To query DateLife’s chronogram database, taxon names provided as
input are processed and matched to the Open Tree of Life taxonomy (OTT).
This is done with the function make_datelife_query().
Next, we present some usage examples of this function.
When input is list or vector of taxon names
We can process a single taxon:
query1 <- make_datelife_query(input = "Canis")
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Making a DateLife query.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|======================================================================| 100%
#> ---> Working with the following taxon: Canis.
#> DateLife query made!Or several taxon names:
query10 <- make_datelife_query(input = rep("Canis", 10))
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Making a DateLife query.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|======================================================================| 100%
#> ---> Working with the following 10 taxa: Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis.
#> DateLife query made!In any case, the output is a list:
query10
#> $cleaned_names
#> [1] "Canis" "Canis" "Canis" "Canis" "Canis" "Canis" "Canis" "Canis" "Canis"
#> [10] "Canis"
#>
#> $ott_ids
#> Canis Canis Canis Canis Canis Canis Canis Canis Canis Canis
#> 372706 372706 372706 372706 372706 372706 372706 372706 372706 372706
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"When input names are not found in the taxonomy
The function returns NA as taxonomic id for the missing
name:
make_datelife_query2(input = c("Canis", "werewolf", "jupiter"))
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|======================= | 33%
#> Warning: werewolf are not matched
#>
|
|=============================================== | 67%
#> Warning: jupiter are not matched
#>
|
|======================================================================| 100%
#> $cleaned_names
#> [1] "Canis" "werewolf" "jupiter"
#>
#> $tnrs_names
#> [1] "Canis" NA NA
#>
#> $ott_ids
#> [1] 372706 NA NA
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"Subspecies can also be searched
make_datelife_query2(input = "Canis mesomelas elongae")
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|======================================================================| 100%
#> $cleaned_names
#> [1] "Canis mesomelas elongae"
#>
#> $tnrs_names
#> [1] "Canis mesomelas elongae"
#>
#> $ott_ids
#> [1] 576165
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"
all_subspecies <- c("Canis mesomelas elongae", "Canis mesomelas elongae")
make_datelife_query2(input = all_subspecies)
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|======================================================================| 100%
#> $cleaned_names
#> [1] "Canis mesomelas elongae" "Canis mesomelas elongae"
#>
#> $tnrs_names
#> [1] "Canis mesomelas elongae" "Canis mesomelas elongae"
#>
#> $ott_ids
#> [1] 576165 576165
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"
one_subspecies <- c("Canis mesomelas elongae", "Canis adustus", "Lycalopex fulvipes")
make_datelife_query2(input = one_subspecies)
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
#> $cleaned_names
#> [1] "Canis mesomelas elongae" "Canis adustus"
#> [3] "Lycalopex fulvipes"
#>
#> $tnrs_names
#> [1] "Canis mesomelas elongae" "Canis adustus"
#> [3] "Lycalopex fulvipes"
#>
#> $ott_ids
#> [1] 576165 621176 996573
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"Choosing between homonyms
Taxonomic homonyms are valid names that are used for different biological entities. For example, the genus name Aotus refers to a monkey and a grass. TNRS is smart enough to choose a taxonomic context for a set of names, but it is not infallible.
