NEWS.md

In VEZY/DynACof: A Process-Based Model to Study Growth, Yield and Ecosystem Services of Coffee Agroforestry Systems

DynACof 1.5.1

• Make the package compatible with newer versions of data.table
• Fix error in starting simulation message
• Modified dynacof_i() implementation

DynACof 1.3.0

• 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)

DynACof 1.2.0

• 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

• 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

• 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

DynACof 1.1.0

• Add soil surface temperature computation
• DynACof now calls mainfun(), which regroups all computations.
• update documentation for metamodels

DynACof 1.0.2

• Add templates for input parameters
• Simulation saved using saveRDS (better coding practice)
• Clean old comments in the model
• Update documentation
• Update Website

DynACof 1.0.1

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

DynACof 0.1.2

First news. Will be updated from now on.

VEZY/DynACof documentation built on Feb. 3, 2021, 8:52 p.m.