Extract species accumulation curves based on specified criteria

Wrapper function to filter_observations() which filters species observations from biodiversity surveys, based on specified criteria. Subsequently forms community matrix, and removes taxon group-level (genus/family) if all species within group are observed in the area (& period), using the function check_taxongrps(). Finally, runs the function specaccum() in package vegan, and extracts output data. Data on both the biodiversity surveys and their species observations (and respective abundances) must be provided.

Usage

calculate_sac(
  observations,
  survey_ref,
  specify_area,
  specify_period,
  specify_taxon,
  survey_id = "survey_id",
  area = "area",
  period = "period",
  taxon = "taxon",
  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.
specify_area: Specify the area.
specify_period: Specify the survey period.
specify_taxon: Specify the taxon group of interest.
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.
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 with columns for the sites, species richness and sd (standard deviation) of results, as well as the information specified in specify_area, specify_period and specify_taxon.