$-methods               ~~ Methods for Function '$' ~~
AbsoluteFractionModern-methods
                        ~~ Methods for Function
                        'AbsoluteFractionModern' ~~
AbsoluteFractionModern_from_Delta14C
                        Converts its argument to an Absolute Fraction
                        Modern representation
AbsoluteFractionModern_from_Delta14C-methods
                        ~~ Methods for Function
                        'AbsoluteFractionModern_from_Delta14C' ~~
AbsoluteFractionModern_from_Delta14C_method__matrix
                        Converts from Delta14C to Absolute Fraction
                        Modern
AbsoluteFractionModern_from_Delta14C_method__numeric
                        Converts from Delta14C to Absolute Fraction
                        Modern
AbsoluteFractionModern_method__BoundFc
                        convert to Absolute Fraction Normal values
BoundFc                 generic constructor
BoundFc-class           Class '"BoundFc"'
BoundFc-methods         ~~ Methods for Function 'BoundFc' ~~
BoundFc_method__data.frame_missing_missing_missing_character_function
                        constructor
BoundFc_method__data.frame_missing_missing_missing_character_missing
                        constructor
BoundFc_method__data.frame_missing_missing_numeric_character_function
                        constructor
BoundFc_method__data.frame_missing_missing_numeric_character_missing
                        constructor
BoundFc_method__function_numeric_numeric_missing_character_missing
                        constructor
BoundFc_method__function_numeric_numeric_numeric_character_missing
                        constructor
BoundInFlux             generic constructor
BoundInFlux-class       Class '"BoundInFlux"'
BoundInFlux-methods     ~~ Methods for Function 'BoundInFlux' ~~
BoundInFlux_method__TimeMap_missing_missing_missing_missing
                        convert to BoundInFlux
BoundInFlux_method__data.frame_missing_missing_missing_missing
                        constructor
BoundInFlux_method__data.frame_missing_missing_numeric_function
                        constructor
BoundInFlux_method__function_numeric_numeric_missing_missing
                        constructor
BoundInFlux_method__function_numeric_numeric_numeric_missing
                        constructor
BoundLinDecompOp        Generic constructor
BoundLinDecompOp-class
                        Class '"BoundLinDecompOp"'
BoundLinDecompOp-methods
                        ~~ Methods for Function 'BoundLinDecompOp' ~~
BoundLinDecompOp_method__ConstLinDecompOp
                        convert a ConstLinDecompOp to a
                        BoundLinDecompOp
BoundLinDecompOp_method__TimeMap_missing_missing_missing
                        create a BoundLinDecompOp from a TimeMap
BoundLinDecompOp_method__function_numeric_numeric_missing
                        a constructor
BoundLinDecompOp_method__function_numeric_numeric_numeric
                        a constructor
C14Atm                  Atmospheric 14C fraction
C14Atm_NH               Post-bomb atmospheric 14C fraction
ConstFc                 creates an object containing the initial values
                        for the 14C fraction needed to create models in
                        SoilR
ConstLinDecompOp        Generic constructor
ConstLinDecompOp-class
                        Class '"ConstLinDecompOp"'
ConstLinDecompOp-methods
                        ~~ Methods for Function 'ConstLinDecompOp' ~~
ConstLinDecompOp_method__matrix
                        construct from matric
DecompOp-class          Class '"DecompOp"'
DecompOp-methods        ~~ Methods for Function 'DecompOp' ~~
DecompOp_method__DecompOp
                        pass through constructor
DecompOp_method__TimeMap
                        creates a BoundLinDecompOp from a TimeMap
                        object
DecompOp_method__matrix
                        creates a ConstanDecompOp from a matrix
DecompositionOperator-class
                        Class '"DecompositionOperator"'
Delta14C-methods        ~~ Methods for Function 'Delta14C' ~~
Delta14C_from_AbsoluteFractionModern
                        Converts its argument from an Absolute Fraction
                        Modern to a Delta14C representation
Delta14C_from_AbsoluteFractionModern-methods
                        ~~ Methods for Function
                        'Delta14C_from_AbsoluteFractionModern' ~~
Delta14C_from_AbsoluteFractionModern_method__matrix
                        Converts Absolute Fraction Modern values to
                        Delta14C
Delta14C_from_AbsoluteFractionModern_method__numeric
                        Converts to Delta14C format
Delta14C_method__BoundFc
                        convert to Absolute Fraction Normal values
GaudinskiModel14        Implementation of a the six-pool C14 model
                        proposed by Gaudinski et al. 2000
GeneralModel            A general constructor
GeneralModel-methods    ~~ Methods for Function 'GeneralModel' ~~
GeneralModel_14         A general constructor
