traits v0.2.0
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Species Trait Data from Around the Web
Species trait data from many different sources, including
sequence data from 'NCBI', plant trait data from 'BETYdb', invasive species
data from the Global Invasive Species Database and 'EOL', 'Traitbank' data
from 'EOL', Coral traits data from http://coraltraits.org, 'nativity' status
('Flora Europaea' or 'ITIS'), and 'Birdlife' International.
Readme
traits
R client for various sources of species trait data.
Included in traits with the associated function prefix:
- BETYdb -
betydb_ - National Center for Biotechnology Information - NCBI -
ncbi_ - Global Invasive Species Database - GISD -
g_ - Encyclopedia of Life Invasive Species -
eol_ - Encyclopedia of Life Traitbank -
traitbank_ - Coral Traits Database -
coral_ - Flora Europaea -
fe_ - Birdlife International -
birdlife_ - LEDA Traitbase -
leda_ - More to come ...
Talk to us on the issues page if you know of a source of traits data with an API, and we'll see about including it.
For an introduction to the package, see the vignette.
Installation
Stable CRAN version
install.packages("traits")
Or development version from GitHub
devtools::install_github("ropensci/traits")
library("traits")
library("dplyr")
BETYdb
Get trait data for Willow (Salix spp.)
(salix <- betydb_search("Salix Vcmax"))
#> Source: local data frame [14 x 31]
#>
#> access_level author checked citation_id citation_year city
#> (int) (chr) (int) (int) (int) (chr)
#> 1 4 Merilo 1 430 2005 Saare
#> 2 4 Merilo 1 430 2005 Saare
#> 3 4 Merilo 1 430 2005 Saare
#> 4 4 Merilo 1 430 2005 Saare
#> 5 4 Wullschleger 1 51 1993 NA
#> 6 4 Merilo 1 430 2005 Saare
#> 7 4 Merilo 1 430 2005 Saare
#> 8 4 Merilo 1 430 2005 Saare
#> 9 4 Merilo 1 430 2005 Saare
#> 10 4 Merilo 1 430 2005 Saare
#> 11 4 Merilo 1 430 2005 Saare
#> 12 4 Merilo 1 430 2005 Saare
#> 13 4 Merilo 1 430 2005 Saare
#> 14 4 Wang 1 381 2010 NA
#> Variables not shown: commonname (chr), cultivar_id (int), date (chr),
#> dateloc (chr), genus (chr), id (int), lat (dbl), lon (dbl), mean (chr),
#> month (dbl), n (int), notes (chr), result_type (chr), scientificname
#> (chr), site_id (int), sitename (chr), species_id (int), stat (chr),
#> statname (chr), trait (chr), trait_description (chr), treatment (chr),
#> treatment_id (int), units (chr), year (dbl)
# equivalent:
# (out <- betydb_search("willow"))
Summarise data from the output data.frame
library("dplyr")
salix %>%
group_by(scientificname, trait) %>%
mutate(.mean = as.numeric(mean)) %>%
summarise(mean = round(mean(.mean, na.rm = TRUE), 2),
min = round(min(.mean, na.rm = TRUE), 2),
max = round(max(.mean, na.rm = TRUE), 2),
n = length(n))
#> Source: local data frame [4 x 6]
#> Groups: scientificname [?]
#>
#> scientificname trait mean min max n
#> (chr) (chr) (dbl) (dbl) (dbl) (int)
#> 1 Salix Vcmax 65.00 65.00 65.00 1
#> 2 Salix dasyclados Vcmax 46.08 34.30 56.68 4
#> 3 Salix sachalinensis × miyabeana Vcmax 79.28 79.28 79.28 1
#> 4 Salix viminalis Vcmax 43.04 19.99 61.29 8
GISD invasive species data
sp <- c("Carpobrotus edulis", "Rosmarinus officinalis")
g_invasive(sp)
#> species
#> 1 Carpobrotus edulis
#> 2 Rosmarinus officinalis
#> status
#> 1 Carpobrotus edulis is a mat-forming succulent native to South Africa which is invasive primarily in coastal habitats in many parts of the world. It was often introduced as an ornamental plant or used for planting along roadsides, from which it has spread to become invasive. Its main impacts are smothering, reduced regeneration of native flora and changes to soil pH and nutrient regimes.; (succulent); Common Names: balsamo, Cape fig, figue marine, freeway iceplant, ghaukum, ghoenavy, highway ice plant, higo del Cabo, higo marino, Hottentosvy, hottentot fig, Hottentottenfeige, iceplant, ikhambi-lamabulawo, Kaapsevy, patata frita, perdevy, pigface, rankvy, sea fig, sour fig, suurvy, umgongozi, vyerank; Synonyms: Mesembryanthemum edule L., Mesembryanthemum edulis
#> 2 Not in GISD
Or as simplified output
g_invasive(sp, simplify = TRUE)
#> species status
#> 1 Carpobrotus edulis Invasive
#> 2 Rosmarinus officinalis Not in GISD
EOL invasive species data
eol_invasive_('Brassica oleracea', dataset = 'gisd')
#> searched_name name eol_object_id db
#> 1 Brassica oleracea Brassica oleracea NaN gisd
Another example, with more species, and from
eol_invasive_(c('Lymantria dispar','Cygnus olor','Hydrilla verticillata','Pinus concolor'),
dataset = 'i3n')
#> searched_name name eol_object_id
#> 1 Lymantria dispar Lymantria dispar NaN
#> 2 Cygnus olor Cygnus olor (Gmelin 1789) 913227
#> 3 Hydrilla verticillata Hydrilla verticillata (L. f.) Royle 1088921
#> 4 Pinus concolor Pinus concolor NaN
#> db
#> 1 i3n
#> 2 i3n
#> 3 i3n
#> 4 i3n
EOL's traitbank trait data
Searching for Mesoplodon bidens, page id 328566
res <- traitbank(846827)
res$graph %>%
select(`dwc:measurementtype.@id`, `dwc:measurementtype.rdfs:label.en`) %>%
filter(!is.na(`dwc:measurementtype.rdfs:label.en`))
#> Source: local data frame [6 x 2]
#>
#> dwc:measurementtype.@id
#> (chr)
#> 1 http://eol.org/schema/terms/TypeSpecimenRepository
#> 2 http://eol.org/schema/terms/TypeSpecimenRepository
#> 3 http://eol.org/schema/terms/Habitat
#> 4 http://eol.org/schema/terms/Habitat
#> 5 http://eol.org/schema/terms/ExtinctionStatus
#> 6 http://eol.org/schema/terms/ExtinctionStatus
#> Variables not shown: dwc:measurementtype.rdfs:label.en (chr)
Coral
Get the species list and their ids
coral_species()
#> Source: local data frame [1,547 x 2]
#>
#> name id
#> (chr) (chr)
#> 1 Acanthastrea brevis 3
#> 2 Acanthastrea echinata 4
#> 3 Acanthastrea hemprichi 6
#> 4 Acanthastrea ishigakiensis 8
#> 5 Acanthastrea regularis 12
#> 6 Acanthastrea rotundoflora 13
#> 7 Acanthastrea subechinata 14
#> 8 Acropora abrolhosensis 16
#> 9 Acropora abrotanoides 17
#> 10 Acropora aculeus 18
#> .. ... ...
