# Models of Soil Organic Matter Decomposition

## Documentation for package ‘SoilR’ version 1.2.107

- DESCRIPTION file
- Package NEWS

## Help Pages

A B C D E F G H I L M N O P R S T U Y misc

SoilR-package | SoilR

## -- A --

AbsoluteFractionModern | Conversion of radiocarbon values
AbsoluteFractionModern-method | automatic title
AbsoluteFractionModern-method | automatic title
AbsoluteFractionModern_from_Delta14C | Conversion of radiocarbon values
AbsoluteFractionModern_from_Delta14C-method | Conversion of radiocarbon values
AbsoluteFractionModern_from_Delta14C-method | Conversion of radiocarbon values, from Delta14C to absolute fraction modern
add_plot | Add elements to plot
add_plot-method | automatic title
as.character-method | automatic title
as.numeric-method | Convert to a numeric vector with the pool names as names
as.numeric-method | Convert to a numeric vector with names of the form 'a->b'
as.numeric-method | Convert to a numeric value with name of the form 'a->b'
as.numeric-method | Convert to a numeric vector with the pool names as names
availableParticleProperties | Available particle properties
availableParticleProperties-method | automatic title
availableParticleSets | Available particle sets
availableParticleSets-method | automatic title
availableResidentSets | Available resident sets
availableResidentSets-method | automatic title
AWBmodel | Implementation of the microbial model AWB (Allison, Wallenstein, Bradford, 2010)

## -- B --

bacwaveModel | Implementation of the microbial model Bacwave (bacterial waves)
bind.C14curves | Binding of pre- and post-bomb Delta14C curves
BoundFc | Bound Fc object
BoundFc-class | S4-class to represent atmospheric 14C concentration as scalar function of time.
BoundFc-method | automatic title
BoundFc-method | automatic title
BoundInFluxes | constructor for BoundInFluxes
BoundInFluxes-class | automatic title
BoundLinDecompOp | Generic constructor for the class with the same name
BoundLinDecompOp-class | A S4 class to represent a linear compartmental operator defined on time interval
BoundLinDecompOp-method | Creates an object of class BoundLinDecompOp
BoundLinDecompOp-method | A converter
by_PoolIndex | automatic title
by_PoolIndex-method | new object with the source pool id converted to a PoolIndex if necessary
by_PoolIndex-method | convert to a list indexed by pool names
by_PoolIndex-method | new object with the source pool id converted to a PoolName if necessary
by_PoolIndex-method | convert to a list indexed by pool names
by_PoolIndex-method | new object with the source pool id converted to a PoolIndex if necessary
by_PoolIndex-method | Transform pool names to indices
by_PoolIndex-method | Convert the pool names to indices
by_PoolIndex-method | automatic title
by_PoolIndex-method | automatic title
by_PoolIndex-method | automatic title
by_PoolIndex-method | automatic title
by_PoolIndex-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-method | convert a function f of to f_vec
by_PoolName | automatic title
by_PoolName-method | convert to a list indexed by pool names
by_PoolName-method | new object with the source pool id converted to a PoolIndex if necessary
by_PoolName-method | new object with the source pool id converted to a PoolIndex if necessary
by_PoolName-method | convert to a list indexed by pool names
by_PoolName-method | convert to a list indexed by pool names
by_PoolName-method | new object with the source pool id converted to a PoolName if necessary