GeneralModel_14-methods
                        ~~ Methods for Function 'GeneralModel_14' ~~
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_missing_missing_missing_logical
                        a constructor for class Model
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_function_logical
                        a constructor for class Model_14
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_function_missing
                        a constructor for class Model <- 14
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_missing_logical
                        a constructor for class Model_ 14
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_missing_missing
                        a constructor for class Model
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_missing_ANY_numeric_missing_missing_missing
                        a constructor for class Model
GeneralModel_method__numeric_ANY_numeric
                        a constructor for class Model
HarvardForest14CO2      Delta14C in soil CO2 efflux from Harvard Forest
Hua2013                 Atmospheric radiocarbon for the period
                        1950-2010 from Hua et al. (2013)
ICBMModel               Implementation of the Introductory Carbon
                        Balance Model (ICBM)
InFlux-class            Class '"InFlux"'
InFlux-methods          ~~ Methods for Function 'InFlux' ~~
InFlux_method__InFlux   pass through constructor
InFlux_method__TimeMap
                        create a BoundInFlux from a TimeMap object
IntCal09                Northern Hemisphere atmospheric radiocarbon for
                        the pre-bomb period
IntCal13                Atmospheric radiocarbon for the 0-50,000 yr BP
                        period
Model                   A general constructor
Model-class             Class '"Model"'
Model-methods           ~~ Methods for Function 'Model' ~~
Model_14                A general constructor
Model_14-class          Class '"Model_14"'
Model_14-methods        ~~ Methods for Function 'Model_14' ~~
Model_method__numeric_ANY_numeric
                        general constructor for class Model
OnepModel               Implementation of a one pool model
OnepModel14             Implementation of a one-pool C14 model
ParallelModel           ParallelModel
RespirationCoefficients
                        helper function to compute respiration
                        coefficients
RothCModel              Implementation of the RothCModel
SoilR-package           Models of Soil Organic Matter Decomposition
ThreepFeedbackModel     Implementation of a three pool model with
                        feedback structure
ThreepFeedbackModel14   Implementation of a three-pool C14 model with
                        feedback structure
ThreepParallelModel     Implementation of a three pool model with
                        parallel structure
ThreepParallelModel14   Implementation of a three-pool C14 model with
                        parallel structure
ThreepSeriesModel       Implementation of a three pool model with
                        series structure
ThreepSeriesModel14     Implementation of a three-pool C14 model with
                        series structure
ThreepairMMmodel        Implementation of a 6-pool Michaelis-Menten
                        model
TimeMap-class           Class '"TimeMap"'
TimeMap.from.Dataframe
                        TimeMap from Dataframe
TimeMap.new             basic constructor of the class TimeMap.
TwopFeedbackModel       Implementation of a two pool model with
                        feedback structure
TwopFeedbackModel14     Implementation of a two-pool C14 model with
                        feedback structure
TwopMMmodel             Implementation of a two-pool Michaelis-Menten
                        model
TwopParallelModel       Implementation of a two pool model with
                        parallel structure
TwopParallelModel14     Implementation of a two-pool C14 model with
                        parallel structure
TwopSeriesModel         Implementation of a two pool model with series
                        structure
TwopSeriesModel14       Implementation of a two-pool C14 model with
                        series structure
Yasso07Model            Implementation of the Yasso07 model
YassoModel              Implementation of the Yasso model.
[-methods               ~~ Methods for Function '[' ~~
[[-methods              ~~ Methods for Function '[[' ~~
[[<--methods            ~~ Methods for Function '[[<-' ~~
[_method__Model_character
                        (experimenta) partially overload [ ] for models
as.character            creates a character representation of the
                        object in question
as.character-methods    ~~ Methods for Function 'as.character' ~~
as.character_method__BoundInFlux
                        convert BoundInFlux Objects to something
                        printable.
as.character_method__TimeMap
                        convert TimeMap Objects to something printable.
