fix script

app.R

@@ -5,6 +5,9 @@ library(tidyverse)
 message("---- load utils function ----")
 source(file = "utils_function.R")
 
+message("---- load any data ----")
+source(file = "data_loader_script.R")
+
 message("---- run plumber ----")
 pr() %>% 
   pr_mount("/a", pr("services/a_services.R")) %>% 

data/raw_data_for_feed_module - ABW Growth.csv

@@ -0,0 +1,121 @@
+DOC,Balanced,Fast Growth
+1,0.01,0.03
+2,0.08,0.1
+3,0.15,0.17
+4,0.22,0.24
+5,0.29,0.31
+6,0.36,0.38
+7,0.43,0.45
+8,0.5,0.52
+9,0.57,0.59
+10,0.64,0.66
+11,0.71,0.73
+12,0.78,0.8
+13,0.85,0.87
+14,0.92,0.94
+15,0.99,1.01
+16,1.06,1.08
+17,1.13,1.15
+18,1.2,1.22
+19,1.27,1.29
+20,1.34,1.36
+21,1.41,1.43
+22,1.48,1.5
+23,1.55,1.57
+24,1.62,1.64
+25,1.69,1.71
+26,1.76,1.78
+27,1.83,1.85
+28,1.9,1.92
+29,1.97,1.99
+30,2.17,2.19
+31,2.37,2.39
+32,2.57,2.59
+33,2.77,2.79
+34,2.97,2.99
+35,3.17,3.19
+36,3.37,3.39
+37,3.57,3.59
+38,3.77,3.79
+39,3.97,3.99
+40,4.17,4.19
+41,4.37,4.39
+42,4.57,4.59
+43,4.77,4.79
+44,4.97,4.99
+45,5.17,5.19
+46,5.37,5.39
+47,5.57,5.59
+48,5.77,5.79
+49,5.97,5.99
+50,6.17,6.37
+51,6.37,6.57
+52,6.57,6.77
+53,6.77,6.97
+54,6.97,7.17
+55,7.17,7.37
+56,7.37,7.57
+57,7.57,7.77
+58,7.77,7.97
+59,7.97,8.17
+60,8.17,8.37
+61,8.47,8.67
+62,8.77,8.97
+63,9.07,9.27
+64,9.37,9.57
+65,9.67,9.87
+66,9.97,10.17
+67,10.27,10.47
+68,10.57,10.77
+69,10.87,11.07
+70,11.17,11.37
+71,11.47,11.67
+72,11.77,11.97
+73,12.07,12.27
+74,12.37,12.57
+75,12.67,12.87
+76,12.97,13.17
+77,13.27,13.47
+78,13.57,13.77
+79,13.87,14.07
+80,14.17,14.67
+81,14.47,14.97
+82,14.77,15.27
+83,15.07,15.57
+84,15.37,15.87
+85,15.67,16.17
+86,15.97,16.47
+87,16.27,16.77
+88,16.57,17.07
+89,16.87,17.37
+90,17.17,18.17
+91,17.47,18.47
+92,17.82,18.82
+93,18.17,19.17
+94,18.52,19.52
+95,18.87,19.87
+96,19.22,20.22
+97,19.57,20.57
+98,19.92,20.92
+99,20.27,21.27
+100,20.62,22.12
+101,20.97,22.47
+102,21.32,22.82
+103,21.67,23.17
+104,22.02,23.52
+105,22.37,23.87
+106,22.72,24.22
+107,23.07,24.57
+108,23.42,24.92
+109,23.77,25.27
+110,24.12,25.62
+111,24.47,25.97
+112,24.82,26.32
+113,25.17,26.67
+114,25.52,27.02
+115,25.87,27.37
+116,26.22,27.72
+117,26.57,28.07
+118,26.92,28.42
+119,27.27,28.77
+120,27.62,29.12

data_loader_script.R

@@ -0,0 +1,2 @@
+# growth by genetics
+growth_by_genetic_data <- read.csv(file = "data/raw_data_for_feed_module - ABW Growth.csv")

function.R

@@ -124,113 +124,123 @@ function(req) {
 function(req) {
   data_from_user <- req$body
   