For example, when referring to the grass, TNRS chooses the correct taxon id:
make_datelife_query2(input = c("Aotus", "Poa", "Arabidopsis"))
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
#> $cleaned_names
#> [1] "Aotus" "Poa" "Arabidopsis"
#>
#> $tnrs_names
#> [1] "Aotus (genus in kingdom Archaeplastida)"
#> [2] "Poa"
#> [3] "Arabidopsis"
#>
#> $ott_ids
#> [1] 559026 985636 309275
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"But when referring to the monkey, TNRS still chooses the grass:
make_datelife_query2(input = c("Aotus", "Insulacebus", "Microcebus"))
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|======================= | 33%
|
|=============================================== | 67%
|
|======================================================================| 100%
#> $cleaned_names
#> [1] "Aotus" "Insulacebus" "Microcebus"
#>
#> $tnrs_names
#> [1] "Aotus (genus in kingdom Archaeplastida)"
#> [2] "Insulacebus"
#> [3] "Microcebus"
#>
#> $ott_ids
#> [1] 559026 6145234 734824
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"To make sure that we get the taxonomic id and data for the taxon we want, we can specify a “taxonomic context”:
rotl::tnrs_contexts()
make_datelife_query2(input = c("Aotus", "Insulacebus", "Microcebus"), context_name = "Mammals")Making a query from an inclusive taxonomic group
You can run it for one taxon name only:
make_datelife_query2(input = "Canis",
get_spp_from_taxon = TRUE,
reference_taxonomy = "ott")
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|======================================================================| 100%
#> ---> Getting species for the following taxon names :Canis.
#> ---> Obtaining taxonomic data from lineages within genus 'Canis' with OTT id number = 372706.
#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank.
#> * There are 21 subspecies.
#> * There are 42 total species.
#> * There are 36 species in OpenTree's synthetic tree.
#> ---> Retrieving taxonomic info for 36 species names within 'Canis' that are in the OpenTree synthetic tree.
#> $cleaned_names
#> [1] "Canis"
#>
#> $tnrs_names
#> 3612500 5835572
#> "Canis dirus" "Canis anthus"
#> 113383 752755
#> "Canis rufus" "Canis simensis"
#> 621168 621176
#> "Canis aureus" "Canis adustus"
#> 247331 346723
#> "Canis latrans" "Canis himalayensis"
#> 346728 4941918
#> "Canis indica" "Canis environmental sample"
#> 7655930 7655947
#> "Canis ameghinoi" "Canis nehringi"
#> 7655949 7655942
#> "Canis palustris" "Canis lanka"
#> 7655948 7655939
#> "Canis pallipes" "Canis gezi"
#> 7655951 7655935
#> "Canis primaevus" "Canis chrysurus"
#> 7655937 7655941
#> "Canis dukhunensis" "Canis kokree"
#> 7655952 7655940
#> "Canis sladeni" "Canis himalaicus"
#> 7655934 7655936
#> "Canis chanco" "Canis curvipalatus"
#> 7655943 7655931
#> "Canis lateralis" "Canis argentinus"
#> 7655953 7655946
#> "Canis tarijensis" "Canis naria"
#> 7655950 7655933
#> "Canis peruanus" "Canis cautleyi"
#> 7655954 6145382
#> "Canis ursinus" "Canis antarticus"
#> 6145383 7655938
#> "Canis dingo" "Canis etruscus"
#> 666235 247341
#> "Canis mesomelas" "Canis lupus"
#>
#> $ott_ids
#> Canis dirus Canis anthus
#> 3612500 5835572
#> Canis rufus Canis simensis
#> 113383 752755
#> Canis aureus Canis adustus
#> 621168 621176
#> Canis latrans Canis himalayensis
#> 247331 346723
#> Canis indica Canis environmental sample
#> 346728 4941918
#> Canis ameghinoi Canis nehringi
#> 7655930 7655947
#> Canis palustris Canis lanka
#> 7655949 7655942
#> Canis pallipes Canis gezi
#> 7655948 7655939
#> Canis primaevus Canis chrysurus
#> 7655951 7655935
#> Canis dukhunensis Canis kokree
#> 7655937 7655941
#> Canis sladeni Canis himalaicus
#> 7655952 7655940
#> Canis chanco Canis curvipalatus
#> 7655934 7655936
#> Canis lateralis Canis argentinus
#> 7655943 7655931
#> Canis tarijensis Canis naria
#> 7655953 7655946
#> Canis peruanus Canis cautleyi
#> 7655950 7655933
#> Canis ursinus Canis antarticus
#> 7655954 6145382
#> Canis dingo Canis etruscus
#> 6145383 7655938
#> Canis mesomelas Canis lupus
#> 666235 247341
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"Or two or more:
make_datelife_query2(input = c("Canis", "Elephas"),
get_spp_from_taxon = TRUE,
reference_taxonomy = "ott")
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
#> ---> Getting species for the following taxon names :Canis, Elephas.
