Typologies Spain by AliceBeckmann · Pull Request #37 · eduaguilera/whep

AliceBeckmann · 2025-07-17T10:33:30Z

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whep/R/Typologies_Josette.R

Line 585 in 2daf52f

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whep/R/Typologies_Josette.R

Lines 623 to 627 in 2daf52f

    
           p_typology_stack <- ggplot2::ggplot(df_total_input_typ, ggplot2::aes( 
        
             x = factor(Year), 
        
             y = Total_N_input, 
        
             fill = Typology 
        
           )) +

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whep/R/Typologies_Josette.R

Line 642 in 2daf52f

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whep/R/Typologies_Josette.R

Lines 678 to 682 in 2daf52f

    
           p_typology_pct <- ggplot2::ggplot(df_total_input_typ_pct, ggplot2::aes( 
        
             x = factor(Year), 
        
             y = Percent_N_input, 
        
             fill = Typology 
        
           )) +

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whep/R/Typologies_Julia.R

Line 56 in 2daf52f

data$Livestock_Prod_ygps$Province_name, "Latin-ASCII"

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whep/R/Typologies_Julia.R

Lines 66 to 68 in 2daf52f

    
           data$sf_provinces <- data$sf_provinces[!data$sf_provinces$name %in% c( 
        
             "Las_Palmas", "Tenerife" 
        
           ), ]

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whep/R/Typologies_Julia.R

Line 104 in 2daf52f

data$GRAFS_Prod_Destiny_git, lu_aggregated

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whep/R/Typologies_Julia.R

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data$PIE_FullDestinies_FM, lu_aggregated

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whep/R/Typologies_Julia.R

Lines 148 to 150 in 2daf52f

    
           sf_provinces_spain <- sf::st_read(shapefile_path, query = paste0( 
        
             "SELECT * FROM ", layer_name, " WHERE iso_a2 = 'ES'" 
        
           ))

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whep/R/Typologies_Julia.R

Line 157 in 2daf52f

Codes_coefs = readxl::read_excel(file.path(inputs_dir, "Codes_coefs.xlsx"),

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whep/R/Typologies_Julia.R

Line 162 in 2daf52f

inputs_dir, "GRAFS_Prod_Destiny_git.csv"

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whep/R/Typologies_Julia.R

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inputs_dir, "PIE_FullDestinies_FM.csv"

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whep/R/Typologies_Julia.R

Lines 177 to 186 in 2daf52f

    
           ~Livestock_cat,    ~Animal_class, 
        
           "Cattle_milk",     "Dairy_cows", 
        
           "Cattle_meat",     "Cattle", 
        
           "Sheep",           "Sheep_goats", 
        
           "Goats",           "Sheep_goats", 
        
           "Donkeys_mules",   "Equines", 
        
           "Horses",          "Equines", 
        
           "Pigs",            "Pigs", 
        
           "Poultry",         "Hens", 
        
           "Rabbits",         "Rabbits"

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whep/R/Typologies_Julia.R

Lines 219 to 220 in 2daf52f

    
           Year, Province_name, Livestock_cat, Animal_class, 
        
           Stock_Number, LU_head, LU_total

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whep/R/Typologies_Julia.R

Lines 238 to 241 in 2daf52f

    
           dplyr::summarise(LU_total = sum( 
        
             LU_total, 
        
             na.rm = TRUE 
        
           ), .groups = "drop") |>

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whep/R/Typologies_Julia.R

Lines 259 to 262 in 2daf52f

    
           dplyr::summarise(Area_ha = sum( 
        
             Area_ygpit_ha, 
        
             na.rm = TRUE 
        
           ), .groups = "drop")

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whep/R/Typologies_Julia.R

Lines 322 to 325 in 2daf52f

    
           dplyr::summarise(Semi_nat_feed_MgN = sum( 
        
             MgN, 
        
             na.rm = TRUE 
        
           ), .groups = "drop")

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whep/R/Typologies_Julia.R

Lines 341 to 344 in 2daf52f

    
           dplyr::summarise(Cropland_feed_MgN = sum( 
        
             MgN, 
        
             na.rm = TRUE 
        
           ), .groups = "drop")

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whep/R/Typologies_Julia.R

Lines 362 to 365 in 2daf52f

    
           dplyr::summarise(Total_feed_MgN = sum( 
        
             MgN, 
        
             na.rm = TRUE 
        
           ), .groups = "drop") |>

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whep/R/Typologies_Julia.R

Line 383 in 2daf52f

dplyr::left_join(total_feed, semi_nat_feed,

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whep/R/Typologies_Julia.R

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is.na(Semi_nat_feed_MgN), 0, Semi_nat_feed_MgN

