fix environments

R/constants.R

@@ -15,9 +15,8 @@ OUTPUT_Export_CSV <- TRUE
 ## Fao raw data folder
 DIR_RAW_DATA_FAOSTAT <- "inst/extdata/aglu/FAO/FAOSTAT"
 ## Output GCAM csv
-#DIR_OUTPUT_CSV <- "inst/extdata/aglu/FAO/temp"
-DIR_OUTPUT_CSV <- "outputs/CSV"
-dir.create(file.path(DIR_OUTPUT_CSV), showWarnings = FALSE)
+DIR_OUTPUT_CSV <- file.path("outputs", "CSV")
+dir.create(DIR_OUTPUT_CSV, recursive = T, showWarnings = FALSE)
 
 
 # Historical years of focus ----

R/xfaostat_L101_RawDataPreProc1_QCL.R

@@ -35,24 +35,25 @@ module_xfaostat_L101_RawDataPreProc1_QCL <- function(command, ...) {
 
     all_data <- list(...)[[1]]
 
-    # Load required inputs ----
-
-    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
+    Curr_Envir <- environment()
 
 
     if(Process_Raw_FAO_Data == FALSE) {
 
-      # Prebuilt data is read here ----
+    # Load from Prebuilt data ----
       QCL_wide <- extract_prebuilt_data("QCL_wide")
       QCL_area_code_map <- extract_prebuilt_data("QCL_area_code_map")
 
       } else {
 
+    # Load required inputs ----
+    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
+
 
     # *[QCL] FAOSTAT Production and area ----
 
     ## Load raw data
-    FAOSTAT_load_raw_data(DATASETCODE = "QCL", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT)
+    FAOSTAT_load_raw_data(DATASETCODE = "QCL", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT, .Envir = Curr_Envir)
 
     QCL %>% distinct(element_code, element)
 

R/xfaostat_L101_RawDataPreProc2_PP_PD_OA.R

@@ -40,27 +40,28 @@ module_xfaostat_L101_RawDataPreProc2_PP_PD_OA <- function(command, ...) {
 
     all_data <- list(...)[[1]]
 
-    # Load required inputs ----
-
-    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
+    Curr_Envir <- environment()
 
 
     if(Process_Raw_FAO_Data == FALSE) {
 
-      # Prebuilt data is read here ----
+      # Load from Prebuilt data ----
       PP_wide <- extract_prebuilt_data("PP_wide")
       PD <- extract_prebuilt_data("PD")
       OA <- extract_prebuilt_data("OA")
 
     } else {
 
+    # Load required inputs ----
+    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
+
     # Get area code ----
     QCL_area_code <- QCL_area_code_map %>% distinct(area_code) %>% pull()
 
 
     # *[PP] Producer price ----
 
-    FAOSTAT_load_raw_data(DATASETCODE = "PP", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT)
+    FAOSTAT_load_raw_data(DATASETCODE = "PP", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT, .Envir = Curr_Envir)
     # check data
     PP %>% distinct(element, element_code, unit)
 
@@ -128,7 +129,7 @@ module_xfaostat_L101_RawDataPreProc2_PP_PD_OA <- function(command, ...) {
     # [PD] FAO_GDP_deflators ----
     #**************************************
 
-    FAOSTAT_load_raw_data(DATASETCODE = "PD", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT)
+    FAOSTAT_load_raw_data(DATASETCODE = "PD", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT, .Envir = Curr_Envir)
     # read in Taiwan values as FAO does not have Taiwan price data
     # GDP_deflator_Taiwan
 
@@ -183,7 +184,7 @@ module_xfaostat_L101_RawDataPreProc2_PP_PD_OA <- function(command, ...) {
 
     # *[OA]: Population ----
 
-    FAOSTAT_load_raw_data(DATASETCODE = "OA", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT)
+    FAOSTAT_load_raw_data(DATASETCODE = "OA", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT, .Envir = Curr_Envir)
 
     OA %>% distinct(element, element_code)
     OA %>% distinct(item, item_code)

R/xfaostat_L101_RawDataPreProc3_SCL_FBS.R

@@ -37,9 +37,7 @@ module_xfaostat_L101_RawDataPreProc3_SCL_FBS <- function(command, ...) {
 
     all_data <- list(...)[[1]]
 
-    # Load required inputs ----
-
-    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
+    Curr_Envir <- environment()
 
 
     if(Process_Raw_FAO_Data == FALSE) {
@@ -50,20 +48,23 @@ module_xfaostat_L101_RawDataPreProc3_SCL_FBS <- function(command, ...) {
 
