$,NlModel-method        automatic title
AWBmodel                Implementation of the microbial model AWB
                        (Allison, Wallenstein, Bradford, 2010)
AbsoluteFractionModern
                        Conversion of radiocarbon values
AbsoluteFractionModern,BoundFc-method
                        automatic title
AbsoluteFractionModern,ConstFc-method
                        automatic title
AbsoluteFractionModern_from_Delta14C
                        Conversion of radiocarbon values
AbsoluteFractionModern_from_Delta14C,matrix-method
                        Conversion of radiocarbon values
AbsoluteFractionModern_from_Delta14C,numeric-method
                        Conversion of radiocarbon values, from Delta14C
                        to absolute fraction modern
BoundFc                 Bound Fc object
BoundFc,character-method
                        automatic title
BoundFc,missing-method
                        automatic title
BoundFc-class           S4-class to represent atmospheric 14C
                        concentration as scalar function of time.
BoundInFluxes           constructor for BoundInFluxes
BoundInFluxes-class     automatic title
BoundLinDecompOp        Generic constructor for the class with the same
                        name
BoundLinDecompOp,ANY-method
                        Creates an object of class BoundLinDecompOp
BoundLinDecompOp,UnBoundLinDecompOp-method
                        A converter
BoundLinDecompOp-class
                        A S4 class to represent a linear compartmental
                        operator defined on time interval
C14Atm                  Atmospheric 14C fraction
C14Atm_NH               Post-bomb atmospheric 14C fraction
CenturyModel            Implementation of the Century model
CenturyModel14          Implementation of a radiocarbon version of the
                        Century model
ConstFc                 creates an object containing the initial values
                        for the 14C fraction needed to create models in
                        SoilR
ConstFc-class           S4 class representing a constant 14C fraction
ConstInFluxes           Constant input fluxes
ConstInFluxes,ConstantInFluxList_by_PoolIndex,numeric-method
                        automatic title
ConstInFluxes,numeric,ANY-method
                        automatic title
ConstInFluxes-class     S4 class for a constant influx vector
ConstLinDecompOp        Generic constructor for the class with the same
                        name
ConstLinDecompOp,matrix,missing,missing,missing,missing-method
                        Constructor of object of ConstLinDecompOp class
ConstLinDecompOp-class
                        A class to represent a constant
                        (=nonautonomous,linear) compartmental matrix or
                        equivalently a combination of ordered constant
                        internal flux rates and constant out flux
                        rates.
ConstLinDecompOpWithLinearScalarFactor
                        Generic constructor for the class with the same
                        name
ConstLinDecompOpWithLinearScalarFactor-class
                        A class to represent a constant
                        (=nonautonomous,linear) compartmental matrix
                        with a time dependent (linear) scalar pre
                        factor This is a special case of a linear
                        compartmental operator/matrix
ConstLinDecompOp_by_PoolName
                        Generic constructor for the class with the same
                        name
ConstantInFluxList_by_PoolIndex
                        Generic constructor for the class with the same
                        name
ConstantInFluxList_by_PoolIndex,ConstInFluxes-method
                        constructor from ConstInFluxes
ConstantInFluxList_by_PoolIndex,list-method
                        constructor from a normal list
ConstantInFluxList_by_PoolIndex,numeric-method
                        constructor from numeric vector
ConstantInFluxList_by_PoolIndex-class
                        Subclass of list that is guaranteed to contain
                        only elements of type
                        ConstantInFlux_by_PoolIndex
ConstantInFluxList_by_PoolName
                        Generic constructor for the class with the same
                        name
ConstantInFluxList_by_PoolName-class
                        Subclass of list that is guaranteed to contain
                        only elements of type
                        ConstantInFlux_by_PoolName
ConstantInFluxRate_by_PoolIndex-class
                        Describes a flux rates.
ConstantInFluxRate_by_PoolName
                        Constructor for the class with the same name
ConstantInFluxRate_by_PoolName-class
                        Describes a flux rates.
ConstantInFlux_by_PoolIndex-class
                        class for a constant influx to a single pool
                        identified by index
ConstantInFlux_by_PoolName-class
                        class for a constant influx to a single pool
                        identified by pool name
ConstantInternalFluxRateList_by_PoolIndex
                        Generic constructor for the class with the same
                        name
ConstantInternalFluxRateList_by_PoolIndex,list-method
                        constructor from a normal list
ConstantInternalFluxRateList_by_PoolIndex,numeric-method
                        automatic title
ConstantInternalFluxRateList_by_PoolIndex-class
                        Describes a list of flux rates.
