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

cran checks Build Status codecov rstudio mirror downloads cran version

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

Meta

  • Please report any issues or bugs.
  • License: MIT
  • Get citation information for traits in R doing citation(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.

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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.
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Vignettes of traits

Name
betydb.Rmd
betydb.Rmd.og
traits.Rmd
traits.Rmd.og
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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

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