traits v0.3.0

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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', plant data from the USDA plants database, data from 'EOL' 'Traitbank', Coral traits data (<https://coraltraits.org>), 'Birdlife' International, and more.

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traits

Build Status codecov.io rstudio mirror downloads cran version

R client for various sources of species trait data.

Included in traits with the associated function prefix or function name:

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"))
#> # A tibble: 14 x 36
#>    access_level       author checked citation_id citation_year  city
#>  *        <int>        <chr>   <int>       <int>         <int> <chr>
#>  1            4 Wullschleger       1          51          1993  <NA>
#>  2            4         Wang       1         381          2010  <NA>
#>  3            4       Merilo       1         430          2005 Saare
#>  4            4       Merilo       1         430          2005 Saare
#>  5            4       Merilo       1         430          2005 Saare
#>  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       Merilo       1         430          2005 Saare
#> # ... with 30 more variables: commonname <chr>, cultivar <chr>,
#> #   cultivar_id <int>, date <chr>, dateloc <chr>, entity <lgl>,
#> #   genus <chr>, id <int>, lat <dbl>, lon <dbl>, mean <dbl>,
#> #   method_name <lgl>, month <int>, n <int>, notes <chr>, raw_date <chr>,
#> #   result_type <chr>, scientificname <chr>, site_id <int>,
#> #   sitename <chr>, species_id <int>, stat <dbl>, statname <chr>,
#> #   time <chr>, trait <chr>, trait_description <chr>, treatment <chr>,
#> #   treatment_id <int>, units <chr>, year <int>
# 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))
#> # A tibble: 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

EOL's traitbank trait data

Searching for Balaenoptera musculus (blue whale), page id 328574

res <- traitbank(328574)
res$graph %>%
  select(`dwc:measurementtype`) %>%
  filter(!is.na(`dwc:measurementtype`))
#> # A tibble: 181 x 1
#>                                   `dwc:measurementtype`
#>                                                   <chr>
#>  1 http://eol.org/schema/terms/MineralCompositionOfMilk
#>  2 http://eol.org/schema/terms/MineralCompositionOfMilk
#>  3 http://eol.org/schema/terms/MineralCompositionOfMilk
#>  4 http://eol.org/schema/terms/MineralCompositionOfMilk
#>  5 http://eol.org/schema/terms/MineralCompositionOfMilk
#>  6 http://eol.org/schema/terms/MineralCompositionOfMilk
#>  7 http://eol.org/schema/terms/MineralCompositionOfMilk
#>  8 http://eol.org/schema/terms/MineralCompositionOfMilk
#>  9 http://eol.org/schema/terms/MineralCompositionOfMilk
#> 10 http://eol.org/schema/terms/MineralCompositionOfMilk
#> # ... with 171 more rows

Coral

Get the species list and their ids

coral_species()
#> # A tibble: 1,548 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
#> # ... with 1,538 more rows

Get data by taxon

coral_taxa(80)
#> # A tibble: 3,540 x 25
#>    observation_id access user_id specie_id         specie_name location_id
#>             <int>  <int>   <int>     <int>               <chr>       <int>
#>  1         157133      1      10        80 Acropora hyacinthus           1
#>  2         156961      1      14        80 Acropora hyacinthus         409
#>  3           5781      1       1        80 Acropora hyacinthus           1
#>  4         156610      1       2        80 Acropora hyacinthus         500
#>  5         158118      1      10        80 Acropora hyacinthus         409
#>  6         119211      1      49        80 Acropora hyacinthus           1
#>  7         158211      1      10        80 Acropora hyacinthus         413
#>  8          90294      1      15        80 Acropora hyacinthus         341
#>  9          90294      1      15        80 Acropora hyacinthus         341
#> 10          90294      1      15        80 Acropora hyacinthus         341
#> # ... with 3,530 more rows, and 19 more variables: 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 traits in R doing citation(package = 'traits')
  • Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

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Functions in traits

Name Description
is_native Check if a species is native somewhere
taxa_search Search for traits by taxa names
traits-package traits - Species trait data from around the web
tr_ernest Amniote life history dataset
traits_cache Caching
traits-defunct Defunct functions in traits
traitbank Search for traits from EOL's Traitbank.
ncbi_searcher Search for gene sequences available for taxa from NCBI.
birdlife_threats Get bird threat information from BirdLife/IUCN
plantatt PLANTATT plant traits dataset
tr_usda USDA plants data
tr_zanne Zanne et al. plant dataset
ncbi_byid Retrieve gene sequences from NCBI by accession number.
ncbi_byname Retrieve gene sequences from NCBI by taxon name and gene names.
g_invasive Check invasive species status for a set of species from GISD database
birdlife_habitat Get bird habitat information from BirdLife/IUCN
betydb_query Query a BETY table
leda Access LEDA trait data
betydb Search for traits from BETYdb
fe_native Check species status (native, exotic, ...) from Flora Europaea webpage
coral Search for coral data on coraltraits.org
eol_invasive_ Search for presence of taxonomic names in EOL invasive species databases
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Vignettes of traits

Name
betydb.Rmd
traits_intro.Rmd
No Results!

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Details

License MIT + file LICENSE
URL https://github.com/ropensci/traits
BugReports https://github.com/ropensci/traits/issues
LazyData true
VignetteBuilder knitr
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2017-09-22 20:56:21 UTC; sacmac
Repository CRAN
Date/Publication 2017-09-22 21:37:25 UTC

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