DELTA User's Guide

The DELTA system is a flexible data-coding format for taxonomic descriptions, and an associated set of programs for producing and typesetting natural-language descriptions and keys, for interactive identification and information retrieval, and for conversion of the data to formats required for phylogenetic and phenetic analysis. This manual is a comprehensive guide to the data format and the program directives.

1. Introduction

When taxonomic descriptions are prepared for input to computer programs, the form of the coding is usually dictated by the requirements of a particular program or set of programs. This restricts the type of data that can be represented, and the number of other programs that can use the data. Even when working with a particular program, it is frequently necessary to set up different versions of the same basic data — for example, when using restricted sets of taxa or characters to make special-purpose keys. The potential advantages of automation, especially in connection with large groups, cannot be realised if the data have to be restructured by hand for every operation. The DELTA (DEscription Language for TAxonomy) system was developed to overcome these problems. It was designed primarily for easy use by people rather than for convenience in computer programming, and is versatile enough to replace the written description as the primary means of recording data. Consequently, it can be used as a shorthand method of recording data, even if computer processing of the data is not envisaged.

Particular attention has been paid to the need to minimize coding errors. The data are written in free format — that is, there is no need to place data in particular columns. The characters may be assigned numbers in any order that suits the user (there is no need to group them by character types, as required by some programs). However, this order need not be adhered to when recording the attributes of a particular taxon. Thus, attributes that are unknown or considered unimportant can be omitted, and later added to the end of the list, if required. An incorrect attribute can be deleted, and the correct one inserted in the same place or at the end. Common character attributes may be made implicit — that is, only the corresponding unusual attributes need appear explicitly in the data.

The system is capable of encoding all of the types of character commonly used for identification and classification: unordered and ordered multistate (including two-state), counts, measurements, and text. Intermediates, ranges, and alternatives can be represented, and distinction is made between ‘variable’, ‘unknown’, and ‘not applicable’. There is provision for comments, which can be used to indicate such things as probability, rarity, uncertainty, qualification, amplification, or references.

There is some redundancy in the coding system, to aid the detection of errors. Most errors have only a local effect, so that a program can continue to scan the rest of the data for other errors.

A format-conversion program, Confor, converts DELTA-format data into natural language, or into formats required by several other programs, including Key (generation of keys), Dist (generation of distance matrices), Paup, MacClade (Nexus), and Hennig86 (cladistic analysis), and Intkey (interactive identification and information retrieval). A complete list of the available translations can be found under the TRANSLATE INTO directive in Section 3.5. R.J. Various other programs use DELTA format directly – see DELTA Programs and Documentation.

This Guide is intended as a reference manual for the DELTA format (Chapter 2), and for the programs Confor, Delfor, Key, and Dist. Intkey has built-in documentation, and there is some further information in Chapter 7 of this Guide.

Introductions to using the DELTA format and programs are available in User’s Guide to the DELTA Editor (Dallwitz, Paine and Zurcher 1999) and A Primer for the DELTA System (Partridge, Dallwitz and Watson 1993).

The programs run on IBM-compatible PC’s under MS-Windows 95/NT or later (see Installation Guide for details). The programs will also run on Macintosh computers, under Windows emulation programs. The programs are free for non-commercial use (see Conditions of Use for details).

2. Characters and Taxon Descriptions

2.1 The character list

The taxa are described in terms of a list of characters, each of which consists of a feature and a set of states. Five main types of character are recognized: unordered multistate (UM), ordered multistate (OM), integer numeric (IN), real numeric (RN), and text (TE). A multistate character has a fixed number of states (one or more), whereas a numeric character has (in principle) an infinite number of states. (Note. One-state ‘characters’ are allowed mainly for convenience when using a hierarchy of ‘characters’ to represent a taxonomic or geographic hierarchy.) Table 1 shows an example of a character list. Characters 1, 2, and 3 are unordered multistate, 4 is ordered multistate, 5 is integer numeric, 6 is real numeric, and 7 is text. (For two-state characters, the distinction between unordered and ordered is arbitrary.)

#1. striated area on maxillary palp <presence>/

1. present/

2. absent/

#2. pronotum <colour>/

1. red/

2. black/

3. yellow/

#3. eyes <size>/

1. of normal size <i.e. less than 0.5mm in diameter>/

2. very large <i.e. more than 0.5mm in diameter>/

#4. frons <setae>/

1. with setae on anterior middle and above eyes/

2. with setae above eyes only/

3. without setae/

#5. number of lamellae in antennal club/

#6. length/ mm/

#7. <comments>/

Each character description starts with a feature description. The feature description starts with a numero (#), which must be at the start of a line or preceded by a blank. The numero is followed by the character number, a full stop (.), and a blank. A blank between the numero and the character number is optional. The feature description is terminated by a slash (/), which must be at the end of a line or followed by a blank. For multistate characters, the feature description is followed by the state descriptions. A state description starts with the state number, followed by a full stop and a blank. It is terminated by a slash, which must be at the end of a line or followed by a blank. For numeric characters, the feature description may optionally be followed by the units in which the character is measured. The units are terminated by a slash, which must be at the end of a line or followed by a blank. The character numbers must be consecutive integers starting at 1, and must be in ascending order in the character list. State numbers must be consecutive integers starting at 1, and must be in ascending order within each character description. A slash not followed by a blank or end of line (e.g. and/or) is allowed, and does not constitute a terminating slash.

The descriptions of the features, states, and units may contain comments delimited by angle brackets (<>). To be interpreted as a delimiting bracket, an opening bracket must be at the start of a line, or be preceded by a blank, a left bracket, or a right bracket; and a closing bracket must be at the end of a line, or be followed by a blank, a right bracket, a left bracket, or the slash which terminates that part of the character description. Nesting of comments is allowed, e.g. <aaa <bbb>>.

