DwCGeneric: R6 DwC Generic class
In LivingNorway/LivingNorwayR: Creates a Darwin Core Standard compliant data archive ("a data package") for biodiversity data
DwCGeneric R Documentation
R6 DwC Generic class
Description
R6 class representing a generic data structure for a Darwin Core archive file
Format
R6Class object.
Details
The DwcGeneric 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/terms/the Darwin core reference guide for more information on Darwin core classes and the terms
supported by them.
Methods
Public methods
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Method setTableName()
Set the name of the file that the data will print to when preparing the Darwin core archive
Usage
DwCGeneric$setTableName(inTableName)
Arguments
inFileNameA character scalar giving the name to give the data file in a Darwin core archive
Method getTableName()
Retrieve the name of the file that the data will print to when preparing the Darwin core archive
Usage
DwCGeneric$getTableName()
Returns
The name currently set as the file name in the output archive
Method importDataTable()
Import data from a data.frame into a DwCGeneric object
Usage
DwCGeneric$importDataTable(objectData, idColumnInfo, ...)
Arguments
objectDataA data.frame containing the data to import into the object
idColumnInfoEither a character scalar containing the column name
of objectData or an integer scalar giving the index of the column of
objectData that corresponds to the ID variable
...A named set of parameter corresponding to Darwin core terms associated
with the DwCGeneric class type. Each is either a a character scalar containing
the column name of objectData or an integer scalar giving the index of
the column of objectData that corresponds to the term
Method new()
Create a new DwCGeneric object
Usage
DwCGeneric$new(
classTermInfo,
associatedTerms,
objectData,
idColumnInfo,
nameAutoMap = FALSE,
defDateFormat = "YYYY-MM-DD",
...
)
Arguments
classTermInfoA DwCTerm object containing the term information for the class
associatedTermsA list of DwCTerm objects that contain all the terms associated with the class
objectDataA data.frame containing the data to import into the object
idColumnInfoEither a character scalar containing the column name
of objectData or an integer scalar giving the index of the column of
objectData that corresponds to the ID variable
nameAutoMapA logical scalar that if TRUE maps the columns of objectData
to their respective Darwin core terms based on the column names
defDateFormatA character scalar providing the default format for strings denoting dates in the
data table. See the https://dwc.tdwg.org/text/#1-introductionDarwin Core text guide for expected values
for this string.
...A named set of parameter corresponding to Darwin core terms associated
with the DwCGeneric class type. Each is either a a character scalar containing
the column name of objectData or an integer scalar giving the index of
the column of objectData that corresponds to the term
Returns
A new DwCGeneric object
Method getDwCClassName()
Retrieve the name of the class used in Darwin core
Usage
DwCGeneric$getDwCClassName()
Returns
A character scalar contining the name of the Darwin core class
Method getDwCTermInfo()
Retrieve the term information of thee Darwin core class of the object
Usage
DwCGeneric$getDwCTermInfo()
Returns
A DwCTerm object containing the term information of the Darwin core class
of the object
Method getTermMapping()
Retrieve the mapping information of the Darwin core terms associated with the class to the
columns in the data table
Usage
DwCGeneric$getTermMapping()
Returns
A data.frame with one row for each Darwin core term associated with the object's
class with two columns: columnIndex containing the column index of the associated term in the
table and columnName containg the name of the column
Method getAssociatedTerms()
Retrieve the terms associated with the Darwin core class of the object
Usage
DwCGeneric$getAssociatedTerms()
Returns
A list of DwCTerm objects containing the term information
Print object to console
Method print()
Print the term information
Usage
DwCGeneric$print()
Method exportAsDataFrame()
Export the data contained in the table as a data.frame
Usage
DwCGeneric$exportAsDataFrame()
Returns
A data.frame of the object's table data
Method exportTable()
Export the table as a text file
Usage
DwCGeneric$exportTable(
fileName,
append = FALSE,
quote = TRUE,
sep = "\t",
eol = "\n",
na = "NA",
dec = ".",
qmethod = "escape",
fileEncoding = "",
renameMapped = FALSE
)
Arguments
fileNameEither a character string naming a file or a connection open for writing.
