MaizeGro: Simulation of Maize, Growth, LAI, Photosynthesis and...
In BioCro: Simulation of Biomass Crops

Description Usage Arguments Details Value Author(s) See Also Examples

It takes weather data as input (hourly timesteps) and several parameters and it produces phenology, photosynthesis, LAI, etc.

MaizeGro(WetDat, plant.day = NULL, emerge.day = NULL, harvest.day = NULL, 
    plant.density = 7, timestep = 1, lat = 40, canopyControl = list(), 
    MaizeSeneControl = list(), photoControl = list(), MaizePhenoControl = list(), 
    MaizeCAllocControl = list(), laiControl = list(), soilControl = list(), 
    MaizeNitroControl = list(), centuryControl = list())

`WetDat`	weather data as produced by the `weach` function.
`plant.day`	Planting date (format 0-365)
`emerge.day`	Emergence date (format 0-365)
`harvest.day`	Harvest date (format 0-365)
`plant.density`	Planting density (plants per meter squared, default = 7)
`timestep`	Simulation timestep, the default of 1 requires houlry weather data. A value of 3 would require weather data every 3 hours. This number should be a divisor of 24.
`lat`	latitude, default 40.
`canopyControl`	List that controls aspects of the canopy simulation. It should be supplied through the `canopyParms` function. `Sp` (specific leaf area) here the units are ha Mg^{-1}. If you have data in m^2 of leaf per kg of dry matter (e.g. 15) then divide by 10 before inputting this coefficient. `SpD` decrease of specific leaf area. Empirical parameter. Default 0. example value (1.7e-3). `nlayers` (number of layers of the canopy) Maximum 50. To increase the number of layers (more than 50) the `C` source code needs to be changed slightly. `kd` (extinction coefficient for diffuse light) between 0 and 1. `mResp` (maintenance respiration) a vector of length 2 with the first component for leaf and stem and the second component for rhizome and root. For other terms see `BioGro`.
`MaizeSeneControl`	List that controls aspects of senescence simulation. It should be supplied through the `MaizeSeneParms` function. `senLeaf` Thermal time at which leaf senescence will start. `senStem` Thermal time at which stem senescence will start. `senRoot` Thermal time at which root senescence will start.
`photoControl`	List that controls aspects of photosynthesis simulation. It should be supplied through the `MaizePhotoParms` function. `vmax` Vmax passed to the `c4photo` function. `alpha` alpha parameter passed to the `c4photo` function. `kparm` kparm parameter passed to the `c4photo` function. `theta` theta parameter passed to the `c4photo` function. `beta` beta parameter passed to the `c4photo` function. `Rd` Rd parameter passed to the `c4photo` function. `Catm` Catm parameter passed to the `c4photo` function. `b0` b0 parameter passed to the `c4photo` function. `b1` b1 parameter passed to the `c4photo` function.
`MaizePhenoControl`	argument used to pass parameters related to phenology characteristics
`MaizeCAllocControl`	Carbon allocation partitioning for maize. Similar to `BioGro`.
`soilControl`	See function `BioGro` for details.
`MaizeNitroControl`	See `MaizeNitroParms`
`centuryControl`	See function `BioGro` for details.
`laiControl`	argument used to pass parameters related to leaf area index. Use the function laiParms for this. The additional parameters depend on the method used. For the "TT" method the leaf area index only depends on the thermal time and the relevant parameters are TTcoef and max.lai. The method "ind-leaf-Lizaso" has been tested more and the reference documentation is the Lizaso et al. (2003) paper. It is currently the default. At the moment it is not sensitive to stress. This need to be fixed.

The phenology follows the 'Corn Growth and Development' Iowa State Publication.

It currently returns a list with the following components

`DayofYear`	Day of the year (1-365)
`Hour`	Hour of the day (0-23)
`TTTc`	Accumulated thermal time
`PhenoStage`	Phenological stage of the crop
`CanopyAssim`	Hourly canopy assimilation, (Mg ha^-1 ground hr^-1).
`CanopyTrans`	Hourly canopy transpiration, (Mg ha^-1 ground hr^-1).
`LAI`	Leaf Area Index
`Leaf`	Leaf biomass (Mg ha-1)
`Stem`	Stem biomass (Mg ha-1)
`Root`	Root biomass (Mg ha-1)
`Grain`	Grain biomass - yield - (Mg ha-1)
`LAImat`	Leaf Area Index matrix - leaf area index by leaf - (m^2 m^-2)
`VmaxVec`	Vmax vector - it changes if a relationship with Nitrogen is defined
`LeafNVec`	Leaf N concentration (g m^-2)
`cwsMat`	current water status matrix - this will have more than one column if the soil model is multilayered (m^3 m^-3)
`psimMat`	soil water potential (MPa)
`rdMat`	root density matrix (Mg ha^-1)
`SCpools`	Soil carbon pools
`SNpools`	soil nitrogen pools
`LeafPsimVec`	Leaf water potential (MPa)
`SoilEvaporation`	soil evaporation (Mg ha-1). plotting with the plot(x,plot.kind="ET") will use mm/day units.
`SoilWatCont`	Average soil water content for all layers (volumetric)
`SomatalCondCoefs`	Stomatal conductance coefficient (0-1)

Fernando E Miguez

BioGro Use plotting methods such as plot(x, plot.kind="DB") for dry biomass plot(x, plot.kind="SW") for soil water plot(x, plot.kind="ET") for EvapoTranspiration plot(x, plot.kind="cumET") for cummulative EvapoTranspiration plot(x, plot.kind="LAI") for Leaf Area Index plot(x, plot.kind="pheno") for phenology

## Not run: 
data(cmi05)
res <- MaizeGro(cmi05, plant.day = 110,
                emerge.day = 120, harvest.day=300)
                

## Explore data with plots
plot(res, plot.kind="DB") ## for dry biomass
plot(res, plot.kind="SW") ## for soil water
plot(res, plot.kind="ET") ## for EvapoTranspiration
plot(res, plot.kind="cumET") ## for cummulative EvapoTranspiration
plot(res, plot.kind="LAI") ## for Leaf Area Index
plot(res, plot.kind="pheno") ## for phenology


## End(Not run)