     } else {
 
+    # Load required inputs ----
+    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
+
     # Get area code ----
     QCL_area_code <-
       QCL_area_code_map %>% distinct(area_code) %>% pull()
 
     ## *[SCL] SUA: supply utilization accounting ----
 
-    FAOSTAT_load_raw_data("SCL")   # SUA      2010+
+    FAOSTAT_load_raw_data("SCL", .Envir = Curr_Envir)   # SUA      2010+
 
     SCL %>% distinct(element, element_code, unit)
 
 
     if (is.character(SCL$item_code)){
 
-      FAOSTAT_load_raw_data("SCL", GET_MAPPINGCODE = "ItemCodes")
+      FAOSTAT_load_raw_data("SCL", GET_MAPPINGCODE = "ItemCodes", .Envir = Curr_Envir)
 
       SCL %>% rename(cpc_code = item_code) %>%
         left_join_error_no_match(
@@ -117,7 +118,7 @@ module_xfaostat_L101_RawDataPreProc3_SCL_FBS <- function(command, ...) {
     ## *[FBS] new food balance sheet (2010-) ----
 
     ## Load raw data
-    FAOSTAT_load_raw_data("FBS") # New FBS  2010+
+    FAOSTAT_load_raw_data("FBS", .Envir = Curr_Envir) # New FBS  2010+
     FBS %>% distinct(element, element_code, unit)
 
     FBS %>% filter(

R/xfaostat_L101_RawDataPreProc4_FBSH_CB.R

@@ -38,9 +38,8 @@ module_xfaostat_L101_RawDataPreProc4_FBSH_CB <- function(command, ...) {
 
     all_data <- list(...)[[1]]
 
-    # Load required inputs ----
+    Curr_Envir <- environment()
 
-    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
 
 
     if(Process_Raw_FAO_Data == FALSE) {
@@ -50,6 +49,9 @@ module_xfaostat_L101_RawDataPreProc4_FBSH_CB <- function(command, ...) {
 
     } else {
 
+    # Load required inputs ----
+    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
+
     ## Get area code ----
     QCL_area_code <-
       QCL_area_code_map %>% distinct(area_code) %>% pull()
@@ -59,7 +61,7 @@ module_xfaostat_L101_RawDataPreProc4_FBSH_CB <- function(command, ...) {
 
     ## *[FBSH] old food balance sheet (-2013) ----
 
-    FAOSTAT_load_raw_data("FBSH")  # Old FBS -2013
+    FAOSTAT_load_raw_data("FBSH", .Envir = Curr_Envir)  # Old FBS -2013
     FBSH %>% distinct(element, element_code, unit)
     # Keep population (old)
     FBSH %>%
@@ -80,7 +82,7 @@ module_xfaostat_L101_RawDataPreProc4_FBSH_CB <- function(command, ...) {
 
     ## *[CB] Non-food Balance ----
 
-    FAOSTAT_load_raw_data("CB")    # Old FBS-nonfood -2013
+    FAOSTAT_load_raw_data("CB", .Envir = Curr_Envir)    # Old FBS-nonfood -2013
 
     CB %>% distinct(element, element_code, unit)
     # Keep population (old)

R/xfaostat_L101_RawDataPreProc5_TCL.R

@@ -36,9 +36,8 @@ module_xfaostat_L101_RawDataPreProc5_TCL <- function(command, ...) {
 
     all_data <- list(...)[[1]]
 
-    # Load required inputs ----
+    Curr_Envir <- environment()
 
-    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
 
 
     if(Process_Raw_FAO_Data == FALSE) {
@@ -48,24 +47,14 @@ module_xfaostat_L101_RawDataPreProc5_TCL <- function(command, ...) {
 
     } else {
 
-
-      # FAOSTAT_RDS <- c("TCL")
-      #
-      # DIR_PREBUILT_FAOSTAT <- "data/PREBUILT_FAOSTAT"
-      #
-      # lapply(FAOSTAT_RDS, function(d){
-      #   assertthat::assert_that(file.exists(file.path(DIR_PREBUILT_FAOSTAT, paste0(d, ".rds"))))
-      #   assign(d, readRDS(file.path(DIR_PREBUILT_FAOSTAT, paste0(d, ".rds"))),
-      #          envir = parent.env(environment()))
-      # })
-      #
-      # TCL %>% filter(year >= min(FAOSTAT_Hist_Year_TCL)) %>%  spread(year, value) -> TCL_wide
+    # Load required inputs ----
+    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
 