"" indicates to the console.
appendA logical scalar. Only relevant if fileName is a character string. If
TRUE, the output is appended to the file. If FALSE, any existing file of the name is
destroyed.
quoteA logical scalar or a numeric vector. If TRUE, any character or factor
columns will be surrounded by double quotes. If a numeric vector, its elements are taken as the
indeces of columns to quote. In both cases, row and column names are quoted if they are written. If FALSE,
nothing is quoted.
sepThe field seperator stirng. Values within each row are separated by this string.
eolThe character(s) to print at the end of each line (row).
naThe string to use for missing values in the data.
decThe string to use for decimal points in numeric or complex columns: must be a single character
qmethodA character string specifying how to deal with embedded double quote characters when
quoting strings. Must be one of "escape", in which case the quote character is escaped in C style by a
backslash, or "double", in which case it is doubled
fileEncodingA character string. If non-empty, declares the encoding to be used on a file so the
character data can be re-encoded as they are written
renameMappedA logical scalar that, if TRUE, replaces mapped column names with their Darwin
core versions
Method getIDIndex()
Retrieve the column index in the dataset that refers to the unique ID in the dataset
Usage
DwCGeneric$getIDIndex()
Returns
An integer scalar giving the index of the column that refers to the unique dataset IDs
Method getIDName()
Retrieve the column name in the dataset that refers to the unique ID in the dataset
Usage
DwCGeneric$getIDName()
Returns
A character scalar giving the column name that refers to the unique dataset IDs
Method setDefaultYearFormat()
Set the default date format in the dataset
Usage
DwCGeneric$setDefaultYearFormat(detDateFormat)
Arguments
detDateFormatA character scalar providing the default format for strings denoting dates in the
data table. See the https://dwc.tdwg.org/text/#1-introductionDarwin Core text guide for expected values
for this string.
Method getDefaultYearFormat()
Retrieve the default date format
Usage
DwCGeneric$getDefaultYearFormat()
Returns
A character scalar containing the default date format
Method getTableTermName()
Retrieve the term name for the table
Usage
DwCGeneric$getTableTermName()
Returns
A character scalar containing the name to the term defining the table
Method clone()
The objects of this class are cloneable with this method.
Usage
DwCGeneric$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
DwCTerm
DwCTerm
LivingNorway/LivingNorwayR documentation built on Jan. 11, 2024, 5:07 a.m.
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| DwCGeneric | R Documentation |
R6 DwC Generic class
Description
R6 class representing a generic data structure for a Darwin Core archive file
Format
R6Class object.
Details
The DwcGeneric class serves a base class to all Darwin Core archive file types. This class supports all kinds of Darwin Core
archive files but may miss some of the specialised functionality of the more specialist classes.
See https://dwc.tdwg.org/terms/the Darwin core reference guide for more information on Darwin core classes and the terms
supported by them.
Methods
Public methods
Method setTableName()
Set the name of the file that the data will print to when preparing the Darwin core archive
Usage
DwCGeneric$setTableName(inTableName)
Arguments
inFileNameA character scalar giving the name to give the data file in a Darwin core archive
Method getTableName()
Retrieve the name of the file that the data will print to when preparing the Darwin core archive
Usage
DwCGeneric$getTableName()
Returns
The name currently set as the file name in the output archive
Method importDataTable()
Import data from a data.frame into a DwCGeneric object
Usage
DwCGeneric$importDataTable(objectData, idColumnInfo, ...)
