In EDIorg/ecocomDP: Tools to Create, Use, and Convert ecocomDP Data

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
options(tibble.print_min = 4L, tibble.print_max = 4L)

library(ecocomDP)

Converting ecocomDP data to another model format can be as simple as calling a single function. We currently support conversion to the Darwin Core Archive (DwC-A) Event Core.

DwC-A Event Core

mypath <- paste0(tempdir(), "/dwca")
dir.create(mypath)

convert_to_dwca(
  path = mypath, 
  core_name = "event", 
  source_id = "edi.193.5", 
  derived_id = "edi.834.2", 
  user_id = "ecocomdp",
  user_domain = "EDI")
#> Reading edi.193.5
#>  [0%] Downloaded 0 bytes...
#>  [0%] Downloaded 0 bytes...
#>  [0%] Downloaded 0 bytes...
#>  [0%] Downloaded 0 bytes...
#>  [0%] Downloaded 0 bytes...
#>  [0%] Downloaded 0 bytes...
#>  [0%] Downloaded 0 bytes...
#>  [0%] Downloaded 0 bytes...
#>
#> Validating edi.193.5:
#>   Required tables
#>   Column names
#>   Required columns
#>   Column classes
#>   Datetime formats
#>   Primary keys
#>   Composite keys
#>   Referential integrity
#>   Latitude and longitude format
#>   Latitude and longitude range
#>   Elevation
#>
#> Creating DwC-A Event Core tables
#> Creating DwC-A Event Core EML
#> Reading EML of L1 data package edi.193.5
#> Reading EML of L0 data package knb-lter-hfr.118.33
#> Creating EML of L2 data package edi.834.2
#> Updating:
#>   <eml>
#>   <access>
#>   <dataset>
#>   <alternateIdentifier>
#>   <title>
#>   <pubDate>
#>   <abstract>
#>   <keywordSet>
#>   <methods>
#>   <dataTable>
#>   <otherEntity>
#>   <annotations>
#>   </eml>
#>   Writing EML
#> Validating EML
#> Validation passed :)
#> Done.

And there you have it! The DwC-A tables and metadata ready for publication in GBIF!

dir(mypath)
#> [1] "edi.834.2.xml"                 "event.csv"                     "extendedmeasurementorfact.csv"
#> [4] "meta.xml"                      "occurrence.csv" 

EDIorg/ecocomDP documentation built on Aug. 22, 2024, 9:34 a.m.