Package {RDelta}

RDelta: 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.

Value

No return value; this is a package-level documentation object.

Author(s)

Maintainer: Mauro Cavalcanti maurobio@gmail.com (Original tDelta C++ library by Denis Ziegler)

Authors:

• Mauro Cavalcanti maurobio@gmail.com (Original tDelta C++ library by Denis Ziegler)

Other contributors:

• Edinaldo Nelson dos Santos Silva nelson@inpa.gov.br [contributor]

See Also

Useful links:

• https://github.com/maurobio/rdelta

• Report bugs at https://github.com/maurobio/rdelta/issues

C++Object Class

Description

Internal class for managing C++ objects in R.

Value

An object of class C++Object wrapping a pointer to a C++ instance.

Rcpp_DeltaParser Class

Description

Internal class for DELTA parser objects from the C++ module.

Value

An object of class Rcpp_DeltaParser representing a parsed DELTA dataset.

Get number of attributes for an item

Description

Get number of attributes for an item

Usage

attribute_count(delta, itemnum)

Arguments

Value

Integer number of attributes

Get attribute string

Description

Get attribute string

Usage

attribute_string(delta, itemnum, attrnum)

Arguments

Value

Character string with the attribute

Get number of characters

Description

Get number of characters

Usage

char_count(delta)

Arguments

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)

Get character feature

Description

Get character feature

Usage

char_feature(delta, charnum)

Arguments

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)

Get character type

Description

Get character type

Usage

char_type(delta, charnum)

Arguments

Value

Integer character type code

Get character type name

Description

Get character type name

Usage

char_type_name(delta, charnum)

Arguments

Value

Character string with type name

Get character unit

Description

Get character unit

Usage

char_unit(delta, charnum)

Arguments

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)

Arguments

Value

A data.frame with character information

Get characters filename

Description

Get characters filename

Usage

chars_filename(delta)

Arguments

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)

Arguments

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)
})

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)

Arguments

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)
})

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)

Arguments

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)
})

Hierarchical Cluster Analysis

Description

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")

Arguments

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")
})

Get all debug output

Description

Get all debug output

Usage

debug_all(delta)

Arguments

Value

Character string with all debug output

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
)

Arguments

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"))
})

Get character type constants

Description

Get character type constants

Usage

delta_char_types()

Value

Named integer vector of DELTA character types

Get package version

Description

Get package version

Usage

delta_version()

Value

Package version string

Get all dependent characters

Description

Get all dependent characters

Usage

dependent_characters(delta, ccnum, ccstate)

Arguments

Value

Integer vector of dependent character numbers

Get number of dependent characters

Description

Get number of dependent characters

Usage

dependent_count(delta, ccnum, ccstate)

Arguments

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
)

Arguments

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)
})

Find all matching items

Description

Find all matching items

Usage

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

Arguments

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)

Arguments

Value

Integer item number or 0 if none

Get all dependent characters

Description

Get all dependent characters

Usage

get_all_depchar(delta, ccnum, ccstate)

Arguments

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)
})

Get all dependency relationships

Description

Get all dependency relationships

Usage

get_all_dependencies(delta)

Arguments

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)
})

Get all implicit values

Description

Get all implicit values

Usage

get_all_implicit_values(delta, iv_type = 1)

Arguments

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)
})

Get attribute string (C++ style)

Description

Get attribute string (C++ style)

Usage

get_attribute(delta, itemnum, attrnum)

Arguments

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)

Arguments

Value

Integer number of attributes

Get character feature (C++ style)

Description

Get character feature (C++ style)

Usage

get_char_feature(delta, charnum)

Arguments

Value

Character string with the feature description

Get character type (C++ style)

Description

Get character type (C++ style)

Usage

get_char_type(delta, charnum)

Arguments

Value

Integer character type code

Get character unit (C++ style)

Description

Get character unit (C++ style)

Usage

get_char_unit(delta, charnum)

Arguments

Value

Character string with the unit

Get character debug output

Description

Get character debug output

Usage

get_chars_debug(delta)

Arguments

Value

Character string with debug output

Get number of characters (C++ style)

Description

Get number of characters (C++ style)

Usage

get_chars_nb(delta)

Arguments

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)

Arguments

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)
})

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)

Arguments

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)
})

Get example file paths for testing

Description

Get example file paths for testing

Usage

get_example_files(dataset = "viola")

Arguments

Value

List with file paths

Get filename (C++ style)

Description

Get filename (C++ style)

Usage

get_filename(delta)

Arguments

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)

Arguments

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)
})

Get complete item data as a list

Description

Retrieves all data for a specific item.