 
     QCL_area_code <- QCL_area_code_map %>% distinct(area_code) %>% pull()
 
     # *[TCL] Gross trade ----
-    FAOSTAT_load_raw_data("TCL")   # Gross trade
+    FAOSTAT_load_raw_data("TCL", .Envir = Curr_Envir)   # Gross trade
 
     TCL %>% distinct(element, element_code, unit)
     TCL %>% distinct(item, item_code)

R/xfaostat_L101_RawDataPreProc6_TM.R

@@ -35,9 +35,7 @@ module_xfaostat_L101_RawDataPreProc6_TM <- function(command, ...) {
 
     all_data <- list(...)[[1]]
 
-    # Load required inputs ----
-
-    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
+    Curr_Envir <- environment()
 
 
     if(Process_Raw_FAO_Data == FALSE) {
@@ -47,17 +45,8 @@ module_xfaostat_L101_RawDataPreProc6_TM <- function(command, ...) {
 
     } else {
 
-
-      # FAOSTAT_RDS <- c("TM_bilateral_wide")
-      #
-      # DIR_PREBUILT_FAOSTAT <- "data"
-      #
-      # lapply(FAOSTAT_RDS, function(d){
-      #   assertthat::assert_that(file.exists(file.path(DIR_PREBUILT_FAOSTAT, paste0(d, ".rds"))))
-      #   assign(d, readRDS(file.path(DIR_PREBUILT_FAOSTAT, paste0(d, ".rds"))),
-      #          envir = parent.env(environment()))
-      # })
-
+      # Load required inputs ----
+      get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
 
 
       # Get area code ----
@@ -66,7 +55,7 @@ module_xfaostat_L101_RawDataPreProc6_TM <- function(command, ...) {
 
     # *[TM] Bilateral trade ----
     #*FAO has better quality bilateral data since 1992, covering most SUA items
-    FAOSTAT_load_raw_data("TM")    # Bilateral trade
+    FAOSTAT_load_raw_data("TM", .Envir = Curr_Envir)    # Bilateral trade
 
     TM %>%
       # Only keep quantities for elements with a unit of tonnes
@@ -143,3 +132,15 @@ module_xfaostat_L101_RawDataPreProc6_TM <- function(command, ...) {
     stop("Unknown command")
   }
 }
+
+# FAOSTAT_RDS <- c("TM_bilateral_wide")
+#
+# DIR_PREBUILT_FAOSTAT <- "data"
+#
+# lapply(FAOSTAT_RDS, function(d){
+#   assertthat::assert_that(file.exists(file.path(DIR_PREBUILT_FAOSTAT, paste0(d, ".rds"))))
+#   assign(d, readRDS(file.path(DIR_PREBUILT_FAOSTAT, paste0(d, ".rds"))),
+#          envir = parent.env(environment()))
+# })
+
+

R/xfaostat_L101_RawDataPreProc7_FO.R

@@ -33,10 +33,7 @@ module_xfaostat_L101_RawDataPreProc7_FO <- function(command, ...) {
 
     all_data <- list(...)[[1]]
 
-    # Load required inputs ----
-
-
-    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
+    Curr_Envir <- environment()
 
 
 
@@ -46,7 +43,11 @@ module_xfaostat_L101_RawDataPreProc7_FO <- function(command, ...) {
 
 
     } else {
-      FAOSTAT_load_raw_data(DATASETCODE = "FO", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT)
+
+      # Load required inputs ----
+      get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
+
+      FAOSTAT_load_raw_data(DATASETCODE = "FO", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT, .Envir = Curr_Envir)
 
       # Only keep roundwood
       FO %>% filter(year %in% FAOSTAT_Hist_Year,

R/xfaostat_L101_RawDataPreProc8_RL_RFN.R

@@ -35,10 +35,7 @@ module_xfaostat_L101_RawDataPreProc8_RL_RFN <- function(command, ...) {
 
     all_data <- list(...)[[1]]
 
-    # Load required inputs ----
-
-    get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
-
+    Curr_Envir <- environment()
 
 
     if(Process_Raw_FAO_Data == FALSE) {
@@ -50,8 +47,10 @@ module_xfaostat_L101_RawDataPreProc8_RL_RFN <- function(command, ...) {
 
     } else {
 
+      # Load required inputs ----
+      get_data_list(all_data, MODULE_INPUTS, strip_attributes = TRUE)
 
