| SoilR | SoilR-package |
| Experimentally overloaded index operator | [,Model,character,missing,missing-method |
| automatic title | [,NlModel,character,ANY,ANY-method |
| automatic title | [[,MCSim-method |
| automatic title | [[<-,MCSim-method |
| automatic title | $,NlModel-method |
| Conversion of radiocarbon values | AbsoluteFractionModern |
| Conversion of radiocarbon values | AbsoluteFractionModern_from_Delta14C |
| Conversion of radiocarbon values | AbsoluteFractionModern_from_Delta14C,matrix-method |
| Conversion of radiocarbon values, from Delta14C to absolute fraction modern | AbsoluteFractionModern_from_Delta14C,numeric-method |
| automatic title | AbsoluteFractionModern,BoundFc-method |
| automatic title | AbsoluteFractionModern,ConstFc-method |
| Add elements to plot | add_plot |
| automatic title | add_plot,TimeMap-method |
| automatic title | as.character,TimeMap-method |
| Convert to a numeric vector with the pool names as names | as.numeric,InFluxList_by_PoolName-method |
| Convert to a numeric value with name of the form 'a->b' | as.numeric,InternalFlux_by_PoolName-method |
| Convert to a numeric vector with names of the form 'a->b' | as.numeric,InternalFluxList_by_PoolName-method |
| Convert to a numeric vector with the pool names as names | as.numeric,OutFluxList_by_PoolName-method |
| Available particle properties | availableParticleProperties |
| automatic title | availableParticleProperties,MCSim-method |
| Available particle sets | availableParticleSets |
| automatic title | availableParticleSets,MCSim-method |
| Available resident sets | availableResidentSets |
| automatic title | availableResidentSets,MCSim-method |
| Implementation of the microbial model AWB (Allison, Wallenstein, Bradford, 2010) | AWBmodel |
| Implementation of the microbial model Bacwave (bacterial waves) | bacwaveModel |
| Binding of pre- and post-bomb Delta14C curves | bind.C14curves |
| Bound Fc object | BoundFc |
| S4-class to represent atmospheric 14C concentration as scalar function of time. | BoundFc-class |
| automatic title | BoundFc,character-method |
| automatic title | BoundFc,missing-method |
| constructor for BoundInFluxes | BoundInFluxes |
| automatic title | BoundInFluxes-class |
| Generic constructor for the class with the same name | BoundLinDecompOp |
| A S4 class to represent a linear compartmental operator defined on time interval | BoundLinDecompOp-class |
| Creates an object of class BoundLinDecompOp | BoundLinDecompOp,ANY-method |
| A converter | BoundLinDecompOp,UnBoundLinDecompOp-method |
| automatic title | by_PoolIndex |
| new object with the source pool id converted to a PoolIndex if necessary | by_PoolIndex,ConstantInFluxRate_by_PoolName,ANY,ANY-method |
| new object with the source pool id converted to a PoolName if necessary | by_PoolIndex,ConstantInternalFluxRate_by_PoolName,ANY,ANY-method |
| convert to a list indexed by pool names | by_PoolIndex,ConstantInternalFluxRateList_by_PoolName,ANY,ANY-method |
| new object with the source pool id converted to a PoolIndex if necessary | by_PoolIndex,ConstantOutFluxRate_by_PoolName,ANY,ANY-method |
| convert to a list indexed by pool names | by_PoolIndex,ConstantOutFluxRateList_by_PoolName,ANY,ANY-method |
| convert a function f of to f_vec | by_PoolIndex,function,character,character-method |
| Convert the pool names to indices | by_PoolIndex,InFlux_by_PoolName,character,character-method |
| Transform pool names to indices | by_PoolIndex,InFluxList_by_PoolName,character,character-method |
| automatic title | by_PoolIndex,InternalFlux_by_PoolName,character,character-method |
| automatic title | by_PoolIndex,InternalFluxList_by_PoolName,character,character-method |
| automatic title | by_PoolIndex,OutFlux_by_PoolName,character,character-method |
| automatic title | by_PoolIndex,OutFluxList_by_PoolName,character,character-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,PoolConnection_by_PoolName,ANY,ANY-method |
| automatic title | by_PoolName |
| new object with the source pool id converted to a PoolIndex if necessary | by_PoolName,ConstantInFlux_by_PoolIndex-method |
| convert to a list indexed by pool names | by_PoolName,ConstantInFluxList_by_PoolIndex-method |
| new object with the source pool id converted to a PoolIndex if necessary | by_PoolName,ConstantInFluxRate_by_PoolIndex-method |
| convert to a list indexed by pool names | by_PoolName,ConstantInternalFluxRateList_by_PoolIndex-method |
| new object with the source pool id converted to a PoolName if necessary | by_PoolName,ConstantOutFluxRate_by_PoolIndex-method |
| convert to a list indexed by pool names | by_PoolName,ConstantOutFluxRateList_by_PoolIndex-method |
| Atmospheric 14C fraction | C14Atm |
| Post-bomb atmospheric 14C fraction | C14Atm_NH |
| Implementation of the Century model | CenturyModel |
| Implementation of a radiocarbon version of the Century model | CenturyModel14 |
| helper function | check_duplicate_pool_names |
| helper function to check that the length of the argument is exactly 1 | check_id_length |
| Check pool ids | check_pool_ids |
| automatic title | check_pool_ids,PoolConnection_by_PoolIndex,integer-method |
| Computes results | computeResults |
| automatic title | computeResults,MCSim-method |
| class for a constant influx to a single pool identified by index | ConstantInFlux_by_PoolIndex-class |
| class for a constant influx to a single pool identified by pool name | ConstantInFlux_by_PoolName-class |
| Generic constructor for the class with the same name | ConstantInFluxList_by_PoolIndex |
| Subclass of list that is guaranteed to contain only elements of