Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/summary.plant3d.R
Summarize the 3D plant in various useful ways. Requires an object of class
plant3d
, made with constructplant
.
1 2 3 4 5 6 |
object |
Object of class 'plant3d' (one 3D plant) or 'plant3dlist' (a list of 3D plants). |
nKErepeat |
Number of replicates for |
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 |
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:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 |
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).
A list with components described above. See also the Examples below.
Remko Duursma
crownhull
, leafdispersion
,
getR
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | # 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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