caviddhen · caviddhen · Oct 30, 2025 · Oct 6, 2025 · Oct 7, 2025 · Oct 8, 2025
diff --git a/.githooks/pre-commit b/.githooks/pre-commit
@@ -22,11 +22,12 @@ if (any(endsWith(stagedFiles, ".gms"))) {
 
 # make sure that files are not too big
 maxFilesize <- 250 # kB
+exemptFromLimit <- "^renv/archive/[0-9\\.]+_renv\\.lock$"
 
 files <- union(system("git ls-tree -r HEAD --name-only", intern = TRUE), stagedFiles)
 out <- data.frame(files = files, size = round(file.size(files) / 1024, 2))
 out <- out[!is.na(out$size), ]
-out <- out[out$size > maxFilesize, ]
+out <- out[out$size > maxFilesize & !grepl(exemptFromLimit, out$files), ]
 if (nrow(out) > 0) {
   stop(nrow(out), " files with size > ", maxFilesize, "kB detected: \n",
        paste0(out$files, " (", out$size, "kB)", collapse = "\n"))

diff --git a/.zenodo.json b/.zenodo.json
@@ -1,6 +1,6 @@
 {
   "title": "MAgPIE - An Open Source land-use modeling framework",
-  "version": "4.12.0dev",
+  "version": "4.13.0dev",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -127,5 +127,5 @@
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2025-09-08"
+  "publication_date": "2025-10-23"
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,21 +7,36 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 ## [Unreleased]
 
 ### changed
-- **inputdata** updated input data to rev4.124, which includes two fixes, one with nitrogen emissions being to low and one about accounting for starches in FAO processing data
-- **inputdata** updated input data to rev4.123, which uses LUH3 instead of LUH2v2
-- **config** input data upgraded from rev4.121 to rev4.122, incorporating new bioenergy demand and GHG price trajectories from REMIND standalone runs with biochar (R34BC).
-- **56_ghg_policy** extended set of available ghg price scenarios
-- **60_bioenergy** extended set of available second generation bioenergy scenarios
+-
 
 ### added
 -
 
 ### removed
 -
 
+### fixed
+-
+
+
+## [4.13.0] - 2025-10-23
+
+### changed
+- **56_ghg_policy** extended set of available ghg price scenarios
+- **60_bioenergy** extended set of available second generation bioenergy scenarios
+- **config** input data upgraded from rev4.121 to rev4.122, incorporating new bioenergy demand and GHG price trajectories from REMIND standalone runs with biochar (R34BC).
+- **inputdata** updated input data to rev4.123, which uses LUH3 instead of LUH2v2
+
+### added
+- **renv/archive** store `renv.lock` for release versions
+
 ### fixed
 - **14_yield** avoid division by zero for special cases
+- **14_yield** avoid too high yields in edge cases (in case of data mismatches between FAO/LUH croparea and LPJmL yield data avoid zero references yields that lead to overestimated yields)
 - **60_bioenergy** Harmonize 2nd gen bioenergy demand for historic period based on default trajectory "R34M410-SSP2-NPi2025"
+- **inputdata** updated input data to rev4.124, which includes two fixes, one with nitrogen emissions being to low and one about accounting for starches in FAO processing data
+- **inputdata** updated input data to rev4.126, including fixes related to inconsistencies as part of LUH3 update and growing primary forest
+- **scripts/output** removed deprecated `dir` option from `disaggBII` in `disaggregation.R`
 
