Package 'RDelta' reference manual

Title:	Parse and Query DELTA-Format Taxonomic Descriptions
Description:	Provides an R interface to the 'tDelta' C++ library for parsing DELTA (DEscription Language for TAxonomy) format files <https://freedelta.sourceforge.net>. Supports loading character lists, item descriptions, and specifications, with efficient searching and matching of items based on character values. It also supports the generation of identification keys, diagnoses, natural-language descriptions, and clustering and ordination analyses by means of the DELTA programs 'CONFOR', 'KEY', and 'DIST'.
Authors:	Mauro Cavalcanti [aut, cre] (Original tDelta C++ library by Denis Ziegler), Edinaldo Nelson dos Santos Silva [ctb]
Maintainer:	Mauro Cavalcanti <[email protected]>
License:	GPL (>= 3)
Version:	0.1.0
Built:	2026-10-28 19:19:58 UTC
Source:	https://github.com/cran/RDelta

Get number of attributes for an item

Description

Get number of attributes for an item

Usage

attribute_count(delta, itemnum)
attribute_count(delta, itemnum)

Arguments

delta

A DeltaParser object

itemnum

Item number

Value

Integer number of attributes

Get attribute string

Description

Get attribute string

Usage

attribute_string(delta, itemnum, attrnum)
attribute_string(delta, itemnum, attrnum)

Arguments

delta

A DeltaParser object

itemnum

Item number

attrnum

Attribute number

Value

Character string with the attribute

Get number of characters

Description

Get number of characters

Usage

char_count(delta)
char_count(delta)

Arguments

delta

A DeltaParser object

Value

Integer number of characters

Examples

delta <- tryCatch(
  load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  ),
  error = function(e) NULL
)
if (!is.null(delta)) char_count(delta)
delta <- tryCatch(
  load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  ),
  error = function(e) NULL
)
if (!is.null(delta)) char_count(delta)

Get character feature

Description

Get character feature

Usage

char_feature(delta, charnum)
char_feature(delta, charnum)

Arguments

delta

A DeltaParser object

charnum

Character number

Value

Character string with the feature description

Examples

delta <- tryCatch(
  load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  ),
  error = function(e) NULL
)
if (!is.null(delta)) char_feature(delta, 1)
delta <- tryCatch(
  load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  ),
  error = function(e) NULL
)
if (!is.null(delta)) char_feature(delta, 1)

Get character type

Description

Get character type

Usage

char_type(delta, charnum)
char_type(delta, charnum)

Arguments

delta

A DeltaParser object

charnum

Character number

Value

Integer character type code

Get character type name

Description

Get character type name

Usage

char_type_name(delta, charnum)
char_type_name(delta, charnum)

Arguments

delta

A DeltaParser object

charnum

Character number

Value

Character string with type name

Get character unit

Description

Get character unit

Usage

char_unit(delta, charnum)
char_unit(delta, charnum)

Arguments

delta

A DeltaParser object

charnum

Character number

Value

Character string with the unit

Get character information as a data frame

Description

Extracts all character definitions from a DELTA dataset and returns them as a data frame.

Usage

characters_df(delta)
characters_df(delta)

Arguments

delta

A DeltaParser object

Value

A data.frame with character information

Get characters filename

Description

Get characters filename

Usage

chars_filename(delta)
chars_filename(delta)

Arguments

delta

A DeltaParser object

Value

Character string with the filename

Check the characters and items

Description

This function creates a directives file for the CONFOR program to check the characters and items in a DELTA dataset.

Usage

check(delta, remove_temp = TRUE)
check(delta, remove_temp = TRUE)

Arguments

delta

A Delta dataset object (created by load_delta)

remove_temp

Logical; if TRUE, remove temporary files after conversion (default = TRUE)

Details

The function assumes that the CONFOR program executable is available in the system PATH or in the current working directory.

Value

Integer: 0 if check is successful, 1 if check fails

Examples

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  check(delta)
})

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  check(delta)
})

Check the characters

Description

This function creates a directives file for the CONFOR program to check the characters in a DELTA dataset.

Usage

checkc(delta, remove_temp = TRUE)
checkc(delta, remove_temp = TRUE)

Arguments

delta

A Delta dataset object (created by load_delta)

remove_temp

Logical; if TRUE, remove temporary files after conversion (default = TRUE)

Details

The function assumes that the CONFOR program executable is available in the system PATH or in the current working directory.

Value

Integer: 0 if check is successful, 1 if check fails

Examples

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  checkc(delta)
})

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  checkc(delta)
})

Check the items

Description

This function creates a directives file for the CONFOR program to check the items in a DELTA dataset.

Usage

checki(delta, remove_temp = TRUE)
checki(delta, remove_temp = TRUE)

Arguments

delta

A Delta dataset object (created by load_delta)

remove_temp

Logical; if TRUE, remove temporary files after conversion (default = TRUE)

Details

The function assumes that the CONFOR program executable is available in the system PATH or in the current working directory.

Value

Integer: 0 if check is successful, 1 if check fails

Examples

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  checki(delta)
})

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  checki(delta)
})

Performs hierarchical cluster analysis on a distance matrix generated by the dist() function. This function reads the distance matrix and item names from the DIST output files and creates a dendrogram.

Usage

cluster(notu, method = "average")
cluster(notu, method = "average")

Arguments

notu

Number of operational taxonomic units (items) in the dataset.

method

The agglomeration method to be used. This should be one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). Default is "average".

