Solving conflicts or merging main branch and my branch

Author: AliceBeckmann

.Rbuildignore

@@ -8,3 +8,5 @@
 ^pkgdown$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^data-raw$
+^README\.Rmd$

.Rprofile

@@ -1,3 +1,7 @@
 if (Sys.getenv("USE_RENV", unset = "TRUE") == "TRUE") {
   source("renv/activate.R")
 }
+
+if (requireNamespace("devtools", quietly = TRUE)) {
+  devtools::load_all()
+}

…hub/workflows/R-CMD-check_and_lintr.yaml .github/workflows/R-CMD-check.yaml.github/workflows/R-CMD-check_and_lintr.yaml renamed to .github/workflows/R-CMD-check.yaml .github/workflows/R-CMD-check_and_lintr.yaml renamed to .github/workflows/R-CMD-check.yaml

@@ -1,9 +1,12 @@
 Package: WHEP
-Title: What the Package Does (One Line, Title Case)
+Title: Who Has Eaten the Planet
 Version: 0.0.0.9000
-Authors@R: 
-    person("First", "Last", , "first.last@example.com", role = c("aut", "cre"))
-Description: What the package does (one paragraph).
+Authors@R: c(
+    person("Catalin", "Covaci", , "catalin.covaci@csic.es", role = c("aut", "cre"), comment = c(ORCID = "0009-0005-2186-5972")),
+    person("Eduardo", "Aguilera", , "eduardo.aguilera@csic.es", role = c("aut"), comment = c(ORCID = "0000-0003-4382-124X")),
+    person("João", "Serra", , "jserra@agro.au.dk", role = c("ctb"), comment = c(ORCID = "0000-0002-3561-5350"))
+  )
+Description: Gather historical agricultural and trade data from 1850.
 License: MIT + file LICENSE
 Imports:
     dplyr,
@@ -34,4 +37,7 @@ Suggests:
     tibble
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-URL: https://eduaguilera.github.io/WHEP/
+URL: https://eduaguilera.github.io/WHEP, https://github.com/eduaguilera/WHEP
+BugReports: https://github.com/eduaguilera/WHEP/issues
+Depends: 
+    R (>= 3.5)

DESCRIPTION

@@ -2,18 +2,21 @@
 
 export(add_area_code)
 export(add_area_name)
-export(add_item_code)
-export(add_item_name)
-export(add_process_code)
-export(add_process_name)
+export(add_item_cbs_code)
+export(add_item_cbs_name)
+export(add_item_prod_code)
+export(add_item_prod_name)
 export(build_supply_use)
 export(create_n_inputs_grafs_spain)
 export(create_typologies_grafs_spain)
 export(create_typologies_of_josette)
 export(expand_trade_sources)
 export(get_bilateral_trade)
 export(get_faostat_data)
+export(get_feed_intake)
 export(get_file_path)
+export(get_primary_production)
+export(get_primary_residues)
 export(get_processing_coefs)
 export(get_wide_cbs)
 importFrom(rlang,":=")

NAMESPACE

@@ -12,16 +12,13 @@
 #' memory usage, the tibble is not exactly in tidy format.
 #' It contains the following columns:
 #' - `year`: The year in which the recorded event occurred.
-#' - `item`: Natural language name for the item that is being traded.
+#' - `item_cbs_code`: FAOSTAT internal code for the item that is being traded.
+#'   For code details see e.g. `add_item_cbs_name()`.
 #' - `bilateral_trade`: Square matrix of `NxN` dimensions where `N` is the
 #'   total number of countries being considered. The matrix row and column
 #'   names are exactly equal and they represent country codes.
-#'   - Row name: FAOSTAT internal code for the country that is exporting the
-#'     item. Equivalences with ISO 3166-1 numeric can be found in the
-#'     _Area Codes_ CSV from the zip file that can be downloaded from
-#'     [FAOSTAT](https://www.fao.org/faostat/en/#data/FBS). TODO: Think about
-#'     this, would be nice to use ISO3 codes but won't be enough for our
-#'     periods
+#'   - Row name: The code of the country where the data is from. For code
+#'    details see e.g. `add_area_name()`.
 #'   - Column name: FAOSTAT internal code for the country that is importing the
 #'     item. See row name explanation above.
 #'
@@ -107,7 +104,7 @@ get_bilateral_trade <- function(file_path) {
   cbs <- "commodity_balance_sheet" |>
     get_file_path() |>
     get_wide_cbs() |>
-    dplyr::select(year, item, area_code, export, import)
+    dplyr::select(year, item_cbs_code, area_code, export, import)
 
