BETYdb is the Biofuel Ecophysiological Traits and Yields Database. You can get many different types of data from this database, including trait data.

Function setup: All functions are prefixed with `betydb_`. Plural function names like `betydb_traits()` accept parameters and always give back a data.frame, while singlur function names like `betydb_trait()` accept an ID and give back a list.

The idea with the functions with plural names is to search for either traits, species, etc., and with the singular function names to get data by one or more IDs.

## Load traits

    library("traits")

## Traits

Get trait data for Miscanthus giganteus

    out <- betydb_search(query = "Switchgrass Yield")

Summarise data from the output `data.frame`

    library("dplyr")
    out %>%
      group_by(id) %>%
      summarise(mean_result = mean(as.numeric(mean), na.rm = TRUE)) %>%
      arrange(desc(mean_result))

    ## Source: local data frame [509 x 2]
    ##
    ##       id mean_result
    ## 1   1666       27.36
    ## 2  16845       27.00
    ## 3   1669       26.36
    ## 4  16518       26.00
    ## 5   1663       25.35
    ## 6  16742       25.00
    ## 7   1594       24.78
    ## 8   1674       22.71
    ## 9   1606       22.54
    ## 10  1665       22.46
    ## ..   ...         ...

Single trait

    betydb_trait(id = 10)

    ## $created_at
    ## NULL
    ##
    ## $description
    ## [1] "Leaf Percent Nitrogen"
    ##
    ## $id
    ## [1] 10
    ##
    ## $label
    ## NULL
    ##
    ## $max
    ## [1] "10"
    ##
    ## $min
    ## [1] "0.02"
    ##
    ## $name
    ## [1] "leafN"
    ##
    ## $notes
    ## [1] ""
    ##
    ## $standard_name
    ## NULL
    ##
    ## $standard_units
    ## NULL
    ##
    ## $units
    ## [1] "percent"
    ##
    ## $updated_at
    ## [1] "2011-06-06T09:40:42-05:00"

## Species

Single species, Acacia karroothorn

    betydb_specie(id = 10)

    ## $AcceptedSymbol
    ## [1] "ACKA2"
    ##
    ## $commonname
    ## [1] "karroothorn"
    ##
    ## $created_at
    ## NULL
    ##
    ## $genus
    ## [1] "Acacia"
    ##
    ## $id
    ## [1] 10
    ##
    ## $notes
    ## [1] ""
    ##
    ## $scientificname
    ## [1] "Acacia karroo"
    ##
    ## $spcd
    ## NULL
    ##
    ## $species
    ## [1] "karroo"
    ##
    ## $updated_at
    ## [1] "2011-03-01T15:02:25-06:00"

## Citations

Get citatons searching for Miscanthus

    betydb_citation(10)

    ## $author
    ## [1] "Casler"
    ##
    ## $created_at
    ## NULL
    ##
    ## $doi
    ## [1] "10.2135/cropsci2003.2226"
    ##
    ## $id
    ## [1] 10
    ##
    ## $journal
    ## [1] "Crop Science"
    ##
    ## $pdf
    ## [1] "http://crop.scijournals.org/cgi/reprint/43/6/2226.pdf"
    ##
    ## $pg
    ## [1] "2226–2233"
    ##
    ## $title
    ## [1] "Cultivar X environment interactions in switchgrass"
    ##
    ## $updated_at
    ## NULL
    ##
    ## $url
    ## [1] "http://crop.scijournals.org/cgi/content/abstract/43/6/2226"
    ##
    ## $user_id
    ## NULL
    ##
    ## $vol
    ## [1] 43
    ##
    ## $year
    ## [1] 2003

## Sites

Single site

    betydb_site(id = 1)

    ## $city
    ## [1] "Aliartos"
    ##
    ## $country
    ## [1] "GR"
    ##
    ## $geometry
    ## [1] "POINT (23.17 38.37 114.0)"
    ##
    ## $greenhouse
    ## [1] FALSE
    ##
    ## $notes
    ## [1] ""
    ##
    ## $sitename
    ## [1] "Aliartos"
    ##
    ## $state
    ## [1] ""