#> ---> Obtaining taxonomic data from lineages within genus 'Canis' with OTT id number = 372706.
#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank.
#> * There are 21 subspecies.
#> * There are 42 total species.
#> * There are 36 species in OpenTree's synthetic tree.
#> ---> Retrieving taxonomic info for 36 species names within 'Canis' that are in the OpenTree synthetic tree.
#> ---> Obtaining taxonomic data from lineages within genus 'Elephas' with OTT id number = 541927.
#> * Found the following taxonomic ranks: subspecies, no rank, no rank - terminal, species.
#> * There are 5 subspecies.
#> * There are 8 total species.
#> * There are 7 species in OpenTree's synthetic tree.
#> ---> Retrieving taxonomic info for 7 species names within 'Elephas' that are in the OpenTree synthetic tree.
#> $cleaned_names
#> [1] "Canis" "Elephas"
#>
#> $tnrs_names
#> 3612500 5835572
#> "Canis dirus" "Canis anthus"
#> 113383 752755
#> "Canis rufus" "Canis simensis"
#> 621168 621176
#> "Canis aureus" "Canis adustus"
#> 247331 346723
#> "Canis latrans" "Canis himalayensis"
#> 346728 4941918
#> "Canis indica" "Canis environmental sample"
#> 7655930 7655947
#> "Canis ameghinoi" "Canis nehringi"
#> 7655949 7655942
#> "Canis palustris" "Canis lanka"
#> 7655948 7655939
#> "Canis pallipes" "Canis gezi"
#> 7655951 7655935
#> "Canis primaevus" "Canis chrysurus"
#> 7655937 7655941
#> "Canis dukhunensis" "Canis kokree"
#> 7655952 7655940
#> "Canis sladeni" "Canis himalaicus"
#> 7655934 7655936
#> "Canis chanco" "Canis curvipalatus"
#> 7655943 7655931
#> "Canis lateralis" "Canis argentinus"
#> 7655953 7655946
#> "Canis tarijensis" "Canis naria"
#> 7655950 7655933
#> "Canis peruanus" "Canis cautleyi"
#> 7655954 6145382
#> "Canis ursinus" "Canis antarticus"
#> 6145383 7655938
#> "Canis dingo" "Canis etruscus"
#> 666235 247341
#> "Canis mesomelas" "Canis lupus"
#> 7654243 7654244
#> "Elephas armeniacus" "Elephas namadicus"
#> 7654245 3607197
#> "Elephas zulu" "Elephas bombifrons"
#> 6144032 7654246
#> "Elephas celebensis" "Palaeoloxodon lomolinoi"
#> 541928
#> "Elephas maximus"
#>
#> $ott_ids
#> Canis dirus Canis anthus
#> 3612500 5835572
#> Canis rufus Canis simensis
#> 113383 752755
#> Canis aureus Canis adustus
#> 621168 621176
#> Canis latrans Canis himalayensis
#> 247331 346723
#> Canis indica Canis environmental sample
#> 346728 4941918
#> Canis ameghinoi Canis nehringi
#> 7655930 7655947
#> Canis palustris Canis lanka
#> 7655949 7655942
#> Canis pallipes Canis gezi
#> 7655948 7655939
#> Canis primaevus Canis chrysurus
#> 7655951 7655935
#> Canis dukhunensis Canis kokree
#> 7655937 7655941
#> Canis sladeni Canis himalaicus
#> 7655952 7655940
#> Canis chanco Canis curvipalatus
#> 7655934 7655936
#> Canis lateralis Canis argentinus
#> 7655943 7655931
#> Canis tarijensis Canis naria
#> 7655953 7655946
#> Canis peruanus Canis cautleyi
#> 7655950 7655933
#> Canis ursinus Canis antarticus
#> 7655954 6145382
#> Canis dingo Canis etruscus
#> 6145383 7655938
#> Canis mesomelas Canis lupus
#> 666235 247341
#> Elephas armeniacus Elephas namadicus
#> 7654243 7654244
#> Elephas zulu Elephas bombifrons
#> 7654245 3607197
#> Elephas celebensis Palaeoloxodon lomolinoi
#> 6144032 7654246
#> Elephas maximus
#> 541928
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"Sometimes, only some input taxon names are inclusive:
make_datelife_query2(input = c("Mus", "Mus musculus"),
get_spp_from_taxon = c(TRUE, FALSE),
reference_taxonomy = "ott")
#> ---> Phylo-processing 'input'.
