Merge pull request #581 from pfuehrlich-pik/master

magpie release 4.6.9

.github/workflows/test-code.yaml

@@ -27,12 +27,6 @@ jobs:
         with:
           extra-repositories: https://cloud.r-project.org https://rse.pik-potsdam.de/r/packages/
 
-      - name: Install R dependencies
-        uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          packages: gms
-          extra-packages: gms
-
       - name: pre-commit Hook
         run: source(".githooks/pre-commit")
         shell: Rscript {0}

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "MAgPIE - An Open Source land-use modeling framework",
-  "version": "4.6.8",
+  "version": "4.6.9",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -109,5 +109,5 @@
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2023-07-17"
+  "publication_date": "2023-07-27"
 }

CHANGELOG.md

@@ -5,11 +5,18 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 
+## [4.6.9] - 2023-07-27
+
+### fixed
+- **70_livestock** consideration of milk demand in the calculation of the pasture management factor
+- **scripts** Fixed inaccuracies and inconsistent application of SNV policies during disaggregation in luscale::interpolateAvlCroplandWeighted(), which is called in extra/disaggregation.R
+
+
 ## [4.6.8] - 2023-07-17
 
 ### changed
 - **41_area_equipped_for_irrigation** new AEI data (Mehta2022) replacing old Siebert data
-- **80_optimization** printing of solprint when solver status is 7 re-activated 
+- **80_optimization** printing of solprint when solver status is 7 re-activated
 - **scripts** start_functions.R can now handle clusters per region flexibly
 - **scripts** the REMIND-MAgPIE coupling now uses renv
 
@@ -33,6 +40,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 - **config** corrected wrong names of parameters for peatland costs
 - **config** updated scenario configs to newest preprocessing (4.87)
 
+
 ## [4.6.7] - 2023-05-10
 
 ### changed
@@ -729,7 +737,8 @@ This release version is focussed on consistency between the MAgPIE setup and the
 First open source release of the framework. See [MAgPIE 4.0 paper](https://doi.org/10.5194/gmd-12-1299-2019) for more information.
 
 
-[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.6.8...develop
+[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.6.9...develop
+[4.6.9]: https://github.com/magpiemodel/magpie/compare/v4.6.8...v4.6.9
 [4.6.8]: https://github.com/magpiemodel/magpie/compare/v4.6.7...v4.6.8
 [4.6.7]: https://github.com/magpiemodel/magpie/compare/v4.6.6...v4.6.7
 [4.6.6]: https://github.com/magpiemodel/magpie/compare/v4.6.5...v4.6.6

CITATION.cff

@@ -125,8 +125,8 @@ authors:
     email: [email protected]
 
 title: MAgPIE - An Open Source land-use modeling framework
-version: 4.6.8
-date-released: 2023-07-17
+version: 4.6.9
+date-released: 2023-07-27
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse

DESCRIPTION

@@ -17,7 +17,7 @@ Imports:
     iamc,
     lucode2 (>= 0.36.0),
     luplot,
-    luscale,
+    luscale (>= 2.27.4),
     lusweave,
     m4fsdp,
     madrat,

README.md

@@ -24,8 +24,8 @@ https://www.pik-potsdam.de/research/projects/activities/land-use-modelling/magpi
 A framework description paper has been published in
 Geoscientific Model Development (GMD): https://doi.org/10.5194/gmd-12-1299-2019
 
-The model documentation for version 4.6.8 can be found at
-https://rse.pik-potsdam.de/doc/magpie/4.6.8/
+The model documentation for version 4.6.9 can be found at
+https://rse.pik-potsdam.de/doc/magpie/4.6.9/
 
 A most recent version of the documentation can also be extracted from the
 model source code via the R package goxygen
@@ -188,7 +188,7 @@ [email protected]
 Please contact [email protected]
 
 ## CITATION
-See file CITATION.cff or the [How-to-Cite section](https://rse.pik-potsdam.de/doc/magpie/4.6.8/#how-to-cite) in the model documentation for information how to cite the model.
+See file CITATION.cff or the [How-to-Cite section](https://rse.pik-potsdam.de/doc/magpie/4.6.9/#how-to-cite) in the model documentation for information how to cite the model.
 