Confor omits character-list comments from much of its output: in particular, they do not appear in natural-language descriptions. They may contain any kind of subsidiary material, such as definitions of the terms being used, or references. In some contexts, such as interactive identification, a feature description may be displayed in isolation; comments should therefore be used, if necessary, to make the feature description convey the nature of the character (see examples in Table 1). Lengthy comments may be more appropriately placed in the Confor directive CHARACTER NOTES (see Section 3.5). Inner nested comments should be used for the author’s private notes; they can be omitted when the character list is printed or translated into other formats (see OMIT INNER COMMENTS in Section 3.5).

The feature and state descriptions should start with lower-case letters (except for proper nouns, etc.). If an initial letter must remain lower case even when at the start of a sentence, it should be preceded by a vertical bar, e.g. |mRNA. If output is to be automatically typeset, any necessary typesetting marks should be included (see Section 3.4).

For input to Confor, the character list must be preceded by the control phrase *CHARACTER LIST (see Chapter 3).

2.2 The taxon descriptions

A taxon description consists of one or more ‘item descriptions’, each of which describes one form or variant of the taxon. Usually one item per taxon is sufficient. However, it may be desirable, for example, to represent two or more subspecies as separate items within one species (taxon), or to represent one variable taxon by several items.

An item description consists of the item name followed by a set of attributes. The item name starts with a numero (#), which must be at the start of a line or preceded by a blank. A blank after the numero is optional. The item name is terminated by a slash (/), which must be at the end of a line or followed by a blank. A slash not followed by a blank or end of line is allowed, and does not constitute a terminating slash.

The item name may contain comments delimited by angle brackets (<>). To be interpreted as a delimiting bracket, an opening bracket must be at the start of a line, or be preceded by a blank, a left bracket, or a right bracket; and a closing bracket must be at the end of a line, or be followed by a blank, a right bracket, a left bracket, or the slash which terminates the item name. Nesting of comments is allowed. It is recommended that item-name comments be used for the authority, as in the example below. (The interpretation of inner nested comments is currently not defined; they may be used in future extensions of the DELTA format.)

An attribute consists of a character number, together with the character values (state numbers or numerical values) that apply to the taxon being described. The special symbols ‘V’, ‘U’, and ‘–’, represent ‘variable’, ‘unknown’, and ‘not applicable’, respectively. These are called pseudo-values. The simplest form of an attribute is

where c is a character number and v is a character value or pseudo-value. Attributes must be separated by at least one blank.

Striated area on maxillary palp present; or absent. Frons without setae. Number of lamellae in antennal club not applicable. Length 8.5mm.

where c is a character number, r_i is a value or combination of values (see below), ‘/’ is a separator denoting ‘or’, and ‘<e_i>’ is optional extra information (a comment). Blanks or line endings are permitted within e_i, but not elsewhere within the attribute. Nesting of comments is allowed. Note that, unlike the syntax in the character list and item names, any occurrence of ‘<’ or ‘>’ is interpreted as a comment delimiter. Inner nested comments should be used for the author’s private notes; they can be omitted when the character list is printed or translated into other formats (see OMIT INNER COMMENTS in Section 3.5). r_i takes one of the forms

where v is any character value or pseudo-value, v_j is any character value (not a pseudo-value), ‘&’ is a separator denoting ‘and’, and ‘-’ is a separator denoting ‘to’.

Text characters are coded simply as c<e₀>. If an initial letter of the value of a text character must remain lower case even when at the start of a sentence, it should be preceded by a vertical bar, e.g. |mRNA.

Striated area on maxillary palp present; or absent <rare>. Pronotum black; or black and yellow <striped>. Eyes of normal size to very large. Length 7 to 8.5mm. Possibly two species.

When the separator ‘-’ is used with ordered multistate or numeric characters, the components of r_i must be in ascending order, and r_i denotes all values between v₁ and v_m. For unordered multistate characters, values between v₁ and v_m are not included in the range.

The attributes 4,1-3 and 4,1-2-3 are equivalent, and indicate that setae may be on the anterior middle and above the eyes, above the eyes only, or absent. However, the attributes 2,1-3 and 2,1-2-3 are not equivalent: the former denotes colours between red and yellow (red, orange, and yellow, but not black), while the latter denotes red, black, yellow, and their intermediates.

For numeric characters, ‘v₁-’ and/or ‘-v_m’ may be enclosed within parentheses, to denote extreme values, and there may be at most 3 normal values (those not enclosed in parentheses). The middle or only normal value is assumed to be a measure of central tendency (mean, median, or mode).

Most current applications do not make use of the distinction between the separators ‘&’ and ‘/’. The only exception (apart from the Confor and Delfor options specifically for maintaining DELTA data) is the TRANSLATE INTO NATURAL LANGUAGE directive of Confor. If the distinction is essential for identification purposes, extra states can be defined for the required combinations. However, this may be less satisfactory for use in classification, as there is no way (within the DELTA system) to express the relationship between the composite states and their components.

Attributes may be recorded in any order within an item. A missing attribute is equivalent to an attribute with pseudo-value ‘U’ (except for variant items in a multi-item taxon, or if character dependencies or implicit values have been specified — see below).

The items of a multi-item taxon must be grouped together. The items are identified as belonging to the same taxon by having a plus sign after the numero of the second and subsequent items (#+). The first item is called the main item, and the other items are called variant items. Missing attributes in the main item denote characters with unknown values (or dependent or implicit values), in the usual way. Missing attributes in the variant items denote attributes that are the same as in the main item.

Confor can be used to produce DELTA-format data in which all the relevant information from the main items is explicit in the variant items (see INSERT REDUNDANT VARIANT ATTRIBUTES in Section 3.5). This process can also be reversed (see OMIT REDUNDANT VARIANT ATTRIBUTES in Section 3.5).

(It is proposed that future versions of the DELTA format will have provision for specifying a taxonomic hierarchy, and for passing attribute information up and down the hierarchy. The ‘variant items’ facility, in its present form, will be then be redundant, and will be removed.)

