grassland changes. added sheets to input data

Functions_cifos/function_collection.R

@@ -37,43 +37,13 @@ FUNload_list_monfreda <- function(path, type) {
 
 # Loading Model data from local repository
 Fun_ModelData = function(sheet){
-  # loads CiFoS model input data
-  # INPUT:
-  # - sheet: string with name of sheet to be read
-  # OUTPUT:
-  # - dataframe with sheet content
   library("readxl")
-  if (Sys.getenv("USERNAME") == "wacke003") {
-    dir = "C:/Users/wacke003/Git/cifos-model.eu/"
-  } else {
-    dir = "D:/GAMS/EU_model_Feb2022/"
-  }
-  return(read_excel(paste0(dir,"European_CiFoS_model_data.xlsx"),
-                    sheet = sheet))
-}
-
-# Loading table with country name mapping
-Fun_CountryMapping = function(){
-  # loads a table with the mapping of ISO3 country names and respective country 
-  # names used in the CiFoS model.
-  # OUTPUT:
-  # - tibble with country name mapping
-  library("readxl")
-  EU_iso3 = c("AUT","BEL", "BGR", "HRV", "CZE", "DNK", "EST","FIN", "FRA", "DEU", 
-              "GRC", "HUN", "IRL", "ITA","LVA", "LTU", "LUX", "MLT", "NLD", "POL",
-              "PRT","ROU", "SVK","SVN", "ESP", "SWE", "GBR", "CYP")
   if (Sys.getenv("USERNAME") == "wacke003") {
     dir_mapping = "C:/Users/wacke003/Git/wolfram/Input_data/Mappings/"
   } else {
-    dir_mapping = "C:/Users/simon083/OneDrive - Wageningen University & Research/PhD_WJS/Academic/RQ1/Data_analysis/Spatial_mod/Modified_scripts/R/CifoS_Crop/Input_data/Mappings/"
+    dir_mapping = "D:/GAMS/EU_model_Feb2022/"
   }
-  dat_map_SPAM_GAUL_CIFOS_FAO = read.csv(paste(dir_mapping,
-                                               "dat_map_SPAM_GAUL_CIFOS_FAO.csv",
-                                               sep="")) %>%  
-    as_tibble() %>% dplyr::select(iso3_SPAM, name_cntr_CIFOS2021) %>% 
-    filter(iso3_SPAM %in% EU_iso3) 
-  return(dat_map_SPAM_GAUL_CIFOS_FAO)
-}
+  read_excel(paste0(dir_mapping,"European_CiFoS_model_data.xlsx"), sheet = sheet) }
 
 # Crop variable conversion ------------------------------------------------
 # Calculate production from yields and area - here: suitable yields

