ModifyPfiles: Modify Yplant input files.

In YplantQMC: Plant architectural analysis with Yplant and QuasiMC.

Description

Reads a plant file (a Yplant input file with extension .p, known as a pfile), and writes a new pfile, by modifying angles, internode lengths, or segment diameters.

Usage

modifypfile(pfile = NA, whichvar = NA, outputfile = "tmp.p", 
newvalues = NULL)

replaceangles(whichangle="An.3", pfile=NA, outputfile = NA,
newangles = NULL, distobj = NULL)

changeinternodes(pfile=NA,outputfile = "tmp.p",method=c("perc","constant"),
	changeperc=50, consvalue = NA)

Arguments

whichangle	By default the leaf angle, or one of the other angles (see Details).
pfile	Name of the .p file.
outputfile	Name of the new file.
distobj	An object of class angledist, that is a leaf angle distribution (See examples).
newangles	A vector of angles to be used in the new p file (optional, in stead of distobj).
whichvar	Name of variable in p file to modify (see readp for list of variables.
newvalues	Vector of new values for the variable that is to be replaced.
method	for changeinternodes, a percentage change ("perc") or a new constant value ("constant").
changeperc	If method="perc", change the internodes by this percentage of their orginal value.
consvalue	If method="constant", change all internodes to this constant value.

Details

The function 'modifypfile' is a general function that can be used to modify any variable in a pfile. The following variables can be changed in a pfile :

Az, An

Azimuth and angle of stem sections

Or

Orientation angle of the midrib of the leaf

Az.1, An.1

Branch sections

Az.2, An.2

Petioles

Az.3, An.3

Leaves

The function replaceangles is a specialized version for replacing leaf angles (and do some specific error checking, or sampling from leaf angle distributions). The function changeinternodes is a special function for lengths of woody segments (technically not quite the same as internodes!).

For replaceangles, an object of class angledist can be constructed with the angledist function in package LeafAngle (See Example below) or from fitting to a sample with fitdistribution. If angles are provided but the vector is too short, the vector will be sampled with replacement.

Value

A new pfile is created, by default with the name "tmp.p", unless the argument outputfile is set.

Author(s)

Remko Duursma

See Also

readp, fitdistribution, readl, constructplant

Examples

## Not run: 

# Replace angles by sampling from an ellipsoidal distribution:
mydist <- angledist("ellipsoid", distpars=0.7)
replaceangles(pfile="someplant.p", distobj=mydist)

# Make constant angles:
replaceangles(pfile="someplant.p", newangles=45)

# Change new file name:
replaceangles(pfile="someplant.p", outputfile="someplant 45degrees.p", newangles=45)

# Change petiole orientation, choose pfile with dialog box:
replaceangles("Az.2", newangles=runif(300, 0, 360))

# Modify various variables in a pfile, until we end up with an artificial plant,
# useful for testing.
# Order of changes, in this case (although it does not matter!):
# Leaf azimuth, leaf orientation, leaf angle, petiole length, petiole angle.
modifypfile("originalplant.p", whichvar="Az.3", outputfile="testplant.p", newvalues=45)
modifypfile("testplant.p", whichvar="Or", outputfile="testplant.p", newvalues=45)
modifypfile("testplant.p", whichvar="An.3", outputfile="testplant.p", newvalues=-45)
modifypfile("testplant.p", whichvar="L.2", outputfile="testplant.p", newvalues=10)
modifypfile("testplant.p", whichvar="An.2", outputfile="testplant.p", newvalues=45)



## End(Not run)

YplantQMC documentation built on May 2, 2019, 5:50 p.m.