-  print(data_from_user)
-  shrimp_stock_data <- data_from_user$shrimp_stock_data %>% 
+  start_date <-  data_from_user$start_date
+  maximum_doc <-  data_from_user$maximum_doc
+  pond_setting <-  data_from_user$pond_setting %>% 
     janitor::clean_names()
-  harvest_setting <- data_from_user$harvest_setting %>% 
+  partial_harvest_setting <-  data_from_user$partial_harvest_setting %>% 
     janitor::clean_names()
-  max_doc <- data_from_user$max_doc
-  growth_scenario_table <- data_from_user$growth_scenario_table %>% 
+  survival_calculation_method <-  data_from_user$survival_calculation_method
+  target_survival <-  data_from_user$target_survival
+  survival_model <-  data_from_user$survival_model
+  feeding_session_setting <-  data_from_user$feeding_session_setting
+  fi_multiplier_setting <-  data_from_user$fi_multiplier_setting
+  fr_type_setting <- data_from_user$fr_type_setting
+  fr_coef_x <-  data_from_user$fr_coef_x
+  fr_coef_y <-  data_from_user$fr_coef_y
+  blind_feeding_start_feeding_setting <-  data_from_user$blind_feeding_start_feeding_setting
+  blind_feeding_increment_setting <-  data_from_user$blind_feeding_increment_setting %>% 
     janitor::clean_names()
-  survival_setting <- data_from_user$survival_setting
-  blind_feeding_day_1_setting <- data_from_user$blind_feeding_day_1_setting
-  blind_feeding_day_2_setting <- data_from_user$blind_feeding_day_2_setting %>% 
+  growth_calculation_method <-  data_from_user$growth_calculation_method
+  initial_abw <-  data_from_user$initial_abw
+  initial_growth_data <-  data_from_user$initial_growth_data %>% 
     janitor::clean_names()
-  date_data <- data_from_user$date_data
-  fi_multiplier <- data_from_user$fi_multiplier_setting
+  
+  print()
   
   message("---- generate feeding for one cycle ----")
   
-  result <- all_feeding_generator_function_v2(
-    shrimp_stock_data = shrimp_stock_data,
-    max_doc = max_doc,
-    harvest_setting = harvest_setting,
-    growth_scenario_table = growth_scenario_table,
-    survival_setting = survival_setting,
-    blind_feeding_day_1_setting = blind_feeding_day_1_setting,
-    blind_feeding_day_2_setting = blind_feeding_day_2_setting,
-    date_data = date_data,
-    fi_multiplier = fi_multiplier
-  )
+  # result <- all_feeding_generator_function_v2(
+  #   shrimp_stock_data = shrimp_stock_data,
+  #   max_doc = max_doc,
+  #   harvest_setting = harvest_setting,
+  #   growth_scenario_table = growth_scenario_table,
+  #   survival_setting = survival_setting,
+  #   blind_feeding_day_1_setting = blind_feeding_day_1_setting,
+  #   blind_feeding_day_2_setting = blind_feeding_day_2_setting,
+  #   date_data = date_data,
+  #   fi_multiplier = fi_multiplier
+  # )
   