 ## AUTHORS
 See list of authors in CITATION.cff

config/default.cfg

@@ -26,7 +26,7 @@ cfg$input <- c(regional    = "rev4.87_h12_magpie.tgz",
                cellular    = "rev4.87_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz",
                validation  = "rev4.87_h12_validation.tgz",
                additional  = "additional_data_rev4.43.tgz",
-               calibration = "calibration_H12_per_ton_fao_may22_glo_08Jul23.tgz")
+               calibration = "calibration_H12_per_ton_fao_may22_glo_14Jul23.tgz")
 
 # NOTE: It is recommended to recalibrate the model when changing cellular input data
 #       as well as for any other setting that would affect initial values in the model,

modules/15_food/anthro_iso_jun22/declarations.gms

@@ -125,8 +125,7 @@ parameters
 
 * before shock
  o15_kcal_regr_initial(t,iso,kfo)             Uncalibrated per capita demand before price shock (kcal per capita per day)
- p15_kcal_pc_initial(t,i,kfo)                 Per capita consumption in food demand model before price shock on regional level (kcal per capita per day)
- pm_kcal_pc_initial(t,i,kfo)                  Per capita consumption in food demand model before price shock (kcal per capita per day)
+ pm_kcal_pc_initial(t,i,kall)                  Per capita consumption in food demand model before price shock (kcal per capita per day)
  p15_kcal_pc_initial_iso(t,iso,kfo)           Per capita consumption in food demand model before price shock on country level (kcal per capita per day)
 
 * after price shock

modules/15_food/anthro_iso_jun22/equations.gms

@@ -9,7 +9,7 @@
 
 q15_food_demand(i2,kfo) ..
                 (vm_dem_food(i2,kfo) + sum(ct, f15_household_balanceflow(ct,i2,kfo,"dm")))
-                * sum(ct,(f15_nutrition_attributes(ct,kfo,"kcal") * 10**6)) =g=
+                * sum(ct,(fm_nutrition_attributes(ct,kfo,"kcal") * 10**6)) =g=
                 sum(ct,im_pop(ct,i2) * p15_kcal_pc_calibrated(ct,i2,kfo)) * 365
                 ;
 

modules/15_food/anthro_iso_jun22/exodietmacro.gms

@@ -28,8 +28,7 @@ if (s15_run_diet_postprocessing = 1,
   p15_bmi_shr_regr(t,iso,sex,age,bmi_group15) = v15_bmi_shr_regr.l(iso,sex,age,bmi_group15);
 
   p15_bmi_shr_calibrated(t,iso,sex,age,bmi_group15) =
-         p15_bmi_shr_regr(t,iso,sex,age,bmi_group15)+
-         i15_bmi_shr_calib(t,iso,sex,age,bmi_group15);
+          p15_bmi_shr_regr(t,iso,sex,age,bmi_group15) + i15_bmi_shr_calib(t,iso,sex,age,bmi_group15) * s15_calibrate;
 
 * The BMI shares are not allowed to exceed the bounds 0 and 1. Values are corrected to the bounds.
   p15_bmi_shr_calibrated(t,iso,sex,age,bmi_group15)$(p15_bmi_shr_calibrated(t,iso,sex,age,bmi_group15)<0) = 0;
@@ -108,7 +107,7 @@ if (s15_run_diet_postprocessing = 1,
                  + p15_kcal_pc_iso_rumdairy_orig(t,iso) * (1- i15_rumdairy_fadeout(t,iso)));
 
