ModifyPfiles: Modify Yplant input files.
In YplantQMC: Plant Architectural Analysis with Yplant and QuasiMC

Description Usage Arguments Value Author(s) See Also Examples

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.

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.

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

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

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

`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.
`newangles`	A vector of angles to be used in the new p file (optional, in stead of distobj).
`distobj`	An object of class `angledist`, that is a leaf angle distribution (See examples).
`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.

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

Remko Duursma

readp, fitdistribution, readl, constructplant

## 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)