WIP: redo the default numbers calculation based on the new file dumped from grendel

Grendel/scenarios/numbers_report.Rmd

@@ -45,33 +45,41 @@ path_desktop("goose", date_stamp, jobs, grain_dist_file) %>%
   fst::read_fst() %>% 
   as_tibble() -> grain_dists
 
-grain_dists %>% group_by(param, value) %>% count(grain_dist)
-
 left_join(goose_numbers, grain_dists, by = c("param", "value", "season")) -> goose_numbers
-goose_numbers %>% 
-  mutate(replicate = 1L) -> goose_numbers
 
-goose_numbers <- bind_rows(goose_numbers, goose_numbers_2)
+default_numbers_file <- glue("{jobs}_scenario-goose-numbers_{date_stamp}.fst")
+path_desktop("goose", date_stamp, jobs, default_numbers_file) %>%
+  fst::read_fst() %>% 
+  as_tibble() %>% 
+  mutate(pinkfoot = pf_families + pf_non_breeders,
+         greylag = gl_families + gl_non_breeders,
+         barnacle = bn_families + bn_non_breeders,
+         day = day - 365L) %>%
+  filter(param == "GOOSE_STARTNO_SCALER",
+         value == 1,
+         season == 1) %>% 
+  select(day, pinkfoot, greylag, barnacle) %>% 
+  gather(key = species, value = numbers, -day) %>% 
+  filter(numbers > 0) -> default_numbers
+
 # Summarize field forage data ----  
 # Mean numbers per day
 goose_numbers %>% 
   mutate(day = day - 365*season) %>% 
-  select(replicate, grain_dist, param, value, season, day, pinkfoot, barnacle, greylag) %>% 
-  group_by(replicate, grain_dist, param, value, season, day) %>% 
+  select(grain_dist, param, value, season, day, pinkfoot, barnacle, greylag) %>% 
+  group_by(grain_dist, param, value, season, day) %>% 
   summarise_at(.vars = vars(pinkfoot, barnacle, greylag),
                .funs = funs(daily = sum)) %>% 
   group_by(grain_dist, param, value, day) %>% 
   summarise_at(.vars = vars(ends_with("daily")),
-               .funs = funs(avg = mean,
-                            min, max)) %>% 
+               .funs = funs(avg = mean, min, max)) %>% 
   ungroup() %>% 
   gather(key = species, value = numbers, -grain_dist, -param, -value, -day) %>% 
   filter(numbers > 0) -> numbers_per_day
 
-numbers_per_day %>% 
-  filter(value == 1) -> default
-left_join(numbers_per_day, default, 
-          by = c("grain_dist", "param",  "day", "species"),
+# Read the default numbers and standardize
+left_join(numbers_per_day, default_numbers, 
+          by = c("day", "species"),
           suffix = c("", "_default")) %>% 
   mutate(standarized = numbers/numbers_default) -> numbers_per_day