ConstantInternalFluxRateList_by_PoolName
                        Generic constructor for the class with the same
                        name
ConstantInternalFluxRateList_by_PoolName,list-method
                        Constructor from a normal list of fluxes
ConstantInternalFluxRateList_by_PoolName-class
                        Describes a list of flux rates.
ConstantInternalFluxRate_by_PoolIndex
                        Generic constructor for the class with the same
                        name
ConstantInternalFluxRate_by_PoolIndex,numeric,numeric,missing,numeric-method
                        automatic title
ConstantInternalFluxRate_by_PoolIndex-class
                        S4 class representing a constant internal flux
                        rate
ConstantInternalFluxRate_by_PoolName
                        Generic constructor for the class with the same
                        name
ConstantInternalFluxRate_by_PoolName,character,character,missing,numeric-method
                        constructor with argument conversion
ConstantInternalFluxRate_by_PoolName,missing,missing,character,numeric-method
                        constructor from strings of the form 'a->b'
ConstantInternalFluxRate_by_PoolName-class
                        S4-class to represent a constant internal flux
                        rate with source and target indexed by name
ConstantOutFluxRateList_by_PoolIndex
                        Generic constructor for the class with the same
                        name
ConstantOutFluxRateList_by_PoolIndex,list-method
                        constructor from a normal list
ConstantOutFluxRateList_by_PoolIndex,numeric-method
                        automatic title
ConstantOutFluxRateList_by_PoolIndex-class
                        Describes a list of flux rates.
ConstantOutFluxRateList_by_PoolName
                        Generic constructor for the class with the same
                        name
ConstantOutFluxRateList_by_PoolName,list-method
                        constructor from a normal list
ConstantOutFluxRateList_by_PoolName,numeric-method
                        automatic title
ConstantOutFluxRateList_by_PoolName-class
                        Describes a list of flux rates.
ConstantOutFluxRate_by_PoolIndex
                        Generic constructor for the class with the same
                        name
ConstantOutFluxRate_by_PoolIndex,numeric,numeric-method
                        automatic title
ConstantOutFluxRate_by_PoolIndex-class
                        S4 Class to represent a single constant
                        out-flux rate with the source pool specified by
                        an index
ConstantOutFluxRate_by_PoolName-class
                        S4 Class to represent a single constant
                        out-flux rate with the source pool specified by
                        name
DecompOp-class          S4-class to represent compartmental operators
DecompositionOperator-class
                        automatic title
Delta14C                Conversion of radiocarbon values
Delta14C,BoundFc-method
                        automatic title
Delta14C,ConstFc-method
                        automatic title
Delta14C_from_AbsoluteFractionModern
                        Conversion of radiocarbon values
Delta14C_from_AbsoluteFractionModern,matrix-method
                        Conversion of radiocarbon values
Delta14C_from_AbsoluteFractionModern,numeric-method
                        Conversion of radiocarbon values
Fc-class                automatic title
FcAtm.from.Dataframe    FcAtm.from.Dataframe
GaudinskiModel14        Implementation of a the six-pool C14 model
                        proposed by Gaudinski et al. 2000
GeneralDecompOp         A generic factory for subclasses of
                        GeneralDecompOp
GeneralDecompOp,DecompOp-method
                        Pass through factory for objects of subclasses
                        of DecompOp
GeneralDecompOp,TimeMap-method
                        automatic title
GeneralDecompOp,function-method
                        automatic title
GeneralDecompOp,list-method
                        automatic title
GeneralDecompOp,matrix-method
                        automatic title
GeneralModel            additional function to create Models
GeneralModel_14         create objects of class Model_14
GeneralNlModel          Use this function to create objects of class
                        NlModel.
GeneralPoolId           General pool Id
GeneralPoolId,character-method
                        automatic title
GeneralPoolId,numeric-method
                        generic factory for this virtual class
Graven2017              Compiled records of radicarbon in atmospheric
                        CO2 for historical simulations in CMIP6
HarvardForest14CO2      Delta14C in soil CO2 efflux from Harvard Forest
Hua2013                 Atmospheric radiocarbon for the period
                        1950-2010 from Hua et al. (2013)
Hua2021                 Atmospheric radiocarbon for the period
                        1950-2019 from Hua et al. (2021)
ICBMModel               Implementation of the Introductory Carbon
                        Balance Model (ICBM)
ICBM_N                  Implementation of the ICBM/N model
InFlux                  Generic constructor for the class with the same
                        name
InFluxList_by_PoolIndex
                        Generic constructor for the class with the same
                        name
InFluxList_by_PoolIndex,list-method
                        constructor from a normal list after checking
                        the elements
InFluxList_by_PoolIndex-class
                        Describes a list of flux rates.
