Name: traits
Owner: rOpenSci
Description: Species traits data
Created: 2014-04-09 20:21:13.0
Updated: 2018-01-08 15:41:19.0
Pushed: 2018-01-05 19:55:13.0
Size: 4496
Language: R
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R client for various sources of species trait data.
Included in traits with the associated function prefix or function name:
betydb_ncbi_traitbank_coral_birdlife_leda_tr_usdatr_zannetr_ernestTalk 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.
Stable CRAN version
all.packages("traits")
Or development version from GitHub
ools::install_github("ropensci/traits")
ary("traits")
ary("dplyr")
Get trait data for Willow (Salix spp.)
ix <- 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
0 4 Merilo 1 430 2005 Saare
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
... 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>
uivalent:
ut <- betydb_search("willow"))
Summarise data from the output data.frame
ary("dplyr")
x %>%
oup_by(scientificname, trait) %>%
tate(.mean = as.numeric(mean)) %>%
mmarise(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>
Salix Vcmax 65.00 65.00 65.00 1
Salix dasyclados Vcmax 46.08 34.30 56.68 4
Salix sachalinensis × miyabeana Vcmax 79.28 79.28 79.28 1
Salix viminalis Vcmax 43.04 19.99 61.29 8
Searching for Balaenoptera musculus (blue whale), page id 328574
<- traitbank(328574)
graph %>%
lect(`dwc:measurementtype`) %>%
lter(!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
0 http://eol.org/schema/terms/MineralCompositionOfMilk
... with 171 more rows
Get the species list and their ids
l_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
0 Acropora aculeus 18
... with 1,538 more rows
Get data by taxon
l_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
0 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>
Habitat data
life_habitat(22721692)
id Habitat (level 1) Habitat (level 2) Importance
22721692 Forest Subtropical/Tropical Dry suitable
22721692 Forest Subtropical/Tropical Moist Montane major
22721692 Forest Temperate suitable
22721692 Shrubland Subtropical/Tropical High Altitude suitable
Occurrence
breeding
non-breeding
breeding
breeding
traits in R doing citation(package = 'traits')