#> * 'input' is not a phylogeny.
#> ---> Runnning TNRS to match input names to reference taxonomy (OTT).
#>
|
| | 0%
|
|=================================== | 50%
|
|======================================================================| 100%
#> ---> Getting species for the following taxon names :Mus.
#> ---> Obtaining taxonomic data from lineages within genus 'Mus' with OTT id number = 1068778.
#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank.
#> * There are 20 subspecies.
#> * There are 84 total species.
#> * There are 60 species in OpenTree's synthetic tree.
#> ---> Retrieving taxonomic info for 60 species names within 'Mus' that are in the OpenTree synthetic tree.
#> ---> Adding species data from inclusive taxon names.
#> $cleaned_names
#> [1] "Mus musculus" "Mus"
#>
#> $tnrs_names
#>
#> "Mus musculus"
#> 7067432
#> "Mus cf. callewaerti"
#> 5857433
#> "Mus cf. setulosus West"
#> 5857432
#> "Mus cf. tenellus TA-2014"
#> 5857436
#> "Mus cf. baoulei West"
#> 5857434
#> "Mus cf. callewaerti TA-2014"
#> 3608901
#> "Mus neavei"
#> 844274
#> "Mus sorella"
#> 844277
#> "Mus tenellus"
#> 844280
#> "Mus cf. musculoides"
#> 844282
#> "Mus bufo"
#> 3608883
#> "Mus callewaerti"
#> 5857435
#> "Mus mahomet"
#> 7067433
#> "Mus sp. musculoides-minutoides DPL-2017"
#> 369735
#> "Mus baoulei"
#> 403204
#> "Mus emesi"
#> 996648
#> "Mus musculoides"
#> 1000695
#> "Mus indutus"
#> 759679
#> "Mus mattheyi"
#> 845966
#> "Mus minutoides"
#> 845980
#> "Mus setulosus"
#> 1000702
#> "Mus haussa"
#> 1000700
#> "Mus cf. saxicola"
#> 887682
#> "Mus shortridgei"
#> 542525
#> "Mus saxicola"
#> 845970
#> "Mus platythrix"
#> 348560
#> "Mus terricolor"
#> 451263
#> "Mus booduga"
#> 289304
#> "Mus triton"
#> 542521
#> "Mus spretus"
#> 542528
#> "Mus cookii"
#> 845976
#> "Mus spicilegus"
#> 1027340
#> "Mus famulus"
#> 922493
#> "Mus caroli"
#> 1010350
#> "Mus fragilicauda"
#> 185328
#> "Mus crociduroides"
#> 542493
#> "Mus pahari"
#> 6144910
#> "Mus terraereginae"
#> 7654766
#> "Mus aegaeus"
#> 7654768
#> "Mus camini"
#> 7654773
#> "Mus paulina"
#> 7654776
#> "Mus vulpinus"
#> 7654767
#> "Mus arboricola"
#> 7654772
#> "Mus nigrita"
#> 7654775
#> "Mus tomentosus"
#> 7654774
#> "Mus proconodon"
#> 7654771
#> "Mus microdontoides"
#> 7654770
#> "Mus leptosoma"
#> 3608899
#> "Mus oubanguii"
#> 3608881
#> "Mus goundae"
#> 3608904
#> "Mus orangiae"
#> 3608880
#> "Mus phillipsi"
#> 3608890
#> "Mus setzeri"
#> 3608886
#> "Mus fernandoni"
#> 3608885
