constructplant: Construct a 3D plant
In YplantQMC: Plant architectural analysis with Yplant and QuasiMC.

Description Usage Arguments Details Value Author(s) See Also Examples

Read in legacy-style Yplant input files into a special object, to be used in any analysis in YplantQMC.

The function constructs an object of class plant3d, based on Yplant input files (.p and .l/.lf). Various methods exist for plant3d objects, in particular plot.plant3d and summary.plant3d.

For batch analyses, the function readplantlist reads a number of files at a time, and stores the results in a special list (of class plant3dlist).

Three plants are provided with YplantQMC (and automatically loaded) :toona, pilularis and sugarmaple. See plantexamples.

To learn about the format of P and L files, read the detailed account on the Prometheus wiki (Pearcy, Falster & Duursma 2011): http://goo.gl/Hmyv6.

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constructplant(pfile = NULL, lfile = NULL, qfile = NULL, multiplier=1.0, 
X0 = 0, Y0 = 0, Z0 = 0, warn=FALSE, quiet=FALSE)
readplantlist(pfiles=NA, lfiles=NA, lpk="leafplantkey.txt", multiplier=1)

`pfile,lfile`	Name of .p and .l (or .lf) file.
`qfile`	Optionally, instead of a pfile, a Q file format. See Details.
`multiplier`	Multiplies length dimensions, e.g. to change units.
`X0,Y0,Z0`	New x,y,z coordinate of the stem base.
`warn`	If TRUE, writes warnings of minor issues with P file format.
`quiet`	If TRUE, no messages are ever shown.
`pfiles,lfiles`	Vectors of .p files and .l files.
`lpk`	Optionally, a 'leafplantkey' file. See Details.

For legacy Yplant users (Pearcy and Yang 1996, see http://goo.gl/Hmyv6), you will find that constructplant is much more robust with respect to malformed input files. It will also attempt to write error messages when things go wrong.

The Q file format is an alternative to .P files, and is much easier to use if the virtual plant does not have stem sections. There are seven columns:

X,Y,Z: Coordinates of the leaf base
ang,az: Angle and azimuth of the normal to the leaf surface
or: Orientation (azimuth angle) of the midrib
L: Leaf length

The file is space-delimited (such as the output of write.table), and includes column headers (exactly named as above).

The leafplantkey file is a convenient way to organize a large number of plant files. This is a simple comma-separated text file without headers. The order is pfile,lfile (without quotes). For example, a "leafplantkey.txt" file may look like this:

acaflo1.p,acaflo.l
acaflo2.p,acaflo.l
acaflo3.p,acaflo.l
acamyr1.p,acamyr.l
acamyr2.p,acamyr.l
acamyr3.p,acamyr.l
acasua1.p,acasua.l
acasua2.p,acasua.l
acasua4.p,acasua.l
acasuaR02.p,acasua.l
acasuaR05.p,acasua.l
acasuaR09.p,acasua.l

In the case of constructplant, an object of class plant3d. For readplantlist, an object of class plant3dlist (which is simply a list of objects as generated by constructplant to ease batch analyses).

Remko Duursma

plot.plant3d,readp

## Not run: 
# Read one plant:
myplant <- constructplant("sompfile.p","somelfile.l")

# Pfile was in cm - should be in mm. Multiply all length dimensions by 10.
myplant <- constructplant("sompfile.p","somelfile.l", multiplier=10)

# Read a couple of plants. 
myplants <- constructplant(pfiles=c("plant1.p","plant2.p"), lfiles=rep("leaf.l",2))


## End(Not run)