Some characters have a common or ‘usual’ state value, which describes the great majority of taxa, and a rare or ‘unusual’ state value, which describes only one or a few taxa. It is possible to specify that the common value is to be implicit unless otherwise indicated (see IMPLICIT VALUES in Section 3.5). Then only the rare values need be explicitly coded in the items. The main purpose of implicit values is to improve natural-language descriptions by omitting the common character values. Confor can be used to insert the implicit values in DELTA-format data or natural-language descriptions (see INSERT IMPLICIT VALUES in Section 3.5). However, if implicit values are inserted in DELTA-format data, the process cannot be reversed.

Sometimes certain attributes imply that other characters are inapplicable. A common example is a character that specifies the presence or absence of some structure: if the structure is absent, then all characters that further describe that structure are inapplicable. If this dependency of the characters is specified (see DEPENDENT CHARACTERS in Section 3.5), then the inapplicable characters can be omitted from items, instead of being explicitly coded as inapplicable.

For input to Confor, the items must be preceded by the control phrase *ITEM DESCRIPTIONS (see Chapter 3).

3. The Format-Conversion Program Confor

3.1 Introduction

Confor is a program for translating DELTA-format data into various other formats, including natural language. Execution of the program is controlled by means of ‘directives’, which are described in detail in Section 3.5. The output formats available are listed in that Section under the directive TRANSLATE INTO.

A directive consists of a star (*), a control phrase of up to four words, and data. The star must be at the start of a line, or be preceded by a blank. A blank following the star is optional. The control phrase must be in upper-case letters. Only the first two or three symbols of each word of the control phrase are examined by the program. However, it is recommended that the words be written in full, to make the directive as readable as possible. The data take different forms, depending on the control phrase, and in some directives are absent. A control phrase must be contained in one line, but its data may extend over several lines. A directive is terminated by the star at the start of the next directive.

The execution of the program is controlled by the contents of the directives, and by the order in which they appear. Not all combinations and orders of directives are permitted. The restrictions are given in full in the individual descriptions of the directives (see Section 3.5).

The order in which the directives may appear are governed by their types. There are 6 types: 0, and 1-5. Type-0 directives have no restrictions on order. Directives of types 1-5 must appear in order of their types — that is, a directive must not precede any directive of lower type. The reason for this restriction is that higher-type directives may need to use information provided by lower-type directives. The directive types for individual directives are given in Section 3.5.

Except for type-0 directives, a directive must not appear more than once in a run. This restriction extends to sets of directives that specify the same or similar information, for example, the directives INCLUDE ITEMS and EXCLUDE ITEMS.

Many of the variables whose values may be set by directives are assigned default values by the program at the start of each run. Variables whose default values are what is required need not be explicitly set: the directives or parts of directives that set these variables may be omitted.

Sets of Confor directives are stored in files (see Section 3.2). To run the program, enter

3.2 Data organization and file names

The Confor directives required for a particular purpose can all be stored in a single computer file. However, it is usually more convenient and flexible to divide the directives into four files, as follows.

The adoption of conventions for naming files makes the names easier to remember. It is best to use a separate subdirectory for each set of data: then the names of corresponding files can always be the same, e.g. ‘specs’ for the specifications file. Some examples are given below.

Special-purpose DELTA-format files. The purpose is indicated by a suffix to the file name.

Key-format files produced by the TRANSLATE INTO KEY FORMAT option of Confor. The format of the files is indicated by a prefix to the file name.

3.3 Error messages

3.3.1 General

When Confor detects an error in the data, it prints: the current line of data, preceded by the file name and line number; an arrow pointing to the column where the error was detected; and an error message. This information is printed on the screen and on the listing file (see LISTING FILE in Section 3.5). If an essential part of the data, such as a delimiter, has been omitted, the omission cannot usually be detected until another delimiter has been found. The site of the omission will then be before the position of the arrow, in some cases on a previous line.

Error messages are often easier to interpret when viewed in full context in the listing file. By default, the CHARACTER LIST and ITEM DESCRIPTIONS directives are omitted from the listing file, but they can be included by means of the LIST CHARACTERS and LIST ITEMS directives. The latter directive was used to produce the listing file shown (in part) in the following example.

Example

¹There should be a blank separating the first two attributes. They should read: 1,1.01-1.25 2,1

^3,4Both of these messages are due to the same mistake: a blank in the middle of an attribute. It should read: 15,1

⁵There should be a slash after the preceding item name (parvispinus Taylor). Note that the error in the fifth attribute (5.1 instead of 5,1) was not detected — because of the missing slash, the program treated all of the attributes as part of the item name.

After detecting errors, the program continues to process the data as long as it is possible and worthwhile to do so. When there is an error in a directive specifying a file name, the program stops immediately. After any other type of error, the program continues until a higher-type directive is encountered.

3.3.2 Storage limitations

None of the DELTA programs has fixed limits on the numbers of items or characters. All storage is allocated from a single pool, whose size depends on the amount of memory (RAM) available in the computer. All of the programs require some storage proportional to the number of characters, and some proportional to the number of items (taxa). Some of the programs also require additional storage. ‘Key’ requires storage proportional to the number of items multiplied by the number of characters.

Confor has a ‘data buffer’, which must be able to hold the longest item. The length of an item is increased by text material (text characters and comments), and decreased if some characters are not coded (for example, because they inapplicable to a particular item). The same storage is also used to hold individual characters from the character list and individual character notes, but these are rarely the limiting factors.

Confor has two error messages that indicate that it does not have enough storage available. The first is

This means that the item (or character, or character note) currently being read will not fit in the data buffer. The default length of the data buffer is 20 times the number of characters. This can be increased or decreased by means of the DATA BUFFER SIZE directive, which should be placed in the ‘specs’ file immediately under the MAXIMUM NUMBER OF ITEMS directive.

This means that the total amount of storage available is insufficient. A reduction in storage requirements is obtained by using a SPECIAL STORAGE directive in the ‘specs’ file, so that the character list is stored on disk instead of in memory. Reducing the size of the data buffer (see above) will also help, but the scope for this is usually limited. However, any reduction is multiplied threefold, because there are three data buffers.

