Address Code Suggestions #9 and Usability Fixes #10

Clear errors and warning in package checking

.Rbuildignore

@@ -19,3 +19,8 @@ coverage.R
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^.drake/
+^tests/testthat/.drake/
+^inst/extdata/aglu/FAO/FAOSTAT_Archive/
+^inst/extdata/aglu/FAO/FAOSTAT/*.zip
+^.github

DESCRIPTION

@@ -29,7 +29,8 @@ Imports:
     ggplot2 (>= 3.3.2),
     xml2 (>= 1.3.2),
     XML (>= 3.99-0.5),
-    rlang
+    rlang,
+    kableExtra
 Suggests:
     igraph (>= 1.0.1),
     testthat (>= 3.0.0),
@@ -41,6 +42,6 @@ Suggests:
     rmarkdown
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Config/testthat/edition: 3

R/constants.R

@@ -61,7 +61,7 @@ Hist_MEAN_Year_NUTRIENT_MASS_CONV <- 2010:2019 # average cal per g
 # decimal places in ggplot
 scaleFUN <- function(x) sprintf("%.0f", x)
 
-
+xml.XML_SUFFIX <- NULL
 
 
 

R/utils.R

@@ -35,7 +35,7 @@ utils::globalVariables(c(
   "FAO_an_items_PRODSTAT", "FAOupdate", "GCAM_AgLU_SUA_APE_1973_2019",
   "GCAM_DATA_MAP", "GCAM_commodity", "GCAM_region_names", "GCAM_subsector",
   "Localupdate", "TM", "Tourist", "consumption", "datasetname", "localfilesize",
-  "moving_avg", "remotefilezize", "unit"))
+  "moving_avg", "remotefilezize", "unit", "Tourist consumption", "xml.XML_SUFFIX"))
 
 #' find_header
 #'

R/xfaostat_helper_funcs.R

@@ -229,7 +229,8 @@ FF_rawdata_info <- function(
            grepl("zip$", filelocation)) %>%
     transmute(filelocation = basename(filelocation),
               ctime = as.Date(ctime), mtime = as.Date(mtime),
-              localfilesize = utils:::format.object_size(size, "MB", digits = 0)) %>%
+              #localfilesize = utils:::format.object_size(size, "MB", digits = 0),
+              localfilesize = paste0(round(size/10^6, digits = 0), " MB" )) %>%
     # Join the latest metadata
     # Note that FAO raw data had a typo (missing space) in Trade_CropsLivestock_E_All_Data_(Normalized).zip
     # Temporary fix here

R/zaglu_L100.FAO_SUA_PrimaryEquivalent.R

@@ -187,13 +187,13 @@ module_aglu_L100.FAO_SUA_PrimaryEquivalent <- function(command, ...) {
     # 2.1 Helper functions for SUA primary equivalent aggregation ----
 
 
-    #' Get extraction rate
-    #' @description Gross extraction rate is calculated for domestic, traded, and lagged values.
-    #' By gross, it means sink items are aggregated.
-    #' The function is used in Proc_primarize.
-    #' @param DF_CURR_NEST Input supply-utilization accounting data frame with one tier of processing
-    #' @param DF_ALL Input supply-utilization accounting data frame with ALL the data
-    #' @return A data frame including regional, traded, and world extraction rates of a processing
+    # Get extraction rate
+    # @description Gross extraction rate is calculated for domestic, traded, and lagged values.
+    # By gross, it means sink items are aggregated.
+    # The function is used in Proc_primarize.
+    # @param DF_CURR_NEST Input supply-utilization accounting data frame with one tier of processing
+    # @param DF_ALL Input supply-utilization accounting data frame with ALL the data
+    # @return A data frame including regional, traded, and world extraction rates of a processing
 
     Get_GROSS_EXTRACTION_RATE <- function(DF_CURR_NEST, DF_ALL) {
       curr_sink_items = unique(DF_CURR_NEST$item_code)
@@ -248,10 +248,10 @@ module_aglu_L100.FAO_SUA_PrimaryEquivalent <- function(command, ...) {
     }
 
 
-    #' Separate the SUA balance into domestic and imported balanced for sink_item
-    #' @description The function is used in Proc_primarize
-    #' @param DF_CURR_NEST Input supply-utilization accounting data frame with one tier of processing
-    #' @return SUA DF
+    # Separate the SUA balance into domestic and imported balanced for sink_item
+    # @description The function is used in Proc_primarize
+    # @param DF_CURR_NEST Input supply-utilization accounting data frame with one tier of processing
+    # @return SUA DF
 
     Get_ARMINGTON_BALANCE <- function(DF_CURR_NEST) {
       Import_Demand_Item <- factor(c("Food", "Feed", "Processed", "Other uses", "Seed", "Loss"), levels=All_Bal_element)
@@ -308,11 +308,11 @@ module_aglu_L100.FAO_SUA_PrimaryEquivalent <- function(command, ...) {
     }
 
 
-    #' Separate the domestic SUA balance into current and lagged balanced for sink_item
-    #' @description The function is used in Proc_primarize
-    #' @param DF_CURR_NEST_TradeAdj Output from Get_ARMINGTON_BALANCE. Input supply-utilization accounting data frame with one tier of processing and
-    #' @param .SINK_ITEM Sink items or processed items in the processing
-    #' @return SUA DF
+    # Separate the domestic SUA balance into current and lagged balanced for sink_item
+    # @description The function is used in Proc_primarize
+    # @param DF_CURR_NEST_TradeAdj Output from Get_ARMINGTON_BALANCE. Input supply-utilization accounting data frame with one tier of processing and
+    # @param .SINK_ITEM Sink items or processed items in the processing
+    # @return SUA DF
 
     Get_STOCK_BALANCE <- function(DF_CURR_NEST_TradeAdj) {
       Opening_Stock_Item <- factor(c("Food", "Feed", "Processed", "Other uses", "Seed", "Loss"), levels=All_Bal_element)
@@ -380,9 +380,9 @@ module_aglu_L100.FAO_SUA_PrimaryEquivalent <- function(command, ...) {
     }
 
 
-    #' Primary equivalent aggregation
-    #' @param DF_ALL Input supply-utilization accounting data frame with all levels of data nested which need to be primarized
-    #' @return A supply-utilization accounting data frame with all levels processed and aggregated to GCAM_commodity
+    # Primary equivalent aggregation
+    # @param DF_ALL Input supply-utilization accounting data frame with all levels of data nested which need to be primarized
+    # @return A supply-utilization accounting data frame with all levels processed and aggregated to GCAM_commodity
 
     Proc_primarize <- function(DF_ALL){
       MaxNest = max(DF_ALL$nest_level)