YplantDay: Run a simulation over a day with YplantQMC
In YplantQMC: Plant architectural analysis with Yplant and QuasiMC.

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

Interface to daily simulations with YplantQMC. Two objects are required to run the simulation: a plant3d object, containing the plant structure information, and a met object, containing weather data, solar position, and number of timesteps.

Optionally, a phy object is used which contains the leaf gas exchange model for the simulation, to calculate photosynthesis (and possibly transpiration rate) from light capture and other weather variables.

Also optional is the use of a hemi object, which specifies shading by a canopy.

If you don't know where to start, run the example at the bottom of this page.

## S3 method for class 'plant3d'
YplantDay(x, met, phy = NULL, hemi = NULL,quiet=FALSE,
writePSR=TRUE, writeOUT=FALSE, ...)
## S3 method for class 'plant3dlist'
YplantDay(x, met, phy=NULL, hemi=NULL, ...)

`x`	An object of class 'plant3d' or 'plant3dlist' (see `constructplant` and `readplantlist`).
`met`	An object of class 'ypmet', see `setMet`
`phy`	An object of class 'ypphy', see `setPhy`
`hemi`	An object of class 'yphemi', see `setHemi`
`quiet`	If TRUE, does not write messages to the console.
`writePSR`	If TRUE, writes a PSR output file.
`writeOUT`	If TRUE, writes an OUT output file.
`...`	Further arguments passed to `runYplant`

See the arguments list above for the functions that are used to generate each of the four objects. Note that the plant and met objects are required, and phy and hemi are optional.

This function is a user-friendly wrapper for runYplant. That function should be used for all advanced simulations.

The YplantDay functions returns a list of class yplantsim, which has print and plot methods (see Examples).

The list has the following components:

plant: The plant object used in the simulation
phy: If provided, the phy object used in the simulation
hemi: If provided, the hemi object used in the simulation
outdata: A very lengthy dataframe with all results (see below)
nsteps: Number of timesteps
psrdata: Totals and averages by timestep (dataframe), see psrdata
met: The met object used in the simulation

The outdata dataframe in the yplantsim object lists results for individual leaves, has the following variables.

timeofday: Time of day for current timestep (hours)
leafnr: Leaf number
timestep: Length of current timestep (seconds)
PAR0: Above-canopy PAR
PARleaf: Total PAR absorption
PARdir: Direct solar radiation PAR absorption
PARdiff: Diffuse PAR absorption
reldiff: Relative diffuse radiation absorption (0-1).
reldir: Relative direct radiation absorption (0-1).
LA: Individual leaf area (mm2)
LAproj: Projected leaf area (mm2)
LAsunlit: Sunlit, or 'displayed' leaf area (mm2)
A: CO2 assimilation rate (mu mol m-2 s-1)
E: Transpiration rate (mmol m-2 s-1)
gs: Stomatal conductance (mol m-2 s-1)
A0: CO2 assimilation rate for a horizontal unshaded leaf (mu mol m-2 s-1)

Where PAR is photosynthetically active radiation (mu mol m-2 s-1).

The absorptions reldiff and reldir are relative to an unshaded horizontal surface.

To extract relative diffuse radiation absorption from an yplantsim object, for example:

1 2	mysim <- YplantDay(myplant, mymet) reldif <- mysim$outdata$reldiff

Remko Duursma

See http://www.remkoduursma/yplantqmc

runYplant,makereport

## Not run: 
# Set location,
southernfrance <- setLocation(lat=44)

# A daily weather object, use a constant beam fraction of 0.4.
sunnyday <- setMet(southernfrance, month=6, day=21, nsteps=12, Tmin=9, Tmax=29, PARday=22,
	fbeamday=0.4, fbeammethod="constant")

# Light response curve:
toonalrc <- setPhy("lightresponse", 
	leafpars=list(Amax=14.5, Rd=1.4, phi=0.05, theta=0.5, reflec=0.1, transmit=0.05))

# Run YplantQMC for a day. Use the built-in 'largegap' hemiphoto.
toonarun <- YplantDay(toona, sunnyday, toonalrc, largegap)

## End(Not run)