Install the development version
install.packages("devtools")
library("devtools")
install_github("ropensci/taxize")Load the library
library("taxize")This works now (there was a slight bug when no accepted names were found), this id doesn't have any accepted names, but of course others do
tp_accnames(25509881)## http://services.tropicos.org/Name/25509881/AcceptedNames?apikey=f3e499d4-1519-42c9-afd1-685a16882f5a&format=json
## Error
## "No accepted names were found"
Your species list
sps <- c("Justicia brasiliana", "Achatocarpus spinulosus", "Cordilyne dracaenoides",
"Astronium concinnum", "Astronium fraxinifolium", "Astronium graveolens",
"Astronium nelson-rosae", "Myracrodruon urundeuva", "Schinopsis brasiliensis",
"Schinus polygamus")You were passing in a string of names as a factor class as i could detect from the code you sent, I've fixed in the new version on github so the function converts to character for you. All these should work, though many names are missing. Note that ITIS (using the function get_tsn) is mostly North America focused.
get_tpsid(sciname = sps)##
## Retrieving data for taxon 'Justicia brasiliana'
##
##
## Retrieving data for taxon 'Achatocarpus spinulosus'
##
##
## Retrieving data for taxon 'Cordilyne dracaenoides'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Astronium concinnum'
##
##
## Retrieving data for taxon 'Astronium fraxinifolium'
##
##
##
##
##
## More than one tpsid found for taxon 'Astronium fraxinifolium'!
##
## Enter rownumber of taxon (other inputs will return 'NA'):
## tpsid name rank status
## 1 1300083 Astronium fraxinifolium sp. No opinion
## 2 1300084 Astronium fraxinifolium fo. glaberrimum fo. No opinion
## 3 1300085 Astronium fraxinifolium fo. subglabrium fo. No opinion
## 4 1300764 Astronium fraxinifolium var. glabrum var. No opinion
## 5 1301070 Astronium fraxinifolium fo. mollissimum fo. No opinion
## 6 50227670 Astronium fraxinifolium var. fraxinifolium var. No opinion
## 7 100295291 Astronium fraxinifolium fo. pilosum fo. No opinion
## Input accepted, took tpsid '1300083'.
##
##
## Retrieving data for taxon 'Astronium graveolens'
##
##
##
##
##
## More than one tpsid found for taxon 'Astronium graveolens'!
##
## Enter rownumber of taxon (other inputs will return 'NA'):
## tpsid name rank status
## 1 1300086 Astronium graveolens sp. No opinion
## 2 1300087 Astronium graveolens var. brenesii var. No opinion
## 3 1300088 Astronium graveolens var. dugandii var. No opinion
## 4 1300089 Astronium graveolens var. planchoniana var. Illegitimate
## 5 1300971 Astronium graveolens var. inodorum var. No opinion
## 6 1300972 Astronium graveolens var. brasiliense var. No opinion
## 7 1301069 Astronium graveolens var. brasiliensis var. No opinion
## 8 50227672 Astronium graveolens var. graveolens var. No opinion
## 9 100295293 Astronium graveolens var. planchonianum var. No opinion
## Input accepted, took tpsid '1300086'.
##
##
## Retrieving data for taxon 'Astronium nelson-rosae'
##
##
## Retrieving data for taxon 'Myracrodruon urundeuva'
##
##
## Retrieving data for taxon 'Schinopsis brasiliensis'
##
##
##
##
##
## More than one tpsid found for taxon 'Schinopsis brasiliensis'!
##
## Enter rownumber of taxon (other inputs will return 'NA'):
## tpsid name rank status
## 1 1300195 Schinopsis brasiliensis sp. No opinion
## 2 1300196 Schinopsis brasiliensis var. glabra var. No opinion
## Input accepted, took tpsid '1300195'.
##
##
## Retrieving data for taxon 'Schinus polygamus'
## [1] "101666" "24800177" NA "50227677" "1300083"
## [6] "1300086" "50227682" "1300765" "1300195" "100350085"
## attr(,"class")
## [1] "tpsid"
get_tsn(sps)##