 *** Substitution of ruminant meat and dairy products (kfo_rd) with single-cell protein (SCP) based on protein/cap/day
-  i15_protein_to_kcal_ratio(t,kfo) =  f15_nutrition_attributes(t,kfo,"protein")/f15_nutrition_attributes(t,kfo,"kcal");
+  i15_protein_to_kcal_ratio(t,kfo) =  fm_nutrition_attributes(t,kfo,"protein")/fm_nutrition_attributes(t,kfo,"kcal");
 * Before the substitution, kfo_rd is converted from kcal/cap/day to g protein/cap/day
 * using i15_protein_to_kcal_ratio(t,kfo_rd).
 * After the substitution of kfo_rd with SCP (1-i15_rumdairy_scp_fadeout), SCP is converted

modules/15_food/anthro_iso_jun22/input.gms

@@ -124,7 +124,7 @@ $ondelim
 $include "./modules/15_food/input/f15_household_balanceflow.cs3"
 $offdelim;
 
-table f15_nutrition_attributes(t_all,kall,nutrition) Nutrition attributes of food items dedicated for fooduse (mio. kcal per tDM | t Protein per tDM)
+table fm_nutrition_attributes(t_all,kall,nutrition) Nutrition attributes of food items dedicated for fooduse (mio. kcal per tDM | t Protein per tDM)
 $ondelim
 $include "./modules/15_food/input/f15_nutrition_attributes.cs3"
 $offdelim;

modules/15_food/anthro_iso_jun22/preloop.gms

@@ -92,7 +92,7 @@ $else
 $endif
 
 * initial prices in $US per Kcal
-i15_prices_initial_kcal(iso,kfo)$(f15_nutrition_attributes("y1995",kfo,"kcal")>0) = f15_prices_initial(kfo)
-                                                                                  / (f15_nutrition_attributes("y1995",kfo,"kcal")*10**6);
+i15_prices_initial_kcal(iso,kfo)$(fm_nutrition_attributes("y1995",kfo,"kcal")>0) = f15_prices_initial(kfo)
+                                                                                  / (fm_nutrition_attributes("y1995",kfo,"kcal")*10**6);
 p15_prices_kcal(t,iso,kfo,"iter1")=i15_prices_initial_kcal(iso,kfo);
 p15_convergence_measure(t,iter15)=NA;

modules/15_food/anthro_iso_jun22/sets.gms

@@ -102,9 +102,6 @@ sets
    kfo_lp(kfo) Livestock food products
    / livst_rum,livst_pig,livst_chick, livst_egg, livst_milk /
 
-   kfo_rd(kfo) Ruminant meat and dairy food products
-   / livst_rum,livst_milk /
-
    kfo_st(kfo) Staple products
    / tece,maiz,trce,rice_pro,soybean,rapeseed,groundnut,sunflower,puls_pro,
    potato,cassav_sp,sugr_cane,sugr_beet,molasses,brans,scp /
@@ -148,6 +145,10 @@ sets
   livst_fadeoutscen15 Scenarios for changed composition of livestock products
        / halving2050, constant /
 
+* The set kfo_rd can be defined in default.cfg and is used in the food substitution scenarios c15_rumdairy_scp_scen and c15_rumdairyscen
+  kfo_rd(kfo) Ruminant meat and dairy food products
+       / livst_rum,livst_milk /
+
   fadeoutscen15  Food substitution scenarios including functional forms with targets and transition periods
        / constant,
          lin_zero_10_50, lin_zero_20_50, lin_zero_20_30, lin_zero_20_70, lin_50pc_20_50, lin_50pc_20_50_extend65, lin_50pc_20_50_extend80,

modules/15_food/anthropometrics_jan18/declarations.gms

@@ -126,8 +126,7 @@ parameters
 
 * before shock
  o15_kcal_regr_initial(t,iso,kfo)             Uncalibrated per capita demand before price shock (kcal per capita per day)
- p15_kcal_pc_initial(t,i,kfo)                 Per capita consumption in food demand model before price shock on regional level (kcal per capita per day)
- pm_kcal_pc_initial(t,i,kfo)                  Per capita consumption in food demand model before price shock (kcal per capita per day)
+ pm_kcal_pc_initial(t,i,kall)                  Per capita consumption in food demand model before price shock (kcal per capita per day)
  p15_kcal_pc_initial_iso(t,iso,kfo)           Per capita consumption in food demand model before price shock on country level (kcal per capita per day)
 