dat_FAO_map.csv

+item,proc_out,FoodGroups
+Apples and products,temperate_fruit_whole,Fruits
+Apples and products,temperate_fruit_juice,Fruits
+Apples and products,temperate_fruit_pulp,Fruits
+Bananas,bananas,Fruits
+Barley and products,barley_pearl,Grains
+Barley and products,barley_flour,Grains
+Barley and products,barley_bran,Grains
+Barley and products,barley_hulls,Grains
+Barley and products,barley_malt,Grains
+Beans,NA,Legumes
+Beer,pearl_millet_beer,Other
+Beer,sorghum_beer,Other
+Beer,barley_beer,Other
+Bovine Meat,Beef_meat,RedMeat
+Bovine Meat,Beef_bone_meal,RedMeat
+Bovine Meat,Beef_blood_meal,RedMeat
+"Butter, Ghee",Butter,Dairy
+Cassava and products,cassava_flour,Tubers
+Cassava and products,cassava_tapioca,Tubers
+Cassava and products,cassava_dry,Tubers
+Cassava and products,cassava_starch,Tubers
+Cephalopods,NA,Fish
+"Cereals, Other",other_cereals_flour,Grains
+"Cereals, Other",other_cereals_bran,Grains
+"Cereals, Other",other_cereals_whole,Grains
+"Citrus, Other",NA,Fruits
+Cloves,NA,Other
+Cocoa Beans and products,cocoa_butter,Other
+Cocoa Beans and products,cocoa_powder_cake,Other
+Cocoa Beans and products,cocoa_husks,Other
+Coconut Oil,coconuts_oil_copra,UnsaturatedOils
+Coconuts - Incl Copra,coconuts_dessicated,NutsSeeds
+Coconuts - Incl Copra,coconuts_cake_copra,NutsSeeds
+Coffee and products,coffee_roasted,Other
+Coffee and products,coffee_hulls,Other
+Cottonseed,NA,NutsSeeds
+Cottonseed Oil,seed_cotton_oil,UnsaturatedOils
+Cream,NA,Dairy
+Crustaceans,Norway_lobster_FOil,Fish
+Crustaceans,Norway_lobster_FMeal,Fish
+Crustaceans,Norway_lobster,Fish
+Crustaceans,Northern_prawn_FOil,Fish
+Crustaceans,Northern_prawn_FMeal,Fish
+Crustaceans,Northern_prawn,Fish
+Dates,NA,Fruits
+Demersal Fish,NA,Fish
+Eggs,Egg,Eggs
+"Fats, Animals, Raw",Beef_Tallow,LardTallow
+"Fats, Animals, Raw",Poultry_fat,LardTallow
+"Fats, Animals, Raw",Pork_Lard,LardTallow
+"Fish, Body Oil",Atlantic_horse_mackerel_FOil,Fish
+"Fish, Body Oil",Atlantic_herring_FOil,Fish
+"Fish, Body Oil",Norway_pout_FOil,Fish
+"Fish, Body Oil",Sandeels_FOil,Fish
+"Fish, Body Oil",Pollock_FOil,Fish
+"Fish, Body Oil",Blue_whiting_FOil,Fish
+"Fish, Body Oil",Ling_FOil,Fish
+"Fish, Body Oil",European_Sprat_FOil,Fish
+"Fish, Body Oil",European_plaice_FOil,Fish
+"Fish, Body Oil",European_pilchard_FOil,Fish
+"Fish, Body Oil",European_hake_FOil,Fish
+"Fish, Body Oil",Haddock_FOil,Fish
+"Fish, Body Oil",Salmon_oil,Fish
+"Fish, Body Oil",Tilapia_oil,Fish
+"Fish, Body Oil",Atlantic_cod_FOil,Fish
+Freshwater Fish,Tilapia_fillet,Fish
+"Fruits, other",NA,Fruits
+Grapefruit and products,NA,Fruits
+Grapes and products (excl wine),NA,Fruits
+Groundnut Oil,groundnut_oil,UnsaturatedOils
+Groundnuts,groundnut_shelled,Legumes
+Groundnuts,groundnut_shell,Legumes
+Groundnuts,groundnut_butter,Legumes
+"Lemons, Limes and products",NA,Fruits
+Maize and products,maize_flour,Grains
+Maize and products,maize_bran,Grains
+Maize and products,maize_germ,Grains
+Maize Germ Oil,maize_oil,UnsaturatedOils
+Maize Germ Oil,maize_oil,UnsaturatedOils
+"Marine Fish, Other",Atlantic_mackerel_FOil,Fish
+"Marine Fish, Other",Atlantic_mackerel_fillet,Fish
+"Marine Fish, Other",Atlantic_horse_mackerel_fillet,Fish
+"Marine Fish, Other",Atlantic_herring_fillet,Fish
+"Marine Fish, Other",Atlantic_cod_fillet,Fish
+"Marine Fish, Other",Norway_pout_fillet,Fish
+"Marine Fish, Other",Sandeels_fillet,Fish
+"Marine Fish, Other",Pollock_fillet,Fish
+"Marine Fish, Other",Blue_whiting_fillet,Fish
+"Marine Fish, Other",Ling_fillet,Fish
+"Marine Fish, Other",European_sprat_fillet,Fish
+"Marine Fish, Other",European_plaice_fillet,Fish
+"Marine Fish, Other",European_pilchard_fillet,Fish
+"Marine Fish, Other",European_hake_fillet,Fish
+"Marine Fish, Other",Haddock_fillet,Fish
+"Marine Fish, Other",Salmon_fillet,Fish
+"Meat, Other",NA,RedMeat
+"Meat, Other",Sheep_Meat,RedMeat
+"Meat, Other",Goat_Meat,RedMeat
+Milk - Excluding Butter,Milk_full,Dairy
+Milk - Excluding Butter,Yoghurt,Dairy
+Milk - Excluding Butter,Cheese,Dairy
+Milk - Excluding Butter,Cream,Dairy
+Milk - Excluding Butter,Whey,Dairy
+Milk - Excluding Butter,Butter_milk,Dairy
+Milk - Excluding Butter,Milk_skimmed,Dairy
+Millet and products,pearl_millet_flour,Grains
+Millet and products,pearl_millet_bran,Grains
+Mutton & Goat Meat,NA,RedMeat
+Nuts and products,walnuts,NutsSeeds
+Nuts and products,nut_shell,NutsSeeds
+Oats,NA,Grains
+"Oilcrops Oil, Other",NA,UnsaturatedOils