Arguments
objectDataA
data.framecontaining the data to import into the objectidColumnInfoEither a
characterscalar containing the column name ofobjectDataor anintegerscalar giving the index of the column ofobjectDatathat corresponds to the ID variable...A named set of parameter corresponding to Darwin core terms associated with the DwCGeneric class type. Each is either a a
characterscalar containing the column name ofobjectDataor anintegerscalar giving the index of the column ofobjectDatathat corresponds to the term
Method new()
Create a new DwCGeneric object
Usage
DwCGeneric$new( classTermInfo, associatedTerms, objectData, idColumnInfo, nameAutoMap = FALSE, defDateFormat = "YYYY-MM-DD", ... )
Arguments
classTermInfoA
DwCTermobject containing the term information for the classassociatedTermsA
listofDwCTermobjects that contain all the terms associated with the classobjectDataA
data.framecontaining the data to import into the objectidColumnInfoEither a
characterscalar containing the column name ofobjectDataor anintegerscalar giving the index of the column ofobjectDatathat corresponds to the ID variablenameAutoMapA
logicalscalar that ifTRUEmaps the columns ofobjectDatato their respective Darwin core terms based on the column namesdefDateFormatA
characterscalar providing the default format for strings denoting dates in the data table. See the https://dwc.tdwg.org/text/#1-introductionDarwin Core text guide for expected values for this string....A named set of parameter corresponding to Darwin core terms associated with the DwCGeneric class type. Each is either a a
characterscalar containing the column name ofobjectDataor anintegerscalar giving the index of the column ofobjectDatathat corresponds to the term
Returns
A new DwCGeneric object
Method getDwCClassName()
Retrieve the name of the class used in Darwin core
Usage
DwCGeneric$getDwCClassName()
Returns
A character scalar contining the name of the Darwin core class
Method getDwCTermInfo()
Retrieve the term information of thee Darwin core class of the object
Usage
DwCGeneric$getDwCTermInfo()
Returns
A DwCTerm object containing the term information of the Darwin core class
of the object
Method getTermMapping()
Retrieve the mapping information of the Darwin core terms associated with the class to the columns in the data table
Usage
DwCGeneric$getTermMapping()
Returns
A data.frame with one row for each Darwin core term associated with the object's
class with two columns: columnIndex containing the column index of the associated term in the
table and columnName containg the name of the column
Method getAssociatedTerms()
Retrieve the terms associated with the Darwin core class of the object
Usage
DwCGeneric$getAssociatedTerms()
Returns
A list of DwCTerm objects containing the term information
Print object to console
Method print()
Print the term information
Usage
DwCGeneric$print()
Method exportAsDataFrame()
Export the data contained in the table as a data.frame
Usage
DwCGeneric$exportAsDataFrame()
Returns
A data.frame of the object's table data
Method exportTable()
Export the table as a text file
Usage
DwCGeneric$exportTable( fileName, append = FALSE, quote = TRUE, sep = "\t", eol = "\n", na = "NA", dec = ".", qmethod = "escape", fileEncoding = "", renameMapped = FALSE )
Arguments
fileNameEither a
characterstring naming a file or a connection open for writing.""indicates to the console.appendA
logicalscalar. Only relevant iffileNameis acharacterstring. IfTRUE, the output is appended to the file. IfFALSE, any existing file of the name is destroyed.quoteA
logicalscalar or anumericvector. IfTRUE, any character or factor columns will be surrounded by double quotes. If anumericvector, its elements are taken as the indeces of columns to quote. In both cases, row and column names are quoted if they are written. IfFALSE, nothing is quoted.sepThe field seperator stirng. Values within each row are separated by this string.
eolThe character(s) to print at the end of each line (row).
naThe string to use for missing values in the data.
decThe string to use for decimal points in numeric or complex columns: must be a single character
qmethodA 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 doubledfileEncodingA 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
renameMappedA
logicalscalar that, ifTRUE, replaces mapped column names with their Darwin core versions
Method getIDIndex()
Retrieve the column index in the dataset that refers to the unique ID in the dataset
Usage
DwCGeneric$getIDIndex()
Returns
An integer scalar giving the index of the column that refers to the unique dataset IDs
Method getIDName()
Retrieve the column name in the dataset that refers to the unique ID in the dataset
Usage
DwCGeneric$getIDName()
Returns
A character scalar giving the column name that refers to the unique dataset IDs
Method setDefaultYearFormat()
Set the default date format in the dataset
Usage
DwCGeneric$setDefaultYearFormat(detDateFormat)
Arguments
detDateFormatA
characterscalar providing the default format for strings denoting dates in the data table. See the https://dwc.tdwg.org/text/#1-introductionDarwin Core text guide for expected values for this string.
Method getDefaultYearFormat()
Retrieve the default date format
Usage
DwCGeneric$getDefaultYearFormat()
Returns
A character scalar containing the default date format
Method getTableTermName()
Retrieve the term name for the table
Usage
DwCGeneric$getTableTermName()
Returns
A character scalar containing the name to the term defining the table
Method clone()
The objects of this class are cloneable with this method.
Usage
DwCGeneric$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
DwCTerm
DwCTerm
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