 * after price shock

modules/15_food/anthropometrics_jan18/equations.gms

@@ -9,7 +9,7 @@
 
 q15_food_demand(i2,kfo) ..
                 (vm_dem_food(i2,kfo) + sum(ct, f15_household_balanceflow(ct,i2,kfo,"dm")))
-                * sum(ct,(f15_nutrition_attributes(ct,kfo,"kcal") * 10**6)) =g=
+                * sum(ct,(fm_nutrition_attributes(ct,kfo,"kcal") * 10**6)) =g=
                 sum(ct,im_pop(ct,i2) * p15_kcal_pc_calibrated(ct,i2,kfo)) * 365
                 ;
 

modules/15_food/anthropometrics_jan18/input.gms

@@ -105,7 +105,7 @@ $ondelim
 $include "./modules/15_food/input/f15_household_balanceflow.cs3"
 $offdelim;
 
-table f15_nutrition_attributes(t_all,kall,nutrition) Nutrition attributes of food items dedicated for fooduse (mio. kcal per tDM | t Protein per tDM)
+table fm_nutrition_attributes(t_all,kall,nutrition) Nutrition attributes of food items dedicated for fooduse (mio. kcal per tDM | t Protein per tDM)
 $ondelim
 $include "./modules/15_food/input/f15_nutrition_attributes.cs3"
 $offdelim;

modules/15_food/anthropometrics_jan18/intersolve.gms

@@ -222,7 +222,7 @@ p15_kcal_pc_calibrated(t,i,kfo_pp) = p15_plant_kcal_structure_orig(t,i,kfo_pp)
                + p15_kcal_pc_calibrated_rumdairy_orig(t,i) * (1-i15_rumdairy_fadeout(t,i)));
 
 *** Substitution of ruminant meat and dairy products (kfo_rd) with single-cell protein (SCP) based on protein/cap/day
-i15_protein_to_kcal_ratio(t,kfo) =  f15_nutrition_attributes(t,kfo,"protein")/f15_nutrition_attributes(t,kfo,"kcal");
+i15_protein_to_kcal_ratio(t,kfo) =  fm_nutrition_attributes(t,kfo,"protein")/fm_nutrition_attributes(t,kfo,"kcal");
 * Before the substitution, kfo_rd is converted from kcal/cap/day to g protein/cap/day 
 * using i15_protein_to_kcal_ratio(t,kfo_rd).
 * After the substitution of kfo_rd with SCP (1-i15_rumdairy_scp_fadeout), SCP is converted

modules/15_food/anthropometrics_jan18/preloop.gms

@@ -98,7 +98,7 @@ i15_exo_foodscen_fader(t,i) = (1-f15_food_substitution_fader(t,"%c15_exo_foodsce
 
 
 * initial prices in $US per Kcal
-i15_prices_initial_kcal(iso,kfo)$(f15_nutrition_attributes("y1995",kfo,"kcal")>0) = f15_prices_initial(kfo)
-                                                                                  / (f15_nutrition_attributes("y1995",kfo,"kcal")*10**6);
+i15_prices_initial_kcal(iso,kfo)$(fm_nutrition_attributes("y1995",kfo,"kcal")>0) = f15_prices_initial(kfo)
+                                                                                  / (fm_nutrition_attributes("y1995",kfo,"kcal")*10**6);
 p15_prices_kcal(t,iso,kfo,"iter1")=i15_prices_initial_kcal(iso,kfo);
 p15_convergence_measure(t,iter15)=NA;

modules/15_food/anthropometrics_jan18/presolve.gms

@@ -429,7 +429,7 @@ p15_kcal_pc_calibrated(t,i,kfo_pp) = p15_plant_kcal_structure_orig(t,i,kfo_pp)
                + p15_kcal_pc_calibrated_rumdairy_orig(t,i) * (1-i15_rumdairy_fadeout(t,i)));
 
