dwcPrepare

Overview

The goal of dwcPrepare is to make it easier to prepare biodiversity data that use Darwin Core terms.

It can be used to generate Darwin Core Event and Location terms from your data set for submission to a service that uses the Darwin Core Archive (e.g. GBIF and ALA).

For users with established data processing pipelines, the most useful utility functions are likely to be dwc_coordinateUncertaintyInMeters(), which as the name suggests, calculates the coordinateUncertaintyInMeters, and the dwc_locality() function that provides text for the Darwin Core locality term.

Installation

You can install the development version of dwcPrepare from GitHub with:

# install.packages("devtools")
devtools::install_github("jdberson/dwcPrepare")

Getting started

All functions in the package start with dwc_ as the prefix, generally followed by the name of the Darwin Core field. For example, dwc_coordinateUncertaintyInMeters() will calculate the value for the Darwin Core coordinateUncertaintyInMeters field.

Exceptions to this rule are utility functions (dwc_format_gco(), dwc_point_cluster() and dwc_polygon_cluster()) or if a function returns multiple Darwin Core fields (dwc_coordinates(), dwc_country_to_county(), dwc_Event() and dwc_Location()).

The dwc_Event() and dwc_Location() functions provide wrappers that can be used with dplyr::mutate() to generate the Darwin Core Event and Location terms supported by dwcPrepare.

For example, using the toy dataset that comes shipped with the package:

# Load packages
library("dwcPrepare")
library("dplyr")
library("tibble")

# Load data
data("thylacine_data")

# Use dplyr::mutate() with dwc_Event() to generate Darwin Core Event fields
thylacine_data |>
  mutate(
    dwc_Event(
      start = date_trap_setup,
      end = date_trap_collected,
      tzone = "Australia/Hobart",
      samplingEffort = "1 trap"
    )
  )

# Use dplyr::mutate() with dwc_Location() to generate Darwin Core Location fields
thylacine_data |>
  mutate(
    dwc_Location(
      longitude = longitude_dd,
      latitude = latitude_dd,
      verbatimCoordinateSystem = "decimal degrees",
      verbatimSRS = "EPSG:4326",
      gps_uncertainty = gps_uncertainty,
      localities_sf = locality_data_aus,
      localities_names = "locality_name",
      county_sf = county_tas
    )
  )

See vignette("dwcPrepare") for more help with getting started.

Citation

The package can be cited as:

Berson J, Manger J (2023). dwcPrepare: Helps Prepare Data for use in a Darwin Core Archive. R package version 0.0.0.9000, https://github.com/jdberson/dwcPrepare.

Issues

If you find an error or a bug we would love to hear from you! Please let us know what you have found by creating an issue at https://github.com/jdberson/dwcPrepare/issues.