1.3.0 release

• Tsoil used for Rm roots now
• Remove MaxTT from GDD
• Replace Tleaf_Coffee by TairCanopy in DegreeDays_Tcan and T_VG (for ratioNodestoLAI) as it should be (see documentation)
• Put CM_Fruit_Cohort_remain to 0 when harvested
• Add option for no harvest at all
• E_Soil take in priority in surface layer, and then possibly in W_1
• LeafWaterPotential is now fully computed
• Rename LeafWaterPotential into PSIL
• Add PSIL_Tree computation
• Update default metamodels and parameters (revision of article)
• Remove LAI_max dependence for leaf C demand computation
• DynACof.jl related:
  • Update dynacof.jl_setup for dev versions
  • Update dynacof.jl_setup doc + website
  • Add Pkg.free when R terminates
  • Update the code following modifs in julia version (from 69cd69ba69d210e0479b8749deebc9585b58c1c0 to 7239c93bc2c50eb761de330cf4c43429fe18b4ef)
• Runs shade tree model only if Stocking_Tree > 0.0 and remove overcomplicated shade tree models (keep only one now), following DynACof.jl
• Update docs to Roxygen 7.0.0.
• Add startup message
• Fix several bugs:
  • Fix issue in the PENMON implementation
  • FileName reading
  • Fix format of simulation Table returned by DynACof with several cycles
  • Fix error in dynacof_i
  • Fix issues in the soil module
  • Fix transpiration metamodel bug
  • Fix the computation of the overriped fruits (could potentially count the same overriped fruits)
  • Fix issue in soil RootWaterExtract_*
  • Fix issue with LeafWaterPotential (was computed before T_Coffee)

Summer release

• Reformat the code so the shade tree, coffee, soil and energy balance are made by separate functions sequentially
• Add dynacof_i to be able to change a simulation from one (or several) time step to another
• Add DynACof.jl compatibility: now the user can use the Julia version of DynACof directly from the R using the R version of the package. This functionnality require Julia (v > 1.1) to be installed on the computer and available in the path.

DynACof 1.1.2: article version (06/2019)

This version of the model is the one used in the article presenting the model.

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Main changes:

• Externalize coffee metamodels to parameter file + remove Tcan_MAESPA_Coffee as it is computed by the model now
• Add tests for user-defined input parameter
• Add option for model parallelization over crop rotations
• Add ZEN to meteo
• Fix issue on Tleaf_Tree + unit of DELM
• Simplify writing of equations for Tleaf_*
• Use markdown in package documentation
• Update CB with flowers per inflorescences + its doc (+ doc for CN)
• Several bugs/typos fix: e.g. VPD unit when not read from meteo file +
• Update parameter values to match those from the article

DynACof 1.1.1: production version

Main changes:

• Add Temperature-dependent correction for buds (CB) as a function
• Add Temperature-dependent correction for nodes (CN) as a function
• Simplify derivative function of the logarithm (logistic_deriv)
• Add an option for harvest: optimize quantity or quality
• Rename the parameters as in the scientific article and update the inputs
• Update documentation
• Add soil surface temperature computation
• DynACof now calls mainfun(), which regroups all computations.
• update documentation for metamodels

DynACof model

Release used for the research article.

Main changes:

• Improved documentation
• Improved website
• Add input parameter files templates

Several improvements to DynACof + Website !

Several imrpovements:

• epsilon parameters are now true growth cost coefficients (1/previous_espilon)
• Renaming : RainForBudBreak -> R_break ; Reserves_Tree -> RE_Tree
• Tree allometries are now into metamodels
• Use Ks from parameter file instead of hard coded values
• Update Coffea sensible heat flux metamodel
• New computation of Rn_Soil using MAESPA metamodels + replace PARcof by PAR_Trans_Tree and add PAR_Trans (PAR transmitted to soil)
• Add website using pkgdown
• Rm now computed using TairCanopy
• Update T_Tree metamodel
• Add WoodPruningRate as a parameter (it was hard coded !)
• Remove unused WoodDensity_kgDMm3

Model is ready for publication

First release

Model development

The model has been intensively developed to correspond to all our scientific expectations. It has been reshaped to enhance collaboration thanks to its availability as an R package, and thanks to a new simpler way to set the input parameters and meteorology. The model was also thoroughly inspected to avoid any bug.

Evaluation of the model

The model was evaluated on many different measurements and yielded outputs close to the observations for GPP, all Coffee organs carbon and/or dry mass and shade tree (Erythrina poeppigiana) aboveground dry mass and height, net radiation, fruit yield, Latent and sensible heat flux, organs mortality, etc...