Here, get identifiers from 5 different sources for Poa annua. Then we can pass those ideas to other functions that act on those ids without any other input
p.s. this also demonstrates the interactive prompt, as you'll see
library(taxize)
out <- get_ids(names = "Poa annua", db = c("ncbi", "itis", "col", "eol", "tropicos"))
## colid name rank status acc_name
## 1 9791858 Poa annua Species accepted name <NA>
## 2 10003530 Poa annua Species synonym Poa infirma
## eolid name source
## 1 43530222 Poa annua L. GBIF
## 2 46196944 Poa annua L. ITIS
## 3 53014630 Poa annua L. COL
## 4 43531857 Poa aestivalis J.Presl & C.Presl GBIF
## 5 43530223 Poa annua var. rigidiuscula L.H. Dewey GBIF
## 6 43530884 Poa royleana Nees ex Steud. GBIF
## 7 43531303 Poa meyenii Nees GBIF
## 8 43531601 Poa hohenackeri Trin. GBIF
## 9 43565964 Ochlopoa annua (L.) H. Scholz GBIF
## 10 50836543 Poa annua NCBI
## 11 43518589 Aira pumila Pursh GBIF
## tpsid name rank status
## 1 25509881 Poa annua sp. Legitimate
## 2 25512377 Poa annua var. reptans var. No opinion
## 3 25514155 Poa annua var. rigidiuscula var. No opinion
## 4 25516124 Poa annua subsp. pratense subsp. No opinion
## 5 25517736 Poa annua var. annua var. No opinion
## 6 25537474 Poa annua fo. annua fo. No opinion
## 7 25538408 Poa annua subsp. annua subsp. No opinion
## 8 25538823 Poa annua var. aquatica var. No opinion
## 9 25538851 Poa annua var. stricta var. No opinion
## 10 25540127 Poa annua var. typica var. Invalid
## 11 25543952 Poa annua subsp. pilantha subsp. No opinion
## 12 25547854 Poa annua var. exilis var. No opinion
## 13 25549585 Poa annua var. pygmaea var. Invalid
## 14 25550450 Poa annua var. sikkimensis var. No opinion
## 15 25550451 Poa annua var. nepalensis var. No opinion
## 16 25550455 Poa annua var. maroccana var. No opinion
## 17 25550983 Poa annua fo. reptans fo. No opinion
## 18 25552610 Poa annua var. hypsophila var. No opinion
## 19 25556963 Poa annua var. pilantha var. No opinion
## 20 25557595 Poa ser. Annuae ser. No opinion
## 21 25558635 Poa annua var. tommasinii var. Illegitimate
## 22 50062684 Poa [ unranked ] Annuae [ unranked ] Legitimate
## 23 50062691 Poa [ unranked ] Annuae [ unranked ] Illegitimate
## 24 50062695 Poa sect. Annuae sect. Invalid
## 25 50063800 Poa annua subsp. exilis subsp. No opinion
## 26 50063801 Poa annua subsp. supina subsp. Illegitimate
## 27 50077909 Poa annua subsp. varia subsp. Invalid
## 28 50077910 Poa annua unranked varia [unranked] No opinion
## 29 50119145 Poa annua var. eriolepis var. No opinion
## 30 50133141 Poa annua subsp. varia subsp. Legitimate
## 31 50154055 Poa annua var. supina var. No opinion
## 32 50155725 Poa annua var. raniglumis var. No opinion
## 33 50157106 Poa annua proles supina proles No opinion
## 34 50157109 Poa annua var. racemosa var. No opinion
## 35 50157110 Poa annua var. rigidula var. No opinion
## 36 50157407 Poa annua var. triflora var. No opinion
## 37 50158097 Poa annua subvar. minima subvar. No opinion
## 38 50158098 Poa annua var. minima var. No opinion
## 39 50182047 Poa annua var. supina var. Legitimate
## 40 50240461 Poa annua fo. maxima fo. No opinion
## 41 50243156 Poa annua fo. macarrima fo. Invalid
## 42 50267768 Poa annua fo. remotiflora fo. No opinion
## 43 50267769 Poa annua var. viridis var. No