Get data by taxon
coral_taxa(80)
#> Source: local data frame [3,121 x 25]
#>
#> observation_id access user_id specie_id specie_name location_id
#> (int) (int) (int) (int) (chr) (int)
#> 1 119211 1 49 80 Acropora hyacinthus 1
#> 2 109330 1 2 80 Acropora hyacinthus 1
#> 3 88793 1 14 80 Acropora hyacinthus 0
#> 4 115791 1 10 80 Acropora hyacinthus 1
#> 5 115792 1 10 80 Acropora hyacinthus 1
#> 6 5696 1 2 80 Acropora hyacinthus 1
#> 7 5741 1 1 80 Acropora hyacinthus 1
#> 8 5751 1 1 80 Acropora hyacinthus 1
#> 9 5773 1 5 80 Acropora hyacinthus 1
#> 10 5766 1 1 80 Acropora hyacinthus 1
#> .. ... ... ... ... ... ...
#> Variables not shown: location_name (chr), latitude (dbl), longitude (dbl),
#> resource_id (int), resource_secondary_id (int), measurement_id (int),
#> trait_id (int), trait_name (chr), standard_id (int), standard_unit
#> (chr), methodology_id (int), methodology_name (chr), value (chr),
#> value_type (chr), precision (dbl), precision_type (chr), precision_upper
#> (dbl), replicates (int), notes (chr)
Birdlife International
Habitat data
birdlife_habitat(22721692)
#> id Habitat (level 1) Habitat (level 2) Importance
#> 1 22721692 Forest Subtropical/Tropical Dry suitable
#> 2 22721692 Forest Subtropical/Tropical Moist Montane major
#> 3 22721692 Forest Temperate suitable
#> 4 22721692 Shrubland Subtropical/Tropical High Altitude suitable
#> Occurrence
#> 1 breeding
#> 2 non-breeding
#> 3 breeding
#> 4 breeding
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
traitsin R doingcitation(package = 'traits')
Functions in traits
| Name | Description | |
| coral | Search for coral data on coraltraits.org | |
| betydb | Search for traits from BETYdb | |
| ncbi_searcher | Search for gene sequences available for taxa from NCBI. | |
| leda | Access LEDA trait data | |
| birdlife_habitat | Get bird habitat information from BirdLife/IUCN | |
| ncbi_byid | Retrieve gene sequences from NCBI by accession number. | |
| traits-package | traits - Species trait data from around the web | |
| ncbi_byname | Retrieve gene sequences from NCBI by taxon name and gene names. | |
| taxa_search | Search for traits by taxa names | |
| fe_native | Check species status (native, exotic, ...) for one species from Flora Europaea webpage | |
| birdlife_threats | Get bird threat information from BirdLife/IUCN | |
| g_invasive | Check invasive species status for a set of species from GISD database | |
| is_native | Check if a species is native somewhere | |
| plantatt | PLANTATT plant traits dataset | |
| traits-deprecated | Deprecated functions in traits | |
| eol_invasive_ | Search for presence of taxonomic names in EOL invasive species databases. | |
| traitbank | Search for traits from EOL's Traitbank. | |
| No Results! | ||
Last month downloads
Details
| License | MIT + file LICENSE |
| URL | https://github.com/ropensci/traits |
| BugReports | http://www.github.com/ropensci/traits/issues |
| LazyData | true |
| VignetteBuilder | knitr |
| RoxygenNote | 5.0.1 |
| NeedsCompilation | no |
| Packaged | 2016-03-18 14:28:13 UTC; sacmac |
| Repository | CRAN |
| Date/Publication | 2016-03-18 15:58:47 |
| depends | base (>= 2.10) , R (>= 2.10) |
| suggests | covr , knitr , plyr , roxygen2 (>= 5.0.1) , testthat |
| imports | data , data.table (>= 1.9.6) , dplyr (>= 0.4.3) , httr (>= 1.1.0) , jsonlite (>= 0.9.19) , methods , readr (>= 0.2.2) , rvest (>= 0.3.1) , stats , taxize (>= 0.7.4) , utils , xml2 (>= 0.1.2) |
| Contributors | Scott Chamberlain, Zachary Foster, Ignasi Bartomeus, David LeBauer, David Harris |
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