Usage

get_item(delta, itemnum, include_comments = FALSE)

Arguments

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)

Arguments

Value

Character string with item name

Get items debug output

Description

Get items debug output

Usage

get_items_debug(delta)

Arguments

Value

Character string with debug output

Get items filename (C++ style)

Description

Get items filename (C++ style)

Usage

get_items_filename(delta)

Arguments

Value

Character string with the filename

Get number of items (C++ style)

Description

Get number of items (C++ style)

Usage

get_items_nb(delta)

Arguments

Value

Integer number of items

Get specifications debug output

Description

Get specifications debug output

Usage

get_specs_debug(delta)

Arguments

Value

Character string with debug output

Get specifications filename (C++ style)

Description

Get specifications filename (C++ style)

Usage

get_specs_filename(delta)

Arguments

Value

Character string with the filename

Get state name (C++ style)

Description

Get state name (C++ style)

Usage

get_state(delta, charnum, statenum)

Arguments

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)

Arguments

Value

Integer number of states

Get version of the underlying C++ library

Description

Get version of the underlying C++ library

Usage

get_version(delta)

Arguments

Value

Version string

Check if specifications are available

Description

Check if specifications are available

Usage

has_specifications(delta)

Arguments

Value

Logical

Get implicit value

Description

Get implicit value

Usage

implicit_value(delta, charnum, iv_type = 1)

Arguments

Value

Integer implicit value

Get all implicit values

Description

Get all implicit values

Usage

implicit_values(delta, iv_type = 1)

Arguments

Value

Integer vector of implicit values

Check if characters are parsed

Description

Check if characters are parsed

Usage

is_chars_parsed(delta)

Arguments

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)

Arguments

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)
})

Check if items are parsed

Description

Check if items are parsed

Usage

is_items_parsed(delta)

Arguments

Value

Logical

Check if parsed (C++ style)

Description

Check if parsed (C++ style)

Usage

is_parsed(delta)

Arguments

Value

Logical

Check if specifications are parsed

Description

Check if specifications are parsed

Usage

is_specs_parsed(delta)

Arguments

Value

Logical

Get item attributes as data frame

Description

Get item attributes as data frame

Usage

item_attributes(delta, itemnum)

Arguments

Value

Data frame with attributes

Get number of items

Description

Get number of items

Usage

item_count(delta)

Arguments

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)

Get item data as list

Description

Get item data as list

Usage

item_data(delta, itemnum, include_comments = FALSE)

Arguments

Value

List with item data

Get item name

Description

Get item name

Usage

item_name(delta, itemnum, include_comments = TRUE)

Arguments

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)

Get all item names

Description

Get all item names

Usage

item_names(delta, include_comments = FALSE)

Arguments

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)

Arguments

Value

A data.frame with item information

Get items filename

Description

Get items filename

Usage

items_filename(delta)

Arguments

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
)

Arguments

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)
})

Load a DELTA dataset

Description

Create a DeltaParser object from DELTA format files.

Usage

load_delta(chars_file, items_file, specs_file = NULL)

Arguments

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)
}

Check if item matches values

Description

Check if item matches values

Usage

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

Arguments

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
)

Arguments

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"
         ))
})

Find next matching item

Description

Find next matching item

Usage

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

Arguments

Value

Integer item number or 0 if none

Parse a DELTA attribute string

Description

Parse a DELTA attribute string

Usage

parse_attribute(attr_string)

Arguments

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)

Arguments

Value

Logical indicating success

Parse items file

Description

Parse items file

Usage

parse_items(delta)

Arguments

Value

Logical indicating success

Parse specifications file

Description

Parse specifications file

Usage

parse_specs(delta)

Arguments

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)

Arguments

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
})

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)

Arguments

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)

Arguments

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)

Arguments

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)

Arguments

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)

Arguments

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)
})

Set character type

Description

Set character type

Usage

set_char_type(delta, charnum, chartype)

Arguments

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)

Arguments

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)

Arguments

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)

Arguments

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)

Arguments

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)

Arguments

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)

Arguments

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)

Arguments

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)

Arguments

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)

Arguments

Value

Integer number of states

Get state name

Description

Get state name

Usage

state_name(delta, charnum, statenum)

Arguments

Value

Character string with state name

Get all states for a character

Description

Get all states for a character

Usage

states(delta, charnum)

Arguments

Value

Character vector of state names

Remove comments from a DELTA string

Description

Remove comments from a DELTA string

Usage

strip_comments(src)

Arguments

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)

Arguments

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")
})

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)

Arguments

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")
})