Sort taxa for further print

Sorting taxa in slot taxonRelations will be reflected in printed list by functions such as summary() and indented_list(). This is a wrapper for order().

Usage

sort_taxa(object, ...)

# S3 method for class 'taxlist'
sort_taxa(object, by = "TaxonName", priority, ...)

Arguments

object

Object of class taxlist.

...

Further arguments passed to order().

by

Character value indicating the column name in slot taxonRelations of object which will be used for the sorting. Additionally you can use by = "TaxonName" (the default) to get an alphabetical sorting by accepted names.

priority

Optional vector with values to be set on top of the list. Its class have to match the class of the column by.

Value

An object of class taxlist with sorted relations.

Examples

## Subset with Boraginaceae
tax <- subset(Easplist, TaxonName %in% c("Boraginaceae"),
    keep_children = TRUE, keep_parents = TRUE
)
indented_list(tax)
#> Boraginaceae working name
#>  Coldenia L.
#>    Coldenia procumbens L.
#>  Heliotropium L.
#>    Heliotropium benadirense Chiov.
#>    Heliotropium curassavicum L.
#>    Heliotropium indicum L.
#>    Heliotropium species 
#>    Heliotropium steudneri Vatke
#>     Heliotropium steudneri ssp. bullatum Verdc.
#>    Heliotropium bullockii Verdc.
#>    Heliotropium scotteae Rendle
#>    Heliotropium longiflorum (A. DC.) Jaub. & Spach
#>  Symphytum L.
#>    Symphytum officinale L.
#>  Trichodesma R. Br.
#>    Trichodesma zeylanicum (Burm. f.) R. Br.
#>  Cordia L.
#>    Cordia monoica Roxb.
#>    Cordia africana Lam.
#>    Cordia sinensis Lam.
#>    Cordia crenata Delile
#>  Cynoglossum L.
#>    Cynoglossum lanceolatum Forssk.
#>    Cynoglossum species 
#>    Cynoglossum coeruleum A. DC.
#>      Cynoglossum coeruleum var. mannii (Baker & C.H. Wright) Verdc.
#>  Ehretia P. Browne
#>    Ehretia cymosa Thonn.
#>      Ehretia cymosa var. silvatica (Gürke) Brenan
#>  Lithospermum L.
#>    Lithospermum afromontanum Weim.
#>  Myosotis L.
#>    Myosotis vestergrenii Stroh
#>  Echiochilon Desf.
#>    Echiochilon arenarium (I.M. Johnst.) I.M. Johnst.
#>  Euploca Nutt.
#>    Euploca strigosa (Willd.) Diane & Hilger
#>    Euploca ovalifolia (Forssk.) Diane & Hilger 

## Sorting names alphabetically
tax <- sort_taxa(tax)
indented_list(tax)
#> Boraginaceae working name
#>  Coldenia L.
#>    Coldenia procumbens L.
#>  Cordia L.
#>    Cordia africana Lam.
#>    Cordia crenata Delile
#>    Cordia monoica Roxb.
#>    Cordia sinensis Lam.
#>  Cynoglossum L.
#>    Cynoglossum coeruleum A. DC.
#>      Cynoglossum coeruleum var. mannii (Baker & C.H. Wright) Verdc.
#>    Cynoglossum lanceolatum Forssk.
#>    Cynoglossum species 
#>  Echiochilon Desf.
#>    Echiochilon arenarium (I.M. Johnst.) I.M. Johnst.
#>  Ehretia P. Browne
#>    Ehretia cymosa Thonn.
#>      Ehretia cymosa var. silvatica (Gürke) Brenan
#>  Euploca Nutt.
#>    Euploca ovalifolia (Forssk.) Diane & Hilger
#>    Euploca strigosa (Willd.) Diane & Hilger
#>  Heliotropium L.
#>    Heliotropium benadirense Chiov.
#>    Heliotropium bullockii Verdc.
#>    Heliotropium curassavicum L.
#>    Heliotropium indicum L.
#>    Heliotropium longiflorum (A. DC.) Jaub. & Spach
#>    Heliotropium scotteae Rendle
#>    Heliotropium species 
#>    Heliotropium steudneri Vatke
#>     Heliotropium steudneri ssp. bullatum Verdc.
#>  Lithospermum L.
#>    Lithospermum afromontanum Weim.
#>  Myosotis L.
#>    Myosotis vestergrenii Stroh
#>  Symphytum L.
#>    Symphytum officinale L.
#>  Trichodesma R. Br.
#>    Trichodesma zeylanicum (Burm. f.) R. Br. 

## Setting some names on top of the sorting
tax <- sort_taxa(tax, priority = c("Euploca", "Myosotis", "Cordia monoica"))
indented_list(tax)
#> Boraginaceae working name
#>  Euploca Nutt.
#>    Euploca ovalifolia (Forssk.) Diane & Hilger
#>    Euploca strigosa (Willd.) Diane & Hilger
#>  Myosotis L.
#>    Myosotis vestergrenii Stroh
#>  Coldenia L.
#>    Coldenia procumbens L.
#>  Cordia L.
#>    Cordia monoica Roxb.
#>    Cordia africana Lam.
#>    Cordia crenata Delile
#>    Cordia sinensis Lam.
#>  Cynoglossum L.
#>    Cynoglossum coeruleum A. DC.
#>      Cynoglossum coeruleum var. mannii (Baker & C.H. Wright) Verdc.
#>    Cynoglossum lanceolatum Forssk.
#>    Cynoglossum species 
#>  Echiochilon Desf.
#>    Echiochilon arenarium (I.M. Johnst.) I.M. Johnst.
#>  Ehretia P. Browne
#>    Ehretia cymosa Thonn.
#>      Ehretia cymosa var. silvatica (Gürke) Brenan
#>  Heliotropium L.
#>    Heliotropium benadirense Chiov.
#>    Heliotropium bullockii Verdc.
#>    Heliotropium curassavicum L.
#>    Heliotropium indicum L.
#>    Heliotropium longiflorum (A. DC.) Jaub. & Spach
#>    Heliotropium scotteae Rendle
#>    Heliotropium species 
#>    Heliotropium steudneri Vatke
#>     Heliotropium steudneri ssp. bullatum Verdc.
#>  Lithospermum L.
#>    Lithospermum afromontanum Weim.
#>  Symphytum L.
#>    Symphytum officinale L.
#>  Trichodesma R. Br.
#>    Trichodesma zeylanicum (Burm. f.) R. Br.