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whep/R/Typologies_Julia.R

Lines 409 to 412 in 2daf52f

    
           dplyr::summarise(Domestic_feed_MgN = sum( 
        
             MgN, 
        
             na.rm = TRUE 
        
           ), .groups = "drop")

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whep/R/Typologies_Julia.R

Lines 436 to 439 in 2daf52f

    
           dplyr::summarise(Total_feed_import = sum( 
        
             Value_destiny, 
        
             na.rm = TRUE 
        
           ), .groups = "drop")

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whep/R/Typologies_Julia.R

Lines 443 to 446 in 2daf52f

    
           dplyr::summarise(LU_total_spain = sum( 
        
             LU_total, 
        
             na.rm = TRUE 
        
           ), .groups = "drop")

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whep/R/Typologies_Julia.R

Line 481 in 2daf52f

is.nan(Imported_feed_share), NA, Imported_feed_share

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whep/R/Typologies_Julia.R

Lines 509 to 510 in 2daf52f

    
           livestock_density, productivity, semi_nat_share, imported_feed_share, 
        
           sf_provinces, year

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whep/R/Typologies_Julia.R

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Productivity_kgN_ha > 60 ~ "Specialized cropping system",

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whep/R/Typologies_Julia.R

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Productivity_kgN_ha <= 60 ~ "Extensive cropping system",

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whep/R/Typologies_Julia.R

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Semi_nat_share > 0.6 ~ "Extensive mixed crop-livestock system",

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whep/R/Typologies_Julia.R

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Imported_feed_share < 0.5 ~ "Intensive mixed crop-livestock system",

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whep/R/Typologies_Julia.R

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Imported_feed_share >= 0.5 ~ "Specialized livestock-farming system",

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whep/R/Typologies_Julia.R

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Productivity_kgN_ha > 60 ~ "Specialized cropping system",

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whep/R/Typologies_Julia.R

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Productivity_kgN_ha <= 60 ~ "Extensive cropping system",

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whep/R/Typologies_Julia.R

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Semi_nat_share > 0.6 ~ "Extensive mixed crop-livestock system",

[air] _{reported by reviewdog 🐶}

whep/R/Typologies_Julia.R

Line 573 in 2daf52f

Imported_feed_share < 0.5 ~ "Intensive mixed crop-livestock system",

[air] _{reported by reviewdog 🐶}

whep/R/Typologies_Julia.R

Line 576 in 2daf52f

Imported_feed_share >= 0.5 ~ "Specialized livestock-farming system",

github-actions

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

air

[air] _{reported by reviewdog 🐶}

whep/R/Typologies_Julia.R

Line 566 in 21966e1

Productivity_kgN_ha > 60 ~ "Specialized cropping system",

[air] _{reported by reviewdog 🐶}

whep/R/Typologies_Julia.R

Line 568 in 21966e1

Productivity_kgN_ha <= 60 ~ "Extensive cropping system",

[air] _{reported by reviewdog 🐶}

whep/R/Typologies_Julia.R

Line 570 in 21966e1

Semi_nat_share > 0.6 ~ "Extensive mixed crop-livestock system",

[air] _{reported by reviewdog 🐶}

whep/R/Typologies_Julia.R

Line 573 in 21966e1

Imported_feed_share < 0.5 ~ "Intensive mixed crop-livestock system",

[air] _{reported by reviewdog 🐶}

whep/R/Typologies_Julia.R

Line 576 in 21966e1

Imported_feed_share >= 0.5 ~ "Specialized livestock-farming system",

Reset non-typology files (bilateral_trade, gapfilling, production, livestock, etc.) to main's version. Restore files deleted by stale sub-branch merges (calculate_lmdi, harmonize, toy_examples). Keep typology-specific work in n_prov_destiny, n_soil_inputs_nue, utils. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Restore example=FALSE parameter to create_n_prov_destiny, create_n_nat_destiny, create_n_soil_inputs, create_n_production, calculate_nue_crops, calculate_nue_livestock, calculate_system_nue to match main's API. Remove non-existent linear_fill, proxy_fill, sum_fill exports from NAMESPACE. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Accept remote updates to typology plot files (typologies_kgN_ha, typologies_spain_plot, typologies_spain_stacked_bar). Merge both sides for DESCRIPTION, _pkgdown.yml, .Rbuildignore, and whep-package.R. All 473 tests pass. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