3.4 Typesetting marks

Confor recognizes RTF (Rich Text Format) typesetting marks embedded in text such as the character list, taxon names, and comments in attributes. The marks are passed through into output files such as RTF natural-language descriptions and Intkey data files (unless suppressed by means of an OMIT TYPESETTING MARKS directive). An OUTPUT FORMAT HTML directive causes the marks to be translated into the corresponding HTML (HyperText Markup Language) marks. Further typesetting marks can be inserted in various contexts in natural-language descriptions and keys by means of the TYPSETTING MARKS directive.

Although they may contain RTF marks, DELTA data files are not RTF files (which require a special header). They must be edited as text files, or by means of the DELTA Editor which is included in the DELTA program package. In a text editor, the marks are edited as such, whereas in the DELTA Editor, the effects of the marks (for example, italics font) are edited as in a word processor.

RTF marks start with a backslash (\), and are terminated by the backslash of a following mark, a space, or braces ({}). However, a space should not be used as a terminator in DELTA files, as it may be removed by Confor when wrapping lines.

Some frequently used marks are given in the table below. N denotes a numeric parameter. Font size is specified in half-points, and other dimensions in twips. A twip is one-twentieth of a point. There are 1440 twips in an inch, and 567 twips in a centimetre (the conversion factor used is 1 inch = 2.5 cm).

RTF Marks	Meaning	Example
RTF Marks	Meaning	Marks	Effect
\i	Start italics	\i{}Agrostis\i0{}	Agrostis
\i0	Stop italics	\i{}Agrostis\i0{}	Agrostis
\b	Start bold	\b{}Habit\b0{}	Habit
\b0	Stop bold	\b{}Habit\b0{}	Habit
\sub	Start subscript	C\sub{}4\nosupersub{}	C₄
\nosupersub	Stop super- or subscript	C\sub{}4\nosupersub{}	C₄
\fsN	Font size	\fs16{}eight point	eight point
\plain	Set default font attributes
\endash	En dash	4\endash{}10mm	4-10mm
\lquote	Left quote	\lquote{}normal\rquote{}	‘normal’
\rquote	Right quote	\lquote{}normal\rquote{}	‘normal’
\par	New paragraph	\par\pard\sb567\sa283{}	Start a new paragraph with 1cm space before and 0.5cm space after
\pard	Default paragraph attributes
\sbN	Space before paragraph
\saN	Space after paragraph
\liN	Line indentation	\par\pard\li850\fi-567{}	Paragraph with the first line indented 0.5cm, and the others 1.5cm
\fiN	First line indentation (relative to line indentation)	\par\pard\li850\fi-567{}

3.5 Directives (in alphabetical order)

Definitions

where c₁ and c₂ are character numbers, and c₁ is less than or equal to c₂. It denotes all character numbers from c₁ to c₂, inclusive. For example, 6-9 denotes the characters 6, 7, 8, and 9.

where t₁ and t₂ are item numbers, and t₁ is less than or equal to t₂. It denotes all item numbers from t₁ to t₂, inclusive. For example, 6-9 denotes the items 6, 7, 8, and 9.

*ABSOLUTE ERROR (Confor; Type 4)

Description

This directive specifies error limits to be applied to real numeric characters when converting to Key and Intkey formats. If an attribute in an item specifies only a single value, the errors specified in this directive are added to and subtracted from the value in the attribute to convert it to a range. See also PERCENT ERROR, OMIT LOWER FOR CHARACTERS.

General form

where c_i is a character number or range of numbers, and r_i is a positive real number. An absolute error r applied to a value v produces a range v-r to v+r.

Default

Example

With this directive in force, attributes 5,95 17,.12 would be equivalent to 5,85-105 17,.115-.125. Attributes 5,55-70 17,2.2-2.6 would be unchanged.

*ACCEPT DUPLICATE VALUES (Confor, Delfor; Type 4)

Description

This directive allows the occurrence of two or more attributes with the same character number in an item. The last attribute with a given character number overrides the previous ones, and a warning message is displayed. This is to enable corrections to be made by appending the correct attribute, without the need to delete the incorrect attribute. This directive should be used with care, because repeated use of the same character number can arise unintentionally through mistyping of a character number.

General form

Default

*ADD CHARACTERS (Confor; Type 4)

Description

This directive specifies additional characters (that is, additional to those specified by means of an INCLUDE CHARACTERS or EXCLUDE CHARACTERS directive) to be included in the natural-language descriptions of specified taxa. Repeated use of the directive has a cumulative effect.

General form

where t_i is an item number, n_i is an item name, and c_ij is a character number or range of numbers.

Default

Example

*ALTERNATE COMMA (Confor; Type 4)

Description

This directive specifies that an alternate comma be used to separate elements in a list of states in natural-language descriptions. The form of the alternate comma is specified in the VOCABULARY directive. (In Chinese, the alternate comma should be used when the states are nouns, for example, for characters specifying geographical distribution or host range.)

General form

Default

Example

*APPLICABLE CHARACTERS (Confor; Type 4)

Description

This directive specifies the values of ‘controlling’ characters which make other ‘dependent’ characters applicable. If, in a given item, a controlling character takes only values which make its dependent characters inapplicable, or if the controlling character itself is inapplicable, then the dependent characters must not be given any values (other than the pseudovalue ‘inapplicable’ (see Section 2.2), which is redundant and will be removed by translation into DELTA format (see TRANSLATE INTO)).

General form

where c_i is a character number (the controlling character), s_i is a set of state numbers, and d_i is a set of character numbers (the dependent characters). s_i takes the form

where e_j is a character number or range of numbers. Characters declared applicable for a given value of a character are considered to be inapplicable for any other value of that character, unless explicitly declared otherwise. The controlling characters must be multistate, and any value of a controlling character may appear only once in the directive.

Default

Example

*APPLICABLE CHARACTERS 10,1:11 16,1:17 20,1:21-24 32,1:33-38 39,2:40-43 47,3:48-51 55,1:56 57,1:58-59 68,1:69 78,1:79-80 78,2:79:81 78,3:82 78,4:83 78,5:79:84

*CHARACTER FOR OUTPUT FILES (Confor; Type 4)

Description

This directive allows the specification, from information coded in the items, of the names of files for natural-language descriptions. It is an alternative to the ITEM OUTPUT FILES directive. See also INDEX OUTPUT FILE, SUBJECT FOR OUTPUT FILES.