Value

Invisibly returns a list with the following components:

hclust: The hclust object produced by hclust, which can be further processed or plotted by the user.
cophenetic: The cophenetic correlation coefficient (a single numeric value between -1 and 1) measuring how faithfully the dendrogram represents the original distance matrix. Values closer to 1 indicate a better fit.
dist: The dist object representing the input distance matrix.

Examples

# Requires the CONFOR and DIST executables on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  dist(delta)
  res <- cluster(delta$get_items_nb())
  res$cophenetic
  res <- cluster(delta$get_items_nb(), method = "complete")
})

# Requires the CONFOR and DIST executables on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  dist(delta)
  res <- cluster(delta$get_items_nb())
  res$cophenetic
  res <- cluster(delta$get_items_nb(), method = "complete")
})

Get all debug output

Description

Get all debug output

Usage

debug_all(delta)
debug_all(delta)

Arguments

delta

A DeltaParser object

Value

Character string with all debug output

Get character type constants

Description

Get character type constants

Usage

delta_char_types()
delta_char_types()

Value

Named integer vector of DELTA character types

Get package version

Description

Get package version

Usage

delta_version()
delta_version()

Value

Package version string

Convert DELTA dataset to SLIKS format

Description

Converts a DELTA dataset to SLIKS (Simple List of Interactive Key States) format, which is used for interactive identification keys.

Usage

delta2sliks(
  delta,
  output_file = "data.js",
  exclude_numeric = TRUE,
  remove_temp = TRUE
)
delta2sliks(
  delta,
  output_file = "data.js",
  exclude_numeric = TRUE,
  remove_temp = TRUE
)

Arguments

delta

A DeltaParser object (created by load_delta)

output_file

Output file name (default: "data.js")

exclude_numeric

Logical; if TRUE, exclude numeric and text characters

remove_temp

Logical; if TRUE, remove temporary files after conversion

Details

The function assumes that the CONFOR program executable is available in the system PATH or in the current working directory.

Value

Invisibly returns the path to the output file

Examples

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  delta2sliks(delta, output_file = file.path(tempdir(), "data.js"))
})

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  delta2sliks(delta, output_file = file.path(tempdir(), "data.js"))
})

Get all dependent characters

Description

Get all dependent characters

Usage

dependent_characters(delta, ccnum, ccstate)
dependent_characters(delta, ccnum, ccstate)

Arguments

delta

A DeltaParser object

ccnum

Control character number

ccstate

Control character state

Value

Integer vector of dependent character numbers

Get number of dependent characters

Description

Get number of dependent characters

Usage

dependent_count(delta, ccnum, ccstate)
dependent_count(delta, ccnum, ccstate)

Arguments

delta

A DeltaParser object

ccnum

Control character number

ccstate

Control character state

Value

Integer count of dependent characters

Generate Distance Matrix using Gower's Coefficient

Description

This function replicates the DIST command in the DELTA system for generating a distance matrix using Gower's coefficient. It creates the necessary directives files and runs the CONFOR and DIST programs.

Usage

dist(
  delta,
  heading = NULL,
  match_overlap = FALSE,
  minimum_comparisons,
  phylip_format = FALSE,
  exclude_items = NULL,
  exclude_characters = NULL,
  remove_temp = TRUE
)
dist(
  delta,
  heading = NULL,
  match_overlap = FALSE,
  minimum_comparisons,
  phylip_format = FALSE,
  exclude_items = NULL,
  exclude_characters = NULL,
  remove_temp = TRUE
)

Arguments

delta

A Delta dataset object (created by load_delta)

heading

Heading for the output (default = NULL, uses heading from specs file)

match_overlap

For unordered multistate characters, the contribution of a character to the distance between two items is 0 if the items have any of the values of the character in common (default = FALSE)

minimum_comparisons

Minimum number of character comparisons required to calculate the distance between two items (default = ceiling(sqrt(number of included characters)))

phylip_format

Causes the taxon names to be interleaved with the rows of the distance matrix, as required by the program Phylip (default = FALSE)

exclude_items

A list of items to be excluded (default = NULL)

exclude_characters

A list of characters to be excluded (default = NULL)

remove_temp

Logical; if TRUE, remove temporary files after conversion

Details

The function assumes that the CONFOR and DIST program executables are available in the system PATH or in the current working directory.

Value

Invisibly returns 0 on success

Examples

# Requires the CONFOR and DIST executables on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  dist(delta)
  dist(delta, match_overlap = TRUE, phylip_format = TRUE,
       minimum_comparisons = 10)
})

# Requires the CONFOR and DIST executables on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  dist(delta)
  dist(delta, match_overlap = TRUE, phylip_format = TRUE,
       minimum_comparisons = 10)
})

Find all matching items

Description

Find all matching items

Usage

find_matching(delta, charnum, values, strict = TRUE, with_extrval = TRUE)
find_matching(delta, charnum, values, strict = TRUE, with_extrval = TRUE)

Arguments

delta

A DeltaParser object

charnum

Character number

values

Numeric vector of values

strict

Logical; strict comparison

with_extrval

Logical; include extreme values

Value

Integer vector of matching item numbers

Find first matching item

Description

Find first matching item

Usage

first_matching(delta, charnum, values, strict = TRUE, with_extrval = TRUE)
first_matching(delta, charnum, values, strict = TRUE, with_extrval = TRUE)

