Simulation of Biomass Crops


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Documentation for package ‘BioCro’ version 0.267-1

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A B C D E I L M N O P R S V W

-- A --

aci A/Ci curves
annualDB Miscanthus dry biomass data.
annualDB2 Miscanthus dry biomass data.
aq A/Q curves

-- B --

ballBerry Coupled photosynthesis-stomatal conductance simulation
BioGro Biomass crops growth simulation
boo14.200 Weather change Iowa Mesonet

-- C --

c3CanA Simulates canopy assimilation for C3 canopies
c3photo Simulates C3 photosynthesis
c4photo Coupled photosynthesis-stomatal conductance simulation
c4photoR Coupled photosynthesis-stomatal conductance simulation
CanA Simulates canopy assimilation
canopyParms Biomass crops growth simulation
Century This function implements the Century model from Parton.
CenturyC This function implements the Century model from Parton.
centuryParms Biomass crops growth simulation
cmi04 Weather data for Champaign Illinois
cmi05 Weather data for Champaign Illinois
cmi0506 Weather data
cmi06 Weather data for Champaign Illinois
cmiWet Weather data
constrOpBioGro Optimization of dry biomass partitioning coefficients.

-- D --

doy124 Weather data

-- E --

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

-- I --

idbp Initial Dry Biomass Partitioning Coefficients
is.leap Simulates the hourly conditions from daily
isom This function implements the Century model from Parton.

-- L --

LayET Weather data
lightME Simulates the light macro environment
lnParms Simulates canopy assimilation

-- M --

MaizeCAllocParms Simulation of Maize, Growth, LAI, Photosynthesis and phenology
MaizeGro Simulation of Maize, Growth, LAI, Photosynthesis and phenology
MaizeNitroParms Simulation of Maize, Growth, LAI, Photosynthesis and phenology
MaizePhenoParms Simulation of Maize, Growth, LAI, Photosynthesis and phenology
MaizePhotoParms Simulation of Maize, Growth, LAI, Photosynthesis and phenology
MaizeSeneParms Simulation of Maize, Growth, LAI, Photosynthesis and phenology
MCMCBioGro Simulated Annealing and Markov chain Monte Carlo for estimating parameters for Biomass Growth
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 conductance) curves.
mOpc4photo Multiple optimization of C4 photosynthesis.

-- N --

nitroParms Biomass crops growth simulation

-- O --

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 model)

-- P --

phenoConv Simulation of Maize, Growth, LAI, Photosynthesis and phenology
phenoParms Biomass crops growth simulation
photoParms Biomass crops growth simulation
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
plot.mOpc4photo Multiple optimization of C4 photosynthesis.
plot.Opc3photo Optimize parameters of the C3 photosynthesis model.
plot.Opc4photo Optimization of C4 photosynthesis parameters
plotAC Plotting function for A/Ci curves
plotAQ Optimization of C4 photosynthesis parameters
predict.Opc3photo Optimize parameters of the C3 photosynthesis model.
predict.Opc4photo Optimization of C4 photosynthesis parameters
print.BioGro Biomass crops growth simulation
print.MCMCBioGro Simulated Annealing and Markov chain Monte Carlo for estimating parameters for Biomass Growth
print.MCMCc4photo Markov chain Monte Carlo for C4 photosynthesis parameters
print.MCMCEc4photo Print an MCMCEc4photo object
print.mOpc4photo Multiple optimization of C4 photosynthesis.
print.OpBioGro Print an OpBioGro object
print.Opc3photo Optimize parameters of the C3 photosynthesis model.
print.Opc4photo Optimization of C4 photosynthesis parameters
print.OpEC4photo Print an OpEC4photo object
print.summary.Opc4photo Optimization of C4 photosynthesis parameters

-- R --

Rmiscanmod RUE-based model to calculate miscanthus growth and yield.
rootDist soil multi-layered
RsqC4photo R-squared for C4 photosynthesis simulation (Collatz model)
RsqEC4photo R-squared for C4 photosynthesis simulation (von Caemmerer model)
RssBioGro Residual sum of squares for BioGro.
RUEmod Radiation use efficiency based model
RUEmodMY Radiation use efficiency based model

-- S --

seneParms Biomass crops growth simulation
showSoilType Biomass crops growth simulation
simDat2 Simulated biomass data.
SoilEvapo Soil Evaporation
soilML soil multi-layered
soilParms Biomass crops growth simulation
SoilType Biomass crops growth simulation
somc This function implements the Century model from Parton.
summary.OpBioGro Optimization of dry biomass partitioning coefficients.
summary.Opc4photo Optimization of C4 photosynthesis parameters
summary.OpEC4photo Optimization of C4 photosynthesis parameters (von Caemmerer model)
sunML Sunlit shaded multi-layer model

-- V --

valid_dbp Validate dry biomass partitioning coefficients

-- W --

WD1979 Randomly picked dataset from the Illinois area from 1979
weach Simulates the hourly conditions from daily
weach_imn Weather change Iowa Mesonet
weach_imn2 Weather change Iowa Mesonet
weather04 Weather data for Champaign Illinois
weather05 Weather data for Champaign Illinois
weather06 Weather data for Champaign Illinois
wsRcoef Simple function to illustrate soil water content effect on plant water stress.
wtrstr Simple function to illustrate soil water content effect on plant water stress.