BioCro 0.93

BioCro

BioCro is a detailed model that scales from leaf-level photosynthesis to ecosystem level carbon and water balance.

BioCro is a plant production model adapted from WIMOVAC, relying on the key physiological and biophysical processes underlying plant production (Humphries & Long, 1995). BioCro has previously been used for predicting biomass yield and LAI of switchgrass and Miscanthus (Miguez et al., 2009). Sugarcane, coppice willow, arundo, and soy modules are under development and will be released following publication.

Recent development has coupled DayCent (Parton et al 1998) to BioCro, expanding the ability of BioCro to predict ecosystem functioning beyond yields, including the production of greenhouse gases and storage of carbon in the soil. BioCro has also been integrated into a suite of tools which link the model directly with crop trait and yield data, streamlining the entire modeling and data collection workflow (LeBauer et al, 2013). The Predictive Ecosystem Analyzer (PEcAn) couples BioCro to the Biofuel Ecophysiological Traits and Yields database, enabling model parameterization and optimization, targeted data collection optimized to reduce uncertainty in model predictions, and the management of informatics and HPC computing resources.

Inputs:

  • species-specific plant physiological traits ** Photosynthetic Parameters ** Phenological stages ** Biomass partitioning
  • soil physical properties: ** (water holding capacity, wilting point, sand, silt, clay, organic matter, rooting depth).
  • meteorological data (daily or hourly) ** precipitation ** solar radiation ** wind speed ** temperature ** humidity

Outputs

  • Yield, NPP, Biomass (leaf, root, storage)
  • Evapotranspiration
  • Leaf Area Index
  • many more

References

Humphries S and Long SP (1995) WIMOVAC - a software package for modeling the dynamics of the plant leaf and canopy photosynthesis. Computer Applications in the Bioscience 11(4):361-371

Miguez FE, Zhu XG, Humphries S, Bollero GA, Long SP (2009) A semimechanistic model predicting the growth and production of the bioenergy crop Miscanthus × giganteus: description, parameterization and validation. Global Change Biology Bioenergy 1: 282-296

