Finish up the PCe development and prepare for the squash merge

JGCRI · Jan 15, 2025 · ed55c7e · ed55c7e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,14 +2,10 @@ Package: gcamfaostat
 Type: Package
 Title: Prepare, process, and synthesize FAOSTAT data for global agroeconomic and multisector dynamic modeling
 Version: 1.1.0
-Date: 2024-12-1
+Date: 2025-11-11
 Authors@R: c(person("Xin", "Zhao", email = "xin.zhao@pnnl.gov", role = c("cre", "aut"), comment = c(ORCID = "0000-0002-1801-4393")),
             person("Maksym", "Chepeliev", role = "aut", comment = c(ORCID = "0000-0001-8585-2314")),
             person("Pralit", "Patel", role = "aut", comment = c(ORCID = "0000-0003-3992-1061")),
-            person("Marshall", "Wise", role = "aut", comment = c(ORCID = "0000-0002-2718-0051")),
-            person("Kate", "Calvin", role = "aut", comment = c(ORCID = "0000-0003-2191-4189")),
-            person("Kanishka", "Narayan", role = "aut", comment = c(ORCID = "0000-0001-8483-6216")),
-            person("Chris", "Vernon", role = "aut", comment = c(ORCID = "0000-0002-3406-6214")),
             person("Pacific Northwest National Laboratory", role = "cph"))
 Description: Clean and balance agricultural input, trade, and supply-utilization data for GCAM and other global agroeconomic modeling.
 License: BSD_2_clause + file LICENSE

diff --git a/R/yfaostat_Traceable_FBS_DataExport.R b/R/yfaostat_Traceable_FBS_DataExport.R
@@ -48,6 +48,10 @@ module_yfaostat_Traceable_FBS_DataExport <- function(command, ...) {
 
     Curr_Envir <- environment()
 
+    # out_filename_suffix is appended to output file names, e.g., dates could be used
+    out_filename_suffix <- paste0("_", Sys.Date())
+    out_filename_suffix <- ""
+
     # adding dummy output ----
     Metadata_GCAMFAOSTAT_Traceable_FBS <-
       tibble(CSV_export = MODULE_OUTPUTS)
@@ -113,7 +117,7 @@ module_yfaostat_Traceable_FBS_DataExport <- function(command, ...) {
 
       output_csv_data(
         gcam_dataset = Nested_Mapping_SUA_To_Traceable_FBS,
-        out_filename = "Nested_Mapping_SUA_To_Traceable_FBS" %>% paste0("_", Sys.Date()),
+        out_filename = "Nested_Mapping_SUA_To_Traceable_FBS" %>% paste0(out_filename_suffix),
         col_type_nonyear = "ccicici",
         title = "Mapping of SUA items to aggregated primary commodity equivalent products by level of nestings",
         unit = "NA",
@@ -150,14 +154,14 @@ module_yfaostat_Traceable_FBS_DataExport <- function(command, ...) {
 
       output_csv_data(
         gcam_dataset = SUA_2010_2022,
-        out_filename = "SUA_2010_2022" %>% paste0("_", Sys.Date()),
+        out_filename = "SUA_2010_2022" %>% paste0(out_filename_suffix),
         col_type_nonyear = "ccifc",
         title = "Supply utilization accounts for all FAO items in 2010 - 2022",
         unit = "1000 tonnes",
         code = "SCL",
         description = "Data is compiled and generated by gcamfaostat. Data is balanced in trade, supply_utilization, and storage",
         out_dir = DIR_OUTPUT_CSV,
-        GZIP = F)
+        GZIP = T)
 
       add_to_output_meta(.df = SUA_2010_2022, "SUA_2010_2022")
 
@@ -179,14 +183,14 @@ module_yfaostat_Traceable_FBS_DataExport <- function(command, ...) {
 
       output_csv_data(
         gcam_dataset = SUA_Food_Calorie_Macronutrient_2010_2022,
-        out_filename = "SUA_Food_Calorie_Macronutrient_2010_2022" %>% paste0("_", Sys.Date()),
+        out_filename = "SUA_Food_Calorie_Macronutrient_2010_2022" %>% paste0(out_filename_suffix),
         col_type_nonyear = "ccicc",
         title = "SUA: food energy and macronutrient in 2010 - 2022",
         unit = "Mt or Mkcal",
         code = "SCL",
         description = "Data is compiled and generated by gcamfaostat. Food energy and macronutrient by iso and SUA items. Item and item code are based on FAO/gcamfaostat definitions",
         out_dir = DIR_OUTPUT_CSV,
-        GZIP = F)
+        GZIP = T)
 
