query_planting.R

library(traits)
library(dplyr)
library(ggplot2)
options(betydb_url = 'https://www.betydb.org/',
        betydb_api_version = 'v1'
) 
yields <- betydb_search(result_type = 'yields', genus = 'Panicum', limit = 'none')

treatments <- betydb_query(table = 'treatments', limit = 'none') %>% 
  dplyr::mutate(treatment_id = id) %>% 
  dplyr::select(treatment_id, name, definition, control)
managements <- betydb_query(table = 'managements', limit = 'none') %>%
  dplyr::filter(mgmttype %in% c('planting', "planting (plants / m2)", "row_spacing")) %>%
  dplyr::mutate(management_id = id) %>%
  dplyr::select(management_id, date, mgmttype, level, units) 
# now link managements to treatments
m <- betydb_query(table = 'managements', associations_mode = 'ids', limit = 'none') 
managements_treatments <- m %>%
  select(treatment_id = `associated treatment ids`, management_id = id) %>% 
  tidyr::unnest(cols = c(treatment_id))
planting <- managements %>%
  left_join(managements_treatments, by = 'management_id') %>%
  left_join(treatments, by = 'treatment_id') %>% 
  select(date, treatment_id) %>% 
  distinct()

y <- yields %>% 
  left_join(planting, by = 'treatment_id')