update develop

.Rprofile

@@ -8,6 +8,15 @@ Sys.setenv(RENV_PATHS_LIBRARY = "renv/library")
 
 source("renv/activate.R")
 
+renvVersion <- "0.16.0"
+if (packageVersion("renv") != renvVersion) {
+  renvLockExisted <- file.exists(renv::paths$lockfile())
+  renv::upgrade(version = renvVersion, reload = TRUE, prompt = FALSE)
+  if (!renvLockExisted) {
+    unlink(renv::paths$lockfile())
+  }
+}
+
 if (!"https://rse.pik-potsdam.de/r/packages" %in% getOption("repos")) {
   options(repos = c(getOption("repos"), pik = "https://rse.pik-potsdam.de/r/packages"))
 }

.github/workflows/test-code.yaml

@@ -18,20 +18,15 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Remove .Rprofile
         run: rm .Rprofile
 
       - uses: r-lib/actions/setup-r@v2
         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
+          use-public-rspm: true
+          extra-repositories: "https://rse.pik-potsdam.de/r/packages"
 
       - name: pre-commit Hook
         run: source(".githooks/pre-commit")

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "MAgPIE - An Open Source land-use modeling framework",
-  "version": "4.6.7dev",
+  "version": "4.6.11dev",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -109,5 +109,5 @@
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2023-05-10"
+  "publication_date": "2023-09-05"
 }

CHANGELOG.md

@@ -8,19 +8,78 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 ## [Unreleased]
 
 ### changed
-- **scripts** start_functions.R can now handle clusters per region flexibly
+-
+
+### added
+- **18_residues** Included cluster-level residue realization, for cluster-level production of residues (but balancing of recycling and burning budgets remains at region-level, for computational lightness)
+- **14_yields/config** Added option for considering impacts of land degradation on yields. If `s14_degradation` is switched to 1, MAgPIE will include cluster-specific information on the state of nature's contributions to people relevant for yields `./modules/14_yields/input/f14_yld_ncp_report.cs3`.
+
+### removed
+-
+
+### fixed
+-
+
+
+## [4.6.11] - 2023-09-05
+
+### changed
+- **scripts** All time steps between 2015 and 2050 are now reported to SEALS
+
+### fixed
+- **70_livestock** fixed division by zero that could occur depending on the scenario set-up
+
+
+## [4.6.10] - 2023-08-16
+
+### changed
+- **config**  update preprocessing to newest input data v4.88 with new transport costs
+- **GitHub action** the github action is now faster, because it installs binary packages from Posit Package Manager
+- **scenario_config.csv** update preprocessing to newest input data v4.88
+- **scripts** output.R is now faster, because it no longer searches runfolder renvs for full.gms files
+
+### fixed
+- **scripts** check_config does not warn about c_input_gdx_path anymore while running empty model
+- **scripts** fixed erronoeous if clause in output.R
+- **scripts** fixed output/extra/disaggregation_LUH2.R. The script was not working any more because magpie4::protectedArea was changed to return protected area for all land types. Moreover, the script now also works for runs without dynamic forestry (default run) but with a warning message.
+
+
+## [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
+- **scripts** start_functions.R can now handle clusters per region flexibly
+- **scripts** the REMIND-MAgPIE coupling now uses renv
 
 ### added
-- **scenario_config.csv** added a scenario for the NGFS project
+- **31_past** added `cc`, `nocc` and `nocc_hist` options for `c31_past_suit_scen` and `c31_grassl_yld_scenario`
+- **32_carbon** added `nocc` and `nocc_hist` option for `c52_land_carbon_sink_rcp`
+- **71_disagg_lvst** added new realisation `foragebased_jul23` which solves GAMS issues at higher spatial resolutions
+- **config** added `cfg$results_folder_highres` which allows to modify the output folder used in the `highres.R` output script
 - **config** new area equipped for irrigation (AEI) data in preprocessing (4.87)
+- **scenario_config.csv** added a scenario for the NGFS project
+- **scripts** New output script for reporting disaggregated land use patterns to the SEALS (Spatial Economic Allocation Landscape Simulator) downscaling model
 
