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Create collection dynamics module

create_trends_report.Rd

Trends: Evolution over time of the capacity and diversity of a collection. Turnover: Dynamics of the gained and lost plants each year.

Usage

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

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

Arguments

enriched_report

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

collection

The name of the living collection

min_year

The minimum year for analyses over time.

coordinates

The coordinates of the collection (long, lat).

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.

wgsrpd3

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

data_type

Either "Accessions" or "Items". Specifies the quantity to use when looking at the trends of provenance, native species, endemic species and threatened species.

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