InFluxList_by_PoolName
                        Generic constructor for the class with the same
                        name
InFluxList_by_PoolName,list-method
                        constructor from a normal list
InFluxList_by_PoolName-class
                        Class for a list of influxes indexed by the
                        names of the target pools
InFlux_by_PoolIndex     Generic constructor for the class with the same
                        name
InFlux_by_PoolIndex,function,numeric-method
                        Constructor from an ordered pair of PoolIndex
                        (integer like) objects
InFlux_by_PoolIndex-class
                        S4 class for the influx to a single pool
                        identified by the index
InFlux_by_PoolName      Generic constructor for an influx to a single
                        pool from an ordered pair of PoolName (string
                        like) and function objects
InFlux_by_PoolName,function,character-method
                        Constructor from an ordered pair of PoolName
                        (string like) and function objects
InFlux_by_PoolName-class
                        S4 class for the influx to a single pool
                        identified by the name
InFluxes                A generic factory for subclasses of InFluxes
InFluxes,ConstantInFluxList_by_PoolIndex-method
                        automatic title
InFluxes,InFluxes-method
                        automatic title
InFluxes,StateIndependentInFluxList_by_PoolIndex-method
                        automatic title
InFluxes,TimeMap-method
                        automatic title
InFluxes,function-method
                        automatic title
InFluxes,list-method    automatic title
InFluxes,numeric-method
                        automatic title
InFluxes-class          A virtual S4-class representing (different
                        subclasses) of in-fluxes to the system
IntCal09                Northern Hemisphere atmospheric radiocarbon for
                        the pre-bomb period
IntCal13                Atmospheric radiocarbon for the 0-50,000 yr BP
                        period
IntCal20                The IntCal20 northern hemisphere radiocarbon
                        curve for the 0-55,000 yr BP period
InternalFluxList_by_PoolIndex
                        Generic constructor for the class with the same
                        name
InternalFluxList_by_PoolIndex,list-method
                        Constructor from a normal list after checking
                        the elements
InternalFluxList_by_PoolIndex-class
                        S4-class for a list of internal fluxes with
                        source and destination pool inidices
InternalFluxList_by_PoolName
                        Generic constructor for the class with the same
                        name
InternalFluxList_by_PoolName,list-method
                        constructor from a normal list
InternalFluxList_by_PoolName-class
                        S4-class for a list of internal fluxes with
                        indexed by (source and destination pool) names
InternalFlux_by_PoolIndex
                        Generic constructor for the class with the same
                        name
InternalFlux_by_PoolIndex,function,numeric,numeric,missing-method
                        constructor from an ordered pair of PoolIndex
                        (integer like) objects and a function with
                        vector argument
InternalFlux_by_PoolIndex-class
                        S4-class for a single internal flux with source
                        and destination pools specified by indices
InternalFlux_by_PoolName
                        Generic constructor for the class with the same
                        name
InternalFlux_by_PoolName,function,character,character,missing-method
                        constructor from an ordered pair of PoolName
                        (string like) objects and a function with the
                        set of formal argument names forming a subset
                        of the state_variable_names
InternalFlux_by_PoolName,function,missing,missing,character-method
                        automatic title
InternalFlux_by_PoolName-class
                        S4-class for a single internal flux with source
                        and destination pools specified by name
MCSim-class             Experimental Class for a Monte Carlo Simulation
                        of particles leaving the pool
Model                   Constructor for class Model
Model-class             S4 class representing a model run
Model_14                general constructor for class Model_14
Model_14-class          S4-class to represent a 14C model run
Model_by_PoolNames      Constructor for 'Model_by_PoolNames'
Model_by_PoolNames-class
                        A model run based on flux functions
NlModel-class           deprecated class for a non-linear model run.
