Description Usage Arguments 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
).
A typical usage of setPhy
is :
1 2 |
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,
1 | myplantlist <- includePhy(myplantlist,leafpardataframe)
|
1 2 3 4 5 6 7 8 9 | includePhy(object, ...)
## S3 method for class 'plant3d'
includePhy(object, ...)
## S3 method for class 'plant3dlist'
includePhy(object, phydfr, ...)
setPhy(leafmodel, leafpars = list())
|
object |
A 'plant3d' object (see |
phydfr |
A dataframe with leaf parameters, for batch analyses (see Details). |
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). |
... |
Further arguments passed to 'setPhy' |
An object of class 'ypphy'.
Remko Duursma
Farquhar
,lightresponse
,ypreport
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