---
title: BETYdb Tutorial
author: Scott Chamberlain
date: "2020-08-25"
output: rmarkdown::html_vignette
vignette: >
    %\VignetteIndexEntry{BETYdb Tutorial}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
---



[BETYdb](https://www.betydb.org/) 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


```r
library("traits")
```

## Traits

Get trait data for _Miscanthus giganteus_


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

Summarise data from the output `data.frame`


```r
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


```r
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_


```r
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_


```r
betydb_citation(10)
```

```
#> # 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


```r
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…
```