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Create diversity module

create_taxonomic_diversity_report.Rd

Taxonomic Diversity:Taxonomic presentation and composition in a collection. Geography: Geographic representation of a collection.

Usage

create_taxonomic_diversity_report(
  enriched_report,
  collection = NULL,
  wcvp = NULL,
  PlantClassification = BGSmartR::Diversity_classification$Classification,
  min_year = 1970,
  earliest_allowable_record = 1700,
  old_accession_year_codes = NULL,
  output_dir = NULL
)

create_geography_report(
  enriched_report,
  collection = NULL,
  wgsrpd3 = NULL,
  wcvp = NULL,
  detailed_IUCN_redlist = NULL,
  native = "Naturally occurring only",
  extinct = TRUE,
  doubtful_locations = FALSE,
  output_dir = NULL,
  endemic_species_per_region = NULL,
  accepted_species_per_region = NULL,
  tree_species_per_region = NULL,
  do_download = TRUE
)

Arguments

enriched_report

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

collection

The name of the living collection

wcvp

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

PlantClassification

plant classification information

min_year

The minimum year for analyses over time.

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.

output_dir

The output directory

wgsrpd3

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

detailed_IUCN_redlist

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

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.

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)

accepted_species_per_region

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

tree_species_per_region

A data frame detailing the number of accepted trees (unique records in WCVP, including subspecies, etc) found in WCVP for each region in wgsrpd3. (if running multiple reports saves having to do the calculation each time)

do_download

A flag (TRUE/FALSE) for whether the download buttons are included.