Merge pull request #660 from pascal-sauer/develop

MAgPIE release 4.7.3

.Rprofile

@@ -27,11 +27,16 @@ if (!"https://rse.pik-potsdam.de/r/packages" %in% getOption("repos")) {
 # bootstrapping, will only run once after this repo is freshly cloned
 if (isTRUE(rownames(installed.packages(priority = "NA")) == "renv")) {
   message("R package dependencies are not installed in this renv, installing now...")
-  renv::hydrate() # auto-detect and install all dependencies
+  renv::hydrate(prompt = FALSE, report = FALSE) # auto-detect and install all dependencies
   message("Finished installing R package dependencies.")
+  if (!("upstream" %in% gert::git_remote_list()$name)) {
+    gert::git_remote_add("https://github.com/magpiemodel/magpie.git", "upstream")
+    message("Added upstream git remote pointing to magpiemodel/magpie.")
+  }
 }
 
 # in case bootstrapping fails halfway, install piamenv and rely on requirement auto-fixing
-if (!requireNamespace("piamenv", quietly = TRUE)) {
+if (tryCatch(packageVersion("piamenv"),
+             error = function(e) package_version("0.0")) < package_version("0.3.4")) {
   renv::install("piamenv", prompt = FALSE)
 }

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "MAgPIE - An Open Source land-use modeling framework",
-  "version": "4.7.2",
+  "version": "4.7.3",
   "creators": [
     {
       "name": "Dietrich, Jan Philipp",
@@ -114,5 +114,5 @@
   "license": {
     "id": "AGPL-3.0-or-later"
   },
-  "publication_date": "2024-04-02"
+  "publication_date": "2024-04-12"
 }

CHANGELOG.md

@@ -4,6 +4,33 @@
 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/).
 
+
+## [4.7.3] - 2024-04-12
+
+### changed
+- **21_trade** Revision of trade module. Replaced `cfg$gms$s21_trade_bal_damper` in favour of `cfg$gms$k_import21`, which allows for additional imports to maintain feasibility
+- **21_trade** v21_import_for_feasibility now available for all countries, not just for importers
+- **70_livestock** if `c70_fac_req_regr` is set to `reg`: use of USDA/FAO values for historic factor requirements for livestock instead of using regression values and change of calibration year from 2005 to 2010 for regional factor requirements regression
+- **config** updated FSEC scenario config for revision and included new calibration file (after cost fix in preprocessing)
+- **default.cfg** updated inputdata revision to 4.104 to have NDC scenarios included
+- **scripts** cfg$gms$s35_secdf_distribution <- 2 for FSEC
+- **scripts** modified output reporting for SEALS to account for forestry plantations
+- **scripts/calibration/landconversion_cost.R** Revised calibration approach for conversion costs for cropland. Information from all calibration time steps in combination with a lowpass filter is now used for deriving the calibration factors, which avoids the previous zickzack pattern. The previous option `cfg$damping_factor_landconversion_cost` has been removed in favor of `cfg$lowpass_filter_landconversion_cost`.
+
+### added
+- **14_yields** added minimum threshold for wood yields. Below this threshold, wood yields are set to zero.
+- **config** added switch for minimum timber yields
+- **56_ghg_policy** added NDC scenarios
+- **60_bioenergy** added NDC scenarios
+- **scripts** start script for EAT2p0 Deep Dive project
+### fixed
+- **15_food** Small number rather 0 in condition checking calorie balancing
+- **34_urban** `static` realization was not working because `vm_carbon_stock` was referenced without the set `stockType`
+- **52_carbon** removing jump of carbon content into fully grown forest when a forest changes from second-last age class to last age-class.
+- **58_peatland** Equation `q58_scalingFactorExp` revised to avoid division by zero.
+- **80_optimization** duplicated solve statement in all instances to avoid non-matchting left- and right-hand sides of equations
+
+
 ## [4.7.2] - 2024-04-02
 
 ### changed
@@ -844,7 +871,8 @@ 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/v4.7.2...develop
+[Unreleased]: https://github.com/magpiemodel/magpie/compare/v4.7.3...develop
+[4.7.3]: https://github.com/magpiemodel/magpie/compare/v4.7.2...v4.7.3
 [4.7.2]: https://github.com/magpiemodel/magpie/compare/v4.7.1...v4.7.2
 [4.7.1]: https://github.com/magpiemodel/magpie/compare/v4.7.0...v4.7.1
 [4.7.0]: https://github.com/magpiemodel/magpie/compare/v4.6.11...v4.7.0

CITATION.cff

@@ -131,8 +131,8 @@ authors:
     email: [email protected]
 
 title: MAgPIE - An Open Source land-use modeling framework
-version: 4.7.2
-date-released: 2024-04-02
+version: 4.7.3
+date-released: 2024-04-12
 repository-code: https://github.com/magpiemodel/magpie
 keywords:
   - landuse