## -- C --

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
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-method | automatic title
computeResults | Computes results
computeResults-method | automatic title
ConstantInFluxList_by_PoolIndex | Generic constructor for the class with the same name
ConstantInFluxList_by_PoolIndex-class | Subclass of list that is guaranteed to contain only elements of type ConstantInFlux_by_PoolIndex
ConstantInFluxList_by_PoolIndex-method | constructor from ConstInFluxes
ConstantInFluxList_by_PoolIndex-method | constructor from a normal list
ConstantInFluxList_by_PoolIndex-method | constructor from numeric vector
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-class | Describes a list of flux rates.
ConstantInternalFluxRateList_by_PoolIndex-method | constructor from a normal list
ConstantInternalFluxRateList_by_PoolIndex-method | automatic title
ConstantInternalFluxRateList_by_PoolName | Generic constructor for the class with the same name
ConstantInternalFluxRateList_by_PoolName-class | Describes a list of flux rates.
ConstantInternalFluxRateList_by_PoolName-method | Constructor from a normal list of fluxes
ConstantInternalFluxRate_by_PoolIndex | Generic constructor for the class with the same name
ConstantInternalFluxRate_by_PoolIndex-class | S4 class representing a constant internal flux rate
ConstantInternalFluxRate_by_PoolIndex-method | automatic title
ConstantInternalFluxRate_by_PoolName | Generic constructor for the class with the same name
ConstantInternalFluxRate_by_PoolName-class | S4-class to represent a constant internal flux rate with source and target indexed by name
ConstantInternalFluxRate_by_PoolName-method | constructor with argument conversion
ConstantInternalFluxRate_by_PoolName-method | constructor from strings of the form 'a->b'
ConstantOutFluxRateList_by_PoolIndex | Generic constructor for the class with the same name
ConstantOutFluxRateList_by_PoolIndex-class | Describes a list of flux rates.
ConstantOutFluxRateList_by_PoolIndex-method | constructor from a normal list
ConstantOutFluxRateList_by_PoolIndex-method | automatic title
ConstantOutFluxRateList_by_PoolName | Generic constructor for the class with the same name
ConstantOutFluxRateList_by_PoolName-class | Describes a list of flux rates.
ConstantOutFluxRateList_by_PoolName-method | constructor from a normal list
ConstantOutFluxRateList_by_PoolName-method | automatic title
ConstantOutFluxRate_by_PoolIndex | Generic constructor for the class with the same name
ConstantOutFluxRate_by_PoolIndex-class | S4 Class to represent a single constant out-flux rate with the source pool specified by an index
ConstantOutFluxRate_by_PoolIndex-method | automatic title
ConstantOutFluxRate_by_PoolName-class | S4 Class to represent a single constant out-flux rate with the source pool specified by name
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-class | S4 class for a constant influx vector
ConstInFluxes-method | automatic title
ConstInFluxes-method | automatic title
ConstLinDecompOp | Generic constructor for the class with the same name
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.
ConstLinDecompOp-method | Constructor of object of ConstLinDecompOp class
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
cycling | Cycling analysis of compartmental matrices

## -- D --

DecompOp-class | S4-class to represent compartmental operators
DecompositionOperator-class | automatic title
Delta14C | Conversion of radiocarbon values
Delta14C-method | automatic title
Delta14C-method | automatic title
Delta14C_from_AbsoluteFractionModern | Conversion of radiocarbon values
Delta14C_from_AbsoluteFractionModern-method | Conversion of radiocarbon values
Delta14C_from_AbsoluteFractionModern-method | Conversion of radiocarbon values
deSolve.lsoda.wrapper | deSolve.lsoda.wrapper

## -- E --

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.nestedTime2DMatrixList | create an example nested list that can be
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

## -- F --

Fc-class | automatic title
FcAtm.from.Dataframe | FcAtm.from.Dataframe
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.linear | Effects of temperature on decomposition rates according to a linear model
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
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