   btd <- file_path |>
     readr::read_csv(show_col_types = FALSE) |>
@@ -116,7 +113,7 @@ get_bilateral_trade <- function(file_path) {
   codes <- .get_all_country_codes(btd, cbs)
 
   btd |>
-    .nest_by_year_item(cbs, codes) |>
+    .nest_by_year_item_code(cbs, codes) |>
     .process_bilateral_trade(codes) |>
     dplyr::select(-total_trade)
 }
@@ -177,14 +174,14 @@ get_bilateral_trade <- function(file_path) {
   btd |>
     dplyr::rename_with(tolower) |>
     dplyr::mutate(
-      item = as.factor(item),
       unit = ifelse(unit == "Head", "heads", unit),
       from_code = ifelse(element == "Export", area_code, area_code_p),
       to_code = ifelse(element == "Export", area_code_p, area_code),
       dplyr::across(c(year, from_code, to_code), as.integer)
     ) |>
+    add_item_cbs_code(name_column = "item") |>
     .prefer_flow_direction("Export") |>
-    dplyr::select(year, from_code, to_code, item, unit, value)
+    dplyr::select(year, from_code, to_code, item_cbs_code, unit, value)
 }
 
 # Keep all rows with preferred direction (Import, Export)
@@ -196,7 +193,7 @@ get_bilateral_trade <- function(file_path) {
   bilateral_trade |>
     dplyr::anti_join(
       preferred_direction,
-      by = c("from_code", "to_code", "year", "item")
+      by = c("from_code", "to_code", "year", "item_cbs_code")
     ) |>
     dplyr::bind_rows(preferred_direction)
 }
@@ -240,7 +237,7 @@ get_bilateral_trade <- function(file_path) {
   }
 }
 
-.nest_by_year_item <- function(btd, cbs, codes) {
+.nest_by_year_item_code <- function(btd, cbs, codes) {
   cbs <- cbs |>
     dplyr::mutate(area_code = factor(area_code, levels = codes))
 
@@ -254,53 +251,52 @@ get_bilateral_trade <- function(file_path) {
     .filter_only_items_in_cbs(cbs) |>
     tidyr::nest(
       bilateral_trade = c(from_code, to_code, value),
-      .by = c(year, item)
+      .by = c(year, item_cbs_code)
     ) |>
-    dplyr::left_join(.get_nested_cbs(cbs, codes), c("year", "item"))
+    dplyr::left_join(.get_nested_cbs(cbs, codes), c("year", "item_cbs_code"))
 }
 
 .get_nested_cbs <- function(cbs, codes) {
   cbs |>
-    dplyr::mutate(item = as.factor(item)) |>
     .complete_total_trade(codes) |>
-    dplyr::group_by(year, item) |>
+    dplyr::group_by(year, item_cbs_code) |>
     .balance_total_trade() |>
     dplyr::ungroup() |>
     tidyr::nest(
       total_trade = c(
         area_code, export, import, balanced_export, balanced_import
       ),
-      .by = c(year, item)
+      .by = c(year, item_cbs_code)
     )
 }
 
 .complete_total_trade <- function(total_trade, codes) {
   df_codes <- tibble::tibble(area_code = codes)
   combs <- total_trade |>
-    dplyr::distinct(year, item) |>
+    dplyr::distinct(year, item_cbs_code) |>
     dplyr::cross_join(df_codes)
 
   total_trade |>
-    dplyr::right_join(combs, by = c("year", "item", "area_code")) |>
+    dplyr::right_join(combs, by = c("year", "item_cbs_code", "area_code")) |>
     tidyr::replace_na(list(export = 0, import = 0))
 }
 
 .filter_only_items_in_cbs <- function(btd, cbs) {
   btd_items <- btd |>
-    dplyr::pull(item) |>
+    dplyr::pull(item_cbs_code) |>
     unique() |>
     sort()
 
   cbs_items <- cbs |>
-    dplyr::pull(item) |>
+    dplyr::pull(item_cbs_code) |>
     unique() |>
     sort()
 
   # TODO: Also include these (need total export/import reports)
   items_not_in_cbs <- btd_items[!btd_items %in% cbs_items]
 
   btd |>
-    dplyr::filter(!item %in% items_not_in_cbs)
+    dplyr::filter(!item_cbs_code %in% items_not_in_cbs)
 }
 
 .get_all_country_codes <- function(btd, cbs) {