R client for various sources of species trait data.
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_
|
http://www.betydb.org |
| NCBI |
ncbi_
|
http://www.ncbi.nlm.nih.gov/ |
| Encylopedia of Life |
traitbank_
|
https://github.com/EOL/eol_website/blob/master/doc/api.md |
| Coral Traits Database |
coral_
|
https://coraltraits.org/ |
| Birdlife International |
birdlife_
|
https://www.birdlife.org/ |
| LEDA Traitbase |
leda_
|
|
| USDA Plants Database |
tr_usda
|
|
| Zanne et al. plant dataset |
tr_zanne
|
|
| Amniote life history dataset |
tr_ernest
|
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.
Stable CRAN version
Or development version from GitHub
Get trait data for Willow (Salix spp.)
(salix <- betydb_search("Salix Vcmax"))
#> # A tibble: 14 x 36
#> checked result_type id citation_id site_id treatment_id sitename
#> <int> <chr> <int> <int> <int> <int> <chr>
#> 1 1 traits 39217 430 645 1342 ""
#> 2 1 traits 39218 430 645 1343 ""
#> 3 1 traits 39219 430 645 1344 ""
#> 4 1 traits 39220 430 645 1345 ""
#> 5 1 traits 25405 51 NA 1 <NA>
#> 6 1 traits 39213 430 645 1342 ""
#> 7 1 traits 39214 430 645 1343 ""
#> 8 1 traits 39215 430 645 1344 ""
#> 9 1 traits 39216 430 645 1345 ""
#> 10 1 traits 39221 430 645 1342 ""
#> 11 1 traits 39222 430 645 1343 ""
#> 12 1 traits 39223 430 645 1344 ""
#> 13 1 traits 39224 430 645 1345 ""
#> 14 1 traits 37519 381 602 1220 <NA>
#> # … with 29 more variables: city <chr>, lat <dbl>, lon <dbl>,
#> # scientificname <chr>, commonname <chr>, genus <chr>, species_id <int>,
#> # cultivar_id <int>, author <chr>, citation_year <int>, treatment <chr>,
#> # date <chr>, time <chr>, raw_date <chr>, month <int>, year <int>,
#> # dateloc <chr>, trait <chr>, trait_description <chr>, mean <dbl>,
#> # units <chr>, n <int>, statname <chr>, stat <dbl>, notes <chr>,
#> # access_level <int>, cultivar <chr>, entity <lgl>, method_name <lgl>
# 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 [4]
#> scientificname trait mean min max n
#> <chr> <chr> <dbl> <dbl> <dbl> <int>
#> 1 Salix Vcmax 65 65 65 1
#> 2 Salix dasyclados Vcmax 46.1 34.3 56.7 4
#> 3 Salix sachalinensis × miyabeana Vcmax 79.3 79.3 79.3 1
#> 4 Salix viminalis Vcmax 43.0 20.0 61.3 8traitbank(query = "MATCH (n:Trait) RETURN n LIMIT 1;")
#> $columns
#> [1] "n"
#>
#> $data
#> $data[[1]]
#> metadata.id metadata.labels
#> 1 20280619 Trait
#> paged_traverse
#> 1 http://10.252.248.44:7474/db/data/node/20280619/paged/traverse/{returnType}{?pageSize,leaseTime}
#> outgoing_relationships
#> 1 http://10.252.248.44:7474/db/data/node/20280619/relationships/out
#> outgoing_typed_relationships
#> 1 http://10.252.248.44:7474/db/data/node/20280619/relationships/out/{-list|&|types}
#> labels
#> 1 http://10.252.248.44:7474/db/data/node/20280619/labels
#> create_relationship
#> 1 http://10.252.248.44:7474/db/data/node/20280619/relationships
#> traverse
#> 1 http://10.252.248.44:7474/db/data/node/20280619/traverse/{returnType}
#> all_relationships
#> 1 http://10.252.248.44:7474/db/data/node/20280619/relationships/all
#> all_typed_relationships
#> 1 http://10.252.248.44:7474/db/data/node/20280619/relationships/all/{-list|&|types}
#> property
#> 1 http://10.252.248.44:7474/db/data/node/20280619/properties/{key}
#> self
#> 1 http://10.252.248.44:7474/db/data/node/20280619
#> incoming_relationships
#> 1 http://10.252.248.44:7474/db/data/node/20280619/relationships/in
#> properties
#> 1 http://10.252.248.44:7474/db/data/node/20280619/properties
#> incoming_typed_relationships
#> 1 http://10.252.248.44:7474/db/data/node/20280619/relationships/in/{-list|&|types}
#> data.eol_pk data.resource_pk
#> 1 R74-PK5014587 110690
#> data.scientific_name
#> 1 <i>Adenopodia floribunda</i> (Kleinhoonte) Brenan
#> data.source
#> 1 http://www.pnas.org/content/114/40/10695
#> data.literal
#> 1 http://eol.org/schema/terms/Tropical_and_subtropical_moist_broadleaf_forestsGet 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 rowsGet 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 h… 1
#> 2 156961 1 14 80 Acropora h… 409
#> 3 5781 1 1 80 Acropora h… 1
#> 4 156610 1 2 80 Acropora h… 500
#> 5 158118 1 10 80 Acropora h… 409
#> 6 119211 1 49 80 Acropora h… 1
#> 7 158211 1 10 80 Acropora h… 413
#> 8 90294 1 15 80 Acropora h… 341
#> 9 90294 1 15 80 Acropora h… 341
#> 10 90294 1 15 80 Acropora h… 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>Habitat data
birdlife_habitat(22721692)
#> id Habitat (level 1) Habitat (level 2) Importance
#> 1 22721692 Forest Subtropical/Tropical Dry major
#> 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 breedingtraits in R doing citation(package = 'traits')