February 19, 2014 From rOpenSci (https://deploy-preview-121--ropensci.netlify.app/blog/2014/02/19/taxize-update/). Except where otherwise noted, content on this site is licensed under the CC-BY license.
We just released a new version of taxize - version 0.2.0. This release contains a number of new features, and bug fixes. Here is a run down of some of the changes:
First, install and load taxize
install.packages("rgbif")
library(taxize)
New things
New functions: class2tree
Sometimes you just want to have a visual of the taxonomic relationships among taxa. If you don’t know how to build a molecular phylogeny, don’t have time, or there just isn’t molecular data, you can sorta build one using taxonomy. Building on our classification function, you can get a bunch of taxonomic hierarchies from the classification function, then pass them to the new function class2tree. Like so:
Define a species list
spnames <- c("Latania lontaroides", "Randia cubana", "Blumea brevipes", "Commelina erecta",
"Miconia pyramidalis", "Aquilegia moorcroftiana", "Acridocarpus austrocaledonicus",
"Vaccinium wrightii", "Riocreuxia flanaganii", "Macroditassa adnata", "Acianthera ochreata",
"Spathodea campanulata", "Leucadendron salicifolium", "Habenaria fluminensis",
"Platostoma siamense", "Bulbophyllum hoehnei", "Aspidosperma polyneuron",
"Rhynchospora fascicularis", "Sida lonchitis", "Ardisia cymosa", "Morinda brachycalyx",
"Tetrastigma hypoglaucum", "Paphiopedilum vietnamense", "Goodenia glabra")
Then collect taxonomic hierarchies for each taxon, and remove those with no results (those with no results are just NA) (I’m setting verbose=TRUE to suppress messages for this example)
out <- classification(spnames, db = "ncbi", verbose = FALSE)
out <- out[!is.na(out)]
Use class2tree to automagically convert the list of hierarchies to a ape phylo object, then plot
tr <- class2tree(out)
plot(tr, no.margin = TRUE)
gistr map
New functions: get_gbfid
The Global Biodiversity Information Facility (GBIF) has their own taxonomy. They allow programmatic access to their taxonomy, see here for details. Also see our rgbif package that wraps all their API services.
We added a similar function to our get_tsn, get_uid, etc. functions for various taxonomies, but for the GBIF taxonomy. Here are some example calls:
get_gbifid(sciname = "Poa annua", verbose = FALSE)
## 1
## "2704179"
## attr(,"class")
## [1] "gbifid"
get_gbifid(sciname = "Pinus contorta", verbose = FALSE)
## 1
## "5285750"
## attr(,"class")
## [1] "gbifid"
get_gbifid(sciname = "Puma concolor", verbose = FALSE)
## 1
## "2435099"
## attr(,"class")
## [1] "gbifid"
get_gbifid(c("Poa annua", "Pinus contorta"), verbose = FALSE)
## [1] "2704179" "5285750"
## attr(,"class")
## [1] "gbifid"
This could be useful if you for example, want to have the exact IDs GBIF uses for your set of species to use at some later point - and at that later point you could use our rgbif package and search for biodiversity occurrence data with the IDs you collected. For example:
library(rgbif)
(id <- get_gbifid(sciname = "Puma concolor", verbose = FALSE))
## 1
## "2435099"
## attr(,"class")
## [1] "gbifid"
occ_search(id)
## $meta
## $meta$offset
## [1] 0
##
## $meta$limit
## [1] 20
##
## $meta$endOfRecords
## [1] FALSE
##
## $meta$count
## [1] 8392
##
##
## $hierarchy
## $hierarchy[[1]]
## name key rank
## 1 Animalia 1 kingdom
## 2 Chordata 44 phylum
## 3 Mammalia 359 clazz
## 4 Carnivora 732 order
## 5 Felidae 9703 family
## 6 Puma 2435098 genus
## 7 Puma concolor 2435099 species
##
##
## $data
## name key longitude latitude
## 1 Puma concolor 866527350 -110.58 31.85
## 2 Puma concolor 866545169 -103.60 29.16
## 3 Puma concolor 866495627 -106.39 35.13
## 4 Puma concolor 866498665 -89.43 20.31
## 5 Puma concolor 866508658 -105.04 19.47
## 6 Puma concolor 866523280 -118.24 34.06
## 7 Puma concolor 866526517 -104.45 29.92
## 8 Puma concolor 866530535 -118.30 34.07
## 9 Puma concolor 860790696 -77.35 2.77
## 10 Puma concolor NA NA NA
## 11 Puma concolor NA NA NA
## 12 Puma concolor NA NA NA
## 13 Puma concolor 866525528 -123.83 40.13
## 14 Puma concolor 866531329 -123.83 40.13
## 15 Puma concolor 866519497 -118.90 34.54
## 16 Puma concolor 866601452 -122.52 38.45
## 17 Puma concolor 866547065 -110.30 41.88
## 18 Puma concolor 866562541 -123.83 40.13
## 19 Puma concolor 866562081 -123.82 40.13
## 20 Puma concolor 866558112 -103.13 29.65
In addition, get_ids now accepts ‘gbif’ as an option for the db parameter - get_ids is our omnibus function to search for taxon ids across all sources available in taxize.
New functions: rbind and cbind for classification
The classification function gives back taxonomic hierarchies from a variety of sources, including NCBI, ITIS, Catalogue of Life, Tropicos, EOL, and now GBIF. If you pass in many taxonomic IDs or taxon names, you get back a list of hierarchies. We added two functions to make it convenient to mash these outputs together, rbind for basically stacking hierarchies on top of one another, and cbind for making a width-wise combination of hierarchies. Our cbind doesn’t do exactly what your used to cbind doing for data.frame’s. The examples below are based on some changed code since the newest CRAN version, but you can install the development version with the changes from Github (see here for instructions).
