DynACof: Dynamic Agroforestry Coffee Crop Model

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

Description

The DynACof process-based model computes plot-scale Net Primary Productivity, carbon allocation, growth, yield, energy, and water balance of coffee plantations according to management, while accounting for spatial effects using metamodels from the 3D process-based model MAESPA. The model also uses cohorts for the development of the coffee buds and fruits to better represent fruit carbon demand distribution along the year.

Usage

DynACof(
  Period = NULL,
  WriteIt = F,
  ...,
  parallel = TRUE,
  output_f = ".RData",
  Inpath = NULL,
  Outpath = Inpath,
  Simulation_Name = "DynACof",
  FileName = list(Site = "1-Site.R", Meteo = NULL, Soil = "3-Soil.R", Coffee =
    "4-Coffee.R", Tree = NULL)
)

Arguments

Period	Period of time to be simulated, see details. Default: NULL
WriteIt	If TRUE, write the outputs to disk using write.results(), see details. Default: FALSE
...	Further arguments to pass to write.results().
parallel	Boolean. Parallelize the computation over crop rotations.
output_f	Output format. If output_f = ".RData", the output list will be saved as a unique .RData file. Any other value: write the output list in several .csv and .txt files. Default: .RData
Inpath	Path to the input parameter list folder, Default: NULL (take package values)
Outpath	Path pointing to the folder were the results will be writen, Default: Outpath = Inpath
Simulation_Name	Character name of the simulation file name if WriteIt = T. Default: "DynACof"
FileName	A list of input file names : Site Site parameters file name, see details. Default: '1-Site.R' Meteo Meteo parameters file name, see details. Default: '2-Meteorology.txt' Soil Soil parameters file name, see details. Default: '3-Soil.R' Coffee Coffee parameters file name, see details. Default: '4-Coffee.R' Tree Shade tree parameters file name, see details. Default: NULL Default input files are provided with the package as an example parameterization.

Details

The user can import a simulation using base::readRDS(). Almost all variables for coffee exist also for shade trees with the suffix _Tree after the name of the variable, e.g. : LAI = coffee LAI, LAI_Tree = shade tree LAI. Special shade tree variables (see return section) are only optional, and it may have more variables upon parameterization because variables can be added in the metamodels parameter file in Metamodels() or Allometries(). Important : It is highly recommended to set the system environment timezone to the one from the meteorology file. For example the default meteorology file (Aquiares()) has to be set to Sys.setenv(TZ="UTC").

Value

Return invisibly a list containing three objects (Parameters, Meteo and Sim):

• Sim: A data.frame of the simulation outputs at daily time-step:

  Type	Var	unit	Definition
  General	Cycle	-	Plantation cycle ID
  	Plot_Age	year	Plantation age (starting at 1)
  	Plot_Age_num	year (numeric)	Numeric age of plantation
  	LAIplot	m2 leaves m-2 soil	Plot (Coffee + Shade Tree if any) Leaf Area Index
  Suffixes for Coffee organs	x_RE	-	Reserves
  	x_SCR	-	Stump and Coarse roots
  	x_Fruit	-	Fruit
  	x_Shoot	-	Resprout wood (= branches)
  	x_FRoot	-	Fine roots
  	x_Leaf		Leaves
  Suffixes for Shade Tree org.	x_RE_Tree	-	Reserves
  	x_Stem_Tree	-	Stem (= trunk)
  	x_Branch_Tree	-	Branches
  	x_CoarseRoot_Tree	-	Coarse roots
  	x_FRoot_Tree	-	Fine roots
  	x_Leaf_Tree		Leaves
  Energy	Rn_tot	MJ m-2 d-1	System net radiation
  	Rn_Tree	MJ m-2 d-1	Shade tree net radiation
  	Rn_Coffee	MJ m-2 d-1	Coffee net radiation
  	Rn_Soil	MJ m-2 d-1	Soil net radiation
  	Rn_Soil_SW	MJ m-2 d-1	Soil net radiation computed using Shuttleworth & Wallace (1985) for reference
  	LE_x	MJ m-2 d-1	System/Coffee/Tree/Soil latent heat
  	H_x	MJ m-2 d-1	System/Coffee/Tree/Soil sensible heat
  	Q_Soil	MJ m-2 d-1	Soil heat transport
  	Transmittance_Tree	fraction	Fraction of light transmitted by the shade trees
  	PAR_Trans_Tree	MJ m-2 d-1	Light transmitted by the shade trees canopy
  	PAR_Trans	MJ m-2 d-1	Light transmitted by the Coffea canopy
  	K_Dir	-	Direct light extinction coefficient
  	K_Dif	-	Diffuse light extinction coefficient
  	APAR	MJ m-2 d-1	Absorbed PAR by the plant
  	APAR_Dif	MJ m-2 d-1	Absorbed diffuse PAR (Direct is APAR-APAR_Dif)
  	lue	gC MJ	Light use efficiency
  	Tleaf_Coffee	deg C	Coffee canopy temperature computed by DynACof
  	WindSpeed_x	m s-1	Wind speed at the center of the layer
  	TairCanopy_x	deg C	Air tempetature at the center of the layer
  	DegreeDays_Tcan	deg C	Growing degree days computed using Coffee Canopy Temperature
  Carbon	GPP	gC m-2 d-1	Gross primary productivity
  	Consumption_RE	gC m-2 d-1	Daily reserve consumption
  	Carbon_Lack_Mortality	gC m-2 d-1	Mortality from a higher carbon consumption than Supply
  	Rm	gC m-2 d-1	Total Coffee maintenance respiration
  	Rm_x	gC m-2 d-1	Maintenance respiration at organ scale
  	Rg	gC m-2 d-1	Total Coffee growth respiration
  	Rg_x	gC m-2 d-1	Growth respiration at organ scale
  	Ra	gC m-2 d-1	Coffee layer autotrophic respiration (=Rm+Rg)
  	Demand_x	gC m-2 d-1	C demand at organ scale (fruit, leaf and fine root only)
  	Alloc_x	gC m-2 d-1	C allocation to organ net of Rm (NPP+Rg)
  	Supply	gC m-2 d-1	C supply at the begining of the day at layer scale (GPP+Reserve consumption-Rm)
  	Supply_x	gC m-2 d-1	C supply to organ, net of Rm
  	NPP	gC m-2 d-1	Net primary productivity at layer scale
  	NPP_x	gC m-2 d-1	Net primary productivity at organ scale
  	Mnat_x	gC m-2 d-1	Organ natural mortality (= due to lifespan)
  	Mprun_x	gC m-2 d-1	Organ mortality due to pruning
  	M_ALS	gC m-2 d-1	Coffee leaf mortality from American Leaf Spot
  	Mortality_x	gC m-2 d-1	Total organ mortality
  	LAI	m2 leaves m-2 soil	Leaf Area Index
  	CM_x	gC m-2 d-1	Organ C mass
  	DM_x	gDM m-2 d-1	Organ dry mass
  Fruit development	BudInitPeriod	boolean	Bud initiation period (BIP)
  	Budinit	Buds d-1	Total Number of Buds Initiated per day
  	ratioNodestoLAI	Nodes LAI-1	Number of fruiting nodes per LAI unit
  	Temp_cor_Bud	fraction	Temperature correction factor for bud development
  	pbreak	0-1	Daily probability of bud dormancy break
  	BudBreak	Buds d-1	Total number of buds breaking dormancy per day
  	SM	g m-2 d-1	Coffee Fruit Sucrose Mass
  	SC	g Sugar gDM	Coffee Fruit Sucrose Content
  	Maturation_duration	days Fruit cohort-1	Coffee Fruit Total Maturation Duration for each cohort
  	Harvest_Maturity_Pot	Fraction	Daily average fruit maturity (0-1)
  	Date_harvest	day of year	date of harvest
  	Harvest_Fruit	gC m-2	Total fruit carbon mass at harvest
  	Harvest_Maturity	Fraction	Average fruit maturity at harvest (0-1)
  	Overriped_Fruit	gC m-2 d-1	Overriped fruits that fall onto the ground
  Water	IntercMax	mm	Maximum potential rainfall interception by canopy
  	CanopyHumect	mm	Rainfall interception by canopy
  	Throughfall	mm	Rainfall not intercepted by the canopy, coming to the soil
  	SuperficialRunoff	mm	Water runoff from the superficial soil layer
  	ExcessRunoff	mm	Discharge from the superficial soil layer
  	TotSuperficialRunoff	mm	Sum of discharge+ExcessRunoff
  	InfilCapa	mm	Superficial water infiltration capacity to first layer of soil
  	Infiltration	mm	Superficial water infiltration to first layer of soil
  	Drain_[1-3]	mm	Water drainage from soil layer 1, 2 or 3
  	WSurfaceRes	mm	Soil water content from the surface layer
  	W_tot	mm	Total soil profile water content
  	W_[1-3]	mm	Soil water content from the layer 1, 2 or 3
  	REW_tot	-	Relative extractable water from the soil
  	REW_[1-3]	-	Relative extractable water from the layer 1, 2 or 3
  	EW_tot	mm	Extractable water from the soil
  	EW_[1-3]	mm	Extractable water from the layer 1, 2 or 3
  	SWD	mm	soil water deficit
  	RootWaterExtract_[1-3]	mm	Root water extraction for soil layer 1 to 3
  	IntercRevapor	mm	Evaporation by canopy
  	T_x	mm	Transpiration at system/Coffee/Tree scale
  	E_Soil	mm	Soil evaporation
  	ETR	mm	System evapotranspiration
  	SoilWaterPot	MPa	Soil water potential
  	PSIL	Mpa	Coffee leaf water potential
  Special shade tree variables	LA_Tree	m2 leaves tree-1	shade tree leaf area
  	Crown_H_Tree	m	Crown height
  	Trunk_H_Tree	m	Trunk height
  	Height_Tree	m	Shade tree total height (used for boundary conductance), set to 0 if no shade trees
  	DBH_Tree	m	Diameter at breast height
  	LAD_Tree	m2 m-3	Shade tree Leaf Area Density
  	CrownRad_Tree	m	Crown radius
  	CrownProj_Tree	m2 crown tree-1	Crown projection
  	Stocking_Tree	tree m-2	Shade tree density
  	TimetoThin_Tree	boolean	Days on which tree is thinned
  	MThinning_x_Tree	gc m-2 d-1	Mortality due to thining at organ scale