#> "Mus vulcani"
#> 3608874
#> "Mus mayori"
#> 7654769
#> "Mus colletti"
#> 6144906
#> "Mus canguru"
#> 542509
#> "Mus musculus"
#> 542519
#> "Mus cervicolor"
#> 845973
#> "Mus macedonicus"
#>
#> $ott_ids
#> Mus cf. callewaerti
#> 542509 7067432
#> Mus cf. setulosus West Mus cf. tenellus TA-2014
#> 5857433 5857432
#> Mus cf. baoulei West Mus cf. callewaerti TA-2014
#> 5857436 5857434
#> Mus neavei Mus sorella
#> 3608901 844274
#> Mus tenellus Mus cf. musculoides
#> 844277 844280
#> Mus bufo Mus callewaerti
#> 844282 3608883
#> Mus mahomet Mus sp. musculoides-minutoides DPL-2017
#> 5857435 7067433
#> Mus baoulei Mus emesi
#> 369735 403204
#> Mus musculoides Mus indutus
#> 996648 1000695
#> Mus mattheyi Mus minutoides
#> 759679 845966
#> Mus setulosus Mus haussa
#> 845980 1000702
#> Mus cf. saxicola Mus shortridgei
#> 1000700 887682
#> Mus saxicola Mus platythrix
#> 542525 845970
#> Mus terricolor Mus booduga
#> 348560 451263
#> Mus triton Mus spretus
#> 289304 542521
#> Mus cookii Mus spicilegus
#> 542528 845976
#> Mus famulus Mus caroli
#> 1027340 922493
#> Mus fragilicauda Mus crociduroides
#> 1010350 185328
#> Mus pahari Mus terraereginae
#> 542493 6144910
#> Mus aegaeus Mus camini
#> 7654766 7654768
#> Mus paulina Mus vulpinus
#> 7654773 7654776
#> Mus arboricola Mus nigrita
#> 7654767 7654772
#> Mus tomentosus Mus proconodon
#> 7654775 7654774
#> Mus microdontoides Mus leptosoma
#> 7654771 7654770
#> Mus oubanguii Mus goundae
#> 3608899 3608881
#> Mus orangiae Mus phillipsi
#> 3608904 3608880
#> Mus setzeri Mus fernandoni
#> 3608890 3608886
#> Mus vulcani Mus mayori
#> 3608885 3608874
#> Mus colletti Mus canguru
#> 7654769 6144906
#> Mus musculus Mus cervicolor
#> 542509 542519
#> Mus macedonicus
#> 845973
#>
#> $phy
#> [1] NA
#>
#> attr(,"class")
#> [1] "datelifeQuery"The function get_opentree_species()
The function get_opentree_species() works under the hood
to extract species names within a given taxonomic group.
This is how it fails:
get_opentree_species()
#> * Both 'taxon_name' and 'ott_id' arguments are missing.
#> Please provide at least one - returning NA.
#> [1] NA
get_opentree_species(taxon_name = c("Canis", "Elephas"))
#> This function can only process one taxon name at a time.
#> Please provide just one taxon name - returning NA.
#> [1] NA
get_opentree_species(ott_id = c(372706, 541927))
#> This function can only process one OTT id at a time.
#> Please provide just one OTT id number - returning NA.
