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Print overviews for taxlist Objects and their content

Source: R/summary.R
summary.Rd

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

Usage

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

# S4 method for class 'taxlist'
show(object)

# S4 method for class '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.

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).

See also

taxlist

Author

Miguel Alvarez kamapu78@gmail.com

Examples

## summary of the object
summary(Easplist, units = "Mb")
#> object size: 0.7 Mb 
#> validation of 'taxlist' object: TRUE 
#> 
#> number of taxon usage names: 5393 
#> number of taxon concepts: 3887 
#> trait entries: 311 
#> number of trait variables: 1 
#> taxon views: 3 
#> 
#> concepts with parents: 3698 
#> concepts with children: 1343 
#> 
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family 
#> number of concepts in level form: 2
#> number of concepts in level variety: 95
#> number of concepts in level subspecies: 71
#> number of concepts in level species: 2521
#> number of concepts in level complex: 1
#> number of concepts in level genus: 1011
#> number of concepts in level family: 186
#> 

## the same output
summary(Easplist)
#> object size: 761.4 Kb 
#> validation of 'taxlist' object: TRUE 
#> 
#> number of taxon usage names: 5393 
#> number of taxon concepts: 3887 
#> trait entries: 311 
#> number of trait variables: 1 
#> taxon views: 3 
#> 
#> concepts with parents: 3698 
#> concepts with children: 1343 
#> 
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family 
#> number of concepts in level form: 2
#> number of concepts in level variety: 95
#> number of concepts in level subspecies: 71
#> number of concepts in level species: 2521
#> number of concepts in level complex: 1
#> number of concepts in level genus: 1011
#> number of concepts in level family: 186
#> 
show(Easplist)
#> object size: 761.4 Kb 
#> validation of 'taxlist' object: TRUE 
#> 
#> number of taxon usage names: 5393 
#> number of taxon concepts: 3887 
#> trait entries: 311 
#> number of trait variables: 1 
#> taxon views: 3 
#> 
#> concepts with parents: 3698 
#> concepts with children: 1343 
#> 
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family 
#> number of concepts in level form: 2
#> number of concepts in level variety: 95
#> number of concepts in level subspecies: 71
#> number of concepts in level species: 2521
#> number of concepts in level complex: 1
#> number of concepts in level genus: 1011
#> number of concepts in level family: 186
#> 
print(Easplist)
#> object size: 761.4 Kb 
#> validation of 'taxlist' object: TRUE 
#> 
#> number of taxon usage names: 5393 
#> number of taxon concepts: 3887 
#> trait entries: 311 
#> number of trait variables: 1 
#> taxon views: 3 
#> 
#> concepts with parents: 3698 
#> concepts with children: 1343 
#> 
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family 
#> number of concepts in level form: 2
#> number of concepts in level variety: 95
#> number of concepts in level subspecies: 71
#> number of concepts in level species: 2521
#> number of concepts in level complex: 1
#> number of concepts in level genus: 1011
#> number of concepts in level family: 186
#> 
Easplist
#> object size: 761.4 Kb 
#> validation of 'taxlist' object: TRUE 
#> 
#> number of taxon usage names: 5393 
#> number of taxon concepts: 3887 
#> trait entries: 311 
#> number of trait variables: 1 
#> taxon views: 3 
#> 
#> concepts with parents: 3698 
#> concepts with children: 1343 
#> 
#> hierarchical levels: form < variety < subspecies < species < complex < genus < family 
#> number of concepts in level form: 2
#> number of concepts in level variety: 95
#> number of concepts in level subspecies: 71
#> number of concepts in level species: 2521
#> number of concepts in level complex: 1
#> number of concepts in level genus: 1011
#> number of concepts in level family: 186
#> 

## summary for two taxa
summary(Easplist, c(51128, 51140))
#> ------------------------------ 
#> concept ID: 51128 
#> view ID: 1 
#> level: species 
#> parent: 54818 Cheilanthes Sw. 
#> 
#> # accepted name: 
#> 51128 Cheilanthes quadripinnata Kuhn 
#> 
#> # synonyms (1): 
#> 51129 Pellaea quadripinnata (Forssk.) Prantl 
#> ------------------------------ 
#> concept ID: 51140 
#> view ID: 1 
#> level: species 
#> parent: 55364 Haplopteris C. Presl 
#> 
#> # accepted name: 
#> 51140 Haplopteris volkensii (Hieron.) E.H. Crane 
#> 
#> # synonyms (1): 
#> 51141 Vittaria volkensii Hieron. 
#> ------------------------------