General form

where c is the number of a text character. The text recorded against this character for an item is used as the main part of the output-file name, from that item onwards. The appropriate file type (.rtf or .htm) is appended.

Default

Example

*CHARACTERS FOR SYNONYMY (Confor; Type 4)

Description

This directive specifies text characters which contain information on synonymy. These characters, as well as the taxon names, are searched by the ‘Find taxa’ option in Intkey (Version 4.04 and later).

General form

Default

Example

*CHARACTER FOR TAXON IMAGES (Confor; Type 4)

Description

This directive specifies a dummy text character, which is used as a placeholder for taxon-image information in natural-language descriptions. The images and associated information are stored in a TAXON IMAGES directive.

General form

Default

Example

*CHARACTER FOR TAXON NAMES (Confor; Type 4)

Description

This directive allows the specification of alternative taxon name for use in output files. It is mainly intended for specifying abbreviated names for output files destined for other programs, in which long names are impossible or inconvenient.

General form

where c is the number of a text character. The text recorded against this character for an item is used as the taxon name in output files.

Default

Example

*CHARACTER HEADINGS (Confor; Type 4)

Description

This directive specifies headings to be placed in the character list produced by a PRINT CHARACTER LIST directive. (It should not be confused with the ITEM SUBHEADINGS directive.)

General form

where ! represents a delimiter symbol, which may be any symbol except the DELTA delimiters *, #, <, and >; c_i is a character number; and t_i is any text. The delimiter ! is optional; its purpose is to allow the use of the DELTA delimiters within the heading. The delimiter may be left undefined, by omitting its first occurrence (after the words CHARACTER HEADINGS). t_i is output immediately before character c_i on a separate line.

Default

Example

*CHARACTER IMAGES (Confor; Type 4)

Description

This directive specifies information on character images and associated annotation for use with Intkey. The directive is normally created and edited by means of the program Intimate (see Chapter 8).

General form

Default

Example

*CHARACTER KEYWORD IMAGES (Confor; Type 4)

Description

This directive specifies information on character keyword images and associated annotation for use with Intkey. It allows selection of character keywords from image screens (instead of from text screens).

The directive is normally created and edited by means of the program Intimate (see Chapter 8).

General form

Default

Example

*CHARACTER LIST (Confor; Type 5)

Description

General form

Default

Example

*CHARACTER NOTES (Confor; Type 4)

Description

This directive specifies text containing supplementary information about characters. This information is placed after the appropriate characters in the output produced by the PRINT CHARACTER LIST directive, and is also available through Intkey.

General form

where s_i is a set of character numbers and t_i is any text. s_i takes the form

Default

Example

*CHARACTER RELIABILITIES (Confor; Type 4)

Description

This directive specifies the reliabilities or weights of the characters. The interpretation of the reliabilities or weights depends on the program for which they are intended. Generally, characters with high reliabilities or weights will be given emphasis in some way — for example, they will tend to be used early in keys.

This directive specifies the same information as the CHARACTER WEIGHTS directive. The relation between a reliability, r, and a weight, w, is given by

For example, reliabilities of 5 and 3 are equivalent to weights of 1 and 0.25, respectively.

General form

where c_i is a character number or range of character numbers, and r_i is a real number in the range 0 to 10.

Default

Example

*CHARACTER TYPES (Confor, Delfor; Type 2)

Description

General form

where c_i is a character number or range of numbers, and t_i is one of the following character types.

Default

Example 1

Example 2

*CHARACTER WEIGHTS (Confor; Type 4)

Description

This directive specifies the weights of the characters. The interpretation of the weights depends on the program for which they are intended. Generally, characters with high weights will be given emphasis in some way — for example, they will tend to be used early in keys.

The directive must not appear with a CHARACTER RELIABILITIES directive, to which it is an alternative.

General form

where c_i is a character number or range of numbers, and w_i is a real number in the range 0.03125 to 32 (corresponding to character reliabilities in the range 0 to 10).

Default

Example

*CHINESE FORMAT (Confor, Delfor; Type 4)

Description

This directive specifies formatting for Chinese and similar languages. Chinese symbols (characters) are assumed to be represented by pairs of bytes with the high-order bit set in the first byte. Capitalization is suppressed, line breaks may occur before or after any Chinese symbol, and spaces are not placed between features and states in natural-language descriptions.

General form

Default

*COMMENT (Confor, Delfor; Type 0)

Description

This directive enables comments to be incorporated in directives files. It is intended for information that is not associated with a particular character, item, or attribute (for example, the date of the last revision of the data). It can also be used to deactivate a directive that is not currently required, but may be required again later. See also SHOW.

General form

where text is any text not containing blank-star. The text may extend over more than one line.

Default

Example 1

Example 2

*DATA BUFFER SIZE (Confor, Delfor; Type 1)

Description

This directive sets the size of arrays used for temporary storage of character and item descriptions. It need be used only if error messages on previous runs have indicated storage problems (see Section 3.3.2). The arrays must be large enough to hold (in the internal representation) the longest character or item description. However, if the arrays are larger than necessary, they occupy storage that could be used for other purposes.

General form

Default

Example

*DATA COMPRESSION (Confor; Type 4)

Description

This directive causes the items produced when translating into DELTA format to be coded more compactly. Successive attributes that have the same character types and the same state values are combined by using a range of character numbers. For example, the attributes 12,2 13,2 14,2 would become 12-14,2.

General form

Default

*DATA LISTING (Confor; Type 0)

Description

This directive causes the data read from the input file to be listed on the listing file (see LISTING FILE). In the listing, each line is preceded by the name of the file from which it was read, and by the line number. The directive is cancelled by the NO DATA LISTING directive.

This directive does not cause the characters and items files to be listed. This is done by means of the LIST CHARACTERS and LIST ITEMS directives.

