summary.plant3d: Summarize 3D plants

Description

Summarize the 3D plant in various useful ways. Requires an object of class plant3d, made with constructplant.

Usage

"summary"(object, nKErepeat = 10, nsignif = 3, calcSTARbar = FALSE, calcpathlen = FALSE, ...)
"summary"(object, writefile = FALSE, ...)

Arguments

object

Object of class 'plant3d' (one 3D plant) or 'plant3dlist' (a list of 3D plants).

nKErepeat

Number of replicates for leafdispersion, see its help page.

nsignif

Number of digits for output (only for printing).

calcSTARbar

If TRUE, also calculates STARbar and adds it to the summary result.

calcpathlen

If TRUE, calculates mean and SD of path length from ground surface to leaves (default is now FALSE, because this feature may be unstable).

writefile

If TRUE, writes a text file with the summary results in the cur. working dir.

...

Further arguments passed to STARbar.

Value

A list with components described above. See also the Examples below.

Details

The summary.plant3d prints a number of plant summary variables. They are also stored in a list. These are the variables that are currently calculated:

 
LA - Total leaf area (m2) 
meanleafsize - Mean leaf size (cm2)
nleavesp - Number of leaves 
leaflen - Mean leaf length (cm) 
meanleafang - Mean leaf angle (deg) 
wmeanleafang - Mean leaf angle weighted by leaf area
(deg) Xellipsoid - Ellipsoidal leaf angle dist. par.  
crownvol - Crown volume (convex hull) (m3) 
crownsurf - Crown surface area (convex hull) (m2) 
ALAC - Crown density (AL/AC) (m2 m-2) 
cw - Crown width (m) 
cl - Crown length (m)
htot - Total height(m) 
cshape - Crown shape index (-) 
stemsurf - Stem + branch surface area (cm2) 
stemvol - Stem + branch volume (cm3) 
stemdiam - Stem base diameter (mm) 
meanpath - Mean pipe length (mm) 
sdpath - Standard deviation of pipe length (mm) 
totlen - Total woody segment length (mm) 
Ek - Expected distance to 5 nearest leaves (no edge corr.)  
Ek2 - Expected distance to 5 nearest leaves (with edge corr.)  
Ok - Observed distance to 5 nearest leaves 
disp - Dispersion parameter (no edge corr.)  
disp2 - Dispersion parameter (with edge corr.)  
STARbar - (Optional, only when calcSTARbar = TRUE).

Note that when generating a summary on a plant3dlist object, the above information is written to an outputfile. The outputfile is tab-delimited, and has the name 'Plant summaries-YYYY-MM-DD.txt', using the current date.

The following functions are called to calculate some of the summary variables: leafdispersion for Ek,Ek2,Ok,disp,disp2; pathlen (hidden function) for meanpath,sdpath,totlen; the fitdistribution function in the LeafAngle package for Xellipsoid; getR for cw; and crownhull for crownsurf, crownvol and ALAC. The remainder of the variables are trivial calculations from the plant input file (the .p file) or the leaf file.

Optionally, the $\overline{STAR}$ is calculated (when calcSTARbar = TRUE), by calling STARbar. See its help page for full details. Note that all options for STARbar can also be set with the summary function (see Examples).

Examples

Run this code



# Print summary (use built-in Toona plant):
summary(toona)

# Or save summary as a list, access single values:
plantsumm <- summary(toona)
plantsumm$meanpath  # mean path length from soil to leaf
# See table above for names of single variables.

## Not run: 
# # Summary on a plant3dlist ('myplants' is constructed with 'readplantlist').
# summary(myplants, writefile=TRUE)
# 
# # Also calculate STARbar (with the exact method).
# summary(myplant, calcSTARbar=TRUE, method="exact")
# ## End(Not run)

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