DESCRIPTION

@@ -39,5 +39,7 @@ Imports:
 Suggests:
     goxygen,
     languageserver,
-    qgraph
+    qgraph,
+    shinyresults,
+    XML
 Encoding: UTF-8

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 4.7.2 can be found at
-https://rse.pik-potsdam.de/doc/magpie/4.7.2/
+The model documentation for version 4.7.3 can be found at
+https://rse.pik-potsdam.de/doc/magpie/4.7.3/
 
 A most recent version of the documentation can also be extracted from the
 model source code via the R package goxygen
@@ -226,7 +226,7 @@ [email protected]
 Please contact [email protected]
 
 ## CITATION
-See file CITATION.cff or the [How-to-Cite section](https://rse.pik-potsdam.de/doc/magpie/4.7.2/#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/4.7.3/#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$input <- c(regional    = "rev4.101_h12_magpie.tgz",
-               cellular    = "rev4.101_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz",
-               validation  = "rev4.101_h12_validation.tgz",
+cfg$input <- c(regional    = "rev4.104_h12_magpie.tgz",
+               cellular    = "rev4.104_h12_fd712c0b_cellularmagpie_c200_MRI-ESM2-0-ssp370_lpjml-8e6c5eb1.tgz",
+               validation  = "rev4.104_h12_validation.tgz",
                additional  = "additional_data_rev4.48.tgz",
-               calibration = "calibration_H12_per_ton_fao_may22_glo_13Mar24.tgz")
+               calibration = "calibration_H12_26Mar24.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,
@@ -85,9 +85,9 @@ cfg$crop_calib_max <- 1.5            # def= 1.5
 cfg$best_calib <- TRUE   # def = TRUE
 
 # Settings for land conversion cost calibration (cropland)
-# The calibration routine derives regional calibration factors for
+# The calibration routine derives a time-series of regional calibration factors for
 # costs of cropland expansion and rewards for cropland reduction,
-# with the goal to match historical regional cropland in 2015.
+# with the goal to match historical regional cropland in the period 1995-2015.
 # * (TRUE): Land conversion cost calibration will be performed
 # * (ifneeded): Land conversion cost calibration will only be executed if the input file "f39_calib.csv" is missing
 # * (FALSE): Land conversion cost calibration will not be performed
@@ -98,9 +98,9 @@ cfg$calib_accuracy_landconversion_cost <- 0.05         # def = 0.05
 cfg$calib_maxiter_landconversion_cost <- 40           # def = 40
 # Restart from existing calibration factors (TRUE or FALSE)
 cfg$restart_landconversion_cost <- FALSE           # def = FALSE
-# Factor determining how much the divergence infuences the new
-# calibration factor in each calibration iteration (0-1)
-cfg$damping_factor_landconversion_cost <- 0.96        # def= 0.96
+# Number of lowpass filter iterations applied on calibration factors 
+# for time steps 1995-2015
+cfg$lowpass_filter_landconversion_cost <- 1        # def= 1
 # Set upper limit for cropland calibration factor
 cfg$cost_calib_max_landconversion_cost <- 3         # def= 3
 # Set lower limit for cropland calibration factor
@@ -198,7 +198,6 @@ cfg$gms$sm_fix_SSP2 <- 2020
 cfg$gms$sm_fix_cc <- 2020
 
 # ***---------------------    10_land   ----------------------------------------
-# * (feb15): default land realization
 # * (landmatrix_dec18): includes a land transition matrix
 cfg$gms$land <- "landmatrix_dec18"          # def = landmatrix_dec18
 
@@ -331,6 +330,10 @@ cfg$gms$s14_degradation <- 0      # def = 0
 # For other realizations, it is recommended not to use this yield calibration.
 cfg$gms$s14_use_yield_calib <- 0    # def = 0
 
+# Include a minimum yield for wood harvest in secondary vegetation (tDM per ha per yr).
+# Age classes with wood yields below this threshold have a production of zero.
+cfg$gms$s14_minimum_wood_yield <- 20   #def = 20
+
 # ***---------------------    15_food    ---------------------------------------
 # * (anthropometrics_jan18): estimates food using scenario dependent regression
 # *                          and demography drivers
@@ -1402,12 +1405,13 @@ cfg$gms$s56_cprice_red_factor <- 1    # def = 1
 # *     R32M46-SSP5-NPi, R32M46-SSP5-NDC, R32M46-SSP5-PkBudg1050, R32M46-SSP5-PkBudg650,
 # * R21M42: Coupled REMIND-MAgPIE runs with REMIND 2.1 and MAgPIE 4.2
 # *   NPi: Current policies; above 3.0°C in 2100
+# *   NDC: Nationally determined contributions; limit peak warming to 2.5°C
 # *   PkBudg900:  Budget with 900 GtCO2; well-below 1.5°C in 2100 (PkBudg1000 for SDP)
 # *   PkBudg1300: Budget with 1300 GtCO2; well-below 2.0°C in 2100
-# *     R21M42-SDP-NPi,  R21M42-SDP-PkBudg1000, R21M42-SDP-PkBudg1100, R21M42-SDP-PkBudg900,
-# *     R21M42-SSP1-NPi, R21M42-SSP1-PkBudg1100, R21M42-SSP1-PkBudg1300, R21M42-SSP1-PkBudg900,
-# *     R21M42-SSP2-NPi, R21M42-SSP2-PkBudg1100, R21M42-SSP2-PkBudg1300, R21M42-SSP2-PkBudg900,
-# *     R21M42-SSP5-NPi, R21M42-SSP5-PkBudg1100, R21M42-SSP5-PkBudg1300, R21M42-SSP5-PkBudg900,
+# *     R21M42-SDP-NPi, R21M42-SDP-NDC, R21M42-SDP-PkBudg1000, R21M42-SDP-PkBudg1100, R21M42-SDP-PkBudg900,
+# *     R21M42-SSP1-NPi, R21M42-SSP1-NDC, R21M42-SSP1-PkBudg1100, R21M42-SSP1-PkBudg1300, R21M42-SSP1-PkBudg900,
+# *     R21M42-SSP2-NPi, R21M42-SSP2-NDC, R21M42-SSP2-PkBudg1100, R21M42-SSP2-PkBudg1300, R21M42-SSP2-PkBudg900,
+# *     R21M42-SSP5-NPi, R21M42-SSP5-NDC, R21M42-SSP5-PkBudg1100, R21M42-SSP5-PkBudg1300, R21M42-SSP5-PkBudg900,
 # * R2M41: Coupled REMIND-MAgPIE runs with REMIND 2.0 and MAgPIE 4.1
 # *     R2M41-SSP2-NPi, R2M41-SSP2-NDC, R2M41-SSP2-Budg1300, R2M41-SSP2-Budg600, R2M41-SSP2-Budg950
 # * Standalone REMIND runs from Strefler et al 2021; well-below 2.0°C in 2100
@@ -1663,12 +1667,13 @@ cfg$gms$c60_1stgen_biodem <- "const2020"               # def = const2020
 # *     R32M46-SSP5-NPi, R32M46-SSP5-NDC, R32M46-SSP5-PkBudg1050, R32M46-SSP5-PkBudg650,
 # * R21M42: Coupled REMIND-MAgPIE runs with REMIND 2.1 and MAgPIE 4.2
 # *   NPi: Current policies; above 3.0°C in 2100
+# *   NDC: Nationally determined contributions; limit peak warming to 2.5°C
 # *   PkBudg900:  Budget with 900 GtCO2; well-below 1.5°C in 2100 (PkBudg1000 for SDP)
 # *   PkBudg1300: Budget with 1300 GtCO2; well-below 2.0°C in 2100
-# *     R21M42-SDP-NPi,  R21M42-SDP-PkBudg1000, R21M42-SDP-PkBudg1100, R21M42-SDP-PkBudg900,
-# *     R21M42-SSP1-NPi, R21M42-SSP1-PkBudg1100, R21M42-SSP1-PkBudg1300, R21M42-SSP1-PkBudg900,
-# *     R21M42-SSP2-NPi, R21M42-SSP2-PkBudg1100, R21M42-SSP2-PkBudg1300, R21M42-SSP2-PkBudg900,
-# *     R21M42-SSP5-NPi, R21M42-SSP5-PkBudg1100, R21M42-SSP5-PkBudg1300, R21M42-SSP5-PkBudg900,
+# *     R21M42-SDP-NPi, R21M42-SDP-NDC, R21M42-SDP-PkBudg1000, R21M42-SDP-PkBudg1100, R21M42-SDP-PkBudg900,
+# *     R21M42-SSP1-NPi, R21M42-SSP1-NDC, R21M42-SSP1-PkBudg1100, R21M42-SSP1-PkBudg1300, R21M42-SSP1-PkBudg900,
+# *     R21M42-SSP2-NPi, R21M42-SSP2-NDC, R21M42-SSP2-PkBudg1100, R21M42-SSP2-PkBudg1300, R21M42-SSP2-PkBudg900,
+# *     R21M42-SSP5-NPi, R21M42-SSP5-NDC, R21M42-SSP5-PkBudg1100, R21M42-SSP5-PkBudg1300, R21M42-SSP5-PkBudg900,
 # * R2M41: Coupled REMIND-MAgPIE runs with REMIND 2.0 and MAgPIE 4.1
 # *     R2M41-SSP2-NPi, R2M41-SSP2-NDC, R2M41-SSP2-Budg1300, R2M41-SSP2-Budg600, R2M41-SSP2-Budg950
 # * Standalone REMIND runs from Strefler et al 2021; well-below 2.0°C in 2100
@@ -1887,7 +1892,7 @@ cfg$gms$c80_nlp_solver <- "conopt4"              # def = conopt4
 
 # * 1: using optfile for specified solver settings
 # * 0: default settings (optfile will be ignored)
-cfg$gms$s80_optfile <- 1
+cfg$gms$s80_optfile <- 0 # def = 0
 
 
 #*******************************END MODULE SETUP********************************