From a call to get_ids, then passed on to classification, we get a object of class classification_ids
(out <- get_ids(names = "Puma concolor", db = c("ncbi", "gbif"), verbose = FALSE))
## $ncbi
## Puma concolor
## "9696"
## attr(,"match")
## [1] "found"
## attr(,"class")
## [1] "uid"
##
## $gbif
## Puma concolor
## "2435099"
## attr(,"class")
## [1] "gbifid"
##
## attr(,"class")
## [1] "ids"
(cl <- classification(out, verbose = FALSE))
## $ncbi
## $`9696`
## name rank
## 1 cellular organisms no rank
## 2 Eukaryota superkingdom
## 3 Opisthokonta no rank
## 4 Metazoa kingdom
## 5 Eumetazoa no rank
## 6 Bilateria no rank
## 7 Deuterostomia no rank
## 8 Chordata phylum
## 9 Craniata subphylum
## 10 Vertebrata no rank
## 11 Gnathostomata superclass
## 12 Teleostomi no rank
## 13 Euteleostomi no rank
## 14 Sarcopterygii no rank
## 15 Dipnotetrapodomorpha no rank
## 16 Tetrapoda no rank
## 17 Amniota no rank
## 18 Mammalia class
## 19 Theria no rank
## 20 Eutheria no rank
## 21 Boreoeutheria no rank
## 22 Laurasiatheria superorder
## 23 Carnivora order
## 24 Feliformia suborder
## 25 Felidae family
## 26 Felinae subfamily
## 27 Puma genus
## 28 Puma concolor species
##
## attr(,"class")
## [1] "classification"
## attr(,"db")
## [1] "ncbi"
##
## $gbif
## $`2435099`
## name rank
## 1 Animalia kingdom
## 2 Chordata phylum
## 3 Mammalia clazz
## 4 Carnivora order
## 5 Felidae family
## 6 Puma genus
## 7 Puma concolor species
##
## attr(,"class")
## [1] "classification"
##
## attr(,"class")
## [1] "classification_ids"
We can bind width-wise
cbind(cl)
## no rank superkingdom kingdom phylum subphylum
## 1 cellular organisms Eukaryota Metazoa Chordata Craniata
## 2 <NA> <NA> Animalia Chordata <NA>
## superclass class superorder order suborder family
## 1 Gnathostomata Mammalia Laurasiatheria Carnivora Feliformia Felidae
## 2 <NA> <NA> <NA> Carnivora <NA> Felidae
## subfamily genus species clazz
## 1 Felinae Puma Puma concolor <NA>
## 2 <NA> Puma Puma concolor Mammalia
Or bind length-wise
rbind(cl)
## source taxonid name rank
## 1 ncbi 9696 cellular organisms no rank
## 2 ncbi 9696 Eukaryota superkingdom
## 3 ncbi 9696 Opisthokonta no rank
## 4 ncbi 9696 Metazoa kingdom
## 5 ncbi 9696 Eumetazoa no rank
## 6 ncbi 9696 Bilateria no rank
## 7 ncbi 9696 Deuterostomia no rank
## 8 ncbi 9696 Chordata phylum
## 9 ncbi 9696 Craniata subphylum
## 10 ncbi 9696 Vertebrata no rank
## 11 ncbi 9696 Gnathostomata superclass
## 12 ncbi 9696 Teleostomi no rank
## 13 ncbi 9696 Euteleostomi no rank
## 14 ncbi 9696 Sarcopterygii no rank
## 15 ncbi 9696 Dipnotetrapodomorpha no rank
## 16 ncbi 9696 Tetrapoda no rank
## 17 ncbi 9696 Amniota no rank
## 18 ncbi 9696 Mammalia class
## 19 ncbi 9696 Theria no rank
## 20 ncbi 9696 Eutheria no rank
## 21 ncbi 9696 Boreoeutheria no rank
## 22 ncbi 9696 Laurasiatheria superorder
## 23 ncbi 9696 Carnivora order
## 24 ncbi 9696 Feliformia suborder
## 25 ncbi 9696 Felidae family
## 26 ncbi 9696 Felinae subfamily
## 27 ncbi 9696 Puma genus
## 28 ncbi 9696 Puma concolor species
## 29 gbif 2435099 Animalia kingdom
## 30 gbif 2435099 Chordata phylum
## 31 gbif 2435099 Mammalia clazz
## 32 gbif 2435099 Carnivora order
## 33 gbif 2435099 Felidae family
## 34 gbif 2435099 Puma genus
## 35 gbif 2435099 Puma concolor species
Or we can do the same thing on the class classification that we get back from a call to one of get_colid, get_tsn, get_eolid, get_tpsid, get_gbifid, or get_uid, that’s then passed on to classification
cl_col <- classification(get_colid(c("Puma concolor", "Accipiter striatus"),
verbose = FALSE))
rbind(cl_col)
## source taxonid name rank
## 1 col 6862841 Animalia Kingdom
## 2 col 6862841 Chordata Phylum
## 3 col 6862841 Mammalia Class
## 4 col 6862841 Carnivora Order
## 5 col 6862841 Felidae Family
## 6 col 6862841 Puma Genus
## 7 col 11909487 Animalia Kingdom
## 8 col 11909487 Chordata Phylum
## 9 col 11909487 Aves Class
## 10 col 11909487 Accipitriformes Order
## 11 col 11909487 Accipitridae Family
## 12 col 11909487 Accipiter Genus
cbind(cl_col)
## kingdom phylum class order family genus
## 1 Animalia Chordata Mammalia Carnivora Felidae Puma
## 2 Animalia Chordata Aves Accipitriformes Accipitridae Accipiter
Read more about changes in v0.2 at Github.
