Title:	Parse Darwin Core Files
Description:	Parse and create Darwin Core (http://rs.tdwg.org/dwc/) Simple and Archives. Functionality includes reading and parsing all the files in a Darwin Core Archive, including the datasets and metadata; read and parse simple Darwin Core files; and validation of Darwin Core Archives.
Version:	0.4.0
License:	MIT + file LICENSE
LazyData:	true
URL:	https://docs.ropensci.org/finch/, https://github.com/ropensci/finch
BugReports:	https://github.com/ropensci/finch/issues
Encoding:	UTF-8
Imports:	xml2 (≥ 1.0.0), EML (≥ 2.0.0), data.table (≥ 1.10.0), digest, hoardr (≥ 0.2.0)
Suggests:	testthat, crul, jsonlite
RoxygenNote:	7.1.1
X-schema.org-applicationCategory:	Biology
X-schema.org-keywords:	biology, occurrences, specimen, biodiversity, collections, species
X-schema.org-isPartOf:	https://ropensci.org
NeedsCompilation:	no
Packaged:	2020-08-10 21:48:08 UTC; sckott
Author:	Scott Chamberlain [aut, cre]
Maintainer:	Scott Chamberlain <myrmecocystus@gmail.com>
Repository:	CRAN
Date/Publication:	2020-08-11 04:50:02 UTC

finch

Description

Parse Darwin Core Archive files

Author(s)

Scott Chamberlain myrmecocystus@gmail.com

Convert a path or URL to a location object

Description

Convert a path or URL to a location object

Usage

as.location(x, ...)

## S3 method for class 'character'
as.location(x, ...)

## S3 method for class 'location'
as.location(x, ...)

## S3 method for class 'location'
print(x, ...)

Arguments

Examples

# A zip file
file <- system.file("examples/0000154-150116162929234.zip",
  package = "finch")
as.location(file)

# A directory
dir <- system.file("examples/0000154-150116162929234",
  package = "finch")
as.location(dir)

# A URL
as.location("https://httpbin.org/get")

Caching

Description

Manage cached finch files with package hoardr

Details

The dafault cache directory is paste0(rappdirs::user_cache_dir(), "/R/finch"), but you can set your own path using cache_path_set()

cache_delete only accepts one file name, while cache_delete_all doesn't accept any names, but deletes all files. For deleting many specific files, use cache_delete in a lapply() type call

Useful user functions

• dwca_cache$cache_path_get() get cache path

• dwca_cache$cache_path_set() set cache path

• dwca_cache$list() returns a character vector of full path file names

• dwca_cache$files() returns file objects with metadata

• dwca_cache$details() returns files with details

• dwca_cache$delete() delete specific files

• dwca_cache$delete_all() delete all files, returns nothing

Examples

## Not run: 
dwca_cache

# list files in cache
dwca_cache$list()

# delete certain database files
# dwca_cache$delete("file path")
# dwca_cache$list()

# delete all files in cache
# dwca_cache$delete_all()
# dwca_cache$list()

# set a different cache path from the default

## End(Not run)

This function is defunct.

Description

This function is defunct.

Usage

dwca_cache_delete(...)

This function is defunct.

Description

This function is defunct.

Usage

dwca_cache_delete_all(...)

This function is defunct.

Description

This function is defunct.

Usage

dwca_cache_details(...)

This function is defunct.

Description

This function is defunct.

Usage

dwca_cache_list(...)

Parse Darwin Core Archive

Description

Parse Darwin Core Archive

Usage

dwca_read(input, read = FALSE, ...)

Arguments

Details

Note that sometimes file reads fail. We use data.table::fread() internally, which is very fast, but can fail sometimes. If so, try reading in the data manually.

When you pass in a URL, we use rappdirs to determine cache path, and if you pass the same URL again, and your cache is not cleared, we'll pull from the cache. Passing a file or directory on your local system won't invoke the caching route, but will go directly to the file/directory.

Examples

## Not run: 
# set up a temporary directory for the example
dwca_cache$cache_path_set(path = "finch", type = "tempdir")

dir <- system.file("examples", "0000154-150116162929234", package = "finch")

# Don't read data in
(x <- dwca_read(dir, read=FALSE))
x$files
x$highmeta
x$dataset_meta[[1]]
x$data

# Read data
(x <- dwca_read(dir, read=TRUE))
head(x$data[[1]])

# Can pass in a zip file
zip <- system.file("examples", "0000154-150116162929234.zip",
  package = "finch")
(out <- dwca_read(zip))
out$files
out$highmeta
out$emlmeta
out$dataset_meta

# Can pass in zip file as a url
url <-
"https://github.com/ropensci/finch/blob/master/inst/examples/0000154-150116162929234.zip?raw=true"
(out <- dwca_read(url))

# another url
url <- "http://ipt.jbrj.gov.br/jbrj/archive.do?r=redlist_2013_taxons&v=3.12"
(out <- dwca_read(url))

## End(Not run)

Validate a Darwin Core Archive

Description

Validate a Darwin Core Archive

Usage

dwca_validate(x, ifModifiedSince = NULL, browse = FALSE, ...)

Arguments

Details

Uses the GBIF DCA validator (http://tools.gbif.org/dwca-validator/)

Examples

## Not run: 
x <- "http://rs.gbif.org/datasets/german_sl.zip"
dwca_validate(x)

## End(Not run)

Defunct functions in finch

Description

• dwca_cache_delete: Defunt - see dwca_cache

• dwca_cache_delete_all: Defunt - see dwca_cache

• dwca_cache_details: Defunt - see dwca_cache

• dwca_cache_list: Defunt - see dwca_cache

Parse a DarwinRecordSet and SimpleDarwinRecordSet files

Description

Parse a DarwinRecordSet and SimpleDarwinRecordSet files

Usage

simple_read(file)

Arguments

Details

Make sure when reading a DarwinRecordSet to access the chunks by position rather than name since duplicate names are allowed in chunks.

Value

a S3 class dwc_recordset when a DarwinRecordSet is given, or a dwc_simplerecordset when a SimpleDarwinRecordSet is given. In each case the object is really just a list, with lightweight S3 class attached for easy downstream usage. Prints summary to screen by default

Examples

## Not run: 
# SimpleDarwinRecordSet examples
file <- system.file("examples", "example_simple.xml", package = "finch")
simple_read(file)
file <- system.file("examples", "example_simple_fossil.xml",
  package = "finch")
simple_read(file)

# DarwinRecordSet examples
file <- system.file("examples", "example_classes_observation.xml",
  package = "finch")
simple_read(file)

file <- system.file("examples", "example_classes_specimen.xml",
  package = "finch")
simple_read(file)

# access elements of the object
file <- system.file("examples", "example_classes_specimen.xml",
  package = "finch")
res <- simple_read(file)
## namespaces
res$meta
## locations
res$locations
## chunks, the first one
res$chunks[[1]]

## End(Not run)