Arguments

delta

A DeltaParser object

charnum

Character number

values

Numeric vector of values

strict

Logical; strict comparison

with_extrval

Logical; include extreme values

Value

Integer item number or 0 if none

Get all dependent characters

Description

Get all dependent characters

Usage

get_all_depchar(delta, ccnum, ccstate)
get_all_depchar(delta, ccnum, ccstate)

Arguments

delta

A DeltaParser object

ccnum

Control character number

ccstate

Control character state

Value

Integer vector of dependent character numbers

Examples


try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_all_depchar(delta, 13, 2)
})

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_all_depchar(delta, 13, 2)
})

Get all dependency relationships

Description

Get all dependency relationships

Usage

get_all_dependencies(delta)
get_all_dependencies(delta)

Arguments

delta

A DeltaParser object

Value

List of all dependency relationships

Examples


try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_all_dependencies(delta)
})

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_all_dependencies(delta)
})

Get all implicit values

Description

Get all implicit values

Usage

get_all_implicit_values(delta, iv_type = 1)
get_all_implicit_values(delta, iv_type = 1)

Arguments

delta

A DeltaParser object

iv_type

Implicit value type (1 or 2, default: 1)

Value

Integer vector of implicit values

Examples


try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_all_implicit_values(delta)
})

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_all_implicit_values(delta)
})

Get attribute string (C++ style)

Description

Get attribute string (C++ style)

Usage

get_attribute(delta, itemnum, attrnum)
get_attribute(delta, itemnum, attrnum)

Arguments

delta

A DeltaParser object

itemnum

Item number

attrnum

Attribute number

Value

Character string with the attribute

Get number of attributes (C++ style)

Description

Get number of attributes (C++ style)

Usage

get_attributes_nb(delta, itemnum)
get_attributes_nb(delta, itemnum)

Arguments

delta

A DeltaParser object

itemnum

Item number

Value

Integer number of attributes

Get character feature (C++ style)

Description

Get character feature (C++ style)

Usage

get_char_feature(delta, charnum)
get_char_feature(delta, charnum)

Arguments

delta

A DeltaParser object

charnum

Character number

Value

Character string with the feature description

Get character type (C++ style)

Description

Get character type (C++ style)

Usage

get_char_type(delta, charnum)
get_char_type(delta, charnum)

Arguments

delta

A DeltaParser object

charnum

Character number

Value

Integer character type code

Get character unit (C++ style)

Description

Get character unit (C++ style)

Usage

get_char_unit(delta, charnum)
get_char_unit(delta, charnum)

Arguments

delta

A DeltaParser object

charnum

Character number

Value

Character string with the unit

Get character debug output

Description

Get character debug output

Usage

get_chars_debug(delta)
get_chars_debug(delta)

Arguments

delta

A DeltaParser object

Value

Character string with debug output

Get number of characters (C++ style)

Description

Get number of characters (C++ style)

Usage

get_chars_nb(delta)
get_chars_nb(delta)

Arguments

delta

A DeltaParser object

Value

Integer number of characters

Get dependent character by rank (C++ style)

Description

Get dependent character by rank (C++ style)

Get dependent character at specific rank

Usage

get_depchar(delta, ccnum, ccstate, rank = 1)

get_depchar(delta, ccnum, ccstate, rank = 1)
get_depchar(delta, ccnum, ccstate, rank = 1)

get_depchar(delta, ccnum, ccstate, rank = 1)

Arguments

delta

A DeltaParser object

ccnum

Control character number

ccstate

Control character state

rank

Rank position (default: 1)

Value

Integer dependent character number

Dependent character number or 0 if none

Examples


try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_depchar(delta, 13, 2, 1)
})

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_depchar(delta, 13, 2, 1)
})

Get number of dependent characters (C++ style)

Description

Get number of dependent characters (C++ style)

Get number of dependent characters

Usage

get_depchar_nb(delta, ccnum, ccstate)

get_depchar_nb(delta, ccnum, ccstate)
get_depchar_nb(delta, ccnum, ccstate)

get_depchar_nb(delta, ccnum, ccstate)

Arguments

delta

A DeltaParser object

ccnum

Control character number

ccstate

Control character state

Value

Integer count of dependent characters

Number of dependent characters

Examples


try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_depchar_nb(delta, 13, 2)
})

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_depchar_nb(delta, 13, 2)
})

Get example file paths for testing

Description

Get example file paths for testing

Usage

get_example_files(dataset = "viola")
get_example_files(dataset = "viola")

Arguments

dataset

Character string: "viola" or "grass"

Value

List with file paths

Get filename (C++ style)

Description

Get filename (C++ style)

Usage

get_filename(delta)
get_filename(delta)

Arguments

delta

A DeltaParser object

Value

Character string with the filename

Get implicit value (C++ style)

Description

Get implicit value (C++ style)

Get implicit value for a character

Usage

get_implicit_value(delta, charnum, iv_type = 1)

get_implicit_value(delta, charnum, iv_type = 1)
get_implicit_value(delta, charnum, iv_type = 1)

get_implicit_value(delta, charnum, iv_type = 1)

Arguments

delta

A DeltaParser object

charnum

Character number

iv_type

Implicit value type (1 or 2, default: 1)

Value

Integer implicit value

Integer value or NA if not defined

Examples


try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_implicit_value(delta, 1)
})

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  get_implicit_value(delta, 1)
})

Get complete item data as a list

Description

Retrieves all data for a specific item.