OnepModel               Implementation of a one pool model
OnepModel14             Implementation of a one-pool C14 model
OutFlux                 Generic constructor for the class with the same
                        name
OutFluxList_by_PoolIndex
                        Generic constructor for the class with the same
                        name
OutFluxList_by_PoolIndex,list-method
                        constructor from a normal list
OutFluxList_by_PoolIndex-class
                        A list of outfluxes
OutFluxList_by_PoolName
                        Generic constructor for the class with the same
                        name
OutFluxList_by_PoolName,list-method
                        constructor from a normal list
OutFluxList_by_PoolName-class
                        S4 class for a list of out-fluxes indexed by
                        source pool name
OutFlux_by_PoolIndex    Generic constructor for the class with the same
                        name
OutFlux_by_PoolIndex,function,numeric-method
                        constructor from a PoolIndex (integer like)
                        objects and a function with vector argument
OutFlux_by_PoolIndex-class
                        S4 class for a single out-flux with source pool
                        index
OutFlux_by_PoolName     Generic constructor for the class with the same
                        name
OutFlux_by_PoolName,function,character-method
                        constructor from a PoolName (integer like)
                        object and a function
OutFlux_by_PoolName-class
                        S4 class for a single out-flux with source pool
                        name
ParallelModel           models for unconnected pools
PoolConnection_by_PoolIndex
                        Pool connection by pool index
PoolConnection_by_PoolIndex,ANY,ANY,missing-method
                        constructor from an ordered pair of PoolId
                        objects
PoolConnection_by_PoolIndex,missing,missing,character-method
                        constructor from strings of the form '1_to_2'
PoolConnection_by_PoolIndex-class
                        Objects that have a source and a destination
                        described by integer like objects ( of class
                        PoolIndex)
PoolConnection_by_PoolName
                        Pool connection by pool name
PoolConnection_by_PoolName,ANY,ANY,missing-method
                        constructor from an ordered pair of PoolName
                        objects
PoolConnection_by_PoolName-class
                        Objects that have a source and a destination
                        determined by a string like object of class
                        PoolName
PoolId-class            common class for pool ids
PoolIndex               Pool index
PoolIndex,PoolIndex-method
                        pass through constructor fron an object of the
                        same class
PoolIndex,PoolName-method
                        convert to number like object
PoolIndex,character-method
                        construct from number string like '1' or '3'
PoolIndex,numeric-method
                        construct from number
PoolIndex-class         S4 class for pool indices
PoolName                Pool name
PoolName,PoolIndex-method
                        convert to string like object
PoolName,PoolName-method
                        pass through constructor fron an object of the
                        same class
PoolName,character-method
                        construct from string with checks
PoolName-class          class for pool-name-strings
RespirationCoefficients
                        helper function to compute respiration
                        coefficients
RothCModel              Implementation of the RothCModel
SHCal20                 The SHCal20 southern hemisphere radiocarbon
                        curve for the 0-55,000 yr BP period
ScalarTimeMap           Constructor for 'ScalarTimeMap-class'
ScalarTimeMap,data.frame,missing,missing,missing,missing-method
                        constructor for data given as 2 column
                        data.frame
ScalarTimeMap,function,missing,missing,missing,missing-method
                        manual constructor for just a function
ScalarTimeMap,function,numeric,numeric,missing,missing-method
                        manual constructor for a function and an
                        interval
ScalarTimeMap,missing,missing,missing,missing,numeric-method
                        special case for a time map from a constant
ScalarTimeMap,missing,missing,missing,numeric,numeric-method
                        constructor for data and times given as vectors
ScalarTimeMap-class     S4 class for a scalar time dependent function
                        on a finite time interval
SeriesLinearModel       General m-pool linear model with series
                        structure
SeriesLinearModel14     General m-pool linear C14 model with series
                        structure
SoilR-package           SoilR
SoilR.F0.new            deprecated function that used to create an
                        object of class SoilR.F0
StateDependentInFluxVector-class
                        Input vector that is a function of the pool
                        contenst and time
StateIndependentInFluxList_by_PoolIndex
                        Generic constructor for the class with the same
                        name
StateIndependentInFluxList_by_PoolIndex,list-method
                        constructor from a normal list
StateIndependentInFluxList_by_PoolIndex-class
                        Subclass of list that is guaranteed to contain
                        only elements of type
                        StateIndependentInFlux_by_PoolIndex
StateIndependentInFluxList_by_PoolName
                        Generic constructor for the class with the same
                        name
StateIndependentInFlux_by_PoolIndex-class
                        Constructor for the class with the same name
SymbolicModel_by_PoolNames-class
                        A symbolic model description based on flux
                        functions
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                 Constructor for 'TimeMap-class'
TimeMap,TimeMap,ANY,ANY,ANY,ANY-method
                        automatic title
TimeMap,data.frame,missing,missing,missing,missing-method
                        automatic title
TimeMap,function,missing,missing,missing,missing-method
                        manual constructor for just a function
TimeMap,function,numeric,numeric,missing,missing-method
                        manual constructor for a function and an
                        interval
TimeMap,list,missing,missing,missing,missing-method
                        automatic title
TimeMap,missing,missing,missing,numeric,array-method
                        automatic title
TimeMap,missing,missing,missing,numeric,list-method
                        automatic title
TimeMap,missing,missing,missing,numeric,matrix-method
                        automatic title
TimeMap,missing,missing,missing,numeric,numeric-method
                        automatic title
TimeMap-class           S4 class for a time dependent function
TimeMap.from.Dataframe
                        TimeMap.from.Dataframe
TimeMap.new             deprecated constructor of the class TimeMap.