 *** Substitution of ruminant meat and dairy products (kfo_rd) with single-cell protein (SCP) based on protein/cap/day
-i15_protein_to_kcal_ratio(t,kfo) =  f15_nutrition_attributes(t,kfo,"protein")/f15_nutrition_attributes(t,kfo,"kcal");
+i15_protein_to_kcal_ratio(t,kfo) =  fm_nutrition_attributes(t,kfo,"protein")/fm_nutrition_attributes(t,kfo,"kcal");
 * Before the substitution, kfo_rd is converted from kcal/cap/day to g protein/cap/day
 * using i15_protein_to_kcal_ratio(t,kfo_rd).
 * After the substitution of kfo_rd with SCP (1-i15_rumdairy_scp_fadeout), SCP is converted

modules/15_food/anthropometrics_jan18/sets.gms

@@ -102,9 +102,6 @@ sets
    kfo_lp(kfo) Livestock food products
    / livst_rum,livst_pig,livst_chick, livst_egg, livst_milk /
 
-   kfo_rd(kfo) Ruminant meat and dairy food products
-   / livst_rum,livst_milk /
-
    kfo_st(kfo) Staple products
    / tece,maiz,trce,rice_pro,soybean,rapeseed,groundnut,sunflower,puls_pro,
    potato,cassav_sp,sugr_cane,sugr_beet,molasses,brans,scp /
@@ -148,6 +145,10 @@ sets
   livst_fadeoutscen15 Scenarios for changed composition of livestock products
        / halving2050, constant /
 
+* The set kfo_rd can be defined in default.cfg and is used in the food substitution scenarios c15_rumdairy_scp_scen and c15_rumdairyscen
+  kfo_rd(kfo) Ruminant meat and dairy food products
+       / livst_rum,livst_milk /
+
   fadeoutscen15  Food substitution scenarios including functional forms with targets and transition periods
        / constant,
          lin_zero_10_50, lin_zero_20_50, lin_zero_20_30, lin_zero_20_70, lin_50pc_20_50, lin_50pc_20_50_extend65, lin_50pc_20_50_extend80,

modules/15_food/module.gms

@@ -15,7 +15,9 @@
 *' agricultural commodities q15_food_demand.m to change food demand and iterates
 *' with MAgPIE until a common solution is found. Outputs include next to food
 *' demand also projections of anthropometric parameters such as body height and
-*' weight distribution, as well as phyiscal activity levels.
+*' weight distribution, as well as phyiscal activity levels. In addition, this
+*' module also provides information about nutrition attributes of foods that can
+*' be used in other modules via the interface fm_nutrition_attributes.
 *' @authors Benjamin Leon Bodirsky, Isabelle Weindl, Jan Philipp Dietrich
 
 *###################### R SECTION START (MODULETYPES) ##########################

modules/16_demand/sector_may15/sets.gms

@@ -21,6 +21,9 @@ sets
    kli(kap) Livestock products
    / livst_rum, livst_pig, livst_chick, livst_egg, livst_milk  /
 
+   kli_rd(kap) Ruminant meat and dairy products
+   / livst_rum,livst_milk /
+
    kforestry(k) forestry products
         / wood, woodfuel /
 

modules/70_livestock/fbask_jan16/declarations.gms

@@ -23,7 +23,9 @@ parameters
  im_slaughter_feed_share(t_all,i,kap,attributes)  Share of feed that is incorporated in animal biomass (1)
  i70_livestock_productivity(t_all,i,sys)          Productivity indicator for livestock production (t FM per animal per yr)
  im_feed_baskets(t_all,i,kap,kall)                Feed baskets in tDM per tDM livestock product (1)
- p70_cattle_stock_proxy(t,i)                      Proxy for cattle stocks needed to fullfil domestic food demand (mio. animals per yr)
+ p70_cattle_stock_proxy(t,i)                      Proxy for cattle stocks needed to fullfil food demand for ruminant meat (mio. animals per yr)
+ p70_milk_cow_proxy(t,i)                          Proxy for milk cows needed to fullfil food demand for milk (mio. animals per yr)
+ p70_cattle_feed_pc_proxy(t,i,kli_rd)             Proxy for daily per capita feed demand for pasture biomass driven by demand for beef and dairy products (tDM per capita per day)
  p70_incr_cattle(t,i)                             Change in estimated cattle stocks attributed to food demand projections (1)
  pm_past_mngmnt_factor(t,i)                       Regional pasture management intensification factor (1)
  i70_cereal_scp_fadeout(t_all,i)                  Cereal feed fadeout (share 0-1) to be replaced by SCP (1)