 
 ## [4.12.0] - 2025-09-08
@@ -1216,7 +1231,8 @@ 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/v4.12.0...develop
+[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.13.0...develop
+[4.13.0]: https://github.com/magpiemodel/magpie/compare/v4.12.0...v4.13.0
 [4.12.0]: https://github.com/magpiemodel/magpie/compare/v4.11.0...v4.12.0
 [4.11.0]: https://github.com/magpiemodel/magpie/compare/v4.10.1...v4.11.0
 [4.10.1]: https://github.com/magpiemodel/magpie/compare/v4.10.0...v4.10.1

diff --git a/CITATION.cff b/CITATION.cff
@@ -161,8 +161,8 @@ abstract: The *Model of Agricultural Production and its Impact on the Environmen
   exogenously given population in 10 food energy categories, based on regional diets.
   Future trends in food demand are derived from a cross-country regression analysis,
   based on future scenarios on GDP and population growth.
-version: 4.12.0dev
-date-released: 2025-09-08
+version: 4.13.0dev
+date-released: 2025-10-23
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,7 +21,7 @@ Imports:
     m4fsdp,
     madrat,
     magclass (>= 6.14.0),
-    magpie4 (>= 2.39.1),
+    magpie4 (>= 2.42.3),
     MagpieNCGains,
     magpiesets (>= 0.46.1),
     mip,

diff --git a/README.md b/README.md
@@ -26,8 +26,8 @@ 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 4.12.0 can be found at
-https://rse.pik-potsdam.de/doc/magpie/4.12.0/
+The model documentation for version 4.13.0 can be found at
+https://rse.pik-potsdam.de/doc/magpie/4.13.0/
 
 A most recent version of the documentation can also be extracted from the
 model source code via the R package goxygen
@@ -236,7 +236,7 @@ Please contact magpie@pik-potsdam.de if you're having troubles installing or run
 - If you're using PowerShell, starting an interactive R session with `R` doesn't work, and you need to type `R.exe` (or `R.bat` if `R.exe` isn't found) instead. The reason behind this is that `r` is a reserved shortcut for repeating the previous command, which is why you'll be getting a cryptic `Invoke-History: Cannot locate most recent history.` error message when trying to start R in a fresh PowerShell session.
 
 ## CITATION
-See file CITATION.cff or the [How-to-Cite section](https://rse.pik-potsdam.de/doc/magpie/4.12.0/#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/4.13.0/#how-to-cite) in the model documentation for information how to cite the model.
 
 ## AUTHORS
 See list of authors in CITATION.cff

diff --git a/config/default.cfg b/config/default.cfg
@@ -17,14 +17,14 @@ cfg <- list()
 cfg$title <- "default"
 
 # path to the submodel to be used relative to main model folder
-cfg$model <- "main.gms"   #def = "main.gms"
+cfg$model <- "main.gms"   # def = "main.gms"
 
 #### input settings ####
 
 # which input data sets should be used?
-cfg$input <- c(regional    = "rev4.124_h12_magpie.tgz",
-               cellular    = "rev4.124_h12_1b5c3817_cellularmagpie_c200_MRI-ESM2-0-ssp245_lpjml-8e6c5eb1.tgz",
-               validation  = "rev4.124_h12_validation.tgz",
+cfg$input <- c(regional    = "rev4.126_h12_magpie.tgz",
+               cellular    = "rev4.126_h12_1b5c3817_cellularmagpie_c200_MRI-ESM2-0-ssp245_lpjml-8e6c5eb1.tgz",
+               validation  = "rev4.126_h12_validation.tgz",
                additional  = "additional_data_rev4.63.tgz",
                calibration = "calibration_H12_FAO_18Sep25.tgz")
 
@@ -2283,7 +2283,7 @@ cfg$files2export$start <- c("input/info.txt",
                             "input/kba_land_0.5.mz",
                             "input/f58_peatland_area_0.5.mz",
                             "input/MAPSPAM_croparea_0.5.mz",
-                            "input/LUH2_croparea_0.5.mz")
+                            "input/LUH3_croparea_0.5.mz")
 
