7 GRIIS mapping

In this chapter we export the unified information to an Excel template that can be used by the Global Register of Introduced and Invasive Species (GRIIS).

7.1 Read Darwin Core data

dwc_taxon <- read_csv(here("data", "processed", "taxon.csv"))
dwc_distribution <- read_csv(here("data", "processed", "distribution.csv"))
dwc_speciesprofile <- read_csv(here("data", "processed", "speciesprofile.csv"))

Select only national distributions

7.2 GRIIS format

7.2.1 Pre-processing

  1. Check if the taxon core, distribution extension and species profile extension contain only one row per taxonID.
## [1] TRUE
## [1] TRUE
## [1] TRUE
  1. Join the 3 files into one dataframe griis.

7.2.2 Term mapping

7.2.2.1 taxonID

griis %<>% mutate(griis_taxonID = taxonID)

7.2.2.2 countryCode

griis %<>% mutate(griis_countryCode = countryCode)

7.2.2.3 island

griis %<>% mutate(griis_island = "")

7.2.2.4 scientificName

griis %<>% mutate(griis_scientificName = scientificName)

7.2.2.5 acceptedNameUsage

griis %<>% mutate(griis_acceptedNameUsage = case_when(
  acceptedNameUsage != scientificName ~ acceptedNameUsage,
  TRUE ~ ""
))

7.2.2.6 taxonRank

griis %<>% mutate(griis_taxonRank = taxonRank)

7.2.2.7 taxonomicStatus

griis %<>% mutate(griis_taxonomicStatus = taxonomicStatus)

7.2.2.8 kingdom

griis %<>% mutate(griis_kingdom = kingdom)

7.2.2.9 phylum

griis %<>% mutate(griis_phylum = phylum)

7.2.2.10 class

griis %<>% mutate(griis_class = class)

7.2.2.11 order

griis %<>% mutate(griis_order = order)

7.2.2.12 family

griis %<>% mutate(griis_family = family)

7.2.2.13 habitat

griis %<>% mutate(griis_habitat = habitat)

7.2.2.14 occurrenceStatus

griis %<>% mutate(griis_occurrenceStatus = occurrenceStatus)

7.2.2.15 establishmentMeans

griis %<>% mutate(griis_establishmentMeans = recode(establishmentMeans,
  "introduced" = "alien",
  .default = "",
  .missing = ""
))

7.2.2.16 isInvasive

griis %<>% mutate(griis_isInvasive = case_when(
  is.na(isInvasive) ~ "Null"
))

7.2.3 eventDate

griis %<>% mutate(griis_eventDate = eventDate)

7.3 Post-processing

  1. Only keep the GRIIS columns.

  2. Drop the griis_ prefix.

  3. Sort on scientificName (the default for GRIIS lists).

  4. Preview data:

  1. Save to Excel.