Usage

get_item(delta, itemnum, include_comments = FALSE)
get_item(delta, itemnum, include_comments = FALSE)

Arguments

delta

A DeltaParser object

itemnum

Integer item number

include_comments

Logical; if TRUE, include comments in item names

Value

A list with item name and attributes

Get item name (C++ style)

Description

Get item name (C++ style)

Usage

get_item_name(delta, itemnum, include_comments = TRUE)
get_item_name(delta, itemnum, include_comments = TRUE)

Arguments

delta

A DeltaParser object

itemnum

Item number

include_comments

Logical; if TRUE, include comments in item names

Value

Character string with item name

Get items debug output

Description

Get items debug output

Usage

get_items_debug(delta)
get_items_debug(delta)

Arguments

delta

A DeltaParser object

Value

Character string with debug output

Get items filename (C++ style)

Description

Get items filename (C++ style)

Usage

get_items_filename(delta)
get_items_filename(delta)

Arguments

delta

A DeltaParser object

Value

Character string with the filename

Get number of items (C++ style)

Description

Get number of items (C++ style)

Usage

get_items_nb(delta)
get_items_nb(delta)

Arguments

delta

A DeltaParser object

Value

Integer number of items

Get specifications debug output

Description

Get specifications debug output

Usage

get_specs_debug(delta)
get_specs_debug(delta)

Arguments

delta

A DeltaParser object

Value

Character string with debug output

Get specifications filename (C++ style)

Description

Get specifications filename (C++ style)

Usage

get_specs_filename(delta)
get_specs_filename(delta)

Arguments

delta

A DeltaParser object

Value

Character string with the filename

Get state name (C++ style)

Description

Get state name (C++ style)

Usage

get_state(delta, charnum, statenum)
get_state(delta, charnum, statenum)

Arguments

delta

A DeltaParser object

charnum

Character number

statenum

State number

Value

Character string with state name

Get number of states (C++ style)

Description

Get number of states (C++ style)

Usage

get_states_nb(delta, charnum)
get_states_nb(delta, charnum)

Arguments

delta

A DeltaParser object

charnum

Character number

Value

Integer number of states

Get version of the underlying C++ library

Description

Get version of the underlying C++ library

Usage

get_version(delta)
get_version(delta)

Arguments

delta

A DeltaParser object

Value

Version string

Check if specifications are available

Description

Check if specifications are available

Usage

has_specifications(delta)
has_specifications(delta)

Arguments

delta

A DeltaParser object

Value

Logical

Get implicit value

Description

Get implicit value

Usage

implicit_value(delta, charnum, iv_type = 1)
implicit_value(delta, charnum, iv_type = 1)

Arguments

delta

A DeltaParser object

charnum

Character number

iv_type

Implicit value type (1 or 2)

Value

Integer implicit value

Get all implicit values

Description

Get all implicit values

Usage

implicit_values(delta, iv_type = 1)
implicit_values(delta, iv_type = 1)

Arguments

delta

A DeltaParser object

iv_type

Implicit value type (1 or 2)

Value

Integer vector of implicit values

Check if characters are parsed

Description

Check if characters are parsed

Usage

is_chars_parsed(delta)
is_chars_parsed(delta)

Arguments

delta

A DeltaParser object

Value

Logical

Check if character is dependent

Description

Check if character is dependent

Check if a character is dependent

Usage

is_dependent(delta, dcnum, ccnum, ccstate)

is_dependent(delta, dcnum, ccnum, ccstate)
is_dependent(delta, dcnum, ccnum, ccstate)

is_dependent(delta, dcnum, ccnum, ccstate)

Arguments

delta

A DeltaParser object

dcnum

Dependent character number

ccnum

Control character number

ccstate

Control character state

Value

Logical indicating if dependent

Logical indicating if dcnum is dependent

Examples


try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  is_dependent(delta, 14, 13, 2)
})

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  is_dependent(delta, 14, 13, 2)
})

Check if items are parsed

Description

Check if items are parsed

Usage

is_items_parsed(delta)
is_items_parsed(delta)

Arguments

delta

A DeltaParser object

Value

Logical

Check if parsed (C++ style)

Description

Check if parsed (C++ style)

Usage

is_parsed(delta)
is_parsed(delta)

Arguments

delta

A DeltaParser object

Value

Logical

Check if specifications are parsed

Description

Check if specifications are parsed

Usage

is_specs_parsed(delta)
is_specs_parsed(delta)

Arguments

delta

A DeltaParser object

Value

Logical

Get item attributes as data frame

Description

Get item attributes as data frame

Usage

item_attributes(delta, itemnum)
item_attributes(delta, itemnum)

Arguments

delta

A DeltaParser object

itemnum

Item number

Value

Data frame with attributes

Get number of items

Description

Get number of items

Usage

item_count(delta)
item_count(delta)

Arguments

delta

A DeltaParser object

Value

Integer number of items

Examples

delta <- tryCatch(
  load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  ),
  error = function(e) NULL
)
if (!is.null(delta)) item_count(delta)
delta <- tryCatch(
  load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  ),
  error = function(e) NULL
)
if (!is.null(delta)) item_count(delta)

Get item data as list

Description

Get item data as list

Usage

item_data(delta, itemnum, include_comments = FALSE)
item_data(delta, itemnum, include_comments = FALSE)

