BioCro: Simulation of Biomass Crops

Simulates C4 photosynthesis, biomass production and estimates parameters for plant phyisiological models using optimization techinques and Markov chains.

AuthorFernando Miguez <femiguez@iastate.edu>
Date of publication2015-12-14 22:47:03
MaintainerFernando Miguez <femiguez@iastate.edu>
LicenseGPL (>= 2)
Version0.268-0

View on R-Forge

Man pages

aci: A/Ci curves

annualDB: Miscanthus dry biomass data.

aq: A/Q curves

BioCro-internal: Internal BioCro functions

BioGro: Biomass crops growth simulation

c3CanA: Simulates canopy assimilation for C3 canopies

c3photo: Simulates C3 photosynthesis

c4photo: Coupled photosynthesis-stomatal conductance simulation

CanA: Simulates canopy assimilation

Century: This function implements the Century model from Parton.

cmi: Weather data for Champaign Illinois

cmi0506: Weather data

cmiWet: Weather data

doy124: Weather data

eC4photo: C4 photosynthesis simulation (von Caemmerer model)

eCanA: Simulates canopy assimilation (von Caemmerer model)

EngWea94i: Weather data corresponding to a paper by Clive Beale (see...

EngWea94rf: Weather data corresponding to a paper by Clive Beale (see...

idbp: Initial Dry Biomass Partitioning Coefficients

LayET: Weather data

lightME: Simulates the light macro environment

MaizeGro: Simulation of Maize, Growth, LAI, Photosynthesis and...

MCMCBioGro: Simulated Annealing and Markov chain Monte Carlo for...

MCMCc4photo: Markov chain Monte Carlo for C4 photosynthesis parameters

MCMCEc4photo: Markov chain Monte Carlo for C4 photosynthesis parameters

mOpc3photo: Multiple optimization of assimilation (or stomatal...

mOpc4photo: Multiple optimization of C4 photosynthesis.

obsBea: Miscanthus assimilation field data

obsBeaC: Complete Miscanthus assimilation field data

obsNaid: Miscanthus assimilation data

OpBioGro: Optimization of dry biomass partitioning coefficients.

Opc3photo: Optimize parameters of the C3 photosynthesis model.

Opc4photo: Optimization of C4 photosynthesis parameters

OpEC4photo: Optimization of C4 photosynthesis parameters (von Caemmerer...

plotAC: Plotting function for A/Ci curves

plot.BioGro: Plotting function for BioGro objects

plot.MCMCBioGro: Plotting function fo the MCMCBioGro class

plot.MCMCc4photo: Plotting function for MCMCc4photo objects

plot.MCMCEc4photo: Plottin function for MCMCEc4photo objects

print.MCMCEc4photo: Print an MCMCEc4photo object

print.OpBioGro: Print an OpBioGro object

print.OpEC4photo: Print an OpEC4photo object

Rmiscanmod: RUE-based model to calculate miscanthus growth and yield.

RsqC4photo: R-squared for C4 photosynthesis simulation (Collatz model)

RsqEC4photo: R-squared for C4 photosynthesis simulation (von Caemmerer...

RssBioGro: Residual sum of squares for BioGro.

RUEmod: Radiation use efficiency based model

RUEmodMY: Radiation use efficiency based model

simDat2: Simulated biomass data.

SoilEvapo: Soil Evaporation

soilML: soil multi-layered

sunML: Sunlit shaded multi-layer model

valid_dbp: Validate dry biomass partitioning coefficients

WD1979: Randomly picked dataset from the Illinois area from 1979

weach: Simulates the hourly conditions from daily

weach_imn: Weather change Iowa Mesonet

wtrstr: Simple function to illustrate soil water content effect on...

Functions

aci Man page
alr Man page
annualDB Man page
annualDB2 Man page
aq Man page
ardBuck Man page
ballBerry Man page
BioGro Man page
boo14.200 Man page
c3CanA Man page
c3photo Man page
c4photo Man page
c4photoR Man page
CanA Man page
canopyParms Man page
Century Man page
CenturyC Man page
centuryParms Man page
cmi04 Man page
cmi05 Man page
cmi0506 Man page
cmi06 Man page
cmiWet Man page
constrOpBioGro Man page
doy124 Man page
eC4photo Man page
eCanA Man page
EngWea94i Man page
EngWea94rf Man page
flow Man page
FmLcFun Man page
fnpsvp Man page
ialr Man page
idbp Man page
indfun Man page
is.leap Man page
isom Man page
LayET Man page
lightME Man page
lnParms Man page
MaizeCAllocParms Man page
MaizeGro Man page
MaizeNitroParms Man page
MaizePhenoParms Man page
MaizePhotoParms Man page
MaizeSeneParms Man page
MCMCBioGro Man page
MCMCc4photo Man page
MCMCEc4photo Man page
mOpc3photo Man page
mOpc4photo Man page
nitroParms Man page
objFun Man page
objFun2 Man page
obsBea Man page
obsBeaC Man page
obsNaid Man page
OpBioGro Man page
Opc3photo Man page
Opc4photo Man page
OpEC4photo Man page
phenoConv Man page
phenoParms Man page
photoParms Man page
plotAC Man page
plotAQ Man page
plot.BioGro Man page
plot.MCMCBioGro Man page
plot.MCMCc4photo Man page
plot.MCMCEc4photo Man page
plot.mOpc4photo Man page
plot.Opc3photo Man page
plot.Opc4photo Man page
predict.Opc3photo Man page
predict.Opc4photo Man page
print.BioGro Man page
print.MCMCBioGro Man page
print.MCMCc4photo Man page
print.MCMCEc4photo Man page
print.mOpc4photo Man page
print.OpBioGro Man page
print.Opc3photo Man page
print.Opc4photo Man page
print.OpEC4photo Man page
print.summary.Opc4photo Man page
Rmiscanmod Man page
rootDist Man page
RsqC4photo Man page
RsqEC4photo Man page
RssBioGro Man page
RUEmod Man page
RUEmodMY Man page
seneParms Man page
showSoilType Man page
simDat2 Man page
SoilEvapo Man page
soilML Man page
soilParms Man page
SoilType Man page
somc Man page
summary.OpBioGro Man page
summary.Opc4photo Man page
summary.OpEC4photo Man page
sunML Man page
TempToDdryA Man page
TempToLHV Man page
TempToSFS Man page
TempToSWVC Man page
valid_dbp Man page
WD1979 Man page
weach Man page
weach_imn Man page
weach_imn2 Man page
weather04 Man page
weather05 Man page
weather06 Man page
wsRcoef Man page
wtrstr Man page

