traits v0.5.0
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Species Trait Data from Around the Web
Species trait data from many different sources, including
sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>),
plant trait data from 'BETYdb', data from 'EOL' 'Traitbank',
'Birdlife' International, and more.
Readme
traits
R client for various sources of species trait data.
Docs: https://docs.ropensci.org/traits/
What is a trait? A "trait" for the purposes of this package is broadly defined as an aspect of a species that can be described or measured, such as physical traits (size, length, height, color), behavioral traits (running speed, etc.), and even variables that make up the niche of the species (e.g., habitat).
Included in traits with the associated function prefix or function name:
| Souce | Function prefix | Link |
|---|---|---|
| BETYdb | betydb |
https://www.betydb.org/ |
| NCBI | ncbi |
https://www.ncbi.nlm.nih.gov/ |
| Encylopedia of Life | traitbank_ |
https://github.com/EOL/eol_website/blob/master/doc/api.md |
| Birdlife International | birdlife |
https://www.birdlife.org/ |
| LEDA Traitbase | leda |
|
| Zanne et al. plant dataset | tr_zanne |
|
| Amniote life history dataset | tr_ernest |
Talk to us on the issues page (https://github.com/ropensci/traits/issues) if you know of a source of traits data with an API, and we'll see about including it.
Installation
Stable CRAN version
install.packages("traits")
Or development version from GitHub
remotes::install_github("ropensci/traits")
library("traits")
library("dplyr")
Contributors
- Scott Chamberlain
- Zachary Foster
- Ignasi Bartomeus
- David LeBauer
- David Harris
- Chris Black
- Rupert Collins
Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
traitsin R doingcitation(package = 'traits') - Please note that this package is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Functions in traits
| Name | Description | |
| fe_native | Check species status (native, exotic, ...) from Flora Europaea webpage | |
| betydb | Search for traits from BETYdb | |
| leda | Access LEDA trait data | |
| is_native | Check if a species is native somewhere | |
| eol_invasive_ | Search for presence of taxonomic names in EOL invasive species databases | |
| g_invasive | Check invasive species status for a set of species from GISD database | |
| betydb_query | Query a BETY table | |
| birdlife_habitat | Get bird habitat information from BirdLife/IUCN | |
| birdlife_threats | Get bird threat information from BirdLife/IUCN | |
| coral-defunct | Search for coral data on coraltraits.org | |
| ncbi_byid | Retrieve gene sequences from NCBI by accession number. | |
| ncbi_searcher | Search for gene sequences available for taxa from NCBI. | |
| traits-defunct | Defunct functions in traits | |
| traitbank | Search for traits from EOL's Traitbank | |
| plantatt | PLANTATT plant traits dataset | |
| tr_zanne | Zanne et al. plant dataset | |
| tr_usda | USDA plants data | |
| taxa_search | Search for traits by taxa names | |
| traits_cache | Caching | |
| tr_ernest | Amniote life history dataset | |
| traits-package | traits - Species trait data from around the web | |
| ncbi_byname | Retrieve gene sequences from NCBI by taxon name and gene names. | |
| No Results! | ||
Vignettes of traits
| Name | ||
| betydb.Rmd | ||
| betydb.Rmd.og | ||
| traits.Rmd | ||
| traits.Rmd.og | ||
| No Results! | ||
Last month downloads
Details
| License | MIT + file LICENSE |
| URL | https://docs.ropensci.org/traits/, https://github.com/ropensci/traits |
| BugReports | https://github.com/ropensci/traits/issues |
| LazyData | true |
| Encoding | UTF-8 |
| VignetteBuilder | knitr |
| RoxygenNote | 7.1.1 |
| X-schema.org-applicationCategory | Biodiversity |
| X-schema.org-keywords | traits, API, web-services, species, taxonomy |
| X-schema.org-isPartOf | https://ropensci.org |
| NeedsCompilation | no |
| Packaged | 2020-08-26 17:54:07 UTC; sckott |
| Repository | CRAN |
| Date/Publication | 2020-08-27 05:10:06 UTC |
| imports | crul (>= 0.6.0) , data.table (>= 1.9.6) , hoardr , httr (>= 1.1.0) , jsonlite (>= 0.9.19) , readr (>= 1.1.1) , rvest (>= 0.3.1) , taxize (>= 0.7.4) , tibble (>= 1.3.4) , xml2 (>= 0.1.2) |
| suggests | dplyr , knitr , plyr , rmarkdown , testthat |
| depends | R (>= 2.10) |
| Contributors | David Harris, Rupert Collins, Zachary Foster, Ignasi Bartomeus, David LeBauer, Chris Black |
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