#> [1] NA
# TOFIX:
# datelife::get_opentree_species(taxon_name = "Canis", ott_id = 541927)By default, it only return species that are in OpenTree’s synthetic tree:
get_opentree_species(taxon_name = "Canis")
#> ---> Obtaining taxonomic info for all children within OTT taxon, genus 'Canis' (input name = Canis), with OTT id number = 372706.
#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank.
#> * There are 21 subspecies.
#> * There are 42 total species.
#> * There are 36 species in OpenTree's synthetic tree.
#> ---> Retrieving taxonomic info for 36 species names within 'Canis' that are in the OpenTree synthetic tree.
#> $tnrs_names
#> 3612500 5835572
#> "Canis dirus" "Canis anthus"
#> 113383 752755
#> "Canis rufus" "Canis simensis"
#> 621168 621176
#> "Canis aureus" "Canis adustus"
#> 247331 346723
#> "Canis latrans" "Canis himalayensis"
#> 346728 4941918
#> "Canis indica" "Canis environmental sample"
#> 7655930 7655947
#> "Canis ameghinoi" "Canis nehringi"
#> 7655949 7655942
#> "Canis palustris" "Canis lanka"
#> 7655948 7655939
#> "Canis pallipes" "Canis gezi"
#> 7655951 7655935
#> "Canis primaevus" "Canis chrysurus"
#> 7655937 7655941
#> "Canis dukhunensis" "Canis kokree"
#> 7655952 7655940
#> "Canis sladeni" "Canis himalaicus"
#> 7655934 7655936
#> "Canis chanco" "Canis curvipalatus"
#> 7655943 7655931
#> "Canis lateralis" "Canis argentinus"
#> 7655953 7655946
#> "Canis tarijensis" "Canis naria"
#> 7655950 7655933
#> "Canis peruanus" "Canis cautleyi"
#> 7655954 6145382
#> "Canis ursinus" "Canis antarticus"
#> 6145383 7655938
#> "Canis dingo" "Canis etruscus"
#> 666235 247341
#> "Canis mesomelas" "Canis lupus"
#>
#> $ott_ids
#> Canis dirus Canis anthus
#> 3612500 5835572
#> Canis rufus Canis simensis
#> 113383 752755
#> Canis aureus Canis adustus
#> 621168 621176
#> Canis latrans Canis himalayensis
#> 247331 346723
#> Canis indica Canis environmental sample
#> 346728 4941918
#> Canis ameghinoi Canis nehringi
#> 7655930 7655947
#> Canis palustris Canis lanka
#> 7655949 7655942
#> Canis pallipes Canis gezi
#> 7655948 7655939
#> Canis primaevus Canis chrysurus
#> 7655951 7655935
#> Canis dukhunensis Canis kokree
#> 7655937 7655941
#> Canis sladeni Canis himalaicus
#> 7655952 7655940
#> Canis chanco Canis curvipalatus
#> 7655934 7655936
#> Canis lateralis Canis argentinus
#> 7655943 7655931
#> Canis tarijensis Canis naria
#> 7655953 7655946
#> Canis peruanus Canis cautleyi
#> 7655950 7655933
#> Canis ursinus Canis antarticus
#> 7655954 6145382
#> Canis dingo Canis etruscus
#> 6145383 7655938
#> Canis mesomelas Canis lupus
#> 666235 247341You can override that behaviour and get all species by setting
synth_tree_only = FALSE:
get_opentree_species(taxon_name = "Canis", synth_tree_only = FALSE)
#> ---> Obtaining taxonomic info for all children within OTT taxon, genus 'Canis' (input name = Canis), with OTT id number = 372706.
#> * Found the following taxonomic ranks: species, subspecies, no rank - terminal, no rank.
#> * There are 21 subspecies.
#> * There are 42 total species.
#> * There are 36 species in OpenTree's synthetic tree.
#> ---> Returning taxonomic info for 42 species names within genus 'Canis'.
