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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.
input
is list or vector of taxon namesWe 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).
#>
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#> ---> Working with the following taxon: Canis.
#> DateLife query done!
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).
#>
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#> ---> Working with the following 10 taxa: Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis | Canis.
#> DateLife query done!
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"
input
names are not found in the taxonomyThe 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).
#>
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#> Warning: werewolf are not matched
#>
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#> Warning: jupiter are not matched
#>
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#> $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"
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).
#>
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#> $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).
#>
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#> $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).
#>
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#> $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"
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).
#>
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#> $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).
#>
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#> $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”:
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).
#>
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#> ---> 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).
#>
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#> ---> 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).
#>
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|
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#> ---> 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"
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 247341
You 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 247341
If 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 541928
To 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
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.