 ### removed
--
+- **config** `s80_num_nonopt_allowed`
+- **scripts** removed .snapshot.Rprofile and the Rprofile.R script, renv now fully supersedes snapshots
 
 ### fixed
+- **30_crop** corrected q30_cropland in module realization rotation_apr22, where fallow land was on the wrong side of the equation
+- **71_disagg_lvst** reworked `foragebased_aug18` (including removal of linear version and correction of balance flow calculation)
+- **80_optimization** resolve was not working in nlp_par realization due to `s80_num_nonopt_allowed`
+- **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
@@ -717,7 +776,11 @@ 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/v4.6.7...develop
+[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.6.11...develop
+[4.6.11]: https://github.com/magpiemodel/magpie/compare/v4.6.10...v4.6.11
+[4.6.10]: https://github.com/magpiemodel/magpie/compare/v4.6.9...v4.6.10
+[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
 [4.6.5]: https://github.com/magpiemodel/magpie/compare/v4.6.4...v4.6.5

CITATION.cff

@@ -125,8 +125,8 @@ authors:
     email: [email protected]
 
 title: MAgPIE - An Open Source land-use modeling framework
-version: 4.6.7dev
-date-released: 2023-05-10
+version: 4.6.11dev
+date-released: 2023-09-05
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse

DESCRIPTION

@@ -17,7 +17,7 @@ Imports:
     iamc,
     lucode2 (>= 0.36.0),
     luplot,
-    luscale,
+    luscale (>= 2.27.9),
     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 4.6.7 can be found at
-https://rse.pik-potsdam.de/doc/magpie/4.6.7/
+The model documentation for version 4.6.11 can be found at
+https://rse.pik-potsdam.de/doc/magpie/4.6.11/
 
 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/4.6.7/#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/4.6.11/#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

@@ -22,11 +22,11 @@ cfg$model <- "main.gms"   #def = "main.gms"
 #### input settings ####
 
 # which input data sets should be used?
-cfg$input <- c(regional    = "rev4.87_h12_magpie.tgz",
-               cellular    = "rev4.87_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz",
-               validation  = "rev4.87_h12_validation.tgz",
-               additional  = "additional_data_rev4.43.tgz",
-               calibration = "calibration_H12_per_ton_fao_may22_glo_23Mar23.tgz")
+cfg$input <- c(regional    = "rev4.88_h12_magpie.tgz",
+               cellular    = "rev4.88_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz",
+               validation  = "rev4.88_h12_validation.tgz",
+               additional  = "additional_data_rev4.45.tgz",
+               calibration = "calibration_H12_per_ton_fao_may22_glo_08Aug23.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,
@@ -95,7 +95,7 @@ cfg$restart_landconversion_cost <- FALSE           # def = FALSE
 # calibration factor in each calibration iteration (0-1)
 cfg$damping_factor_landconversion_cost <- 0.96        # def= 0.96
 # Set upper limit for cropland calibration factor
-cfg$cost_calib_max_landconversion_cost <- 3            # def= 3
+cfg$cost_calib_max_landconversion_cost <- 3         # def= 3
 # Set lower limit for cropland calibration factor
 cfg$cost_calib_min_landconversion_cost <- 0.05            # def= 0.05
 # Selection type of calibration factors.
@@ -307,6 +307,15 @@ cfg$gms$s14_limit_calib <- 1       # def = 1
 # NOTE: It is recommended to recalibrate the model when changing this setting!
 cfg$gms$s14_calib_ir2rf <- 1       # def = 1
 