#> $tnrs_names
#> 3612500 5835572
#> "Canis dirus" "Canis anthus"
#> 113383 752755
#> "Canis rufus" "Canis simensis"
#> 621168 621176
#> "Canis aureus" "Canis adustus"
#> 247331 346723
#> "Canis latrans" "Canis himalayensis"
#> 346728 5925604
#> "Canis indica" "Canis sp. KEB-2016"
#> 470950 5338950
#> "Canis sp. CANInt1" "Canis sp. Russia/33,500"
#> 247325 5338951
#> "Canis sp." "Canis sp. Belgium/36,000"
#> 4941918 7655930
#> "Canis environmental sample" "Canis ameghinoi"
#> 7655947 7655949
#> "Canis nehringi" "Canis palustris"
#> 7655942 7655948
#> "Canis lanka" "Canis pallipes"
#> 7655939 7655951
#> "Canis gezi" "Canis primaevus"
#> 7655935 7655937
#> "Canis chrysurus" "Canis dukhunensis"
#> 7655941 7655952
#> "Canis kokree" "Canis sladeni"
#> 7655940 7655934
#> "Canis himalaicus" "Canis chanco"
#> 7655936 7655943
#> "Canis curvipalatus" "Canis lateralis"
#> 7655931 7655953
#> "Canis argentinus" "Canis tarijensis"
#> 7655946 7655950
#> "Canis naria" "Canis peruanus"
#> 7655933 7655954
#> "Canis cautleyi" "Canis ursinus"
#> 6145382 6145383
#> "Canis antarticus" "Canis dingo"
#> 7655938 3612504
#> "Canis etruscus" "Canis spelaeus"
#> 666235 247341
#> "Canis mesomelas" "Canis lupus"
#>
#> $ott_ids
#> Canis dirus Canis anthus
#> 3612500 5835572
#> Canis rufus Canis simensis
#> 113383 752755
#> Canis aureus Canis adustus
#> 621168 621176
#> Canis latrans Canis himalayensis
#> 247331 346723
#> Canis indica Canis sp. KEB-2016
#> 346728 5925604
#> Canis sp. CANInt1 Canis sp. Russia/33,500
#> 470950 5338950
#> Canis sp. Canis sp. Belgium/36,000
#> 247325 5338951
#> Canis environmental sample Canis ameghinoi
#> 4941918 7655930
#> Canis nehringi Canis palustris
#> 7655947 7655949
#> Canis lanka Canis pallipes
#> 7655942 7655948
#> Canis gezi Canis primaevus
#> 7655939 7655951
#> Canis chrysurus Canis dukhunensis
#> 7655935 7655937
#> Canis kokree Canis sladeni
#> 7655941 7655952
#> Canis himalaicus Canis chanco
#> 7655940 7655934
#> Canis curvipalatus Canis lateralis
#> 7655936 7655943
#> Canis argentinus Canis tarijensis
#> 7655931 7655953
#> Canis naria Canis peruanus
#> 7655946 7655950
#> Canis cautleyi Canis ursinus
#> 7655933 7655954
#> Canis antarticus Canis dingo
#> 6145382 6145383
#> Canis etruscus Canis spelaeus
#> 7655938 3612504
#> Canis mesomelas Canis lupus
#> 666235 247341If you know the OTT id of your group, you can use it:
get_opentree_species(ott_id = 541927)
#> ---> Obtaining taxonomic data from lineages within genus 'Elephas' with OTT id number = 541927.
#> * Found the following taxonomic ranks: subspecies, no rank, no rank - terminal, species.
#> * There are 5 subspecies.
#> * There are 8 total species.
#> * There are 7 species in OpenTree's synthetic tree.
#> ---> Retrieving taxonomic info for 7 species names within 'Elephas' that are in the OpenTree synthetic tree.