TimeRangeIntersection   The time interval where both functions are
                        defined
TransportDecompositionOperator-class
                        automatic title
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 linear 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
UnBoundInFluxes         Unbound input fluxes
UnBoundInFluxes,function-method
                        automatic title
UnBoundInFluxes-class   automatic title
UnBoundLinDecompOp      Generic constructor for the class with the same
                        name
UnBoundLinDecompOp,function-method
                        Generic constructor for the class with the same
                        name
UnBoundLinDecompOp-class
                        An S4 class to represent a linear nonautonomous
                        compartmental matrix
UnBoundNonLinDecompOp   Generic constructor for the class with the same
                        name
UnBoundNonLinDecompOp,function,missing,missing,missing-method
                        Constructor for the class with the same name
UnBoundNonLinDecompOp,missing,vector,vector,numeric-method
                        Constructor for the class with the same name
UnBoundNonLinDecompOp-class
                        An S4 class to represent a nonlinear
                        nonautonomous compartmental matrix
UnBoundNonLinDecompOp_by_PoolNames
                        Generic constructor for the class with the same
                        name
UnBoundNonLinDecompOp_by_PoolNames-class
                        An S4 class to represent the of nonlinear
                        nonautonomous compartmental system
                        independently of the order of state variables
Yasso07Model            Implementation of the Yasso07 model
YassoModel              Implementation of the Yasso model.
[,Model,character,missing,missing-method
                        Experimentally overloaded index operator
[,NlModel,character,ANY,ANY-method
                        automatic title
[[,MCSim-method         automatic title
[[<-,MCSim-method       automatic title
add_plot                Add elements to plot
add_plot,TimeMap-method
                        automatic title
as.character,TimeMap-method
                        automatic title
as.numeric,InFluxList_by_PoolName-method
                        Convert to a numeric vector with the pool names
                        as names
as.numeric,InternalFluxList_by_PoolName-method
                        Convert to a numeric vector with names of the
                        form 'a->b'
as.numeric,InternalFlux_by_PoolName-method
                        Convert to a numeric value with name of the
                        form 'a->b'
as.numeric,OutFluxList_by_PoolName-method
                        Convert to a numeric vector with the pool names
                        as names
availableParticleProperties
                        Available particle properties
availableParticleProperties,MCSim-method
                        automatic title
availableParticleSets   Available particle sets
availableParticleSets,MCSim-method
                        automatic title
availableResidentSets   Available resident sets
availableResidentSets,MCSim-method
                        automatic title
bacwaveModel            Implementation of the microbial model Bacwave
                        (bacterial waves)
bind.C14curves          Binding of pre- and post-bomb Delta14C curves
by_PoolIndex            automatic title
by_PoolIndex,ConstantInFluxRate_by_PoolName,ANY,ANY-method
                        new object with the source pool id converted to
                        a PoolIndex if necessary
by_PoolIndex,ConstantInternalFluxRateList_by_PoolName,ANY,ANY-method
                        convert to a list indexed by pool names
by_PoolIndex,ConstantInternalFluxRate_by_PoolName,ANY,ANY-method
                        new object with the source pool id converted to
                        a PoolName if necessary
by_PoolIndex,ConstantOutFluxRateList_by_PoolName,ANY,ANY-method
                        convert to a list indexed by pool names
by_PoolIndex,ConstantOutFluxRate_by_PoolName,ANY,ANY-method
                        new object with the source pool id converted to
                        a PoolIndex if necessary
by_PoolIndex,InFluxList_by_PoolName,character,character-method
                        Transform pool names to indices
by_PoolIndex,InFlux_by_PoolName,character,character-method
                        Convert the pool names to indices
by_PoolIndex,InternalFluxList_by_PoolName,character,character-method
                        automatic title
by_PoolIndex,InternalFlux_by_PoolName,character,character-method
                        automatic title
by_PoolIndex,OutFluxList_by_PoolName,character,character-method
                        automatic title
by_PoolIndex,OutFlux_by_PoolName,character,character-method
                        automatic title
