summary: Print overviews for taxlist Objects and their content

Description

A method to display either an overview of the content of taxlist objects or an overview of selected taxa.

Usage

# S4 method for taxlist
summary(
  object,
  ConceptID,
  units = "Kb",
  check_validity = TRUE,
  display = "both",
  maxsum = 5,
  secundum = NULL,
  exact = FALSE,
  ...
)
# S4 method for taxlist
show(object)
# S4 method for taxlist
print(x, ...)

Arguments

object, x: A taxlist object.
ConceptID: IDs of concepts to be displayed in the summary.
units: Character value indicating the units shown in the object's allocated space.
check_validity: Logical value indicating whether the validity of object should be checked or not.
display: Character value indicating the field to be displayed (see details).
maxsum: Integer indicating the maximum number of displayed taxa.
secundum: A character value indicating the column from slottaxonViews to be displayed in the summary.
exact: A logical value indicating whether taxon names should match the exact argument in parameter 'ConceptID'. It works only if 'ConceptID' is provided as character value and is not the keyword 'all'.
...: Further arguments passed to or from another methods.

Author

Miguel Alvarez kamapu78@gmail.com

Details

A general overview indicating number of names, concepts and taxon views included in taxlist objects. If argument ConceptID is a vector with concept IDs or names to be matched by grepl(), then a display of all names included in each concept will be produced. Alternative you can use taxon="all" in order to get the listing of names for all concepts included in the object (truncated to the input number of maxsum).

For summaries applied to concepts, there are three alternative displays of names using the argument display. Use display="name" to show the value TaxonName, display="author" to show the value AuthorName or display="both" to show both values. Such values are taken from slot taxonNames.

For big objects it will be recommended to set units="Mb" (see also object.size() for further alternatives).

Examples

Run this code

## summary of the object
summary(Easplist, units = "Mb")

## the same output
summary(Easplist)
show(Easplist)
print(Easplist)
Easplist

## summary for two taxa
summary(Easplist, c(51128, 51140))

## summary by matching a name
summary(Easplist, "Acmella")

## summary for the first 10 taxa
summary(object = Easplist, ConceptID = "all", maxsum = 10)

Run the code above in your browser using DataLab

Get 50% off unlimited learning