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Print hierarchical structure in indented lists

Source: R/indented_list.R
indented_list.Rd

Print taxonomic hierarchies (ranks and parent-child relationships) from taxlist objects in an indented list.

Usage

indented_list(object, ...)

# S4 method for taxlist
indented_list(
  object,
  filter,
  keep_children = TRUE,
  keep_parents = TRUE,
  rankless_as,
  indent = " ",
  lead_br = "",
  print = TRUE,
  author = TRUE,
  level = FALSE,
  synonyms = FALSE,
  syn_encl = c("= ", ""),
  secundum,
  alphabetical = FALSE,
  ...
)

Arguments

object

A taxlist object containing taxonomic concepts.

...

Further arguments (not used yet).

filter

A character value (optional) that will be matched with the taxon usage names to produce a subset of 'object'. Note that this filter will be also applied to synonyms, independent of the argument applied in parameter 'synonyms'.

keep_children

A logical value indicating whether children of matched concept should be included in the result.

keep_parents

A logical value indicating whether parents of matched concept should be included in the result.

rankless_as

A character vector indicating a level (taxonomic rank) to which rankless taxa may be set before doing the list.

indent

Symbol used for indentation. This symbol will be multiplied by the depth of the taxonomic rank. The default is a blank space. This can be also provided as a named vector, with a different indentation symbol for the respective taxonomic ranks.

lead_br

Optional line break symbol leading before the indentation. It may be required for r-markdown documents.

print

A logical value indicating whether the indented list should be printed in the console or not (default = TRUE).

author

A logical value indicating whether the author should be printed with the name (default = TRUE).

level

A logical value indicating whether the name of the level (taxonomic rank) should be included before the name or not (default = FALSE).

synonyms

A logical value indicating whether the synonyms should be included after accepted names or not (default = FALSE).

syn_encl

A character vector of length 2 including the symbols used to enclose synonyms. First value will be set before the synonyms and second value, after the synonyms.

secundum

A character value matching a name in slot 'taxonViews', which will be printed as secundum (taxon view). It is not printed by default.

alphabetical

A logical value indicating whether taxa may be sorted by names or by IDs. The default is FALSE, thus taxa are sorted by IDs. Note that argument TRUE may not work properly if the object contains homonymous taxa.

Value

If 'print = TRUE', the indented list is printed in the console. The result, which is a data frame with the elements used to format the names, can be also assigned to an object.

Author

Miguel Alvarez kamapu78@gmail.com

Examples

## Show taxonomy of papyrus
indented_list(Easplist, "papyrus")
#> Cyperaceae Juss.
#>  Cyperus L.
#>    Cyperus papyrus L. 

## Include synonyms and taxon views
indented_list(Easplist, "papyrus", level = TRUE, synonyms = TRUE,
    secundum = "secundum")
#> family Cyperaceae Juss. sec. The Plant List (2013)
#>  genus Cyperus L. sec. Taxonomic Name Resolution Service (2018)
#>    species Cyperus papyrus L. sec. African Plant Database (2012)
#>    = Cyperus papyrus ssp. antiquorum (Willd.) Chiov.
#>    = Cyperus papyrus ssp. nyassicus Chiov.