Merge pull request #28 from Seafood-Globalization-Lab/develop

Consumption update
Seafood-Globalization-Lab · Sep 23, 2024 · 83ed281 · 83ed281
2 parents ca9cbf4 + 8a9af70
commit 83ed281
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Showing 7 changed files with 311 additions and 193 deletions.
diff --git a/.gitignore b/.gitignore
@@ -12,4 +12,5 @@ model_inputs/*
 outputs/*
 *.zip
 model_inputs_sau/*
+AM_local/*
 grateful-report.html
diff --git a/02-artis-pipeline.R b/02-artis-pipeline.R
@@ -25,11 +25,11 @@ if (run_env == "aws") {
 }
 
 # Set production data type variable
-prod_data_type <- "FAO"
+prod_data_type <- "SAU"
 
 # Set up Start date for finding no solution countries
 start_date <- Sys.Date()
-test_years <- c(2018)
+test_years <- c()
 #--------------------------------------------------------
 # This section generates the solutions for the mass balance problem for all
 # countries across all years and HS versions

diff --git a/03-combine-tables.R b/03-combine-tables.R
@@ -2,10 +2,9 @@
 # Setup based on the kind of analysis and machine you are working with
 
 # Start with a clean working environment
-rm(list=ls())
-
+# rm(list=ls())
 #-------------------------------------------------------------------------------
-run_env <- "demo"
+run_env <- "aws"
 
 if (run_env == "aws") {
   # High Performance Computing on AWS Setup
@@ -40,6 +39,9 @@ outdir_cvxopt <- file.path(outdir, "cvxopt_snet")
 
 final_outdir <- file.path(outdir, "artis_outputs")
 
+# Ensure the 'outputs' directory exists on the aws "local" machine
+if (!dir.exists("outputs")) { dir.create("outputs") }
+# Ensure the 'artis_outputs' directory exists on the aws "local" machine
 if (!dir.exists(final_outdir)) { dir.create(final_outdir) }
 
 build_artis_data(outdir_snet, final_outdir,

diff --git a/04-create-metadata.R b/04-create-metadata.R
@@ -150,18 +150,43 @@ taxa_metadata <- taxa %>%
     sciname = c("arthropoda", "engraulis", "hippoglossinae", "scombrinae", "clupea",     
                 "chondrichthyes", "salmoninae", "mytilinae", "actinopteri", "animalia",    
                 "homarus", "cypriniformes", "dissostichus", "micromesistius", "echinoida"),
+
     common_name = c("arthropods", "anchovies", "flounders", "mackerels, tunas, and bonitos",
                    "herrings", "sharks, skates, rays, and chimaeras", "salmons and trouts",
                    "saltwater mussels", "ray-finned fish", "aquatic animals", "lobsters", 
                    "carps, minnows, loaches, etc", "toothfish", "blue whitings", "sea urchins"),
-    Genus = NA,
-    Subfamily = NA,
-    Family = NA, 
-    Order = NA, 
-    Class = NA,
-    Superclass = NA,
-    Phylum = NA,
-    Kingdom = NA
+
+    Genus = c(NA, "engraulis", NA, NA, "clupea",     
+              NA, NA, NA, NA, NA,    
+              "homarus", NA, "dissostichus", "micromesistius", NA),
+
+    Subfamily = c(NA, "engraulinae", "hippoglossinae", "scombrinae", "clupeinae",     
+                  NA, "salmoninae", "mytilinae", NA, NA,    
+                  NA, NA, NA, NA, NA),
+
+    Family = c(NA, "engraulidae", "pleuronectidae", "scombridae", "clupeidae",     
+               NA, "salmonidae", "mytilidae", NA, NA,    
+               "nephropidae", NA, "nototheniidae", "gadidae", NA), 
+
+    Order = c(NA, "clupeiformes", "pleuronectiformes", "scombriformes", "	clupeiformes",     
+              NA, "salmoniformes", "mytilida", NA, NA,    
+              "decapoda", "cypriniformes", "perciformes", "gadiformes", "echinoida"), 
+
+    Class = c(NA, "actinopterygii", "actinopterygii", "actinopterygii", "actinopterygii",     
+              "chondrichthyes", "actinopterygii", "bivalvia", "actinopterygii", NA,    
+              "malacostraca", "actinopterygii", "actinopterygii", "actinopterygii", "echinoidea"),
+
+    Superclass = c(NA, NA, NA, NA, NA,     
+                   NA, NA, NA, "actinopteri", NA,    
+                   NA, NA, NA, NA, NA),
+
+    Phylum = c("arthropoda", "chordata", "chordata", "chordata", "chordata",     
+               "chordata", "chordata", "mollusca", "chordata", NA,    
+               "arthropoda", "chordata", "chordata", "chordata", "echinodermata"),
+
+    Kingdom = c("animalia", "animalia", "animalia", "animalia", "animalia",     
+                "animalia", "animalia", "animalia", "animalia", "animalia",    
+                "animalia", "animalia", "animalia", "animalia", "animalia")
   )) 
 
 
@@ -400,7 +425,8 @@ for(i in c("96", "02", "07", "12", "17")){
     mutate(Code = if_else(str_detect(Code, "^30"), true = str_replace(Code, pattern = "^30", replacement = "030"),
                           if_else(str_detect(Code, "^511"), true = str_replace(Code, pattern = "^511", replacement = "0511"),
                                   false = Code))) %>%
-    mutate(hs_version = HS_year_rep)
+    mutate(hs_version = HS_year_rep) %>%
+    filter(!is.na(hs_clade))
 
   hs_clade_match <- hs_clade_match %>% 
     bind_rows(hs_clade_match_i) %>%
@@ -446,7 +472,8 @@ prod_taxa_classification <- taxa_metadata %>%
 
 code_max_resolved_taxa <- hs_taxa_match %>%
   rename(hs6 = Code, sciname = SciName) %>%
-  left_join(hs_clade_match %>% mutate(hs_version = paste("HS", hs_version, sep="")),
+  left_join(hs_clade_match %>% 
+              mutate(hs_version = paste("HS", hs_version, sep="")),
             by = c("hs6", "HS_version" = "hs_version")) %>%
   left_join(prod_taxa_classification, by = c("sciname")) %>%
   mutate(code_taxa_level_numeric = case_when(
@@ -484,8 +511,7 @@ code_max_resolved_taxa <- hs_taxa_match %>%
     sciname_hs_modified != "chordata" ~ sciname_hs_modified
   )) %>%
   select("hs_version" = "HS_version", hs6, sciname, sciname_hs_modified) %>%
-  mutate(hs_version = as.integer(parse_number(hs_version)),
-         hs6 = as.character(hs6)) %>%
+  mutate(hs6 = as.character(hs6)) %>%
   distinct()
 
 write.csv(code_max_resolved_taxa, file.path(outdir, "code_max_resolved_taxa.csv"), row.names = FALSE)