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Create a set of climate matching outputs

Source: R/climate_match.R
climate_match.Rd

This function creates a set of climate matching outputs for a species or set of species for a region or nation.

Usage

climate_match(
  region,
  taxon_key,
  zip_file,
  scenario = "all",
  n_limit,
  cm_limit,
  coord_unc,
  BasisOfRecord,
  maps = TRUE
)

Arguments

region

(optional character) the full name of the target nation or region region can also be a custom region (sf object).

taxon_key

(character or vector) containing GBIF - taxonkey(s)

zip_file

(optional character) The path (inclu. extension) of a zipfile from a previous GBIF-download. This zipfile should contain data of the species specified by the taxon_key

scenario

(character) the future scenarios we are interested in. (default) all future scenarios are used.

n_limit

(optional numeric) the minimal number of total observations a species must have to be included in the outputs

cm_limit

(optional numeric) the minimal percentage of the total number of observations within the climate zones of the region a species must have to be included in the outputs

coord_unc

(optional numeric) the maximal coordinate uncertainty a observation can have to be included in the analysis

BasisOfRecord

(optional character) an additional filter for observations based on the GBIF field "BasisOfRecord"

maps

(boolean) indicating whether the maps should be created. (default) TRUE, the maps are created.

Value

list with:

  • unfiltered: a dataframe containing a summary per species and climate classification. The climate classification is a result of a overlay of the observations, filtered by coord_unc & BasisOfRecord, with the climate at the time of observation

  • cm: a dataframe containing the per scenario overlap with the future climate scenarios for the target nation or region and based on the unfiltered dataframe

  • filtered: the climate match dataframe on which the n_limit & climate_limit thresholds have been applied

  • future: a dataframe containing a list per scenario of future climate zones in the target nation or region

  • spatial a sf object containing the observations used in the analysis

  • current_map a leaflet object displaying the degree of worldwide climate match with the climate from 1980 till 2016

  • future_maps a list of leaflet objects for each future climate scenario, displaying the degree of climate match

  • single_species_maps a list of leaflet objects per taxon_key displaying the current and future climate scenarios

Examples

if (FALSE) { # \dontrun{
region <- "europe"

# provide GBIF taxon_key(s)
taxon_key <- c(2865504, 5274858)

# download zip_file from GBIF
# goto https://www.gbif.org/occurrence/download/0001221-210914110416597

zip_file <- "./<path to zip_file>/0001221-210914110416597.zip"

# calculate all climate match outputs
# with GBIF download
climate_match(region,
              taxon_key, 
              n_limit = 90,
              cm_limit = 0.2
)
# calculate only data climate match outputs
# using a pre-downloaded zip_file
climate_match(region,
              taxon_key, 
              zip_file,
              n_limit = 90,
              cm_limit = 0.2,
              maps = FALSE
)
# calculate climate match outputs based 
# on human observations with a 100m 
# coordinate uncertainty
climate_match(region,
              taxon_key, 
              zip_file,
              n_limit = 90,
              cm_limit = 0.2,
              coord_unc = 100,
              BasisOfRecord = "HUMAN_OBSERVATION",
              maps = FALSE
)
} # }