YplantQMC: Plant architectural analysis with Yplant and QuasiMC.
Version 0.5-2

An R implementation of Yplant, combined with the QuasiMC raytracer. Calculate radiation absorption, transmission and scattering, photosynthesis and transpiration of virtual 3D plants.

Browse man pages Browse package API and functions Browse package files

AuthorRemko Duursma. QuasiMC by Mik Cieslak. Uses code by Robert Pearcy (Yplant) and Belinda Medlyn (MAESTRA).
Date of publication2013-03-13 00:19:11
MaintainerRemko Duursma <remkoduursma@gmail.com>
LicenseGPL-2
Version0.5-2
URL http://www.remkoduursma.com/yplantqmc https://r-forge.r-project.org/projects/yplantqmc/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("YplantQMC", repos="http://R-Forge.R-project.org")

Man pages

constructplant: Construct a 3D plant
crownhull: Calculates and plots the convex hull around the plant crown
examplehemi: Two example hemiphotos in YplantQMC format
Farquhar: Farquhar-Ball-Berry coupled leaf gas exchange model
getangles: Read angles from a .p file.
getR: Get crown radius of a plant
installQuasiMC: Download and install the QuasiMC executable
leafdispersion: Leaf dispersion of 3D plants
lightresponse: Non-rectangular hyperbola
makereport: Make a PDF report of several YplantQMC objects
makeStand: Make a stand of virtual plants
ModifyPfiles: Modify Yplant input files.
plantexamples: Three example 3D plants
plot.leaffile: Plots a Yplant leaf file (a file with extension '.l' or...
plot.plant3d: Plots a plant in 3D
projectplant: Project plant coordinates onto a viewing plane
psrdata: Get PSR data.
randomplant: Generate a plant with randomly distributed leaves
readl: Read a Yplant leaf file
readp: Reads the data from a .p file.
runYplant: A single simulation of YplantQMC
setHemi: Generate a hemiphoto object
setLocation: Generate a location object
setMet: Generate a weather object
setPhy: Make a leaf physiology object
Silhouette: Calculates the area of the 2D convex hull of a projected...
STARbar: Calculate displayed and projected leaf areas of a 3D plant
summary.plant3d: Summarize 3D plants
turtle: A turtle sky with 58 points
turtle244: A turtle sky with 244 points
turtle482: A turtle sky with 482 points
viewplot: Make a three panel plot of a 3D plant
xmastime: Is it xmas yet?
yplantaltaz: Altitude and azimuth angles
YplantDay: Run a simulation over a day with YplantQMC
zenaz: Calculates position of the sun

Functions

DAPA Source code
DAPA.plant3d Source code
DAPAQMC Source code
Farquhar Man page Source code
KE Source code
Kn Source code
STARbar Man page Source code
STARbar.plant3d Man page Source code
STARbar.plant3dlist Man page Source code
Silhouette Man page Source code
VPDTdiurnal Source code
VPDtoRH Source code
YplantDay Man page Source code
YplantDay.plant3d Man page Source code
YplantDay.plant3dlist Man page Source code
YplantDay.stand3d Source code
acosangle Source code
areapoly Source code
as.data.frame.STARbarlist Source code
calcparhrly Source code
changeinternodes Man page Source code
checkHemi Source code
checkInstallation Source code
constructplant Man page Source code
crownhull Man page Source code
esat Source code
evalHemi Man page Source code
examplehemi Man page
getR Man page Source code
getangles Man page Source code
getleafnormal Source code
getpsil Source code
gridtrace Source code
includePhy Man page Source code
includePhy.plant3d Man page Source code
includePhy.plant3dlist Man page Source code
installQuasiMC Man page Source code
largegap Man page
leafdata Source code
leafdispersion Man page Source code
lightresponse Man page Source code
madeleafdirection Source code
makeQMCinput Source code
makeStand Man page Source code
makereport Man page Source code
makesolarvec Source code
makevector Source code
makeviewplane Source code
modifypfile Man page Source code
onAttach Source code
onUnload Source code
pathlen Source code
photosyn Source code
photosynfun Source code
pilularis Man page
plantexamples Man page
plot.leaffile Man page Source code
plot.plant3d Man page Source code
plot.plant3dlist Man page Source code
plot.projectedplant3d Man page Source code
plot.stand3d Source code
plot.tracedplant Man page Source code
plot.yphemi Man page Source code
plot.yplantsim Source code
plot.yplocation Source code
plot.ypmet Source code
plot3d.leaffile Man page
plot3dcylinder Source code
plotstemsections Source code
print.STAR Source code
print.plant3d Source code
print.plant3dlist Source code
print.projectedplant3d Man page Source code
print.stand3d Source code
print.summary.plant3d Man page Source code
print.yplantsim Source code
print.yplantsimlist Source code
print.yplocation Source code
print.ypmet Source code
print.ypphy Source code
projectplant Man page Source code
psrdata Man page Source code
randomplant Man page Source code
raytrace Man page
readCAN Source code
readQMCout Source code
readl Man page Source code
readp Man page Source code
readplantlist Man page Source code
replaceangles Man page Source code
runQMCUOC Source code
runYplant Man page Source code
runYplant.plant3d Man page Source code
runYplant.stand3d Man page Source code
runquasimc Source code
setHemi Man page Source code
setLocation Man page Source code
setMet Man page Source code
setPhy Man page Source code
shiftplant Source code
smallgap Man page
sugarmaple Man page
summary.plant3d Man page Source code
summary.plant3dlist Man page Source code
summary.yplantsimlist Source code
toona Man page
trim Source code
turtle Man page
turtle244 Man page
turtle482 Man page
unloadyplant Source code
viewplot Man page Source code
writeOUTfile Source code
writePSRfile Source code
writecfg Source code
writerandomdiffuse Source code
writeturtlediffuse Source code
xmastime Man page Source code
xprod Source code
ypaddonMessage Source code
yplantaltaz Man page
zenaz Man page Source code