availableParticleProperties-methods
                        ~~ Methods for Function
                        'availableParticleProperties' ~~
availableParticleSets-methods
                        ~~ Methods for Function 'availableParticleSets'
                        ~~
bacwaveModel            Implementation of the microbial model Bacwave
                        (bacterial waves)
bind.C14curves          Binding of pre- and post-bomb Delta14C curves
computeResults-methods
                        ~~ Methods for Function 'computeResults' ~~
deSolve.lsoda.wrapper   deSolve lsoda wrapper
eCO2                    Soil CO2 efflux from incubation experiments
fT.Arrhenius            Effects of temperature on decomposition rates
                        according the Arrhenius equation
fT.Century1             Effects of temperature on decomposition rates
                        according the the CENTURY model
fT.Century2             Effects of temperature on decomposition rates
                        according the the CENTURY model
fT.Daycent1             Effects of temperature on decomposition rates
                        according to the DAYCENT model
fT.Daycent2             Effects of temperature on decomposition rates
                        according to the DAYCENT model
fT.Demeter              Effects of temperature on decomposition rates
                        according to the DEMETER model
fT.KB                   Effects of temperature on decomposition rates
                        according to a model proposed by M. Kirschbaum
                        (1995)
fT.LandT                Effects of temperature on decomposition rates
                        according to a function proposed by Lloyd and
                        Taylor (1994)
fT.Q10                  Effects of temperature on decomposition rates
                        according to a Q10 function
fT.RothC                Effects of temperature on decomposition rates
                        according to the functions included in the
                        RothC model
fT.Standcarb            Effects of temperature on decomposition rates
                        according to the StandCarb model
fT.linear               Effects of temperature on decomposition rates
                        according to a linear model
fW.Candy                Effects of moisture on decomposition rates
                        according to the Candy model
fW.Century              Effects of moisture on decomposition rates
                        according to the CENTURY model
fW.Daycent1             Effects of moisture on decomposition rates
                        according to the DAYCENT model
fW.Daycent2             Effects of moisture on decomposition rates
                        according to the DAYCENT model
fW.Demeter              Effects of moisture on decomposition rates
                        according to the DEMETER model
fW.Gompertz             Effects of moisture on decomposition rates
                        according to the Gompertz function
fW.Moyano               Effects of moisture on decomposition rates
                        according to the function proposed by Moyano et
                        al. (2013)
fW.RothC                Effects of moisture on decomposition rates
                        according to the RothC model
fW.Skopp                Effects of moisture on decomposition rates
                        according to the function proposed by Skopp et
                        al. 1990
fW.Standcarb            Effects of moisture on decomposition rates
                        according to the StandCarb model
getAccumulatedRelease   Calculates the accumulated carbon release from
                        the pools as a function of time
getAccumulatedRelease-methods
                        ~~ Methods for Function 'getAccumulatedRelease'
                        ~~
getAccumulatedRelease_method__Model
                        time integrals of release fluxes per pool
getC                    Calculates the C content of the pools
getC-methods            ~~ Methods for Function 'getC' ~~
getC14                  Calculates the mass of radiocarbon (14C
                        fraction times C stock) in all pools
getC14-methods          ~~ Methods for Function 'getC14' ~~
getC14_method__Model_14
                        getC14 method Model 14
getC_method__Model      getC method Model
getDecompOp-methods     ~~ Methods for Function 'getDecompOp' ~~
getDotOut-methods       ~~ Methods for Function 'getDotOut' ~~
getF14                  Calculates the 14C fraction of all pools
getF14-methods          ~~ Methods for Function 'getF14' ~~
getF14C                 Calculates the average radiocarbon fraction
                        weighted by the mass of carbon
getF14C-methods         ~~ Methods for Function 'getF14C' ~~
getF14C_method__Model_14
                        read access to the models F14C variable
getF14R                 Calculates the average radiocarbon fraction
                        weighted by the amount of carbon release
getF14R-methods         ~~ Methods for Function 'getF14R' ~~
getF14R_method__Model_14
                        average radiocarbon fraction weighted by
                        carbonrelease
getF14_method__Model_14
                        radiocarbon
getFormat-methods       ~~ Methods for Function 'getFormat' ~~
getFormat_method__BoundFc
                        extract the format string
getFunctionDefinition   getFunctionDefinition
getFunctionDefinition-methods
                        ~~ Methods for Function 'getFunctionDefinition'
