  specify_taxon = NULL,
  specify_area = NULL,
  specify_period = NULL,
  survey_id = "survey_id",
  area = "area",
  period = "period",
  taxon = "taxon",
  point_id = "point_id",
  species = "species",
  genus = "genus",
  family = "family",
  abundance = "abundance"
)

Arguments

observations: Dataframe of species observations. It should include columns for survey_id, area, period, taxon, species and abundance.
survey_ref: Dataframe of all surveys conducted. Values in the column survey_id should correspond to those in the observations.
level: Specify whether to tally by 'survey' or 'point' (character). Defaults to 'point'.
specify_taxon: Specify the taxon of interest (character). Defaults to NULL, which includes all taxa.
specify_area: Specify the area (character). Defaults to NULL, which includes all areas.
specify_period: Specify the survey period (character). Defaults to NULL, which includes all periods.
survey_id: Column name of the unique identifier for each survey in observations and survey_ref. Defaults to survey_id.
area: Column name of the area specified in observations and survey_ref. Defaults to area.
period: Column name of the sampling period specified in observations and survey_ref. Defaults to period.
taxon: Column name of the taxon of interest specified in observations and survey_ref. Defaults to taxon.
point_id: Column name of the unique identifier for each sampling point specified in observations and survey_ref. Defaults to point_id.
species: Column name of the species specified in observations. Defaults to species.
genus: Column name of the genus specified in observations. Defaults to genus. Used to remove genus-level records in the species column, if all species within the group are observed within the filtered dataset.
family: Column name of the family specified in observations. Defaults to family. Used to remove family-level records in the species column, if all species within the group are observed within the filtered dataset.
abundance: Column name of the species abundance specified in observations. Defaults to abundance.

Value

A dataframe containing the tally of species per survey/sampling point (depends if level ='survey' or 'point').