   message("---- check result ----")
-  print(result)
-  
-  ### blind feed table
-  result$blind_feed_table -> blind_feed_table
-  
-  ### demand feeding table
-  result$demand_feeding_table -> demand_feeding_table
-  
-  ### survival table
-  result$survival_table -> survival_table
-  
-  ### stocking data
-  shrimp_stock_data -> stocking_data
-  
-  ### partial harvest setting
-  harvest_setting -> partial_harvest_setting
-  
-  ### feeding plan generation
-  message("---- blind feeding generation ----")
-  blind_feed_table %>% 
-    pivot_wider(names_from = type, values_from = total_feed) %>% 
-    mutate(
-      feed_per_day_fr = blind_feeding,
-      feed_per_day_indeks = blind_feeding
-    ) %>% 
-    select(-blind_feeding) -> blind_feed_table
-  
-  message("---- demand feeding generation ----")
-  blind_feed_table %>% 
-    bind_rows(
-      demand_feeding_table %>% 
-        select(doc, pond_code, feed_per_day_indeks, feed_per_day_fr) 
-    ) %>% 
-    mutate(feed_type = ifelse(doc <= 30, "blind_feeding", "demand_feeding")) %>% 
-    left_join(growth_scenario_table) %>%
-    left_join(survival_table) %>%
-    # left_join(partial_harvest_setting) %>% 
-    left_join(stocking_data) %>% 
-    arrange(pond_code, doc) %>% 
-    # replace_na(list(harvest_percentage = 0)) %>% 
-    # mutate(harvested = round((population * harvest_percentage/100))) %>% 
-    group_by(pond_code) %>% 
-    mutate(cumulative_harvested = cumsum(harvested)) %>% 
-    ungroup() %>% 
-    mutate(biomass = mbw * population_left/1000) %>% 
-    mutate(biomass_total = biomass + (cumulative_harvested*mbw)/1000) %>% 
-    group_by(pond_code) %>% 
-    mutate(
-      cumulative_feed_indeks = cumsum(feed_per_day_indeks),
-      cumulative_feed_fr = cumsum(feed_per_day_fr),
-    ) %>% 
-    ungroup() %>% 
-    mutate(
-      fcr_indeks = cumulative_feed_indeks/biomass_total,
-      fcr_fr = cumulative_feed_fr/biomass_total
-    ) %>% 
-    mutate(
-      data_type = "planning"
-    ) -> result
-  
-  # variable setting
-  ## datetime information
-  datetime_info <- lubridate::now(tzone = "UTC")
-  
-  ## eeding_strategy_planning_datatable
-  message("---- Save Feeding Plan for One Cycle ----")
-  result %>% 
-    mutate(
-      created_date = datetime_info
-    ) %>% 
-    select(
-      doc, date, pond_code, pond_area, mbw, sr_est, 
-      population, harvest_percentage, harvested, cumulative_harvested, 
-      population_left, biomass, biomass_total, feed_type,
-      feed_per_day_fr, feed_per_day_indeks, 
-      cumulative_feed_fr, cumulative_feed_indeks,
-      fcr_fr, fcr_indeks, 
-      data_type, created_date
-    ) -> result
+
+  # ### blind feed table
+  # result$blind_feed_table -> blind_feed_table
+  # 
+  # ### demand feeding table
+  # result$demand_feeding_table -> demand_feeding_table
+  # 
+  # ### survival table
+  # result$survival_table -> survival_table
+  # 
+  # ### stocking data
+  # shrimp_stock_data -> stocking_data
+  # 
+  # ### partial harvest setting
+  # harvest_setting -> partial_harvest_setting
+  # 
+  # ### feeding plan generation
+  # message("---- blind feeding generation ----")
+  # blind_feed_table %>% 
+  #   pivot_wider(names_from = type, values_from = total_feed) %>% 
+  #   mutate(
+  #     feed_per_day_fr = blind_feeding,
+  #     feed_per_day_indeks = blind_feeding
+  #   ) %>% 
+  #   select(-blind_feeding) -> blind_feed_table
+  # 
+  # message("---- demand feeding generation ----")
+  # blind_feed_table %>% 
+  #   bind_rows(
+  #     demand_feeding_table %>% 
+  #       select(doc, pond_code, feed_per_day_indeks, feed_per_day_fr) 
+  #   ) %>% 
+  #   mutate(feed_type = ifelse(doc <= 30, "blind_feeding", "demand_feeding")) %>% 
+  #   left_join(growth_scenario_table) %>%
+  #   left_join(survival_table) %>%
+  #   # left_join(partial_harvest_setting) %>% 
+  #   left_join(stocking_data) %>% 
+  #   arrange(pond_code, doc) %>% 
+  #   # replace_na(list(harvest_percentage = 0)) %>% 
+  #   # mutate(harvested = round((population * harvest_percentage/100))) %>% 
+  #   group_by(pond_code) %>% 
+  #   mutate(cumulative_harvested = cumsum(harvested)) %>% 
+  #   ungroup() %>% 
+  #   mutate(biomass = mbw * population_left/1000) %>% 
+  #   mutate(biomass_total = biomass + (cumulative_harvested*mbw)/1000) %>% 
+  #   group_by(pond_code) %>% 
+  #   mutate(
+  #     cumulative_feed_indeks = cumsum(feed_per_day_indeks),
+  #     cumulative_feed_fr = cumsum(feed_per_day_fr),
+  #   ) %>% 
+  #   ungroup() %>% 
+  #   mutate(
+  #     fcr_indeks = cumulative_feed_indeks/biomass_total,
+  #     fcr_fr = cumulative_feed_fr/biomass_total
+  #   ) %>% 
+  #   mutate(
+  #     data_type = "planning"
+  #   ) -> result
+  # 
+  # # variable setting
+  # ## datetime information
+  # datetime_info <- lubridate::now(tzone = "UTC")
+  # 
+  # ## eeding_strategy_planning_datatable
+  # message("---- Save Feeding Plan for One Cycle ----")
+  # result %>% 
+  #   mutate(
+  #     created_date = datetime_info
+  #   ) %>% 
+  #   select(
+  #     doc, date, pond_code, pond_area, mbw, sr_est, 
+  #     population, harvest_percentage, harvested, cumulative_harvested, 
+  #     population_left, biomass, biomass_total, feed_type,
+  #     feed_per_day_fr, feed_per_day_indeks, 
+  #     cumulative_feed_fr, cumulative_feed_indeks,
+  #     fcr_fr, fcr_indeks, 
+  #     data_type, created_date
+  #   ) -> result
+  
+  return("Pass")
 }