General form

Default

The input data are not listed. Note, however, that the listing is turned on by the LISTING FILE directive.

*DECIMAL PLACES (Confor; Type 4)

Description

This directive specifies the number of decimal places to be used in outputting real character values, when translating into DELTA format or natural language.

General form

where c_i is a character number or range of numbers, and d_i is an integer in the range 0 to 5. The characters must be real numeric (RN).

Default

Example

The attributes 1,2.6 2,2.6 3,2.6 would be output in DELTA format as 1,2.6 2,3 3,2.60.

*DEPENDENT CHARACTERS (Confor; Type 4)

Description

This directive specifies the values of ‘controlling’ characters that make other ‘dependent’ characters inapplicable. If, in a given item, a controlling character takes only values that make its dependent characters inapplicable, or if the controlling character itself is inapplicable, then the dependent characters must not be given any values (other than the pseudovalue ‘inapplicable’ (see Section 2.2), which is redundant and will be removed by translation into DELTA format (see TRANSLATE INTO)).

General form

where c_i is a character number (the controlling character), s_i is a set of state numbers, and d_i is a set of character numbers (the dependent characters). s_i takes the form

where e_k is a character number or range of numbers. The controlling characters must be multistate, and any value of a controlling character may appear only once in the directive.

Default

Example

Attribute 4,2 implies that character 16 is inapplicable. Attributes 10,1 and 10,3 imply that characters 12, 13, 20, and 30-35 are inapplicable.

*DISABLE DELTA OUTPUT (Confor; Type 4)

Description

This directive, used with TRANSLATE INTO INTKEY FORMAT, disables the Intkey commands OUTPUT DESCRIBE and OUTPUT SUMMARY (which produce DELTA-format data). Note that this cannot prevent Intkey users from capturing data for processing by other programs — it only makes it more difficult.

General form

Default

*DIST OUTPUT FILE (Confor; Type 0)

Description

This directive specifies the file on which data destined for input to the Dist program will be written (see TRANSLATE INTO). The file must not have been used for any other type of input or output. It is a direct-access file, and cannot be viewed or changed with ordinary text editors.

General form

Default

Example

*EMPHASIZE CHARACTERS (Confor; Type 4)

Description

This directive specifies characters to be emphasized in the typeset natural-language descriptions of specified taxa (see TYPESETTING MARKS). The specified characters will appear in the description regardless of whether they have been included by means of an INCLUDE CHARACTERS or EXCLUDE CHARACTERS directive. Repeated use of the directive has a cumulative effect.

General form

where t_i is an item number, n_i is an item name, and c_ij is a character number or range of numbers.

Default

Example

*EMPHASIZE FEATURES (Confor; Type 4)

Description

This directive causes the specified features to be emphasized in natural-language descriptions (see TYPESETTING MARKS). To emphasize the feature in a set of linked characters, all of the features in the set should normally be specified in the EMPHASIZE FEATURES directive, in case the attribute corresponding to the first character is missing.

General form

Default

Example

*END (Confor, Delfor; Type 0)

Description

This directive terminates the program. It is supplied automatically by the program at the end of the main directives file.

General form

Default

*ERROR FILE (Confor, Delfor; Type 0)

Description

This directive specifies the file on which error messages will be output. The file must not have been used for any other type of input or output, apart from listing and print output (see LISTING FILE and PRINT FILE).

General form

Default

Error messages are output on the default output device or file of the particular computer system. This is usually the screen. Also, error messages are always output on the listing file if one has been specified.

Example

*EXCLUDE CHARACTERS (Confor, Delfor; Type 4)

Description

The directive must not appear with an INCLUDE CHARACTERS directive, to which it is an alternative.

General form

Default

Example

*EXCLUDE ITEMS (Confor, Delfor; Type 4)

Description

The directive must not appear with an INCLUDE ITEMS directive, to which it is an alternative.

General form

Default

Example

*HEADING (Confor; Type 0)

Description

This directive specifies a heading, which may subsequently used to label the output. The current time and date may be included in the heading.

The heading is printed on the error file when reading of the HEADING directive is complete; on the listing file (see LISTING FILE) when a new file is started, or after a LIST HEADING directive; and on the print file (see PRINT FILE) after a PRINT HEADING directive. On the ‘output’ file, the heading is written wherever #HEADING (or the equivalent) appears in the data of a OUTPUT PARAMETERS directive (except when translating into DELTA format).

General form

where t is any text not containing blank-star. The words #TIME and #DATE are replaced by the current time and date, respectively. The total number of symbols in the heading, including the time and date, must not exceed 200.

Default

Example

*IMAGE DIRECTORY (Confor; Type 4)

This directive specifies a directory name for images that have links from natural-language descriptions in HTML format. The names of the image files are obtained from a TAXON IMAGES directive, and the specified directory name is prefixed to the file names.

To facilitate moving the output files onto other computers (in particular, onto a WWW server), the image directory should be specified as a relative rather than an absolute path, as shown in the example.

General form

Default

None. Hence, the image files must be in the same directory as the HTML files which reference them.

Example

The ‘..’ refers to the parent of the current directory. Typically, the HTML descriptions are in a subdirectory ‘www’ and the images in a subdirectory ‘images’, both of which are subdirectories of a directory containing the HTML index file and the Intkey files.

*IMPLICIT VALUES (Confor; Type 4)

Description

This directive permits certain attributes or state values to be omitted from items. The omitted attributes or values are assigned default values. The main purpose of the directive is to improve natural-language descriptions by omitting frequently occurring state values.

General form

where c_i is a character number or range of numbers, and s_i and t_i are state values. ‘:t_i’ is optional. Numeric or text characters must not be specified.

If a character specified by c_i does not appear in an item, then the character is assigned the value s_i (unless the item is a variant item, in which case missing characters have their normal interpretation). If a character specified by c_i appears without a value or pseudovalue, it is assigned the value t_i; if ‘:t_i’ is not present in the directive, then no value is assigned. Unknown values must be represented by ‘U’.

When translating into DELTA format, implicit values are not inserted unless an INSERT IMPLICIT VALUES directive is in force.