 # Files that should be copied after the MAgPIE run is finished
 cfg$files2export$end <- NULL

diff --git a/config/projects/scenario_config_el2.csv b/config/projects/scenario_config_el2.csv
@@ -20,5 +20,5 @@ gms$s15_alc_scen;0;0;0
 gms$c30_bioen_water;all;all;all
 gms$factor_costs;sticky_labor;sticky_labor;sticky_labor
 gms$c70_feed_scen;ssp1;ssp2;ssp2
-input['cellular'];rev4.124EL2_h12_c6a7458f_cellularmagpie_c200_IPSL-CM6A-LR-ssp370_lpjml-8e6c5eb1.tgz;;
+input['cellular'];rev4.126EL2_h12_c6a7458f_cellularmagpie_c200_IPSL-CM6A-LR-ssp370_lpjml-8e6c5eb1.tgz;;
 magicc_emis_scen;REMIND_generic_C_SSP2EU-DSPkB650-DS_betax_DeepDive_noNDC-rem-12.mif;REMIND_generic_C_SSP2EU-DSPkB650-DS_betax_DeepDive_noNDC-rem-12.mif;REMIND_generic_C_SSP2EU-DSPkB650-DS_betax_DeepDive_noNDC-rem-12.mif
diff --git a/config/projects/scenario_config_fsec.csv b/config/projects/scenario_config_fsec.csv
@@ -76,8 +76,8 @@ gms$s62_max_dem_bioplastic;0;;;;400;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
 gms$c70_fac_req_regr;reg;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
 gms$c70_feed_scen;;;;;;;;;;;;;;;;;;ssp1;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
 gms$c73_build_demand;;;;;;;;;;;;;;;;;;;;;;;;50pc;;;;;;;;;;;;;;;;;;;;;;;;;;;
-input['cellular'];rev4.124_FSEC_3c888fa5_cellularmagpie_c200_MRI-ESM2-0-ssp460_lpjml-8e6c5eb1.tgz;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;rev4.124_FSEC_0bd54110_cellularmagpie_c200_MRI-ESM2-0-ssp119_lpjml-8e6c5eb1.tgz;rev4.124_FSEC_6819938d_cellularmagpie_c200_MRI-ESM2-0-ssp126_lpjml-8e6c5eb1.tgz;;rev4.124_FSEC_1b5c3817_cellularmagpie_c200_MRI-ESM2-0-ssp245_lpjml-8e6c5eb1.tgz;rev4.124_FSEC_3c888fa5_cellularmagpie_c200_MRI-ESM2-0-ssp460_lpjml-8e6c5eb1.tgz;rev4.124_FSEC_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz;rev4.124_FSEC_09a63995_cellularmagpie_c200_MRI-ESM2-0-ssp585_lpjml-8e6c5eb1.tgz;;;
-input['regional'];rev4.124_FSEC_magpie.tgz;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
-input['validation'];rev4.124_FSEC_validation.tgz;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+input['cellular'];rev4.126_FSEC_3c888fa5_cellularmagpie_c200_MRI-ESM2-0-ssp460_lpjml-8e6c5eb1.tgz;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;rev4.126_FSEC_0bd54110_cellularmagpie_c200_MRI-ESM2-0-ssp119_lpjml-8e6c5eb1.tgz;rev4.126_FSEC_6819938d_cellularmagpie_c200_MRI-ESM2-0-ssp126_lpjml-8e6c5eb1.tgz;;rev4.126_FSEC_1b5c3817_cellularmagpie_c200_MRI-ESM2-0-ssp245_lpjml-8e6c5eb1.tgz;rev4.126_FSEC_3c888fa5_cellularmagpie_c200_MRI-ESM2-0-ssp460_lpjml-8e6c5eb1.tgz;rev4.126_FSEC_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz;rev4.126_FSEC_09a63995_cellularmagpie_c200_MRI-ESM2-0-ssp585_lpjml-8e6c5eb1.tgz;;;
+input['regional'];rev4.126_FSEC_magpie.tgz;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
+input['validation'];rev4.126_FSEC_validation.tgz;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
 input['calibration'];calibration_FSEC_FAO_14Aug25.tgz;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