## Retrieving data for taxon 'Justicia brasiliana'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Achatocarpus spinulosus'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Cordilyne dracaenoides'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Astronium concinnum'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Astronium fraxinifolium'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Astronium graveolens'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Astronium nelson-rosae'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Myracrodruon urundeuva'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Schinopsis brasiliensis'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Schinus polygamus'
## [1] NA NA NA NA NA NA NA
## [8] NA NA "507160"
## attr(,"match")
## [1] "found" "found" "found" "found" "found" "found" "found" "found"
## [9] "found" "found"
## attr(,"class")
## [1] "tsn"
get_ids(sps, db = "ncbi")##
## Retrieving data for taxon 'Justicia brasiliana'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Achatocarpus spinulosus'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Cordilyne dracaenoides'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Astronium concinnum'
##
##
## Retrieving data for taxon 'Astronium fraxinifolium'
##
##
## Retrieving data for taxon 'Astronium graveolens'
##
##
## Retrieving data for taxon 'Astronium nelson-rosae'
##
## Not found. Consider checking the spelling or alternate classification
##
## Retrieving data for taxon 'Myracrodruon urundeuva'
##
##
## Retrieving data for taxon 'Schinopsis brasiliensis'
##
##
## Retrieving data for taxon 'Schinus polygamus'
##
## Not found. Consider checking the spelling or alternate classification
## $ncbi
## Justicia brasiliana Achatocarpus spinulosus Cordilyne dracaenoides
## NA NA NA
## Astronium concinnum Astronium fraxinifolium Astronium graveolens
## "676609" "289699" "263456"
## Astronium nelson-rosae Myracrodruon urundeuva Schinopsis brasiliensis
## NA "261998" "270267"
## Schinus polygamus
## NA
## attr(,"match")
## [1] "not found" "not found" "not found" "found" "found"
## [6] "found" "not found" "found" "found" "not found"
## attr(,"class")
## [1] "uid"
##
## attr(,"class")
## [1] "ids"
You said
I would also like to know the name accepted according to "Catalogue of Vascular Plant Species of Central and Northeastern Brazil" but I haven´t decipher how to do this
There is a service called the global names resolver. You can see what data_source_ids to use by using gnr_datasources
head(gnr_datasources())## id title
## 1 1 Catalogue of Life
## 2 2 Wikispecies
## 3 3 ITIS
## 4 4 NCBI
## 5 5 Index Fungorum
## 6 6 GRIN Taxonomy for Plants
The Brazil catalogue is number 145
gnr_resolve(sps, data_source_ids = 145)## submitted_name matched_name
## 2 Achatocarpus spinulosus
## 4 Astronium concinnum Astronium
## 5 Astronium fraxinifolium Astronium fraxinifolium Schott
## 6 Astronium graveolens Astronium
## 7 Astronium nelson-rosae Astronium nelson-rosae Santin
## 3 Cordilyne dracaenoides
## 1 Justicia brasiliana Justicia brasiliana Roth
## 8 Myracrodruon urundeuva Myracrodruon urundeuva Allemão & M. Allemão
## 9 Schinopsis brasiliensis Schinopsis brasiliensis Engl.
## 10 Schinus polygamus Schinus
## data_source_title
## 2
## 4 Catalogue of Vascular Plant Species of Central and Northeastern Brazil
## 5 Catalogue of Vascular Plant Species of Central and Northeastern Brazil
## 6 Catalogue of Vascular Plant Species of Central and Northeastern Brazil
## 7 Catalogue of Vascular Plant Species of Central and Northeastern Brazil
## 3
## 1 Catalogue of Vascular Plant Species of Central and Northeastern Brazil
## 8 Catalogue of Vascular Plant Species of Central and Northeastern Brazil
## 9 Catalogue of Vascular Plant Species of Central and Northeastern Brazil
## 10 Catalogue of Vascular Plant Species of Central and Northeastern Brazil
## score
## 2 NaN
## 4 0.750
## 5 0.988
## 6 0.750
## 7 0.988
## 3 NaN
## 1 0.988
## 8 0.988
## 9 0.988
## 10 0.750