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...

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

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