Identifies specimens using a key (R.W. Payne).
Options
PRINT = string tokens |
Controls printed output (identification, transcript); if PRINT is unset in an interactive BKIDENTIFY will ask what you want to print, in a batch run the default is iden |
|---|---|
KEY = tree |
Specifies the key |
IDENTIFICATION = variate |
Saves the identification of each specimen |
TERMINALNODE = variate |
Saves numbers of the terminal nodes reached by the specimens |
Parameter
CHARACTER = factors |
Character values of the specimens |
|---|
Description
BKIDENTIFY identifies specimens using an identification key, as constructed by the BKEY procedure. The key can be saved from BKEY as a Genstat tree structure (using the KEY option of BKEY), and supplied to BKIDENTIFY using its own KEY option. Alternatively, BKIDENTIFY will ask you for the identifier of the key if you do not specify KEY when running interactively.
The characteristics of the specimens can be specified by using the CHARACTER parameter. This must be set to a list of factors with names (and levels) identical to those used originally to construct the key. If you do not set CHARACTER when running interactively, BKIDENTIFY will ask you to examine the characters in turn, as required by the key.
The PRINT option controls printed output, with settings:
identification |
prints the identifications obtained using the key; |
|---|---|
transcript |
prints the observed characteristics when supplied in response to questions in an interactive run. |
If you do not set PRINT in an interactive run, BKIDENTIFY will ask what you would like to print. In batch, the default is to print the identifications.
The IDENTIFICATION option allows you to save the identifications (in a text), and the TERMINALNODE option allows you to save a variate containing the numbers of the terminal nodes that the specimens reached in the key.
Options: PRINT, KEY, IDENTIFICATION, TERMINALNODE.
Parameter: CHARACTER.
Method
BKIDENTIFY works its way through the key using the standard tree functions, BNBRANCHES and BNEXT. The QUESTION procedure is used to obtain any information that is required in an interactive run.
Action with RESTRICT
BKIDENTIFY takes account of any restrictions on the CHARACTER factors.
See also
Procedures: BKEY, BKDISPLAY, BKKEEP, IDENTIFY.
Commands for: Multivariate and cluster analysis.
Example
CAPTION 'BKIDENTIFY example',\
'Common clinical yeasts from Payne (1992) COMPSTAT paper';\
STYLE=meta,plain
TEXT [VALUES='Candida albicans','Candida glabrata',\
'Candida parapsilosis','Candida tropicalis',\
'Cryptococcus albidus','Cryptococcus laurentii',\
'Filobasidiella neoformans',\
'Issatchenkia orientalis',\
'Kluyveromyces marxianus',\
'Pichia guilliermondii','Rhodotorula glutinis',\
'Rhodotorula mucilaginosa','Trichosporon beigelii'] Yeasts
FACTOR [NVALUES=Yeasts; LABELS=!t('-','+')]\
C11; EXTRA='Maltose growth'
& C18; EXTRA='Lactose growth'
& C19; EXTRA='Raffinose growth'
& C36; EXTRA='D-Glucuronate growth'
& N1; EXTRA='Nitrate growth'
& V5; EXTRA='Growth w/o Thiamin'
& O2; EXTRA='0.1% Cycloheximide growth'
& E5; EXTRA='Splitting cells'
READ [PRINT=errors] C11,C18,C19,C36,N1,V5,O2,E5; FREPRESENTATION=labels
'+' '-' '-' '-' '-' '+' '+' '-'
'-' '-' '-' '-' '-' '-' '-' '-'
'+' '-' '-' '-' '-' '+' '-' '-'
'+' '-' '-' '-' '-' '+' '+' '-'
'+' * * '+' '+' '-' '-' '-'
'+' '+' '+' '+' '-' * * '-'
'+' '-' * '+' '-' '-' '-' '-'
'-' '-' '-' '-' '-' '+' '-' '-'
'-' * '+' '-' '-' '+' '+' '-'
'+' '-' '+' '-' '-' '+' '+' '-'
'+' '-' * '-' '+' * * '-'
* '-' '+' '-' * '-' * '-'
* '+' * '+' '-' '-' * '+' :
PRINT [MISSING='V'] C11,C18,C19,C36,N1,V5,O2,E5; FIELDWIDTH=4; DECIMALS=0
FACTOR [MODIFY=yes; LABELS=!t(negative,positive)] C11,C18,C19,C36,N1,V5,O2,E5
BKEY [PRINT=bracketed; TAXONNAMES=Yeasts; CRITERION=cme; KEY=YeastKey]\
C11,C18,C19,C36,N1,V5,O2,E5
CAPTION !t('Use BKIDENTIFY to see how the yeasts are identified by the key:',\
'shows that we cannot distinguish Candida albicans & tropicalis.')
BKIDENTIFY [PRINT=identification; KEY=YeastKey] C11,C18,C19,C36,N1,V5,O2,E5