+# * Switch to include yield impacts of land degradation.
+# * The state of yield-relevant nature's contributions to people (NCP)
+# * is reported through ./modules/14_yields/input/f14_yld_ncp_report.cs3
+# * based on estimated outcomes for soil loss or pollination sufficiency
+# * per cluster from an existing model run.
+# * options: 1 (yields are reduced based on yield reduction coefficients)
+# *          0 (land degradation is switched off)
+cfg$gms$s14_degradation <- 0      # def = 0
+
 # ***---------------------    15_food    ---------------------------------------
 # * (anthropometrics_jan18): estimates food using scenario dependent regression
 # *                          and demography drivers
@@ -694,8 +703,17 @@ cfg$gms$s31_fac_req_past  <- 1             # def = 1
 # * reflecting that not all pasture area is grazed.
 cfg$gms$s31_unequal  <- 1             # def = 1
 
+# * Scenario for grassland and pasture yields (only take effect for realization grasslands_apr22)
+# *   options:   cc        (climate change)
+# *             nocc       (no climate change)
+# *             nocc_hist  (no climate change after year defined by sm_fix_cc)
+cfg$gms$c31_grassl_yld_scenario  <- "cc"   # def = "cc"
+
+
 # * SSP scenario switch for pasture suitability areas (only take effect for realization grasslands_apr22)
 # * options: ssp126, ssp245, ssp370, ssp460, ssp585
+# *          nocc  (fixed to values from 1995),
+# *          nocc_hist (ssp245 until year defined in sm_fix_cc, fixed thereafter)
 cfg$gms$c31_past_suit_scen  <- "ssp370"   # def = "ssp370"
 
 # * Switch that allows selecting how yield calibration factors will be calculated.
@@ -1277,7 +1295,9 @@ cfg$gms$nitrogen    <- "rescaled_jan21"                 # def = rescaled_jan21
 cfg$gms$carbon <- "normal_dec17"                       # def = normal_dec17
 
 # * RCP scenario of land carbon sink adjustment factor, from Grassi et al 2021
-# *   options:  RCP19, RCP26, RCP34, RCP45, RCP60, RCPBU
+# *   options:  RCP19, RCP26, RCP34, RCP45, RCP60, RCPBU,
+# *             nocc  (fixed to values from 1995),
+# *             nocc_hist (RCPBU until year defined in sm_fix_cc, fixed thereafter)
 cfg$gms$c52_land_carbon_sink_rcp  <- "RCPBU"
 
 
@@ -1519,8 +1539,8 @@ cfg$gms$peatland  <- "on"                     # def = on
 cfg$gms$s58_rewetting_switch  <- Inf   # def = Inf
 
 # * One-time and recurring costs for peatland rewetting (USD05MER per ha)
-cfg$gms$s58_rewet_cost_onetime  <- 7000   # def = 7000
-cfg$gms$s58_rewet_cost_recur  <- 200   # def = 200
+cfg$gms$s58_cost_rewet_onetime  <- 7000   # def = 7000
+cfg$gms$s58_cost_rewet_recur  <- 200   # def = 200
 
 # * One-time and recurring costs for peatland degradation (USD05MER per ha)
 # * Can be used to test area-based incentives for peatland protection and restoration,
@@ -1529,8 +1549,8 @@ cfg$gms$s58_rewet_cost_recur  <- 200   # def = 200
 # * Therefore, one-time costs can used to incentivize the protection of intact peatlands.
 # * Recurring costs apply on the level of degraded peatland. Therefore, recurring costs,
 # * in combination with one-time costs, can be used to incentivize peatland restoration.
-cfg$gms$s58_degrad_cost_onetime  <- 0   # def = 0
-cfg$gms$s58_degrad_cost_recur  <- 0   # def = 0
+cfg$gms$s58_cost_degrad_onetime  <- 0   # def = 0
+cfg$gms$s58_cost_degrad_recur  <- 0   # def = 0
 