## -- G --

GaudinskiModel14 | Implementation of a the six-pool C14 model proposed by Gaudinski et al. 2000
GeneralDecompOp | A generic factory for subclasses of GeneralDecompOp
GeneralDecompOp-method | Pass through factory for objects of subclasses of DecompOp
GeneralDecompOp-method | automatic title
GeneralDecompOp-method | automatic title
GeneralDecompOp-method | automatic title
GeneralDecompOp-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-method | automatic title
GeneralPoolId-method | generic factory for this virtual class
getAccumulatedRelease | Accumulated release flux out of the pools
getAccumulatedRelease-method | Compute the time integral of the relaese fluxes over time
getC | Calculates the content of the pools
getC-method | Pool Contents for all times
getC-method | Pool Contents for all times
getC-method | Pool Contents for all times
getC14 | Generic that yields the 14C content for all pools and all times
getC14-method | automatic title
getCompartmentalMatrixFunc | Compartmental matrix function
getCompartmentalMatrixFunc-method | automatic title
getCompartmentalMatrixFunc-method | Compartmental matrix function
getCompartmentalMatrixFunc-method | automatic title
getCompartmentalMatrixFunc-method | Extract the matrix valued function of time and state vector for the compartmental matrix
getConstantCompartmentalMatrix | Constant compartmental matrix
getConstantCompartmentalMatrix-method | Constant compartmental matrix
getConstantCompartmentalMatrix-method | automatic title
getConstantInFluxVector | Input flux vector
getConstantInFluxVector-method | automatic title
getConstantInternalFluxRateList_by_PoolIndex | Constant internal flux rate list by pool index
getConstantInternalFluxRateList_by_PoolIndex-method | Constant internal flux rate list by pool index
getConstantOutFluxRateList_by_PoolIndex | Constant out flux rate list by pool index
getConstantOutFluxRateList_by_PoolIndex-method | Constant out flux rate list by pool index
getConstLinDecompOp | Constant linear decomposition operator
getConstLinDecompOp-method | automatic title
getCumulativeC | Cummulative pool contents
getCumulativeC-method | automatic title
getDecompOp | Decomposition operator of a model
getDecompOp-method | Extract the Compartmental Operator
getDecompOp-method | Extract the Compartmental Operator
getDotOut | Dot out
getDotOut-method | automatic title
getF14 | Generic that yields the 14C fraction for the content all pools and all times
getF14-method | automatic title
getF14C | Generic that yields the 14C fraction for the cumulative content of all pools and all times
getF14C-method | automatic title
getF14R | Generic that yields the 14C fraction for the release flux of all pools and all times
getF14R-method | automatic title
getFormat | Get format of SoilR object
getFormat-method | automatic title
getFunctionDefinition | Function definition of SoilR model
getFunctionDefinition-method | automatic title
getFunctionDefinition-method | Function describing an object of class ConstLinDecompOp
getFunctionDefinition-method | convert names of vectors or lists to class ConstantOutFluxRate convert names of vectors or lists to class ConstantInternalFluxRate helper function
getFunctionDefinition-method | automatic title
getFunctionDefinition-method | automatic title
getFunctionDefinition-method | automatic title
getFunctionDefinition-method | automatic title
getFunctionDefinition-method | automatic title
getFunctionDefinition-method | automatic title
getFunctionDefinition-method | automatic title
getFunctionDefinition-method | Extracts the time dependent matrix valued function (compartmental matrix)
getInFluxes | Extract the influxes
getInFluxes-method | Extract the InFluxes as provided during creation of the model
getInFluxes-method | automatic title
getInitialValues | Initial values of SoilR object
getInitialValues-method | automatic title
getLinearScaleFactor | Linear scale factor
getLinearScaleFactor-method | automatic title
getMeanTransitTime | Mean transit time for SoilR objects
getMeanTransitTime-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-method | automatic title
getNumberOfPools-method | automatic title
getNumberOfPools-method | automatic title
getOutputFluxes | Generic Function to obtain the fluxes out of of the pools
getOutputFluxes-method | automatic title
getOutputReceivers | Pools receiving outputs from other pools
getOutputReceivers-method | automatic title
getParticleMonteCarloSimulator | automatic title
getParticleMonteCarloSimulator-method | automatic title
getReleaseFlux | Generic Function to obtain the vector of release fluxes out of the pools for all times.
getReleaseFlux-method | The release fluxes [content]/[time] for all pools.
getReleaseFlux-method | automatic title
getReleaseFlux-method | automatic title
getReleaseFlux14 | Generic that yields the 14C fraction in the release flux
getReleaseFlux14-method | automatic title
getRightHandSideOfODE | Right hand side of ODE of a SoilR model
getRightHandSideOfODE-method | Derivative of the state variables as function
getRightHandSideOfODE-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-method | All Fluxes and stocks for all times
getTimeRange | Time range of a model simulation
getTimeRange-method | automatic title
getTimeRange-method | Time range of a simulation described in an object of class ConstLinDecompOp
getTimeRange-method | automatic title
getTimeRange-method | automatic title
getTimeRange-method | The time interval where the function is defined
getTimeRange-method | automatic title
getTimeRange-method | Extracts the time interval for which the function is valid.
getTimes | Time vector of SoilR object
getTimes-method | Extract the times vector
getTimes-method | Extract the times vector
getTimes-method | automatic title
getTransferCoefficients | Transfer coefficients
getTransferCoefficients-method | automatic title
getTransferCoefficients-method | automatic title
getTransferMatrix | deprecated, use getTransferMatrixFunc instead
getTransferMatrixFunc | Transfer matrix function
getTransferMatrixFunc-method | automatic title
getTransitTimeDistributionDensity | Transit time distribution for SoilR objects
getTransitTimeDistributionDensity-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-method | automatic title
Graven2017 | Compiled records of radicarbon in atmospheric CO2 for historical simulations in CMIP6

## -- H --

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)

