setPhy: Make a leaf physiology object
In YplantQMC: Plant architectural analysis with Yplant and QuasiMC.

Description Usage Arguments Details Value Author(s) See Also

Constructs an object of class 'ypphy', which contains a function that calculates leaf photosynthesis and transpiration (and possibly other variables), from weather data (air temperature, humidity, etc.), and absorbed PAR.

Users can write their own leaf gas exchange functions to be included in a physiology object, or use one of two built in functions: the Farquhar model (see Farquhar), or a simple non-rectangular light response curve (see lightresponse).

setPhy(leafmodel, leafpars = list())

## S3 method for class 'plant3d'
includePhy(object, ...)
## S3 method for class 'plant3dlist'
includePhy(object, phydfr, ...)

`leafmodel`	Name of the leaf gas exchange model ('Farquhar', or 'lightresponse', or user-defined).
`leafpars`	List of parameters that are passed to the leafmodel (and should be arguments of that function).
`object`	A 'plant3d' object (see `constructplant`), or a 'plant3dlist' object.
`phydfr`	A dataframe with leaf parameters, for batch analyses (see Details).
`...`	Further arguments passed to 'setPhy'

A typical usage of setPhy is :

1	eucphy <- setPhy("Farquhar", leafpars=list(Vcmax=80, Jmax=140, Rd=1, G1=7))

This object may be used when running Yplant directly (see YplantDay, or it may be saved into a plant object (which makes it somewhat easier to organize, especially for batch processing). This is achieved with the includePhy function:

1	myplant <- includePhy(myplant, eucphy)

To find out whether a plant has a physiology object saved in it, simply type:

1	myplant$phy

If there is a physiology object, it will print a summary of its contents, otherwise it is NULL.

For batch analyses, includePhy can set the leaf parameters for a list of plants (as constructed with readplantlist). To do this, construct a dataframe where each row corresponds to a set of parameters for a plant, and the columns include pfile (required, to match the parameters to the plants in the list), leafmodel (required, the name of the leaf model), and further any parameters that can be accepted by the leafmodel (for example, Vcmax or Amax, and so on). Then use this command,