These datasets were part of the old version= API approach. The current example=TRUE pattern uses toy_examples.R instead. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

@Keywords

Replace @Keywords internal with @nord on dot-prefixed helper functions to prevent man page generation. Regenerate docs with devtools::document(), removing 16 dot-prefixed and 3 stale man pages. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

@param

Add rename_with(tolower) at the end of create_n_prov_destiny() and create_n_soil_inputs() to output snake_case column names (year, province_name, item, irrig_cat, box, origin, destiny, mg_n) matching main's API. Update all 15 downstream files (typology classifiers, grafs_plot, NUE functions, plots) to use snake_case column references. Add @param example and @examples documentation to all 7 exported N flow functions. Regenerate man pages. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

@return

Update roxygen @return docs to use snake_case column names matching the actual output. Remove decorative dashes from exported function titles. Add detailed column docs to create_n_nat_destiny and irrig_cat to create_n_soil_inputs. Fix stray character at start of n_prov_destiny.R. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

@param

Match main's roxygen style: @param before @return, no decorative dashes in exported function titles, remove duplicate @param. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Merge origin/main into alice/typologies. Keep rename_with(tolower) only at the public create_n_prov_destiny() boundary, not inside internal .add_n_soil_inputs. Take main's version for non-typology files. Add branch-specific typology section to _pkgdown.yml. Add mipfp, ggpattern, patchwork, sf, readxl, stringi deps for typology code. 679/684 tests pass (5 pre-existing failures on main). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Remove linear_fill, proxy_fill, sum_fill from _pkgdown.yml (renamed to fill_linear, fill_sum, fill_proxy_growth on main). Remove mipfp from Imports as it is no longer used. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

- Replace non-ASCII chars (en-dashes, superscripts) with ASCII in intensification_specialization_plot.R and land_use_typology_panel.R. - Add scales to Imports in DESCRIPTION. - Add missing globalVariables() for all typology NSE variables. - Remove Rplots.pdf and typology_kgha_agricultural.jpg from repo. - Add both to .gitignore. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

- Remove explicit return() calls (use implicit returns). - Shorten function names exceeding 30 chars. - Fix T symbol to t_ratio (avoids shadowing TRUE). - Rename recycled_N to recycled_n (snake_case). - Add spaces after commas in tribble definitions. - Replace 1:nrow() with seq_len(nrow()). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Remove explicit return() in land_use_typology_panel.R, Typologies_Josette.R, typologies_spain_plot.R, typologies_spain.R. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

AliceBeckmann added 4 commits July 17, 2025 12:32

Test revision in typologies

f4eb327

Test revision in typologies

ca205b0

Getting Typologies_Josette file back

62a1c73

Getting Typologies_Josette file back

1a2c189

AliceBeckmann requested a review from lbm364dl July 17, 2025 11:10

AliceBeckmann added 2 commits July 17, 2025 14:14

Use of devtools::document

9a506aa

Use of devtools::document

0766c7d

lbm364dl assigned AliceBeckmann Jul 22, 2025

AliceBeckmann added 2 commits July 22, 2025 12:41

Adding plot code for N input shares by typology

1d40f29

Adding plot code for N input shares by typology

91b5907

lbm364dl added this to the v0.2.0 milestone Jul 22, 2025

lbm364dl added the enhancement New feature or request label Jul 22, 2025

lbm364dl force-pushed the alice/model-grafs-spain branch from 98fb05d to 46b433d Compare August 14, 2025 14:35

AliceBeckmann added 2 commits September 12, 2025 13:10

Move typology files to typology branch

2daf52f

Move typology files to typology branch

74074be

github-actions bot reviewed Sep 12, 2025

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AliceBeckmann added 2 commits September 12, 2025 14:04

Merge branch 'alice/model-grafs-spain' into alice/typologies

21966e1

Merge branch 'alice/model-grafs-spain' into alice/typologies

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github-actions bot reviewed Sep 12, 2025