When translating into natural language, implicit values corresponding to s_i are not inserted unless an INSERT IMPLICIT VALUES directive is in force, or the item and character have been specified in an ADD CHARACTERS or EMPHASIZE CHARACTERS directive. Implicit values corresponding to t_i are inserted as though they were explicitly coded in the item; that is, the attributes c_i and c_i,t_i produce the same result.

If an attribute which has been specified as implicit is nevertheless explicitly coded in an item (that is, c_i,s_i appears in the item), the attribute is output when translating into DELTA format or natural language. This explicit coding of otherwise implicit attributes can be used for emphasis, for example, when the attribute is important for distinguishing the taxon from a closely related one.

Default

Example

*INAPPLICABLE CHARACTERS (Confor; Type 4)

Description

*INCLUDE CHARACTERS (Confor, Delfor; Type 4)

Description

The directive must not appear with an EXCLUDE CHARACTERS directive, to which it is an alternative.

General form

Default

Example

*INCLUDE ITEMS (Confor, Delfor; Type 4)

Description

The directive must not appear with an EXCLUDE ITEMS directive, to which it is an alternative.

General form

Default

Example

*INDEX HEADINGS (Confor; Type 4)

This directive specifies headings to be used in the HTML index file (see INDEX OUTPUT FILE), interspersed with the taxon names.

General form

where ! represents a delimiter symbol, which may be any symbol except the DELTA delimiters *, #, <, and >; n_i is a taxon name; and h_i is a heading. The delimiter ! is optional; its purpose is to allow the use of the DELTA delimiters within the heading. The delimiter may be left undefined, by omitting its first occurrence (after the words INDEX HEADINGS). In the output, the headings are positioned before corresponding taxon names.

Default

Example

# F. elmeri/ !Subg. Subulatae Tzvelev, sect. Subulatae Tzvelev !

#F. paradoxa/ !Subg. Subulatae (Tzvelev) E. B. Alexeev, sect. Obtusae E. B. Alexeev !

#F. amethystina/ !Species of Festuca that have been excluded for various reasons, such as limited data or uncertainties related to the correct name, and two species of Lolium. !

*INDEX OUTPUT FILE (Confor; Type 0)

This directive specifies the name of an HTML index file, into which are put links to files containing natural-language descriptions in HTML format. It is used in conjunction with the directives CHARACTER FOR OUTPUT FILES or ITEM OUTPUT FILES, which specify files containing individual taxon descriptions. See also INDEX TEXT.

General form

Default

Example

The ‘.\’ (‘current directory’) overrides the directory specified in a previous OUTPUT DIRECTORY directive. (Usually, the index file is in the main data directory, whereas the HTML files are in a subdirectory ‘www’, which is specified as the ‘output directory’ when these files are being generated.)

*INDEX TEXT (Confor; Type 0)

Description

This directive specifies text to be put in the HTML index file specified by the INDEX OUPUT FILE directive.

General form

where text is any text not containing blank-star. The text may extend over more than one line.

Default

Example

*INPUT DELTA FILE (Confor, Delfor; Type 0)

Description

This directive specifies the file from which directives are next to be read. It differs from the INPUT FILE directive in that if the specified file is not found in the current default directory, the program looks for it in the DELTA directory.

General form

Default

Example

*INPUT FILE (Confor, Delfor; Type 0)

Description

This directive specifies the file from which input lines will be read after the processing of the current input line is finished. The file must not have been used for any other type of input or output.

General form

Default

Input is from a file specified in the command line which started the program running, or a file specified in response to a prompt issued by the program.

Example

*INSERT CHARACTER SEQUENCE NUMBERS (Confor; Type 4)

Description

This directive specifies that sequence numbers are to be inserted in the new characters file, when translating into DELTA format. (It was used when data were saved on punched cards, so that the card deck could be correctly re-assembled if it was dropped.) See also SEQUENCE INCREMENT.

General form

Default

*INSERT IMAGE FILE NAME (Confor; Type 4)

Description

This directive causes the image-file names to be included in the output generated by the CHARACTER FOR TAXON IMAGES and TAXON IMAGES directives. It is intended for constructing an HTML image catalog for use by the author of a data set.

General form

Default

Image-file names are not output (unless no ‘subject’ has been specified for the image — see Chapter 8).

*INSERT IMPLICIT VALUES (Confor; Type 4)

Description

This directive causes implicit values (see IMPLICIT VALUES) to be inserted in natural-language and DELTA-format output. (They are always inserted in all other output.)

General form

Default

*INSERT ITEM SEQUENCE NUMBERS (Confor; Type 4)

Description

This directive specifies that sequence numbers are to be inserted in the new items file, when translating into DELTA format. (It was used when data were saved on punched cards, so that the card deck could be correctly re-assembled if it was dropped.) See also SEQUENCE INCREMENT.

General form

Default

*INSERT REDUNDANT VARIANT ATTRIBUTES (Confor; Type 4)

Description

This directive specifies that, when translating a variant item into DELTA format or natural language, an attribute will be output if it is coded in either the master or variant item — that is, information missing from the variant item will be taken from the master item if possible. (Note that, for all other output formats, this is always done — it is not necessary to use this directive.) See also OMIT REDUNDANT VARIANT ATTRIBUTES.

General form

Default

When translating a variant item into DELTA format or natural language, variant items are output as coded.

*INTKEY OUTPUT FILE (Confor; Type 0)

Description

This directive specifies the file on which data destined for input to the Intkey program will be written (see TRANSLATE INTO). The file must not have been used for any other type of input or output. It is a direct-access file, and cannot be viewed or changed with ordinary text editors.

General form

Default

Example

*ITEM ABUNDANCES (Confor; Type 4)

Description

The interpretation of the abundances or weights depends on the program for which they are intended. Generally, items with high abundances or weights will be given emphasis in some way — for example, they tend to come out early in keys.

This directive specifies the same information as the ITEM WEIGHTS directive. The relation between an abundance, a, and a weight, w, is given by

For example, abundances of 9 and 5 are equivalent to weights of 16 and 1, respectively.