Arguments

delta

A DeltaParser object

itemnum

Item number

include_comments

Logical; if TRUE, include comments in item names

Value

List with item data

Get item name

Description

Get item name

Usage

item_name(delta, itemnum, include_comments = TRUE)
item_name(delta, itemnum, include_comments = TRUE)

Arguments

delta

A DeltaParser object

itemnum

Item number

include_comments

Logical; if TRUE, include comments in item names

Value

Character string with item name

Examples

delta <- tryCatch(
  load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  ),
  error = function(e) NULL
)
if (!is.null(delta)) item_name(delta, 1)
delta <- tryCatch(
  load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  ),
  error = function(e) NULL
)
if (!is.null(delta)) item_name(delta, 1)

Get all item names

Description

Get all item names

Usage

item_names(delta, include_comments = FALSE)
item_names(delta, include_comments = FALSE)

Arguments

delta

A DeltaParser object

include_comments

Logical; if TRUE, include comments in item names

Value

Character vector of item names

Get item information as a data frame

Description

Extracts all item information from a DELTA dataset and returns it as a data frame.

Usage

items_df(delta, include_comments = FALSE)
items_df(delta, include_comments = FALSE)

Arguments

delta

A DeltaParser object

include_comments

Logical; if TRUE, include comments in item names

Value

A data.frame with item information

Get items filename

Description

Get items filename

Usage

items_filename(delta)
items_filename(delta)

Arguments

delta

A DeltaParser object

Value

Character string with the filename

Generate Dichotomous Key using CONFOR/KEY

Description

This function replicates the KEY command in the DELTA system for generating dichotomous keys. It creates the necessary directives files and runs the CONFOR and KEY programs.

Usage

key(
  delta,
  heading = NULL,
  add_character_numbers = FALSE,
  no_bracketted_key = FALSE,
  no_tabular_key = TRUE,
  number_of_confirmatory_characters = 0,
  treat_characters_as_variable = NULL,
  use_normal_values = NULL,
  character_reliabilities = NULL,
  key_states = NULL,
  abase = 2,
  rbase = 1.4,
  reuse = 1.01,
  varywt = 0.8,
  print_width = 80,
  exclude_items = NULL,
  exclude_characters = NULL,
  remove_temp = TRUE
)
key(
  delta,
  heading = NULL,
  add_character_numbers = FALSE,
  no_bracketted_key = FALSE,
  no_tabular_key = TRUE,
  number_of_confirmatory_characters = 0,
  treat_characters_as_variable = NULL,
  use_normal_values = NULL,
  character_reliabilities = NULL,
  key_states = NULL,
  abase = 2,
  rbase = 1.4,
  reuse = 1.01,
  varywt = 0.8,
  print_width = 80,
  exclude_items = NULL,
  exclude_characters = NULL,
  remove_temp = TRUE
)

Arguments

delta

A Delta dataset object (created by load_delta)

heading

Heading for the output (default = NULL, uses heading from specs file)

add_character_numbers

Character numbers are to be inserted in bracketed keys (default = FALSE)

no_bracketted_key

Suppresses the production of a key in the conventional, 'bracketed' format (default = FALSE)

no_tabular_key

Suppresses the production of a key in tabular format (default = TRUE)

number_of_confirmatory_characters

Number of confirmatory characters that will be sought for each main character in the key (default = 0, maximum = 4)

treat_characters_as_variable

A list of characters for which particular attributes are to be treated as 'variable' (default = NULL)

use_normal_values

A list of numeric characters for which extreme values are to be ignored and normal values used when translating into other formats (default = NULL)

character_reliabilities

A list of the 'reliabilities' of the characters (default = NULL)

key_states

A list of numeric character states to be divided into ranges for use as states in identification keys (default = NULL)

abase

Sets the base of the logarithmic item abundance scale (default = 2)

rbase

Sets the base of the logarithmic character-reliability scale (default = 1.4)

reuse

Attempt to minimize the number of different characters used in the key (default = 1.01)

varywt

Sets the value of a parameter that determines the treatment of intra-taxon variability in the process of character selection (default = 0.8)

print_width

Maximum line length for output of the keys (default = 80)

exclude_items

A list of items to be excluded (default = NULL)

exclude_characters

A list of characters to be excluded (default = NULL)

remove_temp

Logical; if TRUE, remove temporary files after conversion (default = TRUE)

Details

The function assumes that the CONFOR and KEY program executables are available in the system PATH or in the current working directory.

Value

Invisibly returns the key as a character vector on success

Examples

# Requires the CONFOR and KEY executables on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  key(delta)
  key(delta, abase = 2, rbase = 1.4,
      no_tabular_key = TRUE, number_of_confirmatory_characters = 2)
})

# Requires the CONFOR and KEY executables on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  key(delta)
  key(delta, abase = 2, rbase = 1.4,
      no_tabular_key = TRUE, number_of_confirmatory_characters = 2)
})

Load a DELTA dataset

Description

Create a DeltaParser object from DELTA format files.