Files

ChangeLog
DESCRIPTION
NAMESPACE
R
R/BioCro.R R/CanA.R R/Century.R R/MCMCBioGro.R R/MaizeGro.R R/OpBioGro.R R/OpEC4photo.R R/OpMaizeGro.R R/Opc3photo.R R/Opc4photo.R R/RUEmod.R R/RUEmodMY.R R/Rmiscanmod.R R/RssBioGro.R R/RssMaizeGro.R R/SatWatVap.R R/SoilEvapo.R R/c3CanA.R R/c3photo.R R/c4photo.R R/constrOpBioGro.R R/eC4photo.R R/idbp.R R/idbpm.R R/lightME.R R/penmon.R R/plotAC.R R/plotAQ.R R/showSoilType.R R/soilML.R R/stemp.r R/sunML.R R/tdebug.R R/valid_dbp.R R/waterStress.R R/weach.R R/weach_imn.R
TODO
build
build/vignette.rds
data
data/EngWea94i.rda
data/EngWea94rf.rda
data/LayET.rda
data/WD1979.rda
data/aci.rda
data/allocP.rda
data/annualDB.rda
data/annualDB2.rda
data/aq.rda
data/ausWea.rda
data/boo14.200.rda
data/cmi04.rda
data/cmi05.rda
data/cmi0506.rda
data/cmi06.rda
data/cmiWet.rda
data/doy124.rda
data/maizeBioA.rda
data/maizeBioB.rda
data/maizeBioC.rda
data/maizeBioD.rda
data/maizeBioE.rda
data/obsBea.rda
data/obsBeaC.rda
data/obsNaid.rda
data/parms.rda
data/simA100.rda
data/simAssim.rda
data/simDat.rda
data/simDat2.rda
data/weather04.rda
data/weather05.rda
data/weather06.rda
inst
inst/doc
inst/doc/BioCro-Manual.Rnw
inst/doc/BioCro-Manual.pdf
man
man/BioCro-internal.Rd man/BioGro.Rd man/CanA.Rd man/Century.Rd man/EngWea94i.Rd man/EngWea94rf.Rd man/LayET.Rd man/MCMCBioGro.Rd man/MCMCEc4photo.Rd man/MCMCc4photo.Rd man/MaizeGro.Rd man/OpBioGro.Rd man/OpEC4photo.Rd man/Opc3photo.Rd man/Opc4photo.Rd man/RUEmod.Rd man/RUEmodMY.Rd man/Rmiscanmod.Rd man/RsqC4photo.Rd man/RsqEC4photo.Rd man/RssBioGro.Rd man/SoilEvapo.Rd man/WD1979.Rd man/aci.Rd man/annualDB.Rd man/aq.Rd man/c3CanA.Rd man/c3photo.Rd man/c4photo.Rd man/cmi.Rd man/cmi0506.Rd man/cmiWet.Rd man/doy124.Rd man/eC4photo.Rd man/eCanA.Rd man/idbp.Rd man/lightME.Rd man/mOpc3photo.Rd man/mOpc4photo.Rd man/obsBea.Rd man/obsBeaC.Rd man/obsNaid.Rd man/plot.BioGro.Rd man/plot.MCMCBioGro.Rd man/plot.MCMCEc4photo.Rd man/plot.MCMCc4photo.Rd man/plotAC.Rd man/print.MCMCEc4photo.Rd man/print.OpBioGro.Rd man/print.OpEC4photo.Rd man/simDat2.Rd man/soilML.Rd man/sunML.Rd man/valid_dbp.Rd man/weach.Rd man/weach_imn.Rd man/wtrstr.Rd
src
src/AuxBioCro.c
src/AuxBioCro.h
src/AuxMaizeGro.c
src/AuxMaizeGro.h
src/BioCro.c
src/BioCro.h
src/CanA.c
src/CanA.h
src/Century.c
src/Century.h
src/Makevars
src/c3CanA.c
src/c3CanA.h
src/c3EvapoTrans.c
src/c3EvapoTrans.h
src/c3photo.c
src/c3photo.h
src/c4photo.c
src/c4photo.h
src/eC4photo.c
src/maizeGro.c
src/maizeGro.h
src/soiltemp.c
src/soiltemp.h
tests
tests/BioGro-ET.R
vignettes
vignettes/BioCro-Manual.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.