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).
A typical usage of setPhy is :
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:
myplant <- includePhy(myplant, eucphy)
To find out whether a plant has a physiology object saved in it, simply type:
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,
myplantlist <- includePhy(myplantlist,leafpardataframe)
includePhy(object, ...)
"includePhy"(object, ...)
"includePhy"(object, phydfr, ...)
setPhy(leafmodel, leafpars = list())constructplant), or a
'plant3dlist' object.Farquhar,lightresponse,ypreport