YplantQMC: Plant architectural analysis with Yplant and QuasiMC.

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

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
http://www.remkoduursma.com/yplantqmc, https://r-forge.r-project.org/projects/yplantqmc/

View on R-Forge

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

changeinternodes Man page
constructplant Man page
crownhull Man page
evalHemi Man page
examplehemi Man page
Farquhar Man page
getangles Man page
getR Man page
includePhy Man page
includePhy.plant3d Man page
includePhy.plant3dlist Man page
installQuasiMC Man page
largegap Man page
leafdispersion Man page
lightresponse Man page
makereport Man page
makeStand Man page
modifypfile Man page
pilularis Man page
plantexamples Man page
plot3d.leaffile Man page
plot.leaffile Man page
plot.plant3d Man page
plot.plant3dlist Man page
plot.projectedplant3d Man page
plot.tracedplant Man page
plot.yphemi Man page
print.projectedplant3d Man page
print.summary.plant3d Man page
projectplant Man page
psrdata Man page
randomplant Man page
raytrace Man page
readl Man page
readp Man page
readplantlist Man page
replaceangles Man page
runYplant Man page
runYplant.plant3d Man page
runYplant.stand3d Man page
setHemi Man page
setLocation Man page
setMet Man page
setPhy Man page
Silhouette Man page
smallgap Man page
STARbar Man page
STARbar.plant3d Man page
STARbar.plant3dlist Man page
sugarmaple Man page
summary.plant3d Man page
summary.plant3dlist Man page
toona Man page
turtle Man page
turtle244 Man page
turtle482 Man page
viewplot Man page
xmastime Man page
yplantaltaz Man page
YplantDay Man page
YplantDay.plant3d Man page
YplantDay.plant3dlist Man page
zenaz Man page

Files

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

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