modules/70_livestock/fbask_jan16/presolve.gms

@@ -12,25 +12,39 @@
 *' biophysical pasture yields in the module [14_yields].
 
 *' The exogenous calculation of pasture management requires information on
-*' the number of cattle reared to fulfil the domestic demand for ruminant 
+*' changes in the number of cattle reared to fulfil the food demand for ruminant
 *' livestock products: 
 
 p70_cattle_stock_proxy(t,i) = im_pop(t,i)*pm_kcal_pc_initial(t,i,"livst_rum")
-                  /i70_livestock_productivity(t,i,"sys_beef");   
+                  /i70_livestock_productivity(t,i,"sys_beef");
 
-*' The lower bound for `p70_cattle_stock_proxy` is set to 20% of initial cattle 
-*' stocks in 1995:
+p70_milk_cow_proxy(t,i) = im_pop(t,i)*pm_kcal_pc_initial(t,i,"livst_milk")
+                  /i70_livestock_productivity(t,i,"sys_dairy");
+
+*' The lower bound for `p70_cattle_stock_proxy` and `p70_milk_cow_proxy` is
+*' set to 20% of initial values in 1995:
 
 p70_cattle_stock_proxy(t,i)$(p70_cattle_stock_proxy(t,i) < 0.2*p70_cattle_stock_proxy("y1995",i)) = 0.2*p70_cattle_stock_proxy("y1995",i);
+p70_milk_cow_proxy(t,i)$(p70_milk_cow_proxy(t,i) < 0.2*p70_milk_cow_proxy("y1995",i)) = 0.2*p70_milk_cow_proxy("y1995",i);
+
+*' The parameter `p70_cattle_feed_pc_proxy` is a proxy for regional daily per capita
+*' feed demand for pasture biomass driven by demand for beef and dairy products,
+*' which is later used for weighted aggregation.
+p70_cattle_feed_pc_proxy(t,i,kli_rd) = pm_kcal_pc_initial(t,i,kli_rd)*im_feed_baskets(t,i,kli_rd,"pasture")/(fm_nutrition_attributes(t,kli_rd,"kcal") * 10**6);
 
-*' The parameter `p70_incr_cattle` describes the changes in cattle stocks 
+*' The parameter `p70_incr_cattle` describes the changes in the number of cattle
 *' relative to the previous time step:
 
 p70_incr_cattle(t,i)  =  1$(ord(t)=1)
-      + (p70_cattle_stock_proxy(t,i)/p70_cattle_stock_proxy(t-1,i))$(ord(t)>1);
+     + (
+          ( p70_cattle_feed_pc_proxy(t,i,"livst_rum") * (p70_cattle_stock_proxy(t,i)/p70_cattle_stock_proxy(t-1,i))
+            +
+            p70_cattle_feed_pc_proxy(t,i,"livst_milk") * (p70_milk_cow_proxy(t,i)/p70_milk_cow_proxy(t-1,i)) )
+          / sum(kli_rd, p70_cattle_feed_pc_proxy(t,i,kli_rd) )
+       )$(ord(t)>1);
 
 *' The pasture management factor is calculated by applying a linear relationship 
-*' that links changes in pasture management with changes in cattle stocks:
+*' that links changes in pasture management with changes in the number of cattle:
 
 if (m_year(t) <= s70_past_mngmnt_factor_fix,
    pm_past_mngmnt_factor(t,i) = 1;