DwCArchive: R6 DwC archive class

In LivingNorway/LivingNorwayR: Creates a Darwin Core Standard compliant data archive ("a data package") for biodiversity data

R6 DwC archive class

Description

R6 class representing a complete data structure for a Darwin Core archive

Format

R6Class object.

Details

The DwcArchive class serves a base class to all Darwin Core archive file types. This class supports all kinds of Darwin Core archive files but may miss some of the specialised functionality of the more specialist classes. See https://dwc.tdwg.org/text/the Darwin core archive guide for more information on the structure of Darwin core archive files.

Methods

Public methods

• DwCArchive$new()

• DwCArchive$exportAsDwCArchive()

• DwCArchive$print()

• DwCArchive$getNumberExtensions()

• DwCArchive$getCoreTable()

• DwCArchive$getExtensionTables()

• DwCArchive$getMetadata()

• DwCArchive$clone()

---

Method new()

Create a new DwCAchive object

Usage

DwCArchive$new(coreDwC, extDwC = NULL, metadata = NULL)

Arguments

coreDwC

A DwCGeneric (or derived class) object that represents the table that corresponds to the 'core' table. Alternatively, this parameter can be character scalar giving the location of the Darwin core archive file to initialize the object from

extDwC

A list of DwCGeneric (or derived class) objects that represent the tables used as extension objects in the Darwin Core archive. If coreDwC is a character scalar then extDwC can also be a character scalar that contains the default file encodings for the files in the Darwin core archive

metadata

A DwCMetadata object that contains the metadata for the archive

---

Method exportAsDwCArchive()

Export the archive as a Darwin core archive file

Usage

DwCArchive$exportAsDwCArchive(
  fileName,
  quote = TRUE,
  sep = "\t",
  eol = "\n",
  na = "",
  dec = ".",
  qmethod = "escape",
  fileEncoding = "",
  emlLocation = "eml.xml"
)

Arguments

fileName

A character string containing the file location of the output Darwin Core Archive.

quote

A logical scalar or a numeric vector. If TRUE, any character or factor columns will be surrounded by double quotes. If a numeric vector, its elements are taken as the indeces of columns to quote. In both cases, row and column names are quoted if they are written. If FALSE, nothing is quoted.

sep

The field seperator stirng. Values within each row are separated by this string.

eol

The character(s) to print at the end of each line (row).

na

The string to use for missing values in the data.

dec

The string to use for decimal points in numeric or complex columns: must be a single character

qmethod

A character string specifying how to deal with embedded double quote characters when quoting strings. Must be one of "escape", in which case the quote character is escaped in C style by a backslash, or "double", in which case it is doubled

fileEncoding

A character string. If non-empty, declares the encoding to be used on a file so the character data can be re-encoded as they are written

emlLocation

The location to store the EML metadata in the Darwin Core archive

---

Method print()

Print the archive information

Usage

DwCArchive$print()

---

Method getNumberExtensions()

Retrieve the number of extensions used in the archive

Usage

DwCArchive$getNumberExtensions()

Returns

An integer scalar containing the number of extensions used in the archive

---

Method getCoreTable()

Retrieve the core table in the archive

Usage

DwCArchive$getCoreTable()

Returns

An object derived from DwCGeneric that contains the core table information

---

Method getExtensionTables()

Retrieve an extension table from the archive

Usage

DwCArchive$getExtensionTables(extIndex = NULL)

Arguments

extIndex

Either an integer vector giving the indeces of the extension tables to retrieve from the archive or a character vector giving the names of the tables to retrieve from the archive. If this parameter is NULL then all extension tables are retrieved

Returns

A list of objects derived from DwCGeneric that contains the extension table information

---

Method getMetadata()

Retrieve the metadata for the archive

Usage

DwCArchive$getMetadata()

Returns

A DwCMetadata object that contains the metadata of the archive

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DwCArchive$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

LivingNorway/LivingNorwayR documentation built on Jan. 11, 2024, 5:07 a.m.