Skip to contents

Create key collections module

create_native_report.Rd

Create an overview of key collections within a living collection including threatened species, endemic species, native species and trees.

Usage

create_native_report(
  enriched_report,
  coordinates = NULL,
  wgsrpd3 = NULL,
  wcvp = NULL,
  collection = NULL,
  native = "Naturally occurring only",
  extinct = TRUE,
  doubtful_locations = FALSE,
  min_year = 1970,
  output_dir = NULL,
  earliest_allowable_record = 1700,
  old_accession_year_codes = NULL,
  bru_codes = NA
)

create_endemic_report(
  enriched_report,
  collection = NULL,
  wgsrpd3 = NULL,
  wcvp = NULL,
  endemic_species_per_region = NULL,
  coordinates = NA,
  output_dir = NULL,
  native = "Naturally occurring only",
  extinct = TRUE,
  doubtful_locations = FALSE,
  min_year = 1970,
  earliest_allowable_record = 1700,
  old_accession_year_codes = NULL
)

create_threatened_report(
  enriched_report,
  collection = NULL,
  wgsrpd3 = NULL,
  wcvp = NULL,
  detailed_IUCN_redlist = NULL,
  coordinates = NA,
  output_dir = NULL,
  native = "Naturally occurring only",
  extinct = TRUE,
  doubtful_locations = FALSE,
  min_year = 1970,
  earliest_allowable_record = 1700,
  old_accession_year_codes = NULL
)

create_trees_report(
  enriched_report,
  collection = NULL,
  wgsrpd3 = NULL,
  wcvp = NULL,
  coordinates = NA,
  output_dir = NULL,
  native = "Naturally occurring only",
  extinct = TRUE,
  doubtful_locations = FALSE,
  min_year = 1970,
  earliest_allowable_record = 1700,
  old_accession_year_codes = NULL
)

Arguments

enriched_report

The enriched report of a living collection (created in BGsmartR)

coordinates

The coordinates of the collection (long, lat).

wgsrpd3

World Geographical Scheme for Recording Plant Distributions. Containing polygons of each level 3 area. Can be obtained from rWCVP package.

wcvp

World Checklist of Vascular Plants (WCVP) database, obtained using the function import_wcvp_names().

collection

The name of the living collection

native

string where 'Naturally occurring only' or 'Introduced only' reduces the locations used to determine native plants.

extinct

Flag (TRUE/FALSE) for whether to include extinct geographic locations.

doubtful_locations

Flag (TRUE/FALSE) for whether to include doubtful locations.

min_year

The minimum year for analyses over time.

output_dir

The output directory

earliest_allowable_record

Number, corresponding to the minimum allowable year in the "AccYear" column.

old_accession_year_codes

Vector of numbers corresponding to values within "AccYear" that indicate that a record is old with unknown accession year. For our analyses over time we assume these records are accessioned on earliest_allowable_record.

bru_codes

A vector of the BRU level 3 codes that want to be considered as the native regions in the report.

endemic_species_per_region

A data frame detailing the number of accepted endemic species found in WCVP for each region in wgsrpd3. (if running multiple reports saves having to do the calculation each time)

detailed_IUCN_redlist

A data frame containing the history and geography of IUCN redlist information.

Value

html report