by_PoolIndex,PoolConnection_by_PoolName,ANY,ANY-method
                        constructor from strings of the form 'x->y' new
                        object with the source pool id and the
                        destination pool id guaranteed to be of class
                        PoolIndex
by_PoolIndex,function,character,character-method
                        convert a function f of to f_vec
by_PoolName             automatic title
by_PoolName,ConstantInFluxList_by_PoolIndex-method
                        convert to a list indexed by pool names
by_PoolName,ConstantInFluxRate_by_PoolIndex-method
                        new object with the source pool id converted to
                        a PoolIndex if necessary
by_PoolName,ConstantInFlux_by_PoolIndex-method
                        new object with the source pool id converted to
                        a PoolIndex if necessary
by_PoolName,ConstantInternalFluxRateList_by_PoolIndex-method
                        convert to a list indexed by pool names
by_PoolName,ConstantOutFluxRateList_by_PoolIndex-method
                        convert to a list indexed by pool names
by_PoolName,ConstantOutFluxRate_by_PoolIndex-method
                        new object with the source pool id converted to
                        a PoolName if necessary
check_duplicate_pool_names
                        helper function
check_id_length         helper function to check that the length of the
                        argument is exactly 1
check_pool_ids          Check pool ids
check_pool_ids,PoolConnection_by_PoolIndex,integer-method
                        automatic title
computeResults          Computes results
computeResults,MCSim-method
                        automatic title
cycling                 Cycling analysis of compartmental matrices
deSolve.lsoda.wrapper   deSolve.lsoda.wrapper
eCO2                    Soil CO2 efflux from an incubation experiment
entropyRatePerJump      Entropy rate per jump
entropyRatePerTime      Entropy rate per time
euler                   euler
example.2DBoundInFluxesFromFunction
                        example.2DBoundInFluxesFromFunction
example.2DBoundLinDecompOpFromFunction
                        example.2DBoundLinDecompOpFromFunction
example.2DConstFc.Args
                        example.2DConstFc.Args
example.2DConstInFluxesFromVector
                        2D example for constant Influx
example.2DGeneralDecompOpArgs
                        example.2DGeneralDecompOpArgs
example.2DInFluxes.Args
                        example.2DInFluxes.Args
example.2DUnBoundLinDecompOpFromFunction
                        example.2DUnBoundLinDecompOpFromFunction
example.ConstlinDecompOpFromMatrix
                        example.ConstlinDecompOpFromMatrix
example.Time2DArrayList
                        create an example TimeMap from 2D array
example.Time3DArrayList
                        create an example TimeFrame from 3D array
example.TimeMapFromArray
                        create an example TimeFrame from 3D array
example.nestedTime2DMatrixList
                        create an example nested list that can be
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   Accumulated release flux out of the pools
getAccumulatedRelease,Model-method
                        Compute the time integral of the relaese fluxes
                        over time
getC                    Calculates the content of the pools
getC,Model-method       Pool Contents for all times
getC,Model_by_PoolNames-method
                        Pool Contents for all times
getC,NlModel-method     Pool Contents for all times
getC14                  Generic that yields the 14C content for all
                        pools and all times
getC14,Model_14-method
                        automatic title
getCompartmentalMatrixFunc
                        Compartmental matrix function
getCompartmentalMatrixFunc,BoundLinDecompOp-method
                        automatic title
getCompartmentalMatrixFunc,ConstLinDecompOp-method
                        Compartmental matrix function
getCompartmentalMatrixFunc,TransportDecompositionOperator-method
                        automatic title
getCompartmentalMatrixFunc,UnBoundNonLinDecompOp-method
                        Extract the matrix valued function of time and
                        state vector for the compartmental matrix
getConstLinDecompOp     Constant linear decomposition operator
getConstLinDecompOp,ConstLinDecompOpWithLinearScalarFactor-method
                        automatic title
getConstantCompartmentalMatrix
                        Constant compartmental matrix
getConstantCompartmentalMatrix,ConstLinDecompOp-method
                        Constant compartmental matrix
getConstantCompartmentalMatrix,ConstLinDecompOpWithLinearScalarFactor-method
                        automatic title
getConstantInFluxVector
                        Input flux vector
getConstantInFluxVector,ConstInFluxes-method
                        automatic title
