betydb.Rmd

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))
## # A tibble: 449 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
## # ... with 439 more rows

Single trait

betydb_trait(id = 10)
## $description
## [1] "Leaf Percent Nitrogen"
## 
## $id
## [1] 10
## 
## $max
## [1] "10"
## 
## $min
## [1] "0.02"
## 
## $name
## [1] "leafN"
## 
## $notes
## [1] ""
## 
## $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"
## 
## $genus
## [1] "Acacia"
## 
## $id
## [1] 10
## 
## $notes
## [1] ""
## 
## $scientificname
## [1] "Acacia karroo"
## 
## $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"
## 
## $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"
## 
## $url
## [1] "http://crop.scijournals.org/cgi/content/abstract/43/6/2226"
## 
## $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] ""
## 
## $time_zone
## [1] "Europe/Athens"