YplantQMC (version 0.6-3)

constructplant: Construct a 3D plant

Description

Read 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. 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: [object Object],[object Object],[object Object],[object Object] 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

Usage

constructplant(input = NULL, lfile = NULL, multiplier = 1, X0 = 0,
  Y0 = 0, Z0 = 0, warn = FALSE, quiet = FALSE)

readplantlist(pfiles = NA, lfiles = NA, lpk = "leafplantkey.txt",
  multiplier = 1)

Arguments

input

One of several possible inputs that contain the plant structure.

lfile

A leaf file. If not provided, a built-in triangle leaf is used.

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.

Value

• 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). An object of class plant3dlist

See Also

plot.plant3d,readp

Examples

# 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))