getConstantInternalFluxRateList_by_PoolIndex
                        Constant internal flux rate list by pool index
getConstantInternalFluxRateList_by_PoolIndex,ConstLinDecompOp-method
                        Constant internal flux rate list by pool index
getConstantOutFluxRateList_by_PoolIndex
                        Constant out flux rate list by pool index
getConstantOutFluxRateList_by_PoolIndex,ConstLinDecompOp-method
                        Constant out flux rate list by pool index
getCumulativeC          Cummulative pool contents
getCumulativeC,NlModel-method
                        automatic title
getDecompOp             Decomposition operator of a model
getDecompOp,Model-method
                        Extract the Compartmental Operator
getDecompOp,NlModel-method
                        Extract the Compartmental Operator
getDotOut               Dot out
getDotOut,TransportDecompositionOperator-method
                        automatic title
getF14                  Generic that yields the 14C fraction for the
                        content all pools and all times
getF14,Model_14-method
                        automatic title
getF14C                 Generic that yields the 14C fraction for the
                        cumulative content of all pools and all times
getF14C,Model_14-method
                        automatic title
getF14R                 Generic that yields the 14C fraction for the
                        release flux of all pools and all times
getF14R,Model_14-method
                        automatic title
getFormat               Get format of SoilR object
getFormat,Fc-method     automatic title
getFunctionDefinition   Function definition of SoilR model
getFunctionDefinition,ConstInFluxes-method
                        automatic title
getFunctionDefinition,ConstLinDecompOp-method
                        Function describing an object of class
                        ConstLinDecompOp
getFunctionDefinition,ConstLinDecompOpWithLinearScalarFactor-method
                        convert names of vectors or lists to class
                        ConstantOutFluxRate convert names of vectors or
                        lists to class ConstantInternalFluxRate helper
                        function
getFunctionDefinition,DecompositionOperator-method
                        automatic title
getFunctionDefinition,InFluxList_by_PoolIndex-method
                        automatic title
getFunctionDefinition,InFluxList_by_PoolName-method
                        automatic title
getFunctionDefinition,StateDependentInFluxVector-method
                        automatic title
getFunctionDefinition,TimeMap-method
                        automatic title
getFunctionDefinition,TransportDecompositionOperator-method
                        automatic title
getFunctionDefinition,UnBoundInFluxes-method
                        automatic title
getFunctionDefinition,UnBoundLinDecompOp-method
                        Extracts the time dependent matrix valued
                        function (compartmental matrix)
getInFluxes             Extract the influxes
getInFluxes,Model-method
                        Extract the InFluxes as provided during
                        creation of the model
getInFluxes,NlModel-method
                        automatic title
getInitialValues        Initial values of SoilR object
getInitialValues,NlModel-method
                        automatic title
getLinearScaleFactor    Linear scale factor
getLinearScaleFactor,ConstLinDecompOpWithLinearScalarFactor-method
                        automatic title
getMeanTransitTime      Mean transit time for SoilR objects
getMeanTransitTime,ConstLinDecompOp-method
                        Mean transit time obtained through a numerical
                        simulation. It produces an estimate with
                        numerical errors. We recommend to use the
                        function transitTime instead.
getNumberOfPools        Number of pools in a model
getNumberOfPools,MCSim-method
                        automatic title
getNumberOfPools,NlModel-method
                        automatic title
getNumberOfPools,TransportDecompositionOperator-method
                        automatic title
getOutputFluxes         Generic Function to obtain the fluxes out of of
                        the pools
getOutputFluxes,NlModel-method
                        automatic title
getOutputReceivers      Pools receiving outputs from other pools
getOutputReceivers,TransportDecompositionOperator,numeric-method
                        automatic title
getParticleMonteCarloSimulator
                        automatic title
getParticleMonteCarloSimulator,NlModel-method
                        automatic title
getReleaseFlux          Generic Function to obtain the vector of
                        release fluxes out of the pools for all times.
getReleaseFlux,Model-method
                        The release fluxes [content]/[time] for all
                        pools.