opinion
## 44 50267770 Poa annua fo. viridis fo. No opinion
## 45 50267771 Poa annua fo. lanuginosa fo. No opinion
## 46 50267772 Poa annua fo. ovalis fo. No opinion
## 47 50267774 Poa annua var. picta var. No opinion
## 48 50267776 Poa annua fo. picta fo. No opinion
## 49 50267778 Poa annua var. rivulorum var. No opinion
## 50 50267779 Poa annua fo. macranthera fo. No opinion
## 51 50278321 Poa annua var. pauciflora var. No opinion
## 52 50315599 Poa annua subsp. notabilis subsp. No opinion
## 53 50315610 Poa annua subsp. raniglunis subsp. No opinion
## 54 50315616 Poa annua fo. purpurea fo. No opinion
## 55 100386563 Poa annua var. arenosa var. Invalid
## 56 100386564 Poa annua var. alpigena var. No opinion
classification(out$itis)
## $`Poa annua`
## rankName taxonName tsn
## 1 Kingdom Plantae 202422
## 2 Subkingdom Viridaeplantae 846492
## 3 Infrakingdom Streptophyta 846494
## 4 Division Tracheophyta 846496
## 5 Subdivision Spermatophytina 846504
## 6 Infradivision Angiospermae 846505
## 7 Class Magnoliopsida 18063
## 8 Superorder Lilianae 846542
## 9 Order Poales 846620
## 10 Family Poaceae 40351
## 11 Genus Poa 41074
## 12 Species Poa annua 41107
synonyms(out$tropicos)
## $`Poa annua`
## NameId ScientificName
## 1 25503923 Aira pumila
## 8 25503925 Aira pumila
## 9 25513515 Catabrosa pumila
## 16 25513642 Eragrostis infirma
## 20 25521823 Festuca tenuiculmis
## 21 25513728 Megastachya infirma
## 24 50231428 Ochlopoa annua
## 28 25512823 Poa aestivalis
## 39 25538791 Poa algida
## 40 25512724 Poa algida
## 48 25550983 Poa annua fo. reptans
## 53 25517736 Poa annua var. annua
## 56 25538823 Poa annua var. aquatica
## 60 50119145 Poa annua var. eriolepis
## 63 25512377 Poa annua var. reptans
## 68 25514155 Poa annua var. rigidiuscula
## 73 25555526 Poa bipollicaris
## 77 25515915 Poa crassinervis
## 79 25561445 Poa hohenackeri
## 81 100391965 Poa humilis
## 82 25514158 Poa infirma
## 87 25512725 Poa meyenii
## 93 50200166 Poa puberula
## 94 25528166 Poa royleana
## ScientificNameWithAuthors Family
## 1 Aira pumila Pursh Poaceae
## 8 Aira pumila Vill. ex Trin. Poaceae
## 9 Catabrosa pumila (Pursh) Roem. & Schult. Poaceae
## 16 Eragrostis infirma (Kunth) Steud. Poaceae
## 20 Festuca tenuiculmis Tovar Poaceae
## 21 Megastachya infirma (Kunth) Roem. & Schult. Poaceae
## 24 Ochlopoa annua (L.) H. Scholz Poaceae
## 28 Poa aestivalis J. Presl Poaceae
## 39 Poa algida (Sol.) Rupr. Poaceae
## 40 Poa algida Trin. Poaceae
## 48 Poa annua fo. reptans (Hausskn.) T. Koyama Poaceae
## 53 Poa annua var. annua Poaceae
## 56 Poa annua var. aquatica Asch. Poaceae
## 60 Poa annua var. eriolepis E. Desv. Poaceae
## 63 Poa annua var. reptans Hausskn. Poaceae
## 68 Poa annua var. rigidiuscula L.H. Dewey Poaceae
## 73 Poa bipollicaris Hochst. Poaceae
## 77 Poa crassinervis Honda Poaceae
## 79 Poa hohenackeri Trin. Poaceae
## 81 Poa humilis Lej. Poaceae
## 82 Poa infirma Kunth Poaceae
## 87 Poa meyenii Nees & Meyen Poaceae
## 93 Poa puberula Steud. Poaceae
## 94 Poa royleana Nees ex Steud. Poaceae
In this case get many identifiers for many names, then pass in identifiers to get many classifications
mynames <- c("Helianthus annuus", "Pinus contorta", "Collomia grandiflora")
out <- get_ids(names = mynames, db = c("ncbi", "itis", "col", "eol", "tropicos"))