Usage

load_delta(chars_file, items_file, specs_file = NULL)
load_delta(chars_file, items_file, specs_file = NULL)

Arguments

chars_file

Path to the DELTA characters file

items_file

Path to the DELTA items file

specs_file

Optional path to the DELTA specifications file

Value

A DeltaParser Rcpp module object

Examples

# Load the packaged example dataset
delta <- tryCatch(
  load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  ),
  error = function(e) NULL
)

if (!is.null(delta)) {
  char_count(delta)
  char_feature(delta, 1)
}
# Load the packaged example dataset
delta <- tryCatch(
  load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  ),
  error = function(e) NULL
)

if (!is.null(delta)) {
  char_count(delta)
  char_feature(delta, 1)
}

Check if item matches values

Description

Check if item matches values

Usage

matches(delta, itemnum, charnum, values, strict = TRUE, with_extrval = TRUE)
matches(delta, itemnum, charnum, values, strict = TRUE, with_extrval = TRUE)

Arguments

delta

A DeltaParser object

itemnum

Item number

charnum

Character number

values

Numeric vector of values

strict

Logical; strict comparison

with_extrval

Logical; include extreme values

Value

Logical indicating if item matches

Translate DELTA-format data into natural language descriptions via CONFOR

Description

This function replicates the TRANSLATE INTO NATURAL LANGUAGE command in the DELTA system. It creates the necessary directives file and runs the CONFOR program to generate natural language descriptions.

Usage

natlan(
  delta,
  heading = NULL,
  replace_angle_brackets = TRUE,
  omit_character_numbers = TRUE,
  omit_inapplicables = TRUE,
  omit_comments = TRUE,
  omit_inner_comments = TRUE,
  omit_final_comma = TRUE,
  translate_implicit_values = FALSE,
  omit_lower_for_characters = NULL,
  omit_or_for_characters = NULL,
  omit_period_for_characters = NULL,
  new_paragraphs_at_characters = NULL,
  item_subheadings = NULL,
  link_characters = NULL,
  replace_semicolon_by_comma = NULL,
  print_width = 80,
  exclude_items = NULL,
  exclude_characters = NULL,
  vocabulary = NULL,
  remove_temp = TRUE
)
natlan(
  delta,
  heading = NULL,
  replace_angle_brackets = TRUE,
  omit_character_numbers = TRUE,
  omit_inapplicables = TRUE,
  omit_comments = TRUE,
  omit_inner_comments = TRUE,
  omit_final_comma = TRUE,
  translate_implicit_values = FALSE,
  omit_lower_for_characters = NULL,
  omit_or_for_characters = NULL,
  omit_period_for_characters = NULL,
  new_paragraphs_at_characters = NULL,
  item_subheadings = NULL,
  link_characters = NULL,
  replace_semicolon_by_comma = NULL,
  print_width = 80,
  exclude_items = NULL,
  exclude_characters = NULL,
  vocabulary = NULL,
  remove_temp = TRUE
)

Arguments

delta

A Delta dataset object (created by load_delta)

heading

Heading for the descriptions (default = NULL, uses heading from specs file)

replace_angle_brackets

Replace angle brackets with parentheses (default = TRUE)

omit_character_numbers

Omit character numbers from descriptions (default = TRUE)

omit_inapplicables

Omit 'or not applicable' from descriptions (default = TRUE)

omit_comments

Omit comments in attributes (default = TRUE)

omit_inner_comments

Omit inner comments in character list and attributes (default = TRUE)

omit_final_comma

Omit final comma before 'and' (default = TRUE)

translate_implicit_values

Output implicit values in descriptions (default = FALSE)

omit_lower_for_characters

List of numeric characters to omit lower values

omit_or_for_characters

List of characters to omit 'or' between alternatives

omit_period_for_characters

List of characters where period would normally terminate a sentence

new_paragraphs_at_characters

List of characters where new paragraphs should start

item_subheadings

List of subheadings for items (delimiter/character/value)

link_characters

List of characters specifying how attributes are combined

replace_semicolon_by_comma

List of characters to use comma instead of semicolon

print_width

Maximum line length for output (default = 80)

exclude_items

List of items to exclude

exclude_characters

List of characters to exclude

vocabulary

List for custom vocabulary (default = NULL)

remove_temp

Logical; if TRUE, remove temporary files after conversion (default = TRUE)

Details

The function assumes that the CONFOR program executable is available in the system PATH or in the current working directory.

Value

Invisibly returns the descriptions as a character vector

Examples

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  natlan(delta)
  natlan(delta,
         heading = "Flora of Region X - species descriptions",
         item_subheadings = list(
           "87" = "Transverse section of lamina",
           "96" = "Leaf epidermis"
         ))
})

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  natlan(delta)
  natlan(delta,
         heading = "Flora of Region X - species descriptions",
         item_subheadings = list(
           "87" = "Transverse section of lamina",
           "96" = "Leaf epidermis"
         ))
})

Find next matching item

Description

Find next matching item

Usage

next_matching(delta, charnum, values, strict = TRUE, with_extrval = TRUE)
next_matching(delta, charnum, values, strict = TRUE, with_extrval = TRUE)

Arguments

delta

A DeltaParser object

charnum

Character number

values

Numeric vector of values

strict

Logical; strict comparison

with_extrval

Logical; include extreme values

Value

Integer item number or 0 if none

Parse a DELTA attribute string

Description

Parse a DELTA attribute string

Usage

parse_attribute(attr_string)
parse_attribute(attr_string)

Arguments

attr_string

A DELTA attribute string

Value

A list with parsed components: charnum (integer), comment (character), and alternatives (list of parsed value lists).