## summary by matching a name
summary(Easplist, "Acmella")
#> ------------------------------ 
#> concept ID: 20 
#> view ID: 1 
#> level: species 
#> parent: 54760 Acmella Pers. 
#> 
#> # accepted name: 
#> 20 Acmella caulirhiza Delile 
#> 
#> # synonyms (19): 
#> 50001 Spilanthes mauritiana (A. Rich. ex Pers.) DC. 
#> 52448 Spilanthes caulirhiza (Delile) DC. 
#> 52449 Acmella mauritiana A. Rich. ex Pers. 
#> 52450 Spilanthes africana DC. 
#> 52451 Spilanthes abyssinica Sch. Bip. ex A. Rich. 
#> 52452 Eclipta filicaulis Schumach. & Thonn. 
#> 52453 Spilanthes filicaulis (Schumach. & Thonn.) C. D. Adams 
#> 52454 Spilanthes acmella var. acmella (L.) Murray 
#> 52455 Verbesina acmella L. 
#> 52456 Spilanthes acmella (L.) Murray 
#> 52457 Blainvillea acmella (L.) Philipson 
#> 52458 Eclipta latifolia L. f. 
#> 52459 Blainvillea latifolia (L. f.) DC. 
#> 52460 Blainvillea rhomboidea Cass. 
#> 52461 Blainvillea dalla-vedovae A. Terracc. 
#> 52462 Verbesina dichotoma Murray 
#> 52463 Blainvillea dichotoma (Murray) Stewart 
#> 52464 Spilanthes caulirhiza var. madagascariensis DC. 
#> 52465 Spilanthes mauritiana f. madagascariensis (DC.) A. H. Moore 
#> ------------------------------ 
#> concept ID: 21 
#> view ID: 1 
#> level: species 
#> parent: 54760 Acmella Pers. 
#> 
#> # accepted name: 
#> 21 Acmella uliginosa (Sw.) Cass. 
#> 
#> # synonyms (1): 
#> 50002 Spilanthes uliginosa Sw. 
#> ------------------------------ 
#> concept ID: 54760 
#> view ID: 2 
#> level: genus 
#> parent: 55936 Compositae Giseke 
#> 
#> # accepted name: 
#> 54762 Acmella Pers. 
#> ------------------------------

## summary for the first 10 taxa
summary(object = Easplist, ConceptID = "all", maxsum = 10)
#> ------------------------------ 
#> concept ID: 1 
#> view ID: 1 
#> level: species 
#> parent: 54753 Abelmoschus Medik. 
#> 
#> # accepted name: 
#> 1 Abelmoschus esculentus (L.) Moench 
#> 
#> # synonyms (1): 
#> 52313 Hibiscus esculentus L. 
#> ------------------------------ 
#> concept ID: 2 
#> view ID: 1 
#> level: species 
#> parent: 54754 Abutilon Mill. 
#> 
#> # accepted name: 
#> 2 Abutilon indicum (L.) 
#> ------------------------------ 
#> concept ID: 3 
#> view ID: 1 
#> level: species 
#> parent: 54754 Abutilon Mill. 
#> 
#> # accepted name: 
#> 3 Abutilon mauritianum (Jacq.) Medik. 
#> 
#> # synonyms (1): 
#> 50361 Pavonia patens (Andrews) Chiov. 
#> ------------------------------ 
#> concept ID: 4 
#> view ID: 1 
#> level: species 
#> parent: 54755 Acacia Mill. 
#> 
#> # accepted name: 
#> 4 Acacia drepanolobium Harms ex Y. Sjöstedt 
#> ------------------------------ 
#> concept ID: 5 
#> view ID: 1 
#> level: species 
#> parent: 54755 Acacia Mill. 
#> 
#> # accepted name: 
#> 5 Acacia elatior Brenan 
#> ------------------------------ 
#> concept ID: 6 
#> view ID: 1 
#> level: species 
#> parent: 54755 Acacia Mill. 
#> 
#> # accepted name: 
#> 6 Acacia kirkii Oliv. 
#> ------------------------------ 
#> concept ID: 7 
#> view ID: 1 
#> level: species 
#> parent: 54755 Acacia Mill. 
#> 
#> # accepted name: 
#> 7 Acacia mearnsii De Wild. 
#> ------------------------------ 
#> concept ID: 8 
#> view ID: 1 
#> level: species 
#> parent: 54755 Acacia Mill. 
#> 
#> # accepted name: 
#> 8 Acacia mellifera (Vahl) Benth. 
#> ------------------------------ 
#> concept ID: 9 
#> view ID: 1 
#> level: species 
#> parent: 54755 Acacia Mill. 
#> 
#> # accepted name: 
#> 9 Acacia polyacantha Willd. 
#> ------------------------------ 
#> concept ID: 10 
#> view ID: 1 
#> level: species 
#> parent: 54755 Acacia Mill. 
#> 
#> # accepted name: 
#> 10 Acacia reficiens Wawra 
#> ------------------------------