General form

where t_i is an item number or range of numbers. and a_i is a real number in the range 0 to 10.

Default

Example

*ITEM DESCRIPTIONS (Confor; Type 5)

Description

General form

Default

Example

*ITEM HEADINGS (Confor; Type 4)

This directive specifies headings to be used in natural-language output, interspersed with the taxon descriptions.

General form

where ! represents a delimiter symbol, which may be any symbol except the DELTA delimiters *, #, <, and >; n_i is a taxon name; and h_i is a heading. The delimiter ! is optional; its purpose is to allow the use of the DELTA delimiters within the heading. The delimiter may be left undefined, by omitting its first occurrence (after the words ITEM HEADINGS). In the output, the headings are positioned before corresponding taxon descriptions.

Default

Example

# F. arundinacea/ \page\b\fs24{}Subg. \i{}Schedonorus\i0{} (Beauv.) Peterm.\b0{}

# F. elmeri/ \page\b\fs24{}Subg. \i{}Subulatae\i0{} Tzvelev, sect. \i{}Subulatae\i0{} Tzvelev\b0{}

#F. paradoxa/ \page\b\fs24{}Subg. \i{}Subulatae\i0{} (Tzvelev) E. B. Alexeev, sect. \i{}Obtusae\i0{} E. B. Alexeev\b0{}

#F. amethystina/ \page\b\fs24{}Species of \i{}Festuca\i0{} that have been excluded for various reasons, such as limited data or uncertainties related to the correct name, and two species of \i{}Lolium\i0{}.\b0{}

*ITEM OUTPUT FILES (Confor; Type 4)

Description

This directive specifies the names of output files for natural-language descriptions. It is an alternative to the CHARACTER FOR OUTPUT FILES directive.

General form

where n_i is a taxon name, and f_i is text specifying a file name. f_i is used as the main part of the output-file name, from the corresponding item onwards. The appropriate file type (.rtf or .htm) is appended by the program.

Default

Example

*ITEM SUBHEADINGS (Confor; Type 4)

Description

This directive specifies subheadings to be placed in natural-language descriptions (see TRANSLATE INTO). (It should not be confused with the CHARACTER HEADINGS directive.)

General form

where ! represents a delimiter symbol, which may be any symbol except the DELTA delimiters *, #, <, and >; c_i is a character number; and t_i is any text. The delimiter ! is optional; its purpose is to allow the use of the DELTA delimiters within the heading. The delimiter may be left undefined, by omitting its first occurrence (after the words ITEM SUBHEADINGS). t_i is output immediately before attribute c_i.

Default

Example

*ITEM WEIGHTS (Confor; Type 4)

Description

The interpretation of the weights depends on the program for which they are intended. Generally, items with high weights will be given emphasis in some way — for example, they tend to come out early in keys.

The directive must not appear with an ITEM ABUNDANCES directive, to which it is an alternative.

General form

where t_i is an item number or range of numbers, and w_i is a real number in the range 0.03125 to 32 (corresponding to item abundances in the range 0 to 10).

Default

Example

*KEY CHARACTER LIST (Confor; Type 5)

Description

This directive specifies an alternative character list, in which the state descriptions conform to the states specified in the KEY STATES directive. It is intended for use when the wording of the new state descriptions generated by the program is unsatisfactory.

The directive must not appear with a CHARACTER LIST directive, to which it is an alternative.

General form

Default

Example

Suppose that the character list in Table 1 (Section 2.1) is used with the following KEY STATES directive.

The following wordings would be generated for the new states of characters 4 to 6.

The following directive could be used to change the wordings of characters 4 and 6.

specs	Specifications.
chars	Character list.
items	Items.

charsf	French character list.
charsk	Character list with special wording appropriate for translation into Key format.

kchars	Character list
kitems	Items.

tokey	Translate into Key format.
topau	Translate into PAUP format.
checki	Check the items.
printc	Print the characters.

UM	Unordered Multistate. Multistate (including 2-state) characters in which the states are not arranged in a natural order.
OM	Ordered Multistate. Multistate characters in which the states are arranged in a natural order.
IN	Integer Numeric. Numeric characters which take only integer (whole-number) values.
RN	Real Numeric. Numeric characters which may take fractional or integer values.
TE	Text.

User’s Guide to the DELTA System: a General System for Processing Taxonomic Descriptions

1. Introduction

2. Characters and Taxon Descriptions

2.1 The character list

2.2 The taxon descriptions

3. The Format-Conversion Program Confor

3.1 Introduction

3.2 Data organization and file names

3.3 Error messages

3.3.1 General

Example

3.3.2 Storage limitations

3.4 Typesetting marks

3.5 Directives (in alphabetical order)

Definitions

*ABSOLUTE ERROR (Confor; Type 4)

Description

General form

Default

Example

*ACCEPT DUPLICATE VALUES (Confor, Delfor; Type 4)

Description

General form

Default

*ADD CHARACTERS (Confor; Type 4)

Description

General form

Default

Example

*ALTERNATE COMMA (Confor; Type 4)

Description

General form

Default

Example

*APPLICABLE CHARACTERS (Confor; Type 4)

Description

General form

Default

Example

*CHARACTER FOR OUTPUT FILES (Confor; Type 4)

Description

General form

Default

Example

*CHARACTERS FOR SYNONYMY (Confor; Type 4)

Description

General form

Default

Example

*CHARACTER FOR TAXON IMAGES (Confor; Type 4)

Description

General form

Default

Example

*CHARACTER FOR TAXON NAMES (Confor; Type 4)

Description

General form

Default

Example

*CHARACTER HEADINGS (Confor; Type 4)

Description

General form

Default

Example

*CHARACTER IMAGES (Confor; Type 4)

Description

General form

Default

Example

*CHARACTER KEYWORD IMAGES (Confor; Type 4)

Description

General form

Default

Example

*CHARACTER LIST (Confor; Type 5)

Description

General form

Default

Example

*CHARACTER NOTES (Confor; Type 4)