 magicc_emis_scen;bjoernAR6_C_SSP2-NDC.mif;;;bjoernAR6_C_SSP2-PkBudg900.mif;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;bjoernAR6_C_SSP1-NDC.mif;;;;;;;;;;;;bjoernAR6_C_RemSDP-900-MagSSP1.mif;;
diff --git a/config/scenario_config.csv b/config/scenario_config.csv
@@ -77,4 +77,4 @@ gms$c60_biodem_level;;;;;;;;;;;;;;;;;;;;;;;;1;0;;;;;;;;;;;;
 gms$c60_res_2ndgenBE_dem;;;;ssp1;ssp2;ssp3;ssp4;ssp5;sdp;ssp2;sdp;sdp;sdp;;;;;;;;;;;;;;;;;;;;;;;;
 gms$c70_feed_scen;;;;ssp1;ssp2;ssp3;ssp4;ssp5;ssp1;ssp5;ssp1;ssp1;ssp2;;;;;;;;;;;;;;;;;;;;;;;;
 gms$s73_timber_demand_switch;;;;;;;;;;;;;;;;;;;;;;;;;;;;;1;1;0;;;;;;
-input['cellular'];;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;rev4.124_h12_0bd54110_cellularmagpie_c200_MRI-ESM2-0-ssp119_lpjml-8e6c5eb1.tgz;rev4.124_h12_6819938d_cellularmagpie_c200_MRI-ESM2-0-ssp126_lpjml-8e6c5eb1.tgz;rev4.124_h12_1b5c3817_cellularmagpie_c200_MRI-ESM2-0-ssp245_lpjml-8e6c5eb1.tgz;rev4.124_h12_3c888fa5_cellularmagpie_c200_MRI-ESM2-0-ssp460_lpjml-8e6c5eb1.tgz;rev4.124_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz;rev4.124_h12_09a63995_cellularmagpie_c200_MRI-ESM2-0-ssp585_lpjml-8e6c5eb1.tgz
+input['cellular'];;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;rev4.126_h12_0bd54110_cellularmagpie_c200_MRI-ESM2-0-ssp119_lpjml-8e6c5eb1.tgz;rev4.126_h12_6819938d_cellularmagpie_c200_MRI-ESM2-0-ssp126_lpjml-8e6c5eb1.tgz;rev4.126_h12_1b5c3817_cellularmagpie_c200_MRI-ESM2-0-ssp245_lpjml-8e6c5eb1.tgz;rev4.126_h12_3c888fa5_cellularmagpie_c200_MRI-ESM2-0-ssp460_lpjml-8e6c5eb1.tgz;rev4.126_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz;rev4.126_h12_09a63995_cellularmagpie_c200_MRI-ESM2-0-ssp585_lpjml-8e6c5eb1.tgz
diff --git a/data-changelog.csv b/data-changelog.csv
@@ -1,4 +1,5 @@
 version,lucEmisRaw2020,lucEmisRaw2050,lucEmisRaw2100,tau2020,tau2050,tau2100,cropland2020,cropland2050,cropland2100,irrigated2020,irrigated2050,irrigated2100,pasture2020,pasture2050,pasture2100,forest2020,forest2050,forest2100,other2020,other2050,other2100,production2020,production2050,production2100,costs2020,costs2050,costs2100,foodExp2020,foodExp2050,foodExp2100
+4.13.0,1990.53,24.95,1285.68,1.28,1.64,1.89,1570.17,1662.21,1923.37,244.01,368.97,471.48,3256.53,3250.17,3171.2,4054.66,3987.36,3960.69,4032.77,3993.42,3828.39,17356.28,22558.33,25170.7,3443728.93,4567396.69,6824370.26,1623.95,2442.77,4916.26
 4.12.0,2640.51,347.36,829.47,1.27,1.61,1.87,1579.89,1695.16,1962.52,245.57,376.49,459.4,3301.45,3295.75,3169.51,4064.46,3993.45,3933.02,3975.83,3902.13,3811.92,16961.85,22246.11,24761.81,3377362.03,4560650.58,6614375.19,1622.25,2443.32,4917.72
 4.11.0,3955.61,609.99,1065.13,1.25,1.6,1.88,1558.03,1640.44,1891.94,242.12,365.49,494.44,3314.14,3324.15,3296.26,4066.85,4006.65,3900.61,3982.6,3915.24,3788.16,16434.28,21917.78,24491.06,3590863.74,4896810.04,6108842.8,1711.18,2540.35,5047.86
 4.10.1,4029.35,937.76,811.98,1.24,1.58,1.86,1570.1,1641.16,1908.36,238.83,369.84,481.77,3312.71,3338.12,3286.4,4064.03,4009.22,3906.25,3974.78,3897.98,3775.96,16532.71,22332.48,24534.96,3595710.82,4904095.84,6267265.88,490.26,541.95,651.09