View reviewed changes

AliceBeckmann added 11 commits September 15, 2025 09:47

added variables to utils

eba5da2

added variables to utils

e9bb774

resolved conflicts and revised whep_typologies_spain

76ebf05

resolved conflicts and revised whep_typologies_spain

6c51d9e

resolved conflicts and revised whep_typologies_spain

e02fdf3

resolved conflicts and revised whep_typologies_spain

d302415

Merge remote-tracking branch 'origin/main' into alice/typologies

a8e4bda

Merge remote-tracking branch 'origin/main' into alice/typologies

2ef1d42

Resolve conflicts

1e3610f

Resolve conflicts

23d8fc2

deleted grafs_plot_df.R

16b778b

lbm364dl added 2 commits February 26, 2026 11:14

Remove R CMD Check warnings

ce0404d

Remove R CMD Check warnings

d3b0d02

lbm364dl modified the milestones: v0.3.0, v0.0.4 Feb 27, 2026

AliceBeckmann and others added 26 commits March 9, 2026 12:07

removed urban systems in stacked bar plots

96a09ad

feat: add calculate_lmdi decomposition function

cc3a71e

feat: add data preparation helpers for lmdi analysis

531a7e5

feat: add provincial land-use typology input panel plots

4b8eb70

feat: expand intensification and circularity plotting workflows

a766666

chore: add generated typology visualization outputs

f4a438f

sync n_prov_destiny.R with main

7646c26

added indicator functions

a8a1b61

fixed a bug in the national function regarding exorts and imports

cd03cae

Update n_prov_destiny

f8987a2

Remove legacy version=example data files from extdata/examples

6494610

These datasets were part of the old version= API approach. The current example=TRUE pattern uses toy_examples.R instead. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Apply air format

301c325

Fix roxygen: remove dashes from titles, put @param before @return

92e8da1

Match main's roxygen style: @param before @return, no decorative dashes in exported function titles, remove duplicate @param. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Reorder rename_with(tolower) before select to minimize diff with main

376e411

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Remove temporary xd.R script

95c92ad

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Fix remaining return_linter issues missed in previous commit

2b34a25

Remove explicit return() in land_use_typology_panel.R, Typologies_Josette.R, typologies_spain_plot.R, typologies_spain.R. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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Typologies Spain#37

Typologies Spain#37
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alice/typologies

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	p_typology_stack <- ggplot2::ggplot(df_total_input_typ, ggplot2::aes(
	x = factor(Year),
	y = Total_N_input,
	fill = Typology
	)) +

	p_typology_pct <- ggplot2::ggplot(df_total_input_typ_pct, ggplot2::aes(
	x = factor(Year),
	y = Percent_N_input,
	fill = Typology
	)) +

	data$sf_provinces <- data$sf_provinces[!data$sf_provinces$name %in% c(
	"Las_Palmas", "Tenerife"
	), ]

	sf_provinces_spain <- sf::st_read(shapefile_path, query = paste0(
	"SELECT * FROM ", layer_name, " WHERE iso_a2 = 'ES'"
	))

	~Livestock_cat, ~Animal_class,
	"Cattle_milk", "Dairy_cows",
	"Cattle_meat", "Cattle",
	"Sheep", "Sheep_goats",
	"Goats", "Sheep_goats",
	"Donkeys_mules", "Equines",
	"Horses", "Equines",
	"Pigs", "Pigs",
	"Poultry", "Hens",
	"Rabbits", "Rabbits"

	Year, Province_name, Livestock_cat, Animal_class,
	Stock_Number, LU_head, LU_total

	dplyr::summarise(LU_total = sum(
	LU_total,
	na.rm = TRUE
	), .groups = "drop") \|>

	dplyr::summarise(Area_ha = sum(
	Area_ygpit_ha,
	na.rm = TRUE
	), .groups = "drop")

	dplyr::summarise(Semi_nat_feed_MgN = sum(
	MgN,
	na.rm = TRUE
	), .groups = "drop")

	dplyr::summarise(Cropland_feed_MgN = sum(
	MgN,
	na.rm = TRUE
	), .groups = "drop")

	dplyr::summarise(Total_feed_MgN = sum(
	MgN,
	na.rm = TRUE
	), .groups = "drop") \|>

	dplyr::summarise(Domestic_feed_MgN = sum(
	MgN,
	na.rm = TRUE
	), .groups = "drop")

	dplyr::summarise(Total_feed_import = sum(
	Value_destiny,
	na.rm = TRUE
	), .groups = "drop")

	dplyr::summarise(LU_total_spain = sum(
	LU_total,
	na.rm = TRUE
	), .groups = "drop")

	livestock_density, productivity, semi_nat_share, imported_feed_share,
	sf_provinces, year

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