Skip to contents

BETYdb Tutorial

Scott Chamberlain

2020-08-25

Source: vignettes/betydb.Rmd
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

Traits

Get trait data for Miscanthus giganteus

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

Summarise data from the output data.frame

suppressPackageStartupMessages(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
#>    <int>       <dbl>
#>  1  1666        27.4
#>  2 16845        27  
#>  3  1669        26.4
#>  4 16518        26  
#>  5  1663        25.4
#>  6 16742        25  
#>  7  1594        24.8
#>  8  1674        22.7
#>  9  1606        22.5
#> 10  1665        22.5
#> # … with 439 more rows

Single trait

betydb_trait(id = 10)
#> # A tibble: 1 x 13
#>      id description units notes created_at updated_at name  max   min  
#>   <int> <chr>       <chr> <chr> <chr>      <chr>      <chr> <chr> <chr>
#> 1    10 Leaf Perce… perc… <NA>  <NA>       2011-06-0… leafN 10    0.02 
#> # … with 4 more variables: standard_name <chr>, standard_units <chr>,
#> #   label <chr>, type <chr>

Species

Single species, Acacia karroothorn

betydb_specie(id = 10)
#> # A tibble: 1 x 10
#>      id spcd  genus species scientificname commonname notes created_at
#>   <int> <chr> <chr> <chr>   <chr>          <chr>      <chr> <chr>     
#> 1    10 <NA>  Acac… karroo  Acacia karroo  karrootho… <NA>  <NA>      
#> # … with 2 more variables: updated_at <chr>, acceptedsymbol <chr>

Citations

Get citatons searching for Miscanthus

#> # A tibble: 1 x 13
#>      id author  year title journal   vol pg    url   pdf   created_at updated_at
#>   <int> <chr>  <int> <chr> <chr>   <int> <chr> <chr> <chr> <chr>      <chr>     
#> 1    10 Casler  2003 Cult… Crop S…    43 2226… http… http… <NA>       <NA>      
#> # … with 2 more variables: doi <chr>, user_id <chr>

Sites

Single site

betydb_site(id = 1)
#> # A tibble: 1 x 8
#>   city    state country notes sitename greenhouse geometry           time_zone  
#>   <chr>   <chr> <chr>   <chr> <chr>    <lgl>      <chr>              <chr>      
#> 1 Aliart… <NA>  GR      <NA>  Aliartos FALSE      POINT (23.17 38.3… Europe/Ath…