In GBIF-Europe/darwinator: Darwin Core Archive Tools For Sampling Event Data

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Introduction

darwinator is an R package that can download sampling event datasets published at GBIF.org from IPT installations.

Installing from github

If you want to install the latest version of the darwinator package from github, you can do it like so:

# First make sure you have the devtools package
# which simplifies installations from github
# Note: Windows users have to first install Rtools to use devtools

install.packages("devtools") 
devtools::install_github("GBIF-Europe/darwinator")

# install a specific released version:
# devtools::install_github("GBIF-Europe/darwinator@v0.1.1")

Quick start

To see some quick usage examples to get you started, open the Vignette.

Load the package in your R environment:

library(darwinator)
sed <- sampling_event_data("78360224-5493-45fd-a9a0-c336557f09c3")

df <- sed$data
dwca <- sed$dwca
citation <- sed$meta$citation

The package bundles a dataset with recommended Darwin Core terms. The labels for the Darwin Core terms can for example be used for validating column names in sampling event datasets. The terms data can be accessed like so:

library(darwinator)
dwc_terms

# read documentation for the dataset
?dwc_terms

Another example - get all GBIF dataset identifiers for Norwegian sampling event based datasets using rgbif. Then download all sampling event data from Norway saving it locally to enable off-line work.

library(tidyverse)
library(rgbif)
library(darwinator)

# make a search for all Norwegian sampling event dataset identfiers
search <-
  dataset_search(
    type = "SAMPLING_EVENT",
    publishingCountry = "NO"
  )
keys <- search$data$datasetKey

# use dplyr::possibly to wrap the sampling_event_data function
# so that it returns NULL if it fails on a particular dataset
library(purrr)
psed <- possibly(function(key) sampling_event_data(key), NULL)
norway <- map(keys, psed)

# exclude failed requests
fails <- unlist(map(norway, is.null))
failed_keys <- keys[fails]
successful_downloads <- norway[!fails]

# save all successful downloads
saveRDS(dl_success, "norway-sed.Rds")

# a report of parsing issues can be generated like this:
parsing_issues <- map_df(successful_downloads, c("dwca", "parsing_issues"))
readr::write_excel_csv(issues_norway, "issues-norway.csv")

For more usage examples, please see the vignette.

Meta

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

• Please report any issues or bugs.
• License: AGPL

GBIF-Europe/darwinator documentation built on May 29, 2019, 12:06 a.m.