Files

man
man/Silhouette.Rd
man/psrdata.Rd
man/zenaz.Rd
man/getangles.Rd
man/setPhy.Rd
man/turtle244.Rd
man/projectplant.Rd
man/viewplot.Rd
man/setHemi.Rd
man/turtle.Rd
man/readl.Rd
man/yplantaltaz.Rd
man/plot.plant3d.Rd
man/installQuasiMC.Rd
man/readp.Rd
man/plot.leaffile.Rd
man/Farquhar.Rd
man/plantexamples.Rd
man/leafdispersion.Rd
man/runYplant.Rd
man/lightresponse.Rd
man/makeStand.Rd
man/STARbar.Rd
man/xmastime.Rd
man/crownhull.Rd
man/makereport.Rd
man/setLocation.Rd
man/turtle482.Rd
man/ModifyPfiles.Rd
man/summary.plant3d.Rd
man/YplantDay.Rd
man/getR.Rd
man/randomplant.Rd
man/constructplant.Rd
man/setMet.Rd
man/examplehemi.Rd
DESCRIPTION
src
src/kn.f
src/bristospitters.f90
src/photosyn.f90
src/PNPOLYR.f
data
data/turtle.RData
data/yplantaltaz.RData
data/plantexamples.RData
data/turtle482.RData
data/hemiphotos.RData
data/turtle244.RData
NAMESPACE
CHANGELOG
R
R/getangles.R
R/STARbar.R
R/readp.R
R/summary.yplantsimlist.R
R/writecfg.R
R/setHemi.R
R/runYplant.R
R/plot.stand3d.R
R/print.plant3dlist.R
R/plot.yplocation.R
R/plot.tracedplant.R
R/checkInstallation.R
R/leafdispersion.R
R/print.ypmet.R
R/makeviewplane.R
R/crownhull.R
R/UNLOAD.R
R/zzz.R
R/includePhy.R
R/Silhouette.R
R/writePSRfile.R
R/YplantDay.R
R/print.summary.plant3d.R
R/summary.plant3dlist.R
R/readCAN.R
R/makeStand.R
R/runQMCUOC.R
R/print.projectedplant3d.R
R/changeinternodes.R
R/writerandomdiffuse.R
R/plot.ypmet.R
R/calcparhrly.R
R/getleafnormal.R
R/print.ypphy.R
R/readQMCout.R
R/ypaddonMessage.R
R/runquasimc.R
R/print.yplocation.R
R/installQuasiMC.R
R/setLocation.R
R/setPhy.R
R/xprod.R
R/constructplant.R
R/psrdata.R
R/print.yplantsim.R
R/plotstemsections.R
R/trim.R
R/print.plant3d.R
R/checkHemi.R
R/plot.plant3d.R
R/as.data.frame.STARbarlist.R
R/summary.plant3d.R
R/DAPA.R
R/plot.projectedplant3d.R
R/getR.R
R/print.STAR.R
R/shiftplant.R
R/zenaz.R
R/plot.yphemi.R
R/projectplant.R
R/replaceangles.R
R/areapoly.R
R/plot3dcylinder.R
R/VPDTdiurnal.R
R/readl.R
R/acosangle.R
R/KE.R
R/print.yplantsimlist.R
R/esat.R
R/pathlen.R
R/lightresponse.R
R/DAPA.plant3d.R
R/xmastime.R
R/randomplant.R
R/Kn.R
R/plot.plant3dlist.R
R/modifypfile.R
R/writeturtlediffuse.R
R/STARbar.plant3dlist.R
R/makesolarvec.R
R/makevector.R
R/evalHemi.R
R/Farquhar.R
R/YplantDay.plant3d.R
R/leafdata.R
R/setMet.R
R/gridtrace.R
R/readplantlist.R
R/plot.leaffile.R
R/viewplot.R
R/print.stand3d.R
R/makereport.R
R/madeleafdirection.R
R/DAPAQMC.R
R/plot.yplantsim.R
R/VPDtoRH.R
R/photosyn.R
R/writeOUTfile.R
R/YplantDay.plant3dlist.R
R/runYplant.stand3d.R
R/makeQMCinput.R
R/getpsil.R
YplantQMC documentation built on May 21, 2017, 2:58 a.m.