## -- I --

ICBMModel | Implementation of the Introductory Carbon Balance Model (ICBM)
ICBM_N | Implementation of the ICBM/N model
incubation_experiment | Soil CO2 efflux from an incubation experiment, along with the soil mass and carbon concentration measurements.
InFlux | Generic constructor for the class with the same name
InFluxes | A generic factory for subclasses of InFluxes
InFluxes-class | A virtual S4-class representing (different subclasses) of in-fluxes to the system
InFluxes-method | automatic title
InFluxes-method | automatic title
InFluxes-method | automatic title
InFluxes-method | automatic title
InFluxes-method | automatic title
InFluxes-method | automatic title
InFluxes-method | automatic title
InFluxList_by_PoolIndex | Generic constructor for the class with the same name
InFluxList_by_PoolIndex-class | Describes a list of flux rates.
InFluxList_by_PoolIndex-method | constructor from a normal list after checking the elements
InFluxList_by_PoolName | Generic constructor for the class with the same name
InFluxList_by_PoolName-class | Class for a list of influxes indexed by the names of the target pools
InFluxList_by_PoolName-method | constructor from a normal list
InFlux_by_PoolIndex | Generic constructor for the class with the same name
InFlux_by_PoolIndex-class | S4 class for the influx to a single pool identified by the index
InFlux_by_PoolIndex-method | Constructor from an ordered pair of PoolIndex (integer like) objects
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-class | S4 class for the influx to a single pool identified by the name
InFlux_by_PoolName-method | Constructor from an ordered pair of PoolName (string like) and function objects
initialize-method | automatic title
initialize-method | automatic title
initialize-method | automatic title
initialize-method | Internal method to supervise creation of objects of this class
initialize-method | Internal method to supervise creation of objects of this class
initialize-method | automatic title
initialize-method | automatic title
initialize-method | automatic title
initialize-method | automatic title
initialize-method | automatic title
initialize-method | automatic title
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-class | S4-class for a list of internal fluxes with source and destination pool inidices
InternalFluxList_by_PoolIndex-method | Constructor from a normal list after checking the elements
InternalFluxList_by_PoolName | Generic constructor for the class with the same name
InternalFluxList_by_PoolName-class | S4-class for a list of internal fluxes with indexed by (source and destination pool) names
InternalFluxList_by_PoolName-method | constructor from a normal list
InternalFlux_by_PoolIndex | Generic constructor for the class with the same name
InternalFlux_by_PoolIndex-class | S4-class for a single internal flux with source and destination pools specified by indices
InternalFlux_by_PoolIndex-method | constructor from an ordered pair of PoolIndex (integer like) objects and a function with vector argument
InternalFlux_by_PoolName | Generic constructor for the class with the same name
InternalFlux_by_PoolName-class | S4-class for a single internal flux with source and destination pools specified by name
InternalFlux_by_PoolName-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-method | automatic title

## -- L --

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

## -- M --

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

## -- N --

NlModel-class | deprecated class for a non-linear model run.

## -- O --

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-class | A list of outfluxes
OutFluxList_by_PoolIndex-method | constructor from a normal list
OutFluxList_by_PoolName | Generic constructor for the class with the same name
OutFluxList_by_PoolName-class | S4 class for a list of out-fluxes indexed by source pool name
OutFluxList_by_PoolName-method | constructor from a normal list
OutFlux_by_PoolIndex | Generic constructor for the class with the same name
OutFlux_by_PoolIndex-class | S4 class for a single out-flux with source pool index
OutFlux_by_PoolIndex-method | constructor from a PoolIndex (integer like) objects and a function with vector argument
OutFlux_by_PoolName | Generic constructor for the class with the same name
OutFlux_by_PoolName-class | S4 class for a single out-flux with source pool name
OutFlux_by_PoolName-method | constructor from a PoolName (integer like) object and a function