                        ~~
getFunctionDefinition_method__BoundFc
                        function definition
getFunctionDefinition_method__BoundInFlux
                        getFunctionDefinition method BoundInFlux
getFunctionDefinition_method__BoundLinDecompOp
                        getFunctionDefinition method BoundLinDecompOp
getFunctionDefinition_method__ConstLinDecompOp
                        creates a constant timedependent function and
                        returns it
getFunctionDefinition_method__DecompositionOperator
                        getFunctionDefinition method
                        DecompositionOperator
getFunctionDefinition_method__TimeMap
                        getFunctionDefinition method TimeMap
getInFluxes-methods     ~~ Methods for Function 'getInFluxes' ~~
getInitialValues-methods
                        ~~ Methods for Function 'getInitialValues' ~~
getMeanTransitTime      Access to the mean transit time
getMeanTransitTime-methods
                        ~~ Methods for Function 'getMeanTransitTime' ~~
getMeanTransitTime_method__ConstLinDecompOp
                        compute the mean transit time
getNumberOfPools-methods
                        ~~ Methods for Function 'getNumberOfPools' ~~
getOutputFluxes-methods
                        ~~ Methods for Function 'getOutputFluxes' ~~
getOutputReceivers-methods
                        ~~ Methods for Function 'getOutputReceivers' ~~
getParticleMonteCarloSimulator-methods
                        ~~ Methods for Function
                        'getParticleMonteCarloSimulator' ~~
getReleaseFlux          Calculates the release of C from each pool
getReleaseFlux-methods
                        ~~ Methods for Function 'getReleaseFlux' ~~
getReleaseFlux14        Calculates the mass of radiocarbon in the
                        release flux (14C fraction times release flux)
getReleaseFlux14-methods
                        ~~ Methods for Function 'getReleaseFlux14' ~~
getReleaseFlux14_method__Model_14
                        14C respiration rate for all pools
getReleaseFlux_method__Model
                        get the release rate for all pools
getTimeRange            getTimeRange
getTimeRange-methods    ~~ Methods for Function 'getTimeRange' ~~
getTimeRange_method__BoundFc
                        ask for the boundaries of the underlying time
                        interval
getTimeRange_method__BoundInFlux
                        time domain of the function
getTimeRange_method__BoundLinDecompOp
                        ask for the boundaries of the underlying time
                        interval
getTimeRange_method__ConstLinDecompOp
                        return an (infinite) time range since the
                        operator is constant
getTimeRange_method__DecompositionOperator
                        ask for the boundaries of the underlying time
                        interval
getTimeRange_method__TimeMap
                        ask for the boundaries of the underlying time
                        interval
getTimes                Extracts the times argument
getTimes-methods        ~~ Methods for Function 'getTimes' ~~
getTimes_method__Model
                        getTimes method Model
getTransferCoefficients-methods
                        ~~ Methods for Function
                        'getTransferCoefficients' ~~
getTransferMatrix-methods
                        ~~ Methods for Function 'getTransferMatrix' ~~
getTransitTimeDistributionDensity
                        methods for transit time distributions
getTransitTimeDistributionDensity-methods
                        ~~ Methods for Function
                        'getTransitTimeDistributionDensity' ~~
getTransitTimeDistributionDensity_method__ConstLinDecompOp
                        compute the TransitTimeDistributionDensity
getValues-methods       ~~ Methods for Function 'getValues' ~~
initialize-methods      ~~ Methods for Function 'initialize' ~~
initialize_method__BoundFc
                        internal constructor (new)
initialize_method__BoundInFlux
                        internal constructor
initialize_method__BoundLinDecompOp
                        initialize called by (new)
initialize_method__ConstLinDecompOp
                        internal constructor
initialize_method__DecompositionOperator
                        initialize called by (new)
initialize_method__Model
                        internal constructor for Model objects
initialize_method__Model_14
                        An internal constructor for 'Model_14' objects
                        not recommended to be used directly in user
                        code.
initialize_method__TimeMap
                        initialize called by (new)
linesCPool              Add lines with the output of 'getC14', 'getC',
                        or 'getReleaseFlux' to an existing plot
plot-methods            ~~ Methods for Function 'plot' ~~
plotC14Pool             Plots the output of 'getC14' for each pool over
                        time
plotCPool               Plots the output of 'getC' or 'getReleaseFlux'
                        for each pool over time
plot_method__Model      plot method Model
print-methods           ~~ Methods for Function 'print' ~~
print_method__Model     print method Model
show-methods            ~~ Methods for Function 'show' ~~
show_method__Model      show method Model
summary-methods         ~~ Methods for Function 'summary' ~~
summary_method__Model   summary method Model
turnoverFit             Estimation of the turnover time from a soil
                        radiocarbon sample.