• Meteo: A data.frame of the input meteorology, potentially coming from the output of Meteorology():

  Var	unit	Definition	If missing
  Date	POSIXct	Date in POSIXct format	Computed from start date parameter, or set a dummy date if missing
  year	year	Year of the simulation	Computed from Date
  DOY	day	day of the year	Computed from Date
  Rain	mm	Rainfall	Assume no rain
  Tair	Celsius	Air temperature (above canopy)	Computed from Tmax and Tmin
  Tmax	Celsius	Maximum air temperature during the day	Required (error)
  Tmin	Celsius	Minimum air temperature during the day	Required (error)
  RH	%	Relative humidity	Not used, but prefered over VPD for Rn computation
  RAD	MJ m-2 d-1	Incident shortwave radiation	Computed from PAR
  Pressure	hPa	Atmospheric pressure	Computed from VPD, Tair and Elevation, or alternatively from Tair and Elevation.
  WindSpeed	m s-1	Wind speed	Taken as constant: Parameters$WindSpeed
  CO2	ppm	Atmospheric CO2 concentration	Taken as constant: Parameters$CO2
  DegreeDays	Celsius	Growing degree days	Computed using GDD()
  PAR	MJ m-2 d-1	Incident photosynthetically active radiation	Computed from RAD
  FDiff	Fraction	Diffuse light fraction	Computed using Diffuse_d() using Spitters et al. (1986) formula
  VPD	hPa	Vapor pressure deficit	Computed from RH
  Rn	MJ m-2 d-1	Net radiation (will be depreciated)	Computed using Rad_net() with RH, or VPD
  DaysWithoutRain	day	Number of consecutive days with no rainfall	Computed from Rain
  Air_Density	kg m-3	Air density of moist air (ρ) above canopy	Computed using bigleaf::air.density()
  ZEN	radian	Solar zenithal angle at noon	Computed from Date, Latitude, Longitude and Timezone

• Parameters: A list of the input parameters (see site())

Note

All variable units are available as attributes (see example).

For simulations with custom initialisations (e.g. at age > 0), or running a simulation day by day, see dynacof_i().

See Also

Meteorology() site()

Examples

## Not run: 
if(interactive()){
 Sys.setenv(TZ="UTC")
 Sim= DynACof(Period= as.POSIXct(c("1979-01-01", "1980-12-31")))

 # Get the units of the input variables:
 attr(Sim$Meteo,"unit")

 # Get the units of the output variables:
 attr(Sim$Sim,"unit")
 }

## End(Not run)

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