       add_to_output_meta(.df = SUA_Food_Calorie_Macronutrient_2010_2022,
                          "SUA_Food_Calorie_Macronutrient_2010_2022")
@@ -208,14 +212,14 @@ module_yfaostat_Traceable_FBS_DataExport <- function(command, ...) {
 
       output_csv_data(
         gcam_dataset = Traceable_FBS_PCe_2010_2022,
-        out_filename = "Traceable_FBS_PCe_2010_2022" %>% paste0("_", Sys.Date()),
+        out_filename = "Traceable_FBS_PCe_2010_2022" %>% paste0(out_filename_suffix),
         col_type_nonyear = "cccc",
         title = "Traceable FBS: supply utilization accounts in primary equivalent for APE items in 2010 - 2022",
         unit = "1000 tonnes",
         code = "SCL",
         description = "Data is compiled and generated by gcamfaostat.",
         out_dir = DIR_OUTPUT_CSV,
-        GZIP = F)
+        GZIP = T)
 
       add_to_output_meta(.df = Traceable_FBS_PCe_2010_2022,
                          "Traceable_FBS_PCe_2010_2022")
@@ -237,14 +241,14 @@ module_yfaostat_Traceable_FBS_DataExport <- function(command, ...) {
 
       output_csv_data(
         gcam_dataset = Traceable_FBS_Food_Calorie_Macronutrient_2010_2022,
-        out_filename = "Traceable_FBS_Food_Calorie_Macronutrient_2010_2022" %>% paste0("_", Sys.Date()),
+        out_filename = "Traceable_FBS_Food_Calorie_Macronutrient_2010_2022" %>% paste0(out_filename_suffix),
         col_type_nonyear = "cccc",
         title = "Traceable FBS: food energy and macronutrient in 2010 - 2022",
         unit = "Mt or Mkcal",
         code = "SCL",
         description = "Data is compiled and generated by gcamfaostat. Food energy and macronutrient by iso and APE items",
         out_dir = DIR_OUTPUT_CSV,
-        GZIP = F)
+        GZIP = T)
 
       add_to_output_meta(.df = Traceable_FBS_Food_Calorie_Macronutrient_2010_2022,
                          "Traceable_FBS_Food_Calorie_Macronutrient_2010_2022")
@@ -302,14 +306,14 @@ module_yfaostat_Traceable_FBS_DataExport <- function(command, ...) {
 
       output_csv_data(
         gcam_dataset = Traceable_FBS_Extraction_Rate_2010_2022,
-        out_filename = "Traceable_FBS_Extraction_Rate_2010_2022" %>% paste0("_", Sys.Date()),
+        out_filename = "Traceable_FBS_Extraction_Rate_2010_2022" %>% paste0(out_filename_suffix),
         col_type_nonyear = "cciiccc",
         title = "Extraction rates used for compiling the traceable FBS dataset",
         unit = "NA",
         code = "NA",
         description = "Data is compiled and generated by gcamfaostat.",
         out_dir = DIR_OUTPUT_CSV,
-        GZIP = F)
+        GZIP = T)
 
       add_to_output_meta(.df = Traceable_FBS_Extraction_Rate_2010_2022 %>% rename(item = sink_item),
                          "Traceable_FBS_Extraction_Rate_2010_2022")

diff --git a/README.md b/README.md
@@ -59,7 +59,8 @@ The package is documented in the [online manual](https://jgcri.github.io/gcamfao
 
 #### 4. Run the driver
 * `driver_drake()` 
-* if `write_csv_model = GCAM` in the function, related CSV will be exported to `output/gcamfaostat_GCAM`
+* if `driver_drake(write_csv_model = GCAM)`, related CSV for GCAM will be exported to `output/gcamfaostat_GCAM`
+* if `driver_drake(write_csv_model = "Traceable_FBS")`, related CSV for generating traceable FBS (T-FBS) will be exported to `output/gcamfaostat_Traceable_FBS`
 * Users can add and design data flows for other models.
 
 #### 5. Use data and package functions

diff --git a/data/GCAM_DATA_MAP.rda b/data/GCAM_DATA_MAP.rda
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/vignette_getting_started.html b/docs/articles/vignette_getting_started.html
diff --git a/docs/articles/vignette_news.html b/docs/articles/vignette_news.html
diff --git a/docs/articles/vignette_preparing_data.html b/docs/articles/vignette_preparing_data.html