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.

Author
Remko Duursma. QuasiMC by Mik Cieslak. Uses code by Robert Pearcy (Yplant) and Belinda Medlyn (MAESTRA)
Date of publication
2016-05-23 06:34:50
Maintainer
Remko Duursma <remkoduursma@gmail.com>
License
GPL-2
Version
0.6-6
URLs

View on CRAN

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
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
ypreport
Make a PDF report of several YplantQMC objects
zenaz
Calculates position of the sun

Files in this package

YplantQMC
YplantQMC/src
YplantQMC/src/PNPOLYR.f
YplantQMC/src/bristospitters.f90
YplantQMC/src/photosyn.f90
YplantQMC/src/kn.f
YplantQMC/NAMESPACE
YplantQMC/CHANGELOG
YplantQMC/data
YplantQMC/data/yplantaltaz.RData
YplantQMC/data/turtle244.RData
YplantQMC/data/turtle.RData
YplantQMC/data/turtle482.RData
YplantQMC/data/plantexamples.RData
YplantQMC/data/hemiphotos.RData
YplantQMC/R
YplantQMC/R/crownhull.R
YplantQMC/R/KE.R
YplantQMC/R/viewplot.R
YplantQMC/R/xmastime.R
YplantQMC/R/randomplant.R
YplantQMC/R/print.plant3d.R
YplantQMC/R/writeturtlediffuse.R
YplantQMC/R/readQMCout.R
YplantQMC/R/replaceangles.R
YplantQMC/R/writerandomdiffuse.R
YplantQMC/R/madeleafdirection.R
YplantQMC/R/plot.yplantsim.R
YplantQMC/R/constructplant.R
YplantQMC/R/makeStand.R
YplantQMC/R/makeQMCinput.R
YplantQMC/R/Farquhar.R
YplantQMC/R/summary.plant3d.R
YplantQMC/R/lightresponse.R
YplantQMC/R/getangles.R
YplantQMC/R/psrdata.R
YplantQMC/R/plot.yphemi.R
YplantQMC/R/Kn.R
YplantQMC/R/STARbar.R
YplantQMC/R/writePSRfile.R
YplantQMC/R/makesolarvec.R
YplantQMC/R/as.data.frame.STARbarlist.R
YplantQMC/R/installQuasiMC.R
YplantQMC/R/xprod.R
YplantQMC/R/DAPA.plant3d.R
YplantQMC/R/checkHemi.R
YplantQMC/R/summary.yplantsimlist.R
YplantQMC/R/makeviewplane.R
YplantQMC/R/readCAN.R
YplantQMC/R/yplantqmc-package.R
YplantQMC/R/acosangle.R
YplantQMC/R/VPDtoRH.R
YplantQMC/R/VPDTdiurnal.R
YplantQMC/R/projectplant.R
YplantQMC/R/plot.ypmet.R
YplantQMC/R/evalHemi.R
YplantQMC/R/runYplant.R
YplantQMC/R/print.STAR.R
YplantQMC/R/getR.R
YplantQMC/R/print.projectedplant3d.R
YplantQMC/R/print.plant3dlist.R
YplantQMC/R/makevector.R
YplantQMC/R/photosyn.R
YplantQMC/R/plot.tracedplant.R
YplantQMC/R/plot.leaffile.R
YplantQMC/R/print.yplocation.R
YplantQMC/R/includePhy.R
YplantQMC/R/plot.yplocation.R
YplantQMC/R/print.yplantsim.R
YplantQMC/R/calcparhrly.R
YplantQMC/R/readp.R
YplantQMC/R/DAPA.R
YplantQMC/R/writeOUTfile.R
YplantQMC/R/runQMCUOC.R
YplantQMC/R/print.ypphy.R
YplantQMC/R/GramSchmidt.R
YplantQMC/R/leafdata.R
YplantQMC/R/Silhouette.R
YplantQMC/R/getpsil.R
YplantQMC/R/leafdispersion.R
YplantQMC/R/setPhy.R
YplantQMC/R/plot.projectedplant3d.R
YplantQMC/R/print.summary.plant3d.R
YplantQMC/R/print.ypmet.R
YplantQMC/R/trim.R
YplantQMC/R/DAPAQMC.R
YplantQMC/R/plot.plant3d.R
YplantQMC/R/setLocation.R
YplantQMC/R/runquasimc.R
YplantQMC/R/YplantDay.R
YplantQMC/R/setMet.R
YplantQMC/R/shiftplant.R
YplantQMC/R/zenaz.R
YplantQMC/R/setHemi.R
YplantQMC/R/writecfg.R
YplantQMC/R/readl.R
YplantQMC/R/getleafnormal.R
YplantQMC/R/print.stand3d.R
YplantQMC/R/pathlen.R
YplantQMC/R/checkInstallation.R
YplantQMC/R/ypreport.R
YplantQMC/R/areapoly.R
YplantQMC/R/esat.R
YplantQMC/R/zzz.R
YplantQMC/R/plotstemsections.R
YplantQMC/R/print.yplantsimlist.R
YplantQMC/R/plot3dcylinder.R
YplantQMC/R/gridtrace.R
YplantQMC/R/summary.plant3dlist.R
YplantQMC/MD5
YplantQMC/DESCRIPTION
YplantQMC/man
YplantQMC/man/crownhull.Rd
YplantQMC/man/Farquhar.Rd
YplantQMC/man/turtle482.Rd
YplantQMC/man/getangles.Rd
YplantQMC/man/setMet.Rd
YplantQMC/man/setLocation.Rd
YplantQMC/man/ModifyPfiles.Rd
YplantQMC/man/randomplant.Rd
YplantQMC/man/plot.leaffile.Rd
YplantQMC/man/runYplant.Rd
YplantQMC/man/setPhy.Rd
YplantQMC/man/YplantDay.Rd
YplantQMC/man/readp.Rd
YplantQMC/man/xmastime.Rd
YplantQMC/man/summary.plant3d.Rd
YplantQMC/man/leafdispersion.Rd
YplantQMC/man/examplehemi.Rd
YplantQMC/man/psrdata.Rd
YplantQMC/man/lightresponse.Rd
YplantQMC/man/yplantaltaz.Rd
YplantQMC/man/plot.plant3d.Rd
YplantQMC/man/plantexamples.Rd
YplantQMC/man/constructplant.Rd
YplantQMC/man/makeStand.Rd
YplantQMC/man/ypreport.Rd
YplantQMC/man/zenaz.Rd
YplantQMC/man/projectplant.Rd
YplantQMC/man/setHemi.Rd
YplantQMC/man/getR.Rd
YplantQMC/man/Silhouette.Rd
YplantQMC/man/viewplot.Rd
YplantQMC/man/turtle244.Rd
YplantQMC/man/readl.Rd
YplantQMC/man/installQuasiMC.Rd
YplantQMC/man/STARbar.Rd
YplantQMC/man/turtle.Rd