Comments (2)
The list of taxa would still be in the object, but the function would not convert its output to taxon
or hierarchy
objects.
EG
> subtaxa(ex_taxmap)
$`1`
[1] "3" "7" "12" "8" "13" "4" "9" "14" "5" "10" "15"
$`2`
[1] "6" "11" "16" "17"
...
vs
> subtaxa(ex_taxmap, return_type = "taxa")
$`1`
$`1`$`3`
<Taxon>
name: Felidae
rank: family
id: 9681
authority: none
$`1`$`7`
<Taxon>
name: Panthera
rank: genus
id: 146712
authority: none
$`1`$`12`
<Taxon>
name: tigris
rank: species
id: 9696
authority: none
$`1`$`8`
<Taxon>
name: Felis
rank: genus
id: 9682
authority: none
$`1`$`13`
<Taxon>
name: catus
rank: species
id: 9685
authority: none
$`1`$`4`
<Taxon>
name: Notoryctidae
rank: family
id: 4479
authority: none
$`1`$`9`
<Taxon>
name: Notoryctes
rank: genus
id: 4544
authority: none
$`1`$`14`
<Taxon>
name: typhlops
rank: species
id: 93036
authority: none
$`1`$`5`
<Taxon>
name: Hominidae
rank: family
id: 9604
authority: none
$`1`$`10`
<Taxon>
name: homo
rank: genus
id: 9605
authority: none
$`1`$`15`
<Taxon>
name: sapiens
rank: species
id: 9606
authority: none
$`2`
$`2`$`6`
<Taxon>
name: Solanaceae
rank: family
id: 4070
authority: none
$`2`$`11`
<Taxon>
name: Solanum
rank: genus
id: 4107
authority: none
$`2`$`16`
<Taxon>
name: lycopersicum
rank: species
id: 49274
authority: none
.
.
.
vs
> ex_taxmap$taxa
$`1`
<Taxon>
name: Mammalia
rank: class
id: 9681
authority: none
$`2`
<Taxon>
name: Plantae
rank: kingdom
id: 33090
authority: none
$`3`
<Taxon>
name: Felidae
rank: family
id: 9681
authority: none
$`4`
<Taxon>
name: Notoryctidae
rank: family
id: 4479
authority: none
$`5`
<Taxon>
name: Hominidae
rank: family
id: 9604
authority: none
from taxa.
This will however remove return_type's ability to return taxa and hierarchies objects
but they can still be accessed via $
?
from taxa.
Related Issues (20)
- taxonomy_table function issue with add_id_column parameter. HOT 1
- Support matrix data type in parsers and subsetting functions
- news HOT 1
- Print method idea: tidy lists
- Is a `head` function needed for `taxmap`? HOT 2
- `taxa`: way to do operations on objects within it HOT 4
- Vectorizing some classes and reorganizing inheritance hierarchy HOT 49
- possible to put taxize in Suggests? HOT 2
- Assign taxon_rank based on n_supertaxa HOT 1
- Function to produce html/latex table of taxonomic and associated data ? HOT 3
- use cases section a bit outdated HOT 4
- HTTP errors when parsing long taxon_id list HOT 12
- No taxon_rank information when parsing from NCBI taxonomy HOT 1
- import of taxdump files HOT 3
- Error: Failed to install 'taxa' from GitHub HOT 1
- error in db_ref$get() after using $set() HOT 2
- creating a taxonomy database for PR2 HOT 10
- Error when using parse_tax_data function HOT 1
- Issues with CRAN check on 2022-03-10 HOT 1
- vctrs revdep issues HOT 3
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from taxa.