#> $tnrs_names
#> 7654243 7654244 7654245
#> "Elephas armeniacus" "Elephas namadicus" "Elephas zulu"
#> 3607197 6144032 7654246
#> "Elephas bombifrons" "Elephas celebensis" "Palaeoloxodon lomolinoi"
#> 541928
#> "Elephas maximus"
#>
#> $ott_ids
#> Elephas armeniacus Elephas namadicus Elephas zulu
#> 7654243 7654244 7654245
#> Elephas bombifrons Elephas celebensis Palaeoloxodon lomolinoi
#> 3607197 6144032 7654246
#> Elephas maximus
#> 541928
get_opentree_species(ott_id = 541927, synth_tree_only = FALSE)
#> ---> Obtaining taxonomic data from lineages within genus 'Elephas' with OTT id number = 541927.
#> * Found the following taxonomic ranks: subspecies, no rank, no rank - terminal, species.
#> * There are 5 subspecies.
#> * There are 8 total species.
#> * There are 7 species in OpenTree's synthetic tree.
#> ---> Returning taxonomic info for 8 species names within genus 'Elephas'.
#> $tnrs_names
#> 7654243 7654244 7654245
#> "Elephas armeniacus" "Elephas namadicus" "Elephas zulu"
#> 3607197 6144032 7654246
#> "Elephas bombifrons" "Elephas celebensis" "Palaeoloxodon lomolinoi"
#> 3607200 541928
#> "Elephas planifrons" "Elephas maximus"
#>
#> $ott_ids
#> Elephas armeniacus Elephas namadicus Elephas zulu
#> 7654243 7654244 7654245
#> Elephas bombifrons Elephas celebensis Palaeoloxodon lomolinoi
#> 3607197 6144032 7654246
#> Elephas planifrons Elephas maximus
#> 3607200 541928To get species for multiple (more than one) taxon names:
ott_ids <- c(541927, 100)
# TODO: make a function out of the following code
# then it can replace code inside datelife_query_get_spp, section # getting species
species_list <- lapply(ott_ids,
function(x) {
datelife::get_opentree_species(ott_id = x,
synth_tree_only = TRUE)
})
#> ---> Obtaining taxonomic data from lineages within genus 'Elephas' with OTT id number = 541927.
#> * Found the following taxonomic ranks: subspecies, no rank, no rank - terminal, species.
#> * There are 5 subspecies.
#> * There are 8 total species.
#> * There are 7 species in OpenTree's synthetic tree.
#> ---> Retrieving taxonomic info for 7 species names within 'Elephas' that are in the OpenTree synthetic tree.
#> ---> Obtaining taxonomic data from lineages within species 'Schidax sp. 'squamaria'' with OTT id number = 100.
#> * Found the following taxonomic ranks: species.
#> * There are 0 subspecies.
#> * There are 1 total species.
#> * There are 1 species in OpenTree's synthetic tree.
#> ---> Retrieving taxonomic info for 1 species names within 'Schidax sp. 'squamaria'' that are in the OpenTree synthetic tree.
return_names <- unlist(sapply(species_list, "[", "tnrs_names"))
return_ott_ids <- unlist(sapply(species_list, "[", "ott_ids"))
names(return_names) <- return_ott_ids
names(return_ott_ids) <- return_names
list(tnrs_names = return_names,
ott_ids = return_ott_ids)
#> $tnrs_names
#> 7654243 7654244 7654245
#> "Elephas armeniacus" "Elephas namadicus" "Elephas zulu"
#> 3607197 6144032 7654246
#> "Elephas bombifrons" "Elephas celebensis" "Palaeoloxodon lomolinoi"
#> 541928 100
#> "Elephas maximus" "Schidax sp. 'squamaria'"
#>
#> $ott_ids
#> Elephas armeniacus Elephas namadicus Elephas zulu
#> 7654243 7654244 7654245
#> Elephas bombifrons Elephas celebensis Palaeoloxodon lomolinoi
#> 3607197 6144032 7654246
#> Elephas maximus Schidax sp. 'squamaria'
#> 541928 100