Help topics

  • aci
    A/Ci curves
  • annualDB(annualDB2)
    Miscanthus dry biomass data.
  • aq
    A/Q curves
  • ardBuck
    Arden Buck Equation from Buck Research Manual (1996)
  • BioGro(SoilType, canopyParms, centuryParms, nitroParms, phenoParms, photoParms, print.BioGro, seneParms, showSoilType, soilParms)
    Biomass crops growth simulation
  • c3CanA
    Simulates canopy assimilation for C3 canopies
  • c3photo
    Simulates C3 photosynthesis
  • c4photo
    Coupled photosynthesis-stomatal conductance simulation
  • CanA(lnParms)
    Simulates canopy assimilation
  • caneGro
    Simulation of cane, Growth, LAI, Photosynthesis and phenology
  • Century(CenturyC)
    This function implements the Century model from Parton.
  • CenturyC
    C version of the Century function
  • CheckLeapYear
    This fuction checks if year is a leap year. If yes, then returns 1 or 0.
  • cmi0506
    Weather data
  • cmiWet
    Weather data
  • CropGro(BioGro, SoilType, canopyParms, centuryParms, nitroParms, phenoParms, photoParms, print.BioGro, seneParms, showSoilType, soilParms)
    Biomass crops growth simulation
  • 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 source).
  • EngWea94rf
    Weather data corresponding to a paper by Clive Beale (see source).
  • flow
    Returns values based on if kno is less than, equal to, or greater than three.
  • FmLcFun
    Returns values for Fm and Lc
  • fnpsvp
    The Goff Gratch equation from Smithsonian Tables, 1984.
  • idbp
    Initial Dry Biomass Partitioning Coefficients
  • idbpm
    idpm
  • LayET
    Weather data
  • lightME
    Simulates the light macro environment
  • MaizeGro
    Simulation of Maize, Growth, LAI, Photosynthesis and phenology
  • MaizePhenoParms
    Lists values for phenology parameters
  • MaizeSeneParms
    Lists values for senecence parameters
  • MCMCBioGro(print.MCMCBioGro)
    Simulated annealing and MCMC function
  • MCMCc4photo(print.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(plot.mOpc4photo, print.mOpc4photo)
    Multiple optimization of C4 photosynthesis.
  • obsBea
    Miscanthus assimilation field data
  • obsBeaC
    Complete Miscanthus assimilation field data
  • obsNaid
    Miscanthus assimilation data
  • OpBioGro(constrOpBioGro, summary.OpBioGro)
    Optimization of dry biomass partitioning coefficients.
  • Opc3photo(plot.Opc3photo, predict.Opc3photo, print.Opc3photo)
    Optimize parameters of the C3 photosynthesis model.
  • Opc4photo(plot.Opc4photo, plotAQ, predict.Opc4photo, print.Opc4photo, print.summary.Opc4photo, summary.Opc4photo)
    Optimization of C4 photosynthesis parameters
  • OpEC4photo(summary.OpEC4photo)
    Optimization of C4 photosynthesis parameters (von Caemmerer model)
  • OpMaizeGro
    Optimization of dry biomass partitioning coefficients.
  • plotAC
    plot A/Ci curve
  • plotAQ
    plot A/Q curve
  • plot.BioGro
    Plotting function for BioGro objects
  • plot.MaizeGro
    Plotting function for MaizeGro objects
  • plot.MCMCBioGro
    Plotting function fo the MCMCBioGro class
  • plot.MCMCc4photo
    Plotting function for MCMCc4photo objects
  • plot.MCMCEc4photo
    Plottin function for MCMCEc4photo objects
  • plot.mOpc3photo
    Plotting method
  • plot.mOpc4photo
    Plotting method
  • plot.willowGro
    Plotting function for willowGro objects
  • predict.Opc3photo
    Predict method
  • predict.Opc4photo
    Predict method
  • print.BioGro
    printing method for BioGro
  • print.MaizeGro
    printing method for MaizeGro
  • print.MCMCBioGro
    printing method for MCMCBioGro
  • print.MCMCc4photo
    Function for printing the MCMCc4photo objects
  • print.MCMCEc4photo
    Print an MCMCEc4photo object
  • print.mOpc3photo
    Printing method
  • print.mOpc4photo
    Printing method
  • print.OpBioGro
    Print an OpBioGro object
  • print.Opc3photo
    Display methods for Opc4photo and OpEC4photo
  • print.Opc4photo
    Display methods for Opc4photo and OpEC4photo
  • print.OpEC4photo
    Print an OpEC4photo object
  • Rmiscanmod
    RUE-based model to calculate miscanthus growth and yield.
  • rootDist
    Finds rootDist for the soilML function
  • 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.
  • RssMaizeGro
    Very simple function to compare the distance between simulated
  • RUEmod
    Radiation use efficiency based model
  • RUEmodMY
    Radiation use efficiency based model
  • showSoilType
    the function that deinfes the soil types
  • simDat2
    Simulated biomass data.
  • SoilEvapo
    Soil Evaporation
  • soilML(rootDist)
    soil multi-layered
  • SoilType
    takes an interger from 0 to 10 that coresponds to a specifically defined soil type and returns the composition of the soil in a list.
  • summary.OpBioGro
    This function will implement simple calculations
  • summary.Opc4photo
    This function will implement simple calculations
  • summary.OpEC4photo
    This function will implement simple calculations
  • sunML
    Sunlit shaded multi-layer model
  • TempToDdryA
    Returns a value for TempToDdryA
  • TempToLHV
    Returns a value for TempToLHV
  • TempToSFS
    Returns a value for SlopeFS from a function of temperature
  • TempToSWVC
    Returns a value for TempToSWC
  • valid_dbp
    Validate dry biomass partitioning coefficients
  • WD1979
    Randomly picked dataset from the Illinois area from 1979
  • weach
    Simulates the hourly conditions from daily
  • weach365
    if the function CheckLeapYear returns 0 this function will be used
  • weach366
    if the function CheckLeapYear returns 1 this function will be used
  • weachDT
    weachDT
  • weach_imn
    Weather change Iowa Mesonet
  • weachNEW
    algorithm that decides weather weach365 or weach366 will be used based on the output of CheckLeapYear
  • weather05(weather04)
    Weather data
  • weather06
    Weather data
  • willowCent(SoilType, canopyParms, centuryParms, nitroParms, phenoParms, photoParms, print.willowGro, seneParms, showSoilType, soilParms, willowGro)
    willowmass crops growth simulation
  • willowGro(SoilType, canopyParms, centuryParms, nitroParms, phenoParms, photoParms, print.willowGro, seneParms, showSoilType, soilParms)
    willowmass crops growth simulation
  • wsRcoef
    R coefficient for water stress
  • wtrstr(ws, wsRcoef)
    Simple function to illustrate soil water content effect on plant water

Dependencies

  • Depends: lattice, data.table
  • Imports: stats, lattice, data.table
  • Suggests: coda, knitr
  • Extends:

Authors