+"Oilcrops, Other",NA,UnsaturatedOils
+Olive Oil,other_oil_crops_oil,UnsaturatedOils
+Olives (including preserved),other_oil_crops_cake,Vegetables
+Onions,NA,Vegetables
+"Oranges, Mandarines",tropical_fruits_whole,Fruits
+"Oranges, Mandarines",tropical_fruits_juice,Fruits
+"Oranges, Mandarines",tropical_fruits_pulp,Fruits
+Palm kernels,oil_palm_kernels_cake,PalmOil
+Palm Oil,oil_palm_fruits_oil,PalmOil
+Palmkernel Oil,oil_palm_kernels_oil,PalmOil
+Peas,NA,Legumes
+Pelagic Fish,NA,Fish
+Pepper,NA,Other
+Pigmeat,Pork_meat,RedMeat
+Pigmeat,Pork_bone_meal,RedMeat
+Pigmeat,Pork_blood_meal,RedMeat
+Pimento,NA,Other
+Pineapples and products,NA,Fruits
+Plantains,plantains,Vegetables
+Potatoes and products,potatoes,Tubers
+Potatoes and products,tuber_peel,Tubers
+Potatoes and products,potatoes_flour,Tubers
+Potatoes and products,potatoes_starch,Tubers
+Poultry Meat,Chicken_meat,Chicken
+Poultry Meat,Chicken_feather_meal,Chicken
+Poultry Meat,Chicken_bone_meal,Chicken
+"Pulses, Other and products",other_crops,Legumes
+"Pulses, Other and products",chickpea_vegetable,Legumes
+"Pulses, Other and products",chickpea_flour,Legumes
+"Pulses, Other and products",chickpea_bran,Legumes
+"Pulses, Other and products",beans_dry_vegetable,Legumes
+"Pulses, Other and products",beans_dry_flour,Legumes
+"Pulses, Other and products",beans_dry_bran,Legumes
+"Pulses, Other and products",other_pulses_vegetable,Legumes
+"Pulses, Other and products",other_pulses_flour,Legumes
+"Pulses, Other and products",other_pulses_bran,Legumes
+"Pulses, Other and products",lentils_vegetable,Legumes
+"Pulses, Other and products",lentils_flour,Legumes
+"Pulses, Other and products",lentils_bran,Legumes
+"Pulses, Other and products",pigeon_peas_vegetable,Legumes
+"Pulses, Other and products",pigeon_peas_flour,Legumes
+"Pulses, Other and products",pigeon_peas_bran,Legumes
+"Pulses, Other and products",cow_peas_dry_vegetable,Legumes
+"Pulses, Other and products",cow_peas_dry_flour,Legumes
+"Pulses, Other and products",cow_peas_dry_bran,Legumes
+Rape and Mustard Oil,rapeseed_oil,UnsaturatedOils
+Rice and products,rice_husked,Grains
+Rice and products,rice_hulls,Grains
+Rice and products,rice_husked_milled,Grains
+Rice and products,rice_bran,Grains
+Rice and products,rice_paddy_milled,Grains
+Rice and products,hulls_paddy_milled,Grains
+Rice and products,bran_paddy_milled,Grains
+"Roots, Other",yams_flour,Tubers
+"Roots, Other",yams_dry,Tubers
+"Roots, Other",other_tubers_flour,Tubers
+"Roots, Other",other_tubers_dry,Tubers
+Rye and products,NA,Grains
+Sesameseed Oil,sesame_oil,UnsaturatedOils
+Sorghum and products,sorghum_flour,Grains
+Sorghum and products,sorghum_bran,Grains
+Soyabean Oil,soyabean_oil,UnsaturatedOils
+Soyabean Oil,soyabean_feed_oil,UnsaturatedOils
+Soyabeans,soyabean_table,Legumes
+Soyabeans,soyabean_hulls,Legumes
+Soyabeans,soyabean_feed_hulls,Legumes
+Spices,NA,Other
+"Spices, Other",NA,Other
+Sugar (Raw Equivalent),sugar_raw,Sugar
+Sugar (Raw Equivalent),sugar_white,Sugar
+Sugar (Raw Equivalent),sugar_refined,Sugar
+Sugar beet,sugarbeet_toptails,Sugar
+Sugar beet,sugarbeet_pulp,Sugar
+Sugar beet,sugarbeet_molasses,Sugar
+Sugar cane,sugarcane_molasse,Sugar
+Sugar cane,sugarcane_bagasse,Sugar
+Sunflower seed,sunflower_hulls,NutsSeeds
+Sunflower seed,sunflower_seed,NutsSeeds
+Sunflowerseed Oil,sunflower_oil,UnsaturatedOils
+Sweet potatoes,sweet_potatoe_flour,Tubers
+Sweet potatoes,sweet_potatoe_starch,Tubers
+"Sweeteners, Other",NA,Sugar
+Tea (including mate),tea_leave,Other
+Tomatoes and products,NA,Vegetables
+"Vegetables, other",other_vegetables_whole,Vegetables
+"Vegetables, other",red_vegetables_whole,Vegetables
+"Vegetables, other",green_vegetables_whole,Vegetables
+Wheat and products,wheat_wholemeal,Grains
+Wheat and products,wheat_wholemeal_germ,Grains
+Wheat and products,wheat_germ,Grains
+Wheat and products,wheat_flour,Grains
+Wheat and products,wheat_bran,Grains
+Yams,NA,Tubers

test.Rmd

+---
+title: "test"
+author: "wjs"
+date: "11/02/2022"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## R Markdown
+
+This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
+
+When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
+
+```{r cars}
+summary(cars)
+```
+
+## Including Plots
+
+You can also embed plots, for example:
+
+```{r pressure, echo=TRUE}
+plot(pressure)
+```
+
+Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.