getReleaseFlux,Model_by_PoolNames-method
                        automatic title
getReleaseFlux,NlModel-method
                        automatic title
getReleaseFlux14        Generic that yields the 14C fraction in the
                        release flux
getReleaseFlux14,Model_14-method
                        automatic title
getRightHandSideOfODE   Right hand side of ODE of a SoilR model
getRightHandSideOfODE,Model-method
                        Derivative of the state variables as function
getRightHandSideOfODE,Model_by_PoolNames-method
                        Provide the (vector valued) derivative of the
                        stocks with respect to time
getSolution             Calculates all stocks all fluxes to ,in and out
                        of the compartment system and also their
                        integrals over time
getSolution,Model_by_PoolNames-method
                        All Fluxes and stocks for all times
getTimeRange            Time range of a model simulation
getTimeRange,ConstInFluxes-method
                        automatic title
getTimeRange,ConstLinDecompOp-method
                        Time range of a simulation described in an
                        object of class ConstLinDecompOp
getTimeRange,ConstLinDecompOpWithLinearScalarFactor-method
                        automatic title
getTimeRange,DecompositionOperator-method
                        automatic title
getTimeRange,TimeMap-method
                        The time interval where the function is defined
getTimeRange,UnBoundInFluxes-method
                        automatic title
getTimeRange,UnBoundLinDecompOp-method
                        Extracts the time interval for which the
                        function is valid.
getTimes                Time vector of SoilR object
getTimes,Model-method   Extract the times vector
getTimes,Model_by_PoolNames-method
                        Extract the times vector
getTimes,NlModel-method
                        automatic title
getTransferCoefficients
                        Transfer coefficients
getTransferCoefficients,NlModel-method
                        automatic title
getTransferCoefficients,TransportDecompositionOperator-method
                        automatic title
getTransferMatrix       deprecated, use getTransferMatrixFunc instead
getTransferMatrixFunc   Transfer matrix function
getTransferMatrixFunc,TransportDecompositionOperator-method
                        automatic title
getTransitTimeDistributionDensity
                        Transit time distribution for SoilR objects
getTransitTimeDistributionDensity,ConstLinDecompOp-method
                        Transit time distribution obtained through a
                        numerical simulation. It introduces numerical
                        errors. We recommend to use the function
                        transitTime instead
getValues               Get values of SoilR object
getValues,ConstFc-method
                        automatic title
incubation_experiment   Soil CO2 efflux from an incubation experiment,
                        along with the soil mass and carbon
                        concentration measurements.
initialize,ConstLinDecompOp-method
                        automatic title
initialize,DecompositionOperator-method
                        automatic title
initialize,MCSim-method
                        automatic title
initialize,Model-method
                        Internal method to supervise creation of
                        objects of this class
initialize,Model_14-method
                        Internal method to supervise creation of
                        objects of this class
initialize,Model_by_PoolNames-method
                        automatic title
initialize,NlModel-method
                        automatic title
initialize,TimeMap-method
                        automatic title
initialize,TransportDecompositionOperator-method
                        automatic title
initialize,UnBoundInFluxes-method
                        automatic title
initialize,UnBoundLinDecompOp-method
                        automatic title
linearScalarModel       Implementation of a general model for linear
                        non-autonomous systems with scalar modifiers
linesCPool              Add lines with the output of 'getC14', 'getC',
                        or 'getReleaseFlux' to an existing plot
listProduct             tensor product of lists
pathEntropy             Path Entropy
plot,MCSim-method       automatic title
plot,Model-method       Create an overview plot
plot,Model_by_PoolNames-method
                        Plot the graph of pool connections
plot,NlModel-method     automatic title
plot,TimeMap-method     automatic title
plotC14Pool             Plots the output of 'getF14' for each pool over
                        time
plotCPool               Plots the output of 'getC' or 'getReleaseFlux'
                        for each pool over time
plotPoolGraph           Generic plotter
plotPoolGraph,SymbolicModel_by_PoolNames-method
                        Plot the graph of pool connections
plotPoolGraphFromTupleLists
                        Helper function to draw connectivity graphs
predefinedModels        PREDEFINED MODELS
print,NlModel-method    automatic title
show,NlModel-method     automatic title
state_variable_names    determine the minimum set of statevariables
systemAge               System and pool age for constant compartment
                        models
transitTime             Transit times for compartment models
turnoverFit             Estimation of the turnover time from a
                        radiocarbon sample.