Parse characters file

Description

Parse characters file

Usage

parse_characters(delta)
parse_characters(delta)

Arguments

delta

A DeltaParser object

Value

Logical indicating success

Parse items file

Description

Parse items file

Usage

parse_items(delta)
parse_items(delta)

Arguments

delta

A DeltaParser object

Value

Logical indicating success

Parse specifications file

Description

Parse specifications file

Usage

parse_specs(delta)
parse_specs(delta)

Arguments

delta

A DeltaParser object

Value

Logical indicating success

Principal Coordinates Analysis

Description

Performs principal coordinates analysis (PCoA) on a distance matrix generated by the dist() function. This function reads the distance matrix and item names from the DIST output files and creates a PCoA scatterplot.

Usage

pcoa(notu)
pcoa(notu)

Arguments

notu

Number of operational taxonomic units (items) in the dataset.

Value

Invisibly returns a list with the following components:

points: A two-column matrix of the coordinates of the items on the first two principal coordinate axes.
eig: The eigenvalues of the PCoA solution, as returned by cmdscale.
variance: A numeric vector of length 2 giving the proportion of total variance explained by Axis 1 and Axis 2 (values between 0 and 1).
cumulative: A single numeric value giving the cumulative proportion of variance explained by the first two axes combined.
cmdscale: The full result object returned by cmdscale, for users who need access to all components.

Examples

# Requires the CONFOR and DIST executables on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  dist(delta)
  res <- pcoa(delta$get_items_nb())
  res$variance
  res$cumulative
})

# Requires the CONFOR and DIST executables on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  dist(delta)
  res <- pcoa(delta$get_items_nb())
  res$variance
  res$cumulative
})

Retrieve ALL information for debugging

Description

This matches the C++ retrieve_all() method from the original tDelta library, combining characters, items, and specifications output.

Usage

retrieve_all(delta)
retrieve_all(delta)

Arguments

delta

A DeltaParser object

Value

Character string with all debug information

Retrieve all character information for debugging

Description

This matches the C++ retrieve_all() method from the original tDelta library.

Usage

retrieve_all_chars(delta)
retrieve_all_chars(delta)

Arguments

delta

A DeltaParser object

Value

Character string with debug information

Retrieve all item information for debugging

Description

This matches the C++ retrieve_all() method from the original tDelta library.

Usage

retrieve_all_items(delta)
retrieve_all_items(delta)

Arguments

delta

A DeltaParser object

Value

Character string with debug information

Retrieve all specifications information for debugging

Description

This matches the C++ retrieve_all() method from the original tDelta library.

Usage

retrieve_all_specs(delta)
retrieve_all_specs(delta)

Arguments

delta

A DeltaParser object

Value

Character string with debug information

Save a Delta dataset to disk

Description

This function saves a Delta dataset object to disk as three plain text files: "chars", "items", and "specs" in the DELTA format.

Usage

save_delta(delta, dir, prefix = "", overwrite = FALSE, width = 79)
save_delta(delta, dir, prefix = "", overwrite = FALSE, width = 79)

Arguments

delta

A Delta dataset object (Rcpp_DeltaParser from load_delta())

dir

Path to the directory where files should be saved. This argument is required: the function never writes to the current working directory by default. Use tempdir() if you only need a scratch location.

prefix

Optional prefix for filenames (default: "")

overwrite

Whether to overwrite existing files (default: FALSE)

width

Maximum line width for output files (default: 79, range: 40-132)

Value

Invisibly returns the input delta object

Examples


try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )

  # Write to a temporary directory
  save_delta(delta, dir = tempdir())

  # Write to a user-chosen directory with a prefix
  save_delta(delta, dir = tempdir(), prefix = "my_", overwrite = TRUE)

  # Use a wider output width
  save_delta(delta, dir = tempdir(), width = 120)
})

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )

  # Write to a temporary directory
  save_delta(delta, dir = tempdir())

  # Write to a user-chosen directory with a prefix
  save_delta(delta, dir = tempdir(), prefix = "my_", overwrite = TRUE)

  # Use a wider output width
  save_delta(delta, dir = tempdir(), width = 120)
})

Set character type

Description

Set character type

Usage

set_char_type(delta, charnum, chartype)
set_char_type(delta, charnum, chartype)

Arguments

delta

A DeltaParser object

charnum

Character number

chartype

Integer character type code

Value

No return value, called for side effects. The character type of charnum is modified in delta in place.

Set character type by name

Description

Set character type by name

Usage

set_char_type_by_name(delta, charnum, type_name)
set_char_type_by_name(delta, charnum, type_name)

Arguments

delta

A DeltaParser object

charnum

Character number

type_name

Character type name

Value

No return value, called for side effects. The character type of charnum is modified in delta in place.

Set characters filename

Description

Set characters filename

Usage

set_chars_filename(delta, fname, parse = TRUE)
set_chars_filename(delta, fname, parse = TRUE)

Arguments

delta

A DeltaParser object

fname

New filename

parse

Logical, parse the file immediately

Value

No return value, called for side effects. The characters filename stored in delta is updated.

Set filename (C++ style)

Description

Set filename (C++ style)

Usage

set_filename(delta, fname, parse = TRUE)
set_filename(delta, fname, parse = TRUE)

Arguments

delta

A DeltaParser object

fname

New filename

parse

Logical, parse the file immediately

Value

No return value, called for side effects. The characters filename stored in delta is updated.

