BioCro: Simulation of Biomass Crops

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

Author
Fernando Miguez <femiguez@iastate.edu>
Date of publication
2015-12-14 22:47:03
Maintainer
Fernando Miguez <femiguez@iastate.edu>
License
GPL (>= 2)
Version
0.268-0

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...

Files in this package

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