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rsofun (development version)

rsofun 5.1.0

New features

  • P-model:

    • New run_pmodel_onestep_f_bysite() adds single-step leaf-level simulations of the P-model
    • Changed temperature dependencies of Vcmax and Jmax (see breaking changes below)
    • Added support for carbon isotope tracking
      • run_pmodel_onestep_f_bysite() returns bigdelta, i.e. the carbon fractionation of fresh assimilate cleafd13c relative to d13c_atm, thereby avoiding any assumptions for d13c_atm.
      • run_pmodel_f_bysite() and runread_pmodel() newly return cleaf and cleafd13c, assuming a constant atmospheric signature d13c_atm = -8.4 permil. In a future version daily values of d13c_atm could/should be included in the input forcing.

  • BiomeE:

    • Added support for LULUC (land use, land-use change) in BiomeE. See vignette biome_luluc for details.
    • New BiomeE behavior to recycle last year of forcing if requested simulation time span (nyeartrend) is longer than available forcing data.
    • Prepared support for carbon isotope tracking
      • run_biomee_f_bysite() and runread_biomee() do track carbon isotopes internally, currently without output. Note that when method_photosynth == "gs_leuning", then bigdelta = 20, whereas when method_photosynth == "pmodel" then bigdelta is computed based on the pmodel-derived chi.

  • calib_sofun() now passes parameters as a named vector to cost-functions for easier processing within cost-functions. Default cost-functions were updated, but currently ignore the names. This is fully backward compatible, but allows to use the names in user-created cost functions.

Breaking changes

  • P-model now computes temperature dependencies of jmax and vcmax with Kumarathunge et al. (2019) instead of Kattge & Knorr (2007), effectively using a dampened signal for tc_growth and long-term averages for tc_home. This alters the simulation results. Formatting of inputs remains unchanged.

  • Breaking changes in BiomeE drivers:

    • init_cohort$init_n_cohorts column has been phased out and must not be present in
      drivers to protect against data corruption.
    • update_annualLAImax flag was removed and the behavior is now slightly altered since LAImax and underLAImax are set and kept constant at the start of the simulation:
      • LAImax takes value max(LAI_light, 0.5)
      • underLAImax takes value min(LAImax, 1.2)
    • do_closedN_run flag now uses initial inorganic N setting rather than arbitrary value and is false by default.
    • Modified drivers to use more sensibles values
      • Species 1 is now a C4 crop
      • N_input is set to 0.01 to limit N starvation.

  • Breaking changes in BiomeE output

    • renamed the following column names in output_daily_tile:
      • totWs=>SoilWater
      • Trsp=>Transp
      • SW_C=>sapwoodC and SW_N=>sapwoodN
      • HW_C=>heartwoodC and HW_N=>heartwoodN
      • McrbC=>mcrbC and McrbN=>mcrbN
      • added NPP
    • renamed the following column names in output_annual_tile and output_annual_cell:
      • rain=>Prcp
      • SeedC=>seedC (and for N)
      • SapwoodC=>sapwoodC (and for N)
      • WoodC=>heartwoodC (and for N)
      • SlowSOM=>slowSOM
      • McrbC=>mcrbC and McrbN=>mcrbN
      • added totC
    • renamed the following column names in output_annual_cohorts:
      • nsc=>NSC and nsn=>NSN
      • sapwC=>sapwoodC
      • woodC=>heartwoodC
      • Nupt=>N_uptk
      • Nfix=>N_fxed
      • switched column positions of NPP and GPP

rsofun v5.0.1

  • This model version behaves exactly as the version before.
  • Update was necessary to include description of scripts and data used for the model documentation paper into archive on Zenodo

rsofun v5.0.0

  • new BiomeE forcing data matching that of P-model
    • prec is now called rain
    • rh is now provided as vpd
    • See biomee_gs_leuning_drivers for an example
  • fix Fortran modules leading to segmentation faults using BiomeE model
  • improved documentation

rsofun v4.4.1

  • bugfix Fortran modules and derived types
  • compilation flags for different platforms

rsofun v4.4

  • bugfix on input data type P-model
  • LM3-PPA to BiomeE renaming
  • cost function rewrite
  • update output format (consistency)
  • add water balance variables to P-model output
  • new p-model calibratable parameters
  • rewrite of temperature and soil moisture stress functions
  • update simulation parameters to take netrad, ppfd and ccov as input forcing
  • documentation parameter sensitivity analysis
  • documentation on the data format
  • document calibration diagnostic and model uncertainty calculation
  • more transparent licensing and copyright statements in COPYING file

rsofun v4.3

  • Consistent variable names p-model / biomee
  • optimization stability BayesianTools
  • documentation
  • Bugfixes

rsofun v4.2

  • Canopy transfer solved for BiomeE with P-model
  • Bugfixes

rsofun v4.1

  • Catching aborting in FORTRAN part to avoid R session crashes

rsofun v4.0

  • Public release after refactored code