Set items filename

Description

Set items filename

Usage

set_items_file(delta, fname, parse = TRUE)
set_items_file(delta, fname, parse = TRUE)

Arguments

delta

A DeltaParser object

fname

New filename

parse

Logical, parse the file immediately

Value

No return value, called for side effects. The items filename stored in delta is updated.

Set items filename (C++ style)

Description

Set items filename (C++ style)

Usage

set_items_filename(delta, fname, parse = TRUE)
set_items_filename(delta, fname, parse = TRUE)

Arguments

delta

A DeltaParser object

fname

New filename

parse

Logical, parse the file immediately

Value

No return value, called for side effects. The items filename stored in delta is updated.

Set specifications filename

Description

Set specifications filename

Usage

set_specs_file(delta, fname, parse = TRUE)
set_specs_file(delta, fname, parse = TRUE)

Arguments

delta

A DeltaParser object

fname

New filename

parse

Logical, parse the file immediately

Value

No return value, called for side effects. The specifications filename stored in delta is updated.

Set specifications filename (C++ style)

Description

Set specifications filename (C++ style)

Usage

set_specs_filename(delta, fname, parse = TRUE)
set_specs_filename(delta, fname, parse = TRUE)

Arguments

delta

A DeltaParser object

fname

New filename

parse

Logical, parse the file immediately

Value

No return value, called for side effects. The specifications filename stored in delta is updated.

Get specifications filename

Description

Get specifications filename

Usage

specs_filename(delta)
specs_filename(delta)

Arguments

delta

A DeltaParser object

Value

Character string with the filename

Get number of states for a character

Description

Get number of states for a character

Usage

state_count(delta, charnum)
state_count(delta, charnum)

Arguments

delta

A DeltaParser object

charnum

Character number

Value

Integer number of states

Get state name

Description

Get state name

Usage

state_name(delta, charnum, statenum)
state_name(delta, charnum, statenum)

Arguments

delta

A DeltaParser object

charnum

Character number

statenum

State number

Value

Character string with state name

Get all states for a character

Description

Get all states for a character

Usage

states(delta, charnum)
states(delta, charnum)

Arguments

delta

A DeltaParser object

charnum

Character number

Value

Character vector of state names

Remove comments from a DELTA string

Description

Remove comments from a DELTA string

Usage

strip_comments(src)
strip_comments(src)

Arguments

src

A string with DELTA comments

Value

A character string with all DELTA comments (delimited by < and >) removed.

Generate a statistical summary of taxonomic characters using CONFOR

Description

This function creates a directives file for the CONFOR program to generate a statistical summary of characters for a DELTA dataset. The summary includes character types, states, and frequency distributions.

Usage

summary(delta, heading = NULL, remove_temp = TRUE)
summary(delta, heading = NULL, remove_temp = TRUE)

Arguments

delta

A Delta dataset object (created by load_delta)

heading

Heading for the summary (default = NULL, uses heading from specs file)

remove_temp

Logical; if TRUE, remove temporary files after conversion (default = TRUE)

Details

The function assumes that the CONFOR program executable is available in the system PATH or in the current working directory.

Value

Invisibly returns the path to the generated summary file

Examples

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  summary(delta)
  summary(delta, heading = "Genre Viola")
})

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  summary(delta)
  summary(delta, heading = "Genre Viola")
})

Generate a list of uncoded characters using CONFOR

Description

This function creates a directives file for the CONFOR program to generate a list of characters that are not coded (i.e., have no data) in a DELTA dataset. This is useful for identifying missing data and gaps in taxonomic descriptions.

Usage

uncoded(delta, heading = NULL, remove_temp = TRUE)
uncoded(delta, heading = NULL, remove_temp = TRUE)

Arguments

delta

A Delta dataset object (created by load_delta)

heading

Heading for the output (default = NULL, uses heading from specs file)

remove_temp

Logical; if TRUE, remove temporary files after conversion (default = TRUE)

Details

The function assumes that the CONFOR program executable is available in the system PATH or in the current working directory.

Value

Invisibly returns the path to the generated uncoded characters file

Examples

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  uncoded(delta)
  uncoded(delta, heading = "Genre Viola - Missing data report")
})

# Requires the CONFOR executable on the PATH.

try({
  delta <- load_delta(
    system.file("extdata", "chars_viola", package = "RDelta"),
    system.file("extdata", "items_viola", package = "RDelta"),
    system.file("extdata", "specs_viola", package = "RDelta")
  )
  uncoded(delta)
  uncoded(delta, heading = "Genre Viola - Missing data report")
})

Package 'RDelta'

Help Index

Get number of attributes for an item

Description

Usage

Arguments

Value

Get attribute string

Description

Usage

Arguments

Value

Get number of characters

Description

Usage

Arguments

Value

Examples

Get character feature

Description

Usage

Arguments

Value

Examples

Get character type

Description

Usage

Arguments

Value

Get character type name

Description

Usage

Arguments

Value

Get character unit

Description

Usage

Arguments

Value

Get character information as a data frame

Description

Usage

Arguments

Value

Get characters filename

Description

Usage

Arguments

Value

Check the characters and items

Description

Usage

Arguments

Details

Value

Examples

Check the characters

Description

Usage

Arguments

Details

Value

Examples

Check the items

Description

Usage

Arguments

Details

Value

Examples

Hierarchical Cluster Analysis

Description

Usage

Arguments

Value

Examples

Get all debug output

Description

Usage

Arguments