R/setPhy.R

In YplantQMC: Plant Architectural Analysis with Yplant and QuasiMC

#'@title Make a leaf physiology object
#'
#'@description 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 \code{\link{Farquhar}}), or a simple non-rectangular light response
#'curve (see \code{\link{lightresponse}}).
#'
#'A typical usage of \code{setPhy} is : 
#'\preformatted{ 
#'eucphy <- setPhy("Farquhar", leafpars=list(Vcmax=80, Jmax=140, Rd=1, G1=7)) 
#'} 
#'This object may be used when running Yplant directly (see \code{\link{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
#'\code{includePhy} function: 
#'\preformatted{ myplant <- includePhy(myplant, eucphy) } 
#'
#'To find out whether a plant has a physiology object saved in it,
#'simply type: 
#'
#'\preformatted{ myplant$phy } 
#'
#'If there is a physiology object, it
#'will print a summary of its contents, otherwise it is \code{NULL}.
#'
#'For batch analyses, \code{includePhy} can set the leaf parameters for a list
#'of plants (as constructed with \code{\link{readplantlist}}). To do this,
#'construct a dataframe where each row corresponds to a set of parameters for a
#'plant, and the columns include \code{pfile} (required, to match the
#'parameters to the plants in the list), \code{leafmodel} (required, the name
#'of the leaf model), and further any parameters that can be accepted by the
#'leafmodel (for example, \code{Vcmax} or \code{Amax}, and so on). Then use
#'this command, 
#'
#'\preformatted{ myplantlist <- includePhy(myplantlist,leafpardataframe) }
#'
#'@aliases setPhy includePhy.plant3d includePhy includePhy.plant3dlist
#'@param leafmodel Name of the leaf gas exchange model ('Farquhar', or
#''lightresponse', or user-defined).
#'@param leafpars List of parameters that are passed to the leafmodel (and
#'should be arguments of that function).
#'@param object A 'plant3d' object (see \code{\link{constructplant}}), or a
#''plant3dlist' object.
#'@param phydfr A dataframe with leaf parameters, for batch analyses (see
#'Details).
#'@param \dots Further arguments passed to 'setPhy'
#'@return An object of class 'ypphy'.
#'@author Remko Duursma
#'@seealso
#'\code{\link{Farquhar}},\code{\link{lightresponse}},\code{\link{ypreport}}
#'@keywords misc
#'@export
setPhy <- function(leafmodel, leafpars=list()){

	l <- list()
		
	# Store leafmodel
	l$leaffunction <- get(leafmodel)  # function
	l$leafmodel <- leafmodel          # name of function
	
	# Store leaf parameters.
	l$leafpars <- leafpars
	
	class(l) <- "ypphy"

return(l)
}