## -- P --

ParallelModel | models for unconnected pools
pathEntropy | Path Entropy
plot-method | automatic title
plot-method | Create an overview plot
plot-method | Plot the graph of pool connections
plot-method | automatic title
plot-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-method | Plot the graph of pool connections
plotPoolGraphFromTupleLists | Helper function to draw connectivity graphs
PoolConnection_by_PoolIndex | Pool connection by pool index
PoolConnection_by_PoolIndex-class | Objects that have a source and a destination described by integer like objects ( of class PoolIndex)
PoolConnection_by_PoolIndex-method | constructor from an ordered pair of PoolId objects
PoolConnection_by_PoolIndex-method | constructor from strings of the form '1_to_2'
PoolConnection_by_PoolName | Pool connection by pool name
PoolConnection_by_PoolName-class | Objects that have a source and a destination determined by a string like object of class PoolName
PoolConnection_by_PoolName-method | constructor from an ordered pair of PoolName objects
PoolId-class | common class for pool ids
PoolIndex | Pool index
PoolIndex-class | S4 class for pool indices
PoolIndex-method | pass through constructor fron an object of the same class
PoolIndex-method | convert to number like object
PoolIndex-method | construct from number string like '1' or '3'
PoolIndex-method | construct from number
PoolName | Pool name
PoolName-class | class for pool-name-strings
PoolName-method | convert to string like object
PoolName-method | pass through constructor fron an object of the same class
PoolName-method | construct from string with checks
predefinedModels | PREDEFINED MODELS
print-method | automatic title

## -- R --

RespirationCoefficients | helper function to compute respiration coefficients
RothCModel | Implementation of the RothCModel

## -- S --

ScalarTimeMap | Constructor for 'ScalarTimeMap-class'
ScalarTimeMap-class | S4 class for a scalar time dependent function on a finite time interval
ScalarTimeMap-method | constructor for data given as 2 column data.frame
ScalarTimeMap-method | manual constructor for just a function
ScalarTimeMap-method | manual constructor for a function and an interval
ScalarTimeMap-method | special case for a time map from a constant
ScalarTimeMap-method | constructor for data and times given as vectors
SeriesLinearModel | General m-pool linear model with series structure
SeriesLinearModel14 | General m-pool linear C14 model with series structure
SHCal20 | The SHCal20 southern hemisphere radiocarbon curve for the 0-55,000 yr BP period
show-method | automatic title
SoilR.F0.new | deprecated function that used to create an object of class SoilR.F0
StateDependentInFluxVector | Input vector that is a function of the pool contenst and time
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-class | Subclass of list that is guaranteed to contain only elements of type StateIndependentInFlux_by_PoolIndex
StateIndependentInFluxList_by_PoolIndex-method | constructor from a normal list
StateIndependentInFluxList_by_PoolName | Generic constructor for the class with the same name
StateIndependentInFlux_by_PoolIndex | Constructor for the class with the same name
StateIndependentInFlux_by_PoolIndex-class | Constructor for the class with the same name
state_variable_names | determine the minimum set of statevariables
SymbolicModel_by_PoolNames | A symbolic model description based on flux functions
SymbolicModel_by_PoolNames-class | A symbolic model description based on flux functions
systemAge | System and pool age for constant compartment models

## -- T --

ThreepairMMmodel | Implementation of a 6-pool Michaelis-Menten model
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
TimeMap | Constructor for 'TimeMap-class'
TimeMap-class | S4 class for a time dependent function
TimeMap-method | automatic title
TimeMap-method | automatic title
TimeMap-method | manual constructor for just a function
TimeMap-method | manual constructor for a function and an interval
TimeMap-method | automatic title
TimeMap-method | automatic title
TimeMap-method | automatic title
TimeMap-method | automatic title
TimeMap-method | automatic title
TimeMap.from.Dataframe | TimeMap.from.Dataframe
TimeMap.new | deprecated constructor of the class TimeMap.
TimeRangeIntersection | The time interval where both functions are defined
transitTime | Transit times for compartment models
TransportDecompositionOperator-class | automatic title
turnoverFit | Estimation of the turnover time from a radiocarbon sample.
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

## -- U --

UnBoundInFluxes | Unbound input fluxes
UnBoundInFluxes-class | automatic title
UnBoundInFluxes-method | automatic title
UnBoundLinDecompOp | Generic constructor for the class with the same name
UnBoundLinDecompOp-class | An S4 class to represent a linear nonautonomous compartmental matrix
UnBoundLinDecompOp-method | Generic constructor for the class with the same name
UnBoundNonLinDecompOp | Generic constructor for the class with the same name
UnBoundNonLinDecompOp-class | An S4 class to represent a nonlinear nonautonomous compartmental matrix
UnBoundNonLinDecompOp-method | Constructor for the class with the same name
UnBoundNonLinDecompOp-method | Constructor for the class with the same name
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

## -- Y --

Yasso07Model | Implementation of the Yasso07 model
YassoModel | Implementation of the Yasso model.

## -- misc --

$-method | automatic title
[-method | Experimentally overloaded index operator
[-method | automatic title
[[-method | automatic title
[[<--method | automatic title