-      FAOSTAT_load_raw_data(DATASETCODE = "RL", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT)
+      FAOSTAT_load_raw_data(DATASETCODE = "RL", DATA_FOLDER = DIR_RAW_DATA_FAOSTAT, .Envir = Curr_Envir)
 
       RL %>%
         filter(year %in% FAOSTAT_Hist_Year,

R/xfaostat_L102_ProductionArea.R

@@ -354,9 +354,13 @@ module_xfaostat_L102_ProductionArea <- function(command, ...) {
     FBS %>% distinct(element, element_code, unit)
 
     # Get fish items through mapping
-
+    Curr_Envir <- environment()
     checkitem <-
-      FF_join_checkmap(c("QCL_COMM_AN_PRIMARY", "FAO_an_items_PRODSTAT"), "item_code", "item") %>%
+      FF_join_checkmap(DFs = c("QCL_COMM_AN_PRIMARY", "FAO_an_items_PRODSTAT"),
+                       COL_by = "item_code",
+                       COL_rename =  "item",
+                       .ENVIR = Curr_Envir
+                       ) %>%
       mutate(match = if_else(QCL_COMM_AN_PRIMARY_item == FAO_an_items_PRODSTAT_item, T, F))
 
 
@@ -467,13 +471,13 @@ module_xfaostat_L102_ProductionArea <- function(command, ...) {
     # P.S.  Check primary product mapping ----
 
     # checkitem <-
-    #   FF_join_checkmap(c("QCL_COMM_CROP_PRIMARY", "FAO_ag_items_PRODSTAT"), "item_code", "item") %>%
+    #  FF_join_checkmap(c("QCL_COMM_CROP_PRIMARY", "FAO_ag_items_PRODSTAT"), "item_code", "item",.ENVIR = Curr_Envir) %>%
     #   mutate(match = if_else(QCL_COMM_CROP_PRIMARY_item == FAO_ag_items_PRODSTAT_item , T, F))
     # checkitem %>% filter(is.na(match)|match == F)
     # # 160 primary items (matching here) + 15/16 fodder crops
     #
     # checkitem <-
-    #   FF_join_checkmap(c("QCL_COMM_AN_PRIMARY", "FAO_an_items_PRODSTAT"), "item_code", "item") %>%
+    #   FF_join_checkmap(c("QCL_COMM_AN_PRIMARY", "FAO_an_items_PRODSTAT"), "item_code", "item",.ENVIR = Curr_Envir) %>%
     #   mutate(match = if_else(QCL_COMM_AN_PRIMARY_item == FAO_an_items_PRODSTAT_item, T, F))
     # checkitem %>% filter(is.na(match)|match == F)
     # # Snails, not sea production came from SCL

R/xfaostat_L103_ProducerPrices.R

@@ -66,9 +66,9 @@ module_xfaostat_L103_ProducerPrices <- function(command, ...) {
 
     #FF_check_count_plot(QCL_PRIMARY) # 205 items
     #FF_check_count_plot(PP) # PP %>% distinct(area)
-
+    Curr_Envir <- environment()
     # check items
-    FF_join_checkmap(c("QCL_PRIMARY", "PP"), "item_code", "item") -> A
+    FF_join_checkmap(c("QCL_PRIMARY", "PP"), "item_code", "item", .ENVIR = Curr_Envir) -> A
     A %>% filter(!is.na(QCL_PRIMARY_item)) %>% filter(is.na(PP_item)) -> PP_NO_DATA_ITEM
     # 20 items out of 205 were missing; mostly animal offals, fats or skins
 

R/xfaostat_L104_ProductionAreaAddFodder.R

@@ -107,9 +107,11 @@ module_xfaostat_L104_ProductionAreaAddFodder <- function(command, ...) {
                      "QCL_area_code_map")->
       QCL_FODDERCROP
 
-
+    Curr_Envir <- environment()
     # 160 primary items +16 fodder crops
-    FF_join_checkmap(c("QCL_FODDERCROP", "FAO_ag_items_PRODSTAT"), "item_code", "item") %>%
+    FF_join_checkmap(DFs = c("QCL_FODDERCROP", "FAO_ag_items_PRODSTAT"),
+                     COL_by = "item_code",
+                     COL_rename = "item", .ENVIR = Curr_Envir) %>%
       mutate(match = if_else(QCL_FODDERCROP_item == FAO_ag_items_PRODSTAT_item , T, F))-> checkitem
     checkitem %>% filter(match == T)
     # 15 fodder crops + 1 pumpkin removed in mapping