utils_function.R

@@ -1,3 +1,95 @@
+# growth function v2 ----
+growth_function_training <- function(
+    data, 
+    init_size = 0.01, 
+    max_doc = 120, 
+    method = "ADG"
+) {
+  # set maximum doc
+  doc_vec <- 1:max_doc
+  if (method == "Growth Model") {
+    message("---- use Growth Model ----")
+    model_res <-nls(
+      mbw ~ asymptotic_growth*(1-(1-(init_size/asymptotic_growth)^(1/allometric_scale))*exp(-growth_rate*doc))^allometric_scale,
+      data = data,
+      start = list(
+        asymptotic_growth = 40, 
+        allometric_scale = 3, 
+        growth_rate = 0.015
+      )
+    )
+    
+    pred_res <- predict(
+      model_res, 
+      list(
+        doc = doc_vec
+      )
+    )
+    
+    tibble(
+      doc = doc_vec,
+      mbw = round(pred_res,3)
+    ) -> growth_res
+  } else if(method == "ABW Interpolation") {
+    message("---- use ABW Interpolation ----")
+    min_doc <- min(data$doc)
+    max_doc <- max(data$doc)
+    
+    growth_res <- data.frame(
+      with(data,
+           approx(doc, mbw, xout = seq(min_doc, max_doc, by = 1), method = "linear")
+      )
+    ) %>%
+      rename(doc = x, mbw = y)
+  } else if(method == "Genetics - Balanced") {
+    message("---- use Genetics - Balanced Data ----")
+    growth_res <- growth_by_genetic_data %>% 
+      select(DOC, Balanced) %>% 
+      rename(
+        doc = DOC,
+        mbw = Balanced
+      ) %>% 
+      filter(doc <= max_doc)
+  } else if(method == "Genetics - Fast Growth") {
+    message("---- use Genetics - Fast Growth Data ----")
+    growth_res <- growth_by_genetic_data %>% 
+      select(DOC, Fast.Growth) %>% 
+      rename(
+        mbw = Fast.Growth,
+        doc = DOC
+      ) %>% 
+      filter(doc <= max_doc)
+  } else {
+    message("---- use ADG Interpolation ----")
+    initial_weight <- init_size 
+    final_doc <- max_doc
+    adg_data <- data
+    
+    abw_container <- list()
+    
+    for (indeks in 1:nrow(adg_data)) {
+      if (indeks == 1) {
+        abw_container[[indeks]] <- c(initial_weight, initial_weight + cumsum(rep(adg_data$adg[indeks], adg_data$doc[indeks + 1] - adg_data$doc[indeks] - 1)))
+      } else if(indeks == nrow(adg_data)) {
+        initial_weight <- max(abw_container[[indeks-1]])
+        abw_container[[indeks]] <- c(initial_weight + cumsum(rep(adg_data$adg[indeks], final_doc - adg_data$doc[indeks] + 1)))
+      } else {
+        initial_weight <- max(abw_container[[indeks-1]])
+        abw_container[[indeks]] <- c(initial_weight + cumsum(rep(adg_data$adg[indeks], adg_data$doc[indeks + 1] - adg_data$doc[indeks])))
+      }
+    }
+    
+    mbw_ <- unlist(abw_container)
+    
+    tibble(
+      doc = 1:final_doc,
+      mbw = mbw_
+    ) -> growth_res
+  }
+  return(growth_res)
+}
+
+
 # survival function v2 ----
 ## function ----
 survival_function_v2 <- function(