Function to build a reference dataframe selecting a case for each taxon from the available specimens in the references' database.

AssembleReference(
  combination,
  ref.db = referencesDatabase,
  thesaurus = zoologThesaurus$taxon
)

Arguments

combination

A dataframe or named list. Each (column) name identifies a taxon. Each column or list element must have a single element of type character, identifying one of the sources included in the references' database.

ref.db

A reference database. This is a named list of named lists of dataframes. The first level is named by taxon and the second level is named by reference source. Each dataframe includes the reference for the corresponding taxon and source. The default ref.db = referencesDatabase is provided as package zoolog data.

thesaurus

A thesaurus for taxa.

Value

A reference dataframe.

Examples

## `referenceSets` includes a series of predefined reference compositions. referenceSets
#> Bos taurus Bos primigenius Ovis aries Ovis orientalis #> NietoDavisAlbarella Nieto <NA> Davis <NA> #> Basel Basel <NA> <NA> Basel #> Combi Nieto <NA> Clutton <NA> #> Groningen <NA> Degerbol <NA> Uerpmann #> Capra hircus Capra aegagrus Sus domesticus Sus scrofa #> NietoDavisAlbarella <NA> <NA> Albarella <NA> #> Basel Basel <NA> <NA> Basel #> Combi Clutton <NA> <NA> Basel #> Groningen <NA> Uerpmann <NA> Hongo #> Cervus elaphus Dama mesopotamica Gazella gazella #> NietoDavisAlbarella <NA> <NA> <NA> #> Basel Basel <NA> <NA> #> Combi Basel Haifa Haifa #> Groningen <NA> <NA> <NA> #> Equus asinus Equus caballus Oryctolagus cuniculus #> NietoDavisAlbarella <NA> <NA> <NA> #> Basel <NA> <NA> <NA> #> Combi Haifa Johnstone Nottingham #> Groningen <NA> <NA> <NA>
## Actually the package `references` is build from them. ## We can rebuild any of them: referenceCombi <- AssembleReference(referenceSets["Combi", ]) ## Define an altenative reference combining differently the references' ## database: refComb <- list(cattle = "Nieto", sheep = "Davis", Goat = "Clutton", pig = "Albarella", redDeer = "Basel") userReference <- AssembleReference(refComb)