 # * Artificial cost for balance variables (USD05MER per ha)
 # * The balance variables in the peatland module avoid infeasibilities due to
@@ -1724,7 +1744,10 @@ cfg$gms$c70_fac_req_regr <- "glo"                               # def = glo
 # * (off):               default
 # * (foragebased_aug18): Disaggregation of livestock to cells
 # *                      with high pasture and fodder availability
-cfg$gms$disagg_lvst <- "foragebased_aug18"                  # def = foragebased_aug18
+# * (foragebased_jul23): Disaggregation of livestock to cells
+# *                      with high pasture and fodder availability
+# *                      (improved and flexibitized)
+cfg$gms$disagg_lvst <- "foragebased_jul23"                  # def = foragebased_jul23
 
 
 # ***---------------------    73_timber   -----------------------------------
@@ -1812,11 +1835,6 @@ cfg$gms$s80_maxiter <- 30
 # * (conopt4+conopt3): conopt4 followed by conopt3
 cfg$gms$c80_nlp_solver <- "conopt4"              # def = conopt4
 
-# number of allowed non-optimal variables
-# Should be set to 0 for GAMS version 25.x.x or earlier
-# Should be set to Inf for GAMS version 26.x.x or later
-cfg$gms$s80_num_nonopt_allowed <- Inf
-
 # * 1: using optfile for specified solver settings
 # * 0: default settings (optfile will be ignored)
 cfg$gms$s80_optfile <- 1
@@ -1870,6 +1888,12 @@ cfg$output <- c("output_check", "extra/disaggregation", "rds_report")
 # :title: is a placeholder for the current run title (cfg$title)
 cfg$results_folder <- "output/:title::date:"
 
+# Results folder used by the "highres.R" output script
+# If NULL, the default set in "highres.R" is used (currently a subfolder in "output")
+# To place highres runs directly in the "output" folder, change to "output"
+# To place highres runs in a specific subfolder change to "output/HR"
+cfg$results_folder_highres <- NULL
+
 # Which files should be copied into the output folder?
 cfg$files2export <- list()
 # Files that should be copied before MAgPIE is started
@@ -1900,6 +1924,10 @@ cfg$files2export$start <- c("input/info.txt",
 # Files that should be copied after the MAgPIE run is finished
 cfg$files2export$end <- NULL
 
+# Expert use only, should not be set manually. Path to a renv.lock file
+# defining the package environment for newly started runs.
+cfg$renv_lock <- NULL
+
 # Folder run statistics should be submitted to
 cfg$runstatistics <- "/p/projects/rd3mod/models/statistics/magpie"
 

config/scenario_config.csv

@@ -30,7 +30,8 @@ gms$c30_bioen_water;;;;rainfed;rainfed;rainfed;rainfed;rainfed;rainfed;rainfed;a
 gms$s30_snv_shr;;;;0;0;0;0;0;0;0;0;0;0.2;;;;;;;0;;0.2;0.2;0.2;0.2;0.2;;;;;;;;;;;;;;;;;;;
 gms$s30_snv_shr_noselect;;;;;;;;;;;;;;;;;;;;;;0;0;0.2;0;0.2;;;;;;;;;;;;;;;;;;;
 gms$s30_snv_scenario_target;;;;;;;;;;;;;2030;;;;;;;;;2030;2030;2030;2030;2030;;;;;;;;;;;;;;;;;;;
-gms$c31_past_suit_scen;;;;ssp126;ssp245;ssp245;ssp370;ssp460;ssp585;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;ssp126;ssp126;ssp245;ssp460;ssp370;ssp585;
+gms$c31_past_suit_scen;;nocc;nocc_hist;ssp126;ssp245;ssp245;ssp370;ssp460;ssp585;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;ssp126;ssp126;ssp245;ssp460;ssp370;ssp585;
+gms$c31_grassl_yld_scenario;cc;nocc;nocc_hist;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
 gms$s32_aff_plantation;;;;0;0;0;0;0;0;0;1;0;0;;;;;;;0;;;;;;;;;;;;;;;;;;;;;;;;;
 gms$s32_aff_bii_coeff;;;;0;0;0;0;0;0;0;1;0;0;;;;;;;0;;;;;;;;;;;;;;;;;;;;;;;;;
 gms$s32_max_aff_area;;;;Inf;Inf;Inf;Inf;Inf;Inf;500;350;0;700;;;;;;;500;;Inf;Inf;Inf;500;500;;;;;;;;;;;;;;;;;;;
@@ -78,8 +79,8 @@ gms$s73_timber_demand_switch;;;;;;;;;;;;;;;;;;;;;;1;1;1;1;1;;;;;1;1;0;;;;;;;;;;;
 gms$s35_forest_damage;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;4;4;4;4;4;;;;;;;
 gms$c32_shock_scenario;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;none;002lin2030;004lin2030;008lin2030;016lin2030;;;;;;;
 gms$c35_shock_scenario;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;none;002lin2030;004lin2030;008lin2030;016lin2030;;;;;;;
-input['cellular'];;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;rev4.87_h12_0bd54110_cellularmagpie_c200_MRI-ESM2-0-ssp119_lpjml-8e6c5eb1.tgz;rev4.87_h12_6819938d_cellularmagpie_c200_MRI-ESM2-0-ssp126_lpjml-8e6c5eb1.tgz;rev4.87_h12_1b5c3817_cellularmagpie_c200_MRI-ESM2-0-ssp245_lpjml-8e6c5eb1.tgz;rev4.87_h12_3c888fa5_cellularmagpie_c200_MRI-ESM2-0-ssp460_lpjml-8e6c5eb1.tgz;rev4.87_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz;rev4.87_h12_09a63995_cellularmagpie_c200_MRI-ESM2-0-ssp585_lpjml-8e6c5eb1.tgz;
-gms$c52_land_carbon_sink_rcp;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;RCP19;RCP26;RCP45;RCP60;RCPBU;RCPBU;
+input['cellular'];;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;rev4.88_h12_0bd54110_cellularmagpie_c200_MRI-ESM2-0-ssp119_lpjml-8e6c5eb1.tgz;rev4.88_h12_6819938d_cellularmagpie_c200_MRI-ESM2-0-ssp126_lpjml-8e6c5eb1.tgz;rev4.88_h12_1b5c3817_cellularmagpie_c200_MRI-ESM2-0-ssp245_lpjml-8e6c5eb1.tgz;rev4.88_h12_3c888fa5_cellularmagpie_c200_MRI-ESM2-0-ssp460_lpjml-8e6c5eb1.tgz;rev4.88_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz;rev4.88_h12_09a63995_cellularmagpie_c200_MRI-ESM2-0-ssp585_lpjml-8e6c5eb1.tgz;
+gms$c52_land_carbon_sink_rcp;;nocc;nocc_hist;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;RCP19;RCP26;RCP45;RCP60;RCPBU;RCPBU;
 gms$c57_macc_version;;;;;;;;;;;;;;;;;;;;;;;;;;;PBL_2022;PBL_2022;PBL_2022;PBL_2022;;;;;;;;;;;;;;;
 gms$c57_macc_scenario;;;;;;;;;;;;;;;;;;;;;;;;;;;Default;Optimistic;Default;Optimistic;;;;;;;;;;;;;;;
 gms$s58_rewetting_switch;;;;;;;;;;;;;;;;;;;;;;;;;;;0;1;0;1;;;;;;;;;;;;;;;

core/sets.gms

@@ -59,7 +59,7 @@ sets
       CHA_7*CHA_23,
       EUR_24*EUR_32,
       IND_33*IND_40,
-      JPN_41,
+      JPN_41*JPN_41,
       LAM_42*LAM_85,
       MEA_86*MEA_111,
       NEU_112*NEU_118,
@@ -73,7 +73,7 @@ sets
       CHA . (CHA_7*CHA_23)
       EUR . (EUR_24*EUR_32)
       IND . (IND_33*IND_40)
-      JPN . (JPN_41)
+      JPN . (JPN_41*JPN_41)
       LAM . (LAM_42*LAM_85)
       MEA . (MEA_86*MEA_111)
       NEU . (NEU_112*NEU_118)