diff --git a/modules/14_yields/managementcalib_aug19/preloop.gms b/modules/14_yields/managementcalib_aug19/preloop.gms
@@ -59,9 +59,11 @@ i14_croparea_total(t_all,w,j) = sum(kcr, fm_croparea(t_all,j,w,kcr));
 
 i14_modeled_yields_hist(t_past,i,knbe14)
    = (sum((cell(i,j),w), fm_croparea(t_past,j,w,knbe14) * f14_yields(t_past,j,knbe14,w)) /
-      sum((cell(i,j),w), fm_croparea(t_past,j,w,knbe14)))$(sum((cell(i,j),w), fm_croparea(t_past,j,w,knbe14))>0.00001)
+      sum((cell(i,j),w), fm_croparea(t_past,j,w,knbe14)))$(sum((cell(i,j),w), fm_croparea(t_past,j,w,knbe14)) > 0.00001 AND
+                                                           sum((cell(i,j),w), fm_croparea(t_past,j,w,knbe14) * f14_yields(t_past,j,knbe14,w)) > 0.00001)
    + (sum((cell(i,j),w), i14_croparea_total(t_past,w,j) * f14_yields(t_past,j,knbe14,w)) /
-      sum((cell(i,j),w), i14_croparea_total(t_past,w,j)))$(sum((cell(i,j),w), fm_croparea(t_past,j,w,knbe14))<=0.00001);
+      sum((cell(i,j),w), i14_croparea_total(t_past,w,j)))$(sum((cell(i,j),w), fm_croparea(t_past,j,w,knbe14)) <= 0.00001 OR
+                                                           sum((cell(i,j),w), fm_croparea(t_past,j,w,knbe14) * f14_yields(t_past,j,knbe14,w)) <= 0.00001);
 
 
 *' The factor `i14_lambda_yields` is calculated for the initial time step depending
@@ -127,9 +129,11 @@ if ((s14_calib_ir2rf = 1),
 * Calibrate newly calibrated yields to FAO yields
   i14_modeled_yields_hist2(i,knbe14)
    = (sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14) * i14_yields_calib("y1995",j,knbe14,w)) /
-      sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14)))$(sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14))>0.00001 AND sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14) * i14_yields_calib("y1995",j,knbe14,w)) > 0.00001)
+      sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14)))$(sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14)) > 0.00001 AND
+                                                            sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14) * i14_yields_calib("y1995",j,knbe14,w)) > 0.00001)
    + (sum((cell(i,j),w), i14_croparea_total("y1995",w,j) * i14_yields_calib("y1995",j,knbe14,w)) /
-      sum((cell(i,j),w), i14_croparea_total("y1995",w,j)))$(sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14))<=0.00001 OR sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14) * i14_yields_calib("y1995",j,knbe14,w)) <= 0.00001);
+      sum((cell(i,j),w), i14_croparea_total("y1995",w,j)))$(sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14)) <= 0.00001 OR
+                                                                 sum((cell(i,j),w), fm_croparea("y1995",j,w,knbe14) * i14_yields_calib("y1995",j,knbe14,w)) <= 0.00001);
 
   i14_yields_calib(t,j,knbe14,w) = sum((cell(i,j)), i14_fao_yields_hist("y1995",i,knbe14) /
                                                       i14_modeled_yields_hist2(i,knbe14)) *