Team Two

> library(dplyr)
>
> bety_src <- src_postgres(dbname = "bety",
+                    password = "bety",
+                    host = "terra-bety.default",
+                    user = "bety",
+                    port = 5432)
>
> traits <- tbl(bety_src, "traits")
>
> variables <- tbl(bety_src, "variables") %>%
+   mutate(variable_id = id)
>
> traits_variables <- traits %>%
+   left_join(variables, by = "variable_id") %>%
+   select(name, mean)
>
> head(traits_variables)
> library(dplyr)
>
> bety_src <- src_postgres(dbname = "bety",
+                    password = "bety",
+                    host = "terra-bety.default",
+                    user = "bety",
+                    port = 5432)
>
> traits <- tbl(bety_src, "traits")
>
> variables <- tbl(bety_src, "variables")
>
> traits_variables <- traits %>%
+   left_join(variables, by = "id") %>%
+   select(name, mean)
>
> head(traits_variables)
> library(dplyr)
>
> bety_src <- src_postgres(dbname = "bety",
+                    password = "bety",
+                    host = "terra-bety.default",
+                    user = "bety",
+                    port = 5432)
>
> traits <- tbl(bety_src, "traits")
>
> variables <- tbl(bety_src, "variables") %>%
+   mutate(variable_id = id)
>
> traits_variables <- traits %>%
+   left_join(variables, by = "variable_id") %>%
+   select(name, mean)
>
> head(traits_variables)
> library(traits)
> library(dplyr)
>
> bety_src <- src_postgres(dbname = "bety",
+                          password = 'bety',
+                          host = 'terra-bety.default',
+                          user = 'bety',
+                          port = 5432)
>
> species <- betydb_query(table = 'species', limit = 'none') %>%
+   mutate(specie_id = id)

Error in curl::curl_fetch_memory(url, handle = handle) :
  Operation was aborted by an application callback
> library(traits)
> library(dplyr)
>
> bety <- src_postgres(dbname = "bety",
+                      password = 'bety',
+                      host = 'terra-bety.default',
+                      user = 'bety',
+                      port = 5432)
>
> species <- betydb_query(table = 'species', limit = 'none') %>%
+   mutate(specie_id = id)
Auto-disconnecting postgres connection (231, 4)
Auto-disconnecting postgres connection (231, 3)
Auto-disconnecting postgres connection (231, 2)
>
> sites <- betydb_query(table = 'sites', limit = 'none') %>%
+   mutate(site_id = id)
Error in mutate_impl(.data, dots) :
  Unsupported type CLOSXP for column "site_id"
>
> yields <- betydb_query(table = 'yields', limit = 'none') %>%
+   select(id, date, mean, n, statname, stat, site_id, specie_id, treatment_id, citation_id, cultivar_id) %>%
+   left_join(species, by = 'specie_id') %>%
+   left_join(sites, by = 'site_id')
Error in is.data.frame(y) : object 'sites' not found
>
> managements_treatments <- tbl(bety, 'managements_treatments') %>%
+   select(treatment_id, management_id)
>
> treatments <- tbl(bety, 'treatments') %>%
+   dplyr::mutate(treatment_id = id) %>%
+   dplyr::select(treatment_id, name, definition, control)
>
> managements <- tbl(bety, 'managements') %>%
+   filter(mgmttype %in% c('fertilizer_N', 'fertilizer_N_rate', 'planting', 'irrigation')) %>%
+   dplyr::mutate(management_id = id) %>%
+   dplyr::select(management_id, date, mgmttype, level, units) %>%
+   left_join(managements_treatments, by = 'management_id') %>%
+   left_join(treatments, by = 'treatment_id')
>
>
> nitrogen <- managements %>%
+   filter(mgmttype == "fertilizer_N_rate") %>%
+   select(treatment_id, nrate = level)
>
> planting <- managements %>% filter(mgmttype == "planting") %>%
+   select(treatment_id, planting_date = date)
>
> planting_rate <- managements %>% filter(mgmttype == "planting") %>%
+   select(treatment_id, planting_date = date, planting_density = level)
>
> irrigation <- managements %>%
+   filter(mgmttype == 'irrigation')
>
> irrigation_rate <- irrigation %>%
+   filter(units == 'mm', !is.na(treatment_id)) %>%
+   group_by(treatment_id, year = sql("extract(year from date)"), units) %>%
+   summarise(irrig.mm = sum(level)) %>%
+   group_by(treatment_id) %>%
+   summarise(irrig.mm.y = mean(irrig.mm))
>
> irrigation_boolean <- irrigation %>%
+   collect %>%
+   group_by(treatment_id) %>%
+   mutate(irrig = as.logical(mean(level))) %>%
+   select(treatment_id, irrig = irrig)
Error in resolve_vars(new_groups, tbl_vars(.data)) :
  unknown variable to group by : treatment_id
>
> irrigation_all <- irrigation_boolean %>%
+   full_join(irrigation_rate, copy = TRUE, by = 'treatment_id')
Error in eval(lhs, parent, parent) :
  object 'irrigation_boolean' not found
>
> grass_yields <- yields %>%
+   filter(genus %in% c('Miscanthus', 'Panicum')) %>%
+   left_join(nitrogen, by = 'treatment_id') %>%
+   #left_join(planting, by = 'treatment_id') %>%
+   left_join(planting_rate, by = 'treatment_id') %>%
+   left_join(irrigation_all, by = 'treatment_id', copy = TRUE) %>%
+   collect %>%
+   mutate(age = year(date)- year(planting_date),
+          nrate = ifelse(is.na(nrate), 0, nrate),
+          SE = ifelse(statname == "SE", stat, ifelse(statname == 'SD', stat / sqrt(n), NA)),
+          continent = ifelse(lon < -30, 'united_states', ifelse(lon < 75, 'europe', 'asia'))) %>%
+   filter(!duplicated(.))
Error in eval(lhs, parent, parent) : object 'yields' not found
>