## eolid name
## 1 43835813 Helianthus annuus L.
## 2 46180859 Helianthus annuus L.
## 3 52926497 Helianthus annuus L.
## 4 43835841 Helianthus annuus L. subsp. lenticularis (Douglas) Cockerell
## 5 43835842 Helianthus annuus subsp. jaegeri (Heiser) Heiser
## 6 43835826 Helianthus annuus L. var. texanus (Heiser) Shinners
## 7 50883433 Helianthus annuus
## 8 53417541 Helianthus annuus fasciation phytoplasma
## 9 50883498 Helianthus annuus x Helianthus argophyllus
## 10 43836079 Helianthus annuus × Helianthus argophyllus
## 11 50883499 Helianthus annuus x Helianthus debilis subsp. debilis
## 12 43836080 Helianthus annuus × Helianthus debilis subsp. debilis
## source
## 1 GBIF
## 2 ITIS
## 3 COL
## 4 GBIF
## 5 GBIF
## 6 GBIF
## 7 NCBI
## 8 NCBI
## 9 NCBI
## 10 GBIF
## 11 NCBI
## 12 GBIF
## eolid name source
## 1 44398364 Pinus contorta Douglas ex Loudon GBIF
## 2 46216292 Pinus contorta Douglas ex Loudon ITIS
## 3 53084713 Pinus contorta Douglas ex Loudon COL
## 4 24954444 Pinus contorta IUCN
## 5 50827991 Pinus contorta NCBI
## 6 44398365 Pinus contorta var. murrayana (Balf.) Engelm. GBIF
## 7 46216296 Pinus contorta var. murrayana (Balf.) Engelm. ITIS
## 8 53084715 Pinus contorta var. murrayana (Balf.) Engelm. COL
## 9 50827994 Pinus contorta var. murrayana NCBI
## 10 46216294 Pinus contorta var. bolanderi (Parl.) Vasey ITIS
## 11 50827993 Pinus contorta var. bolanderi NCBI
## 12 44398367 Pinus contorta var. latifolia Engelm. GBIF
## 13 53084714 Pinus contorta var. latifolia Engelm. COL
## 14 46216295 Pinus contorta var. latifolia Engelm. ex S. Watson ITIS
## 15 53084716 Pinus contorta var. contorta COL
## 16 50827992 Pinus contorta subsp. contorta NCBI
## 17 44398366 Pinus contorta var. contorta Douglas ex Loudon GBIF
## 18 46216293 Pinus contorta var. contorta Douglas ex Loudon ITIS
## 19 44398369 Pinus contorta var. yukonensis W.L. Strong GBIF
## eolid name source
## 1 46170153 Collomia grandiflora Douglas ex Lindl. ITIS
## 2 52804720 Collomia grandiflora Douglas ex Lindl. COL
## 3 50873299 Collomia grandiflora NCBI
## 4 44178704 Collomia grandiflora Dougl. ex Lindl. GBIF
## tpsid name rank status
## 1 2700851 Helianthus annuus sp. Legitimate
## 2 2700852 Helianthus annuus subsp. couplandii subsp. No opinion
## 3 2700853 Helianthus annuus subsp. lenticularis subsp. No opinion
## 4 2702619 Helianthus annuus var. annuus var. No opinion
## 5 2702620 Helianthus annuus var. armavirskij var. No opinion
## 6 2702621 Helianthus annuus var. bicolor var. No opinion
## 7 2702622 Helianthus annuus var. californicus var. No opinion
## 8 2702623 Helianthus annuus var. gallardiflorus var. No opinion
## 9 2702624 Helianthus annuus var. globosus var. Invalid
## 10 2702625 Helianthus annuus var. intermedius var. No opinion
## 11 2702626 Helianthus annuus var. primulinus var. No opinion
## 12 2702627 Helianthus annuus var. uniflorus var. No opinion
## 13 2702628 Helianthus annuus var. vinossissimus var. No opinion
## 14 2702629 Helianthus annuus var. zonatus var. No opinion
## 15 2724044 Helianthus annuus var. macrocarpus var. No opinion
## 16 2724045 Helianthus annuus subsp. jaegeri subsp. No opinion
## 17 2724046 Helianthus annuus subsp. annuus subsp. No opinion
## 18 2724756 Helianthus annuus fo. fallax fo. No opinion
## 19 2724757 Helianthus annuus fo. annuus fo. No opinion
## 20 2726013 Helianthus annuus subsp. texanus subsp. No opinion
## 21 50069938 Helianthus annuus var. coronatus var. No opinion
## 22 50069939 Helianthus annuus var. aridus var. No opinion
## 23 50069940 Helianthus annuus var. latibasis var. No opinion
## 24 50069941 Helianthus annuus fo. lenticularis fo. No opinion
## 25 50071063 Helianthus annuus subsp. petiolaris subsp. No opinion
## 26 50071132 Helianthus annuus var. lenticularis var. No opinion
## 27 50229527 Helianthus annuus var. texanus var. No opinion
## 28 50289543 Helianthus annuus var. citrinus var. No opinion
## 29 100000278 Helianthus annuus x petiolaris var. No opinion
## tpsid name rank status
## 1 24900183 Pinus contorta sp. No opinion
## 2 24900184 Pinus contorta var. bolanderi var. No opinion
## 3 24900185 Pinus contorta var. latifolia var. No opinion
## 4 24900186 Pinus contorta var. murrayana var. No opinion
## 5 24900317 Pinus contorta subsp. murrayana subsp. No opinion
## 6 24900318 Pinus contorta subsp. latifolia subsp. No opinion
## 7 24900433 Pinus contorta var. hendersonii var. No opinion
## 8 24900487 Pinus contorta unranked hendersonii [unranked] No opinion
## 9 24900528 Pinus contorta var. contorta var. No opinion
## 10 24900627 Pinus contorta subsp. contorta subsp. No opinion
## 11 24900810 Pinus contorta subsp. bolanderi subsp. No opinion
## 12 24901682 Pinus contorta var. bolanderi var. No opinion
## 13 50231950 Pinus contorta var. bolanderi var. No opinion
## 14 50231960 Pinus contorta subsp. murrayana subsp. No opinion
## 15 100351799 Pinus subsect. Contorta subsect. No opinion
## 16 100363705 Pinus contorta var. yukonensis var. No opinion
## tpsid name rank status
## 1 25800485 Collomia grandiflora sp. No opinion
## 2 50130471 Collomia grandiflora var. axillaris var. No opinion
## 3 50130472 Collomia grandiflora var. grandiflora var. No opinion
## 4 100314137 Collomia grandiflora fo. axillaris fo. No opinion
## 5 100314138 Collomia grandiflora fo. cryptantha fo. No opinion
## 6 100314139 Collomia grandiflora fo. diffusa fo. No opinion
## 7 100314140 Collomia grandiflora fo. scabra fo. No opinion
## 8 100314141 Collomia grandiflora fo. tenuiflora fo. No opinion
## 9 100314142 Collomia grandiflora var. diffusa var. No opinion
## 10 100314143 Collomia grandiflora var. tenuiflora var. No opinion
classification(out)
## $ncbi
## $ncbi$`Helianthus annuus`
## ScientificName Rank UID
## 1 cellular organisms no rank 131567
## 2 Eukaryota superkingdom 2759
## 3 Viridiplantae kingdom 33090
## 4 Streptophyta phylum 35493
## 5 Streptophytina no rank 131221
## 6 Embryophyta no rank 3193
## 7 Tracheophyta no rank 58023
## 8 Euphyllophyta no rank 78536
## 9 Spermatophyta no rank 58024
## 10 Magnoliophyta no rank 3398
## 11 eudicotyledons no rank 71240
## 12 core eudicotyledons no rank 91827
## 13 asterids subclass 71274
## 14 campanulids no rank 91882
## 15 Asterales order 4209
## 16 Asteraceae family 4210
## 17 Asteroideae subfamily 102804
## 18 Heliantheae alliance no rank 911341
## 19 Heliantheae tribe 102814
## 20 Helianthus genus 4231
## 21 Helianthus annuus species 4232
##
## $ncbi$`Pinus contorta`
## ScientificName Rank UID
## 1 cellular organisms no rank 131567
## 2 Eukaryota superkingdom 2759
## 3 Viridiplantae kingdom 33090
## 4 Streptophyta phylum 35493
## 5 Streptophytina no rank 131221
## 6 Embryophyta no rank 3193
## 7 Tracheophyta no rank 58023
## 8 Euphyllophyta no rank 78536
## 9 Spermatophyta no rank 58024
## 10 Coniferophyta no rank 3312
## 11 Coniferopsida class 58019
## 12 Coniferales order 3313
## 13 Pinaceae family 3318
## 14 Pinus genus 3337
## 15 Pinus subgenus 139271
## 16 Pinus contorta species 3339
##
## $ncbi$`Collomia grandiflora`
## ScientificName Rank UID
## 1 cellular organisms no rank 131567
## 2 Eukaryota superkingdom 2759
## 3 Viridiplantae kingdom 33090
## 4 Streptophyta phylum 35493
## 5 Streptophytina no rank 131221
## 6 Embryophyta no rank 3193
## 7 Tracheophyta no rank 58023
## 8 Euphyllophyta no rank 78536
## 9 Spermatophyta no rank 58024
## 10 Magnoliophyta no rank 3398
## 11 eudicotyledons no rank 71240
## 12 core eudicotyledons no rank 91827
## 13 asterids subclass 71274
## 14 Ericales order 41945
## 15 Polemoniaceae family 24584
## 16 Collomia genus 40760
## 17 Collomia grandiflora species 66234
##
##
## $itis
## $itis$`Helianthus annuus`
## rankName taxonName tsn
## 1 Kingdom Plantae 202422
## 2 Subkingdom Viridaeplantae 846492
## 3 Infrakingdom Streptophyta 846494
## 4 Division Tracheophyta 846496
## 5 Subdivision Spermatophytina 846504
## 6 Infradivision Angiospermae 846505
## 7 Class Magnoliopsida 18063
## 8 Superorder Asteranae 846535
## 9 Order Asterales 35419
## 10 Family Asteraceae 35420
## 11 Genus Helianthus 36611
## 12 Species Helianthus annuus 36616
##
## $itis$`Pinus contorta`
## rankName taxonName tsn
## 1 Kingdom Plantae 202422
## 2 Subkingdom Viridaeplantae 846492
## 3 Infrakingdom Streptophyta 846494
## 4 Division Tracheophyta 846496
## 5 Subdivision Spermatophytina 846504
## 6 Infradivision Gymnospermae 846506
## 7 Class Pinopsida 500009
## 8 Order Pinales 500028
## 9 Family Pinaceae 18030
## 10 Genus Pinus 18035
## 11 Species Pinus contorta 183327
##
## $itis$`Collomia grandiflora`
## rankName taxonName tsn
## 1 Kingdom Plantae 202422
## 2 Subkingdom Viridaeplantae 846492
## 3 Infrakingdom Streptophyta 846494
## 4 Division Tracheophyta 846496
## 5 Subdivision Spermatophytina 846504
## 6 Infradivision Angiospermae 846505
## 7 Class Magnoliopsida 18063
## 8 Superorder Asteranae 846535
## 9 Order Ericales 23443
## 10 Family Polemoniaceae 30896
## 11 Genus Collomia 31035
## 12 Species Collomia grandiflora 31037
##
##
## $col
## $col$`Helianthus annuus`
## classif_name classif_rank classif_id
## 1 Plantae Kingdom 15610504
## 2 Tracheophyta Phylum 15610505
## 3 Magnoliopsida Class 15610506
## 4 Asterales Order 15614747
## 5 Asteraceae Family 15617169
## 6 Helianthus Genus 15691642
##
## $col$`Pinus contorta`
## classif_name classif_rank classif_id
## 1 Plantae Kingdom 15610504
## 2 Tracheophyta Phylum 15610505
## 3 Pinopsida Class 15612223
## 4 Pinales Order 15612224
## 5 Pinaceae Family 15613661
## 6 Pinus Genus 15661926
##
## $col$`Collomia grandiflora`
## classif_name classif_rank classif_id
## 1 Plantae Kingdom 15610504
## 2 Tracheophyta Phylum 15610505
## 3 Magnoliopsida Class 15610506
## 4 Ericales Order 15610507
## 5 Polemoniaceae Family 15617189
## 6 Collomia Genus 15702987
##
##
## $eol
## $eol$`Helianthus annuus`
## [1] "No hierarchy information for 43835813"
##
## $eol$`Pinus contorta`
## [1] "No hierarchy information for 44398364"
##
## $eol$`Collomia grandiflora`
## taxonID scientificName taxonRank
## 1 46150613 Plantae kingdom
## 2 46159776 Viridaeplantae subkingdom
## 3 46161961 Streptophyta infrakingdom
## 4 46167532 Tracheophyta division
## 5 46169010 Spermatophytina subdivision
## 6 46169011 Angiospermae infradivision
## 7 46169012 Magnoliopsida class
## 8 46169016 Asteranae superorder
## 9 46169017 Ericales order
## 10 46169946 Polemoniaceae family
## 11 46170148 Collomia Nutt. genus
##
##
## $tropicos
## $tropicos$`Helianthus annuus`
## NameId ScientificName Rank
## 1 43000109 Equisetopsida class
## 2 43000013 Magnoliidae subclass
## 3 100352415 Asteranae superorder
## 4 43000082 Asterales order
## 5 50307371 Asteraceae family
## 6 40022652 Helianthus genus
##
## $tropicos$`Pinus contorta`
## NameId ScientificName Rank
## 1 43000109 Equisetopsida class
## 2 50324780 Pinidae subclass
## 3 50324779 Pinales order
## 4 42000417 Pinaceae family
## 5 40009142 Pinus genus
##
## $tropicos$`Collomia grandiflora`
## NameId ScientificName Rank
## 1 43000109 Equisetopsida class
## 2 43000013 Magnoliidae subclass
## 3 100352415 Asteranae superorder
## 4 43000048 Ericales order
## 5 42000286 Polemoniaceae family
## 6 40012270 Collomia genus