Reference

Main function Call to the DynACof model (either in pure R or in Julia)
DynACof()	Dynamic Agroforestry Coffee Crop Model
dynacof_i()	Step-by-step DynACof
dynacof.jl()	Run DynACof.jl (Julia version of DynACof)
dynacof_i.jl()	Step-by-step dynacof.jl()
Julia version utilities Functions used to instantiate Julia + DynACof.jl
dynacof.jl_setup()	Setup Julia call
dynacof.jl_update()	Update DynACof.jl
Imports Imports values from files or default, check consistancy, and compute missing variables if needed
Meteorology()	Import Meteorology for model input
Import_Parameters()	Import model parameters
Meteorology functions Compute missing meteorology variables
Rad_ext()	Daily extra-terrestrial radiation
Rad_net()	Daily net radiation
GDD()	Daily growing degree days (GDD)
Diffuse_d()	Diffuse fraction
Evapotranspiration Compute the daily evaporation or transpiration
PENMON()	Evapotranspiration
Aerodynamic conductance Different functions to compute the aerodynamic conductances
Gb_hForced() Gb_hFree()	Leaf boundary layer conductance for heat under forced and free convection
Gb_h()	Leaf boundary layer conductance for heat
GetWind()	Get the average wind speed at center of canopy layer
G_bulk()	Bulk aerodynamic conductance
G_interlay()	Canopy layer to canopy layer aerodynamic conductance
G_soilcan()	Canopy to soil aerodynamic conductance
GBCANMS()	Canopy and Soil boundary layer conductance (depreciated)
Modules Functions used to compute allometries, metamodels or diseases that the user can change (from input parameter files)
Light_extinction_K() Metamodels_soil()	MAESPA metamodels
Allometries()	Shade tree allometries (optional)
ALS()	American Leaf Spot
Fruiting Helpers to compute coffee fruit related variables
Sucrose_cont_perc()	Fruit sucrose accumulation
CB()	Temperature-dependent correction function for buds (CB)
CN()	Temperature-dependent correction coefficient for nodes (CN)
Helpers Little functions used as helpers
cos_deg() sin_deg() tan_deg() acos_deg() asin_deg() atan_deg()	Trigonometric Functions (degree)
Paliv_dis()	Continuous percentage of living tissue distribution
logistic() logistic_deriv()	Logistic function helpers
Simulation-class	Generator for class Simulation (simulation object)
test_parameters()	Tests on input parameters
Data Example data or parameters
Aquiares	Aquiares meteorology.
coffee() site() soil() Tree()	Default (example) parameter functions
Constants()	Constants used in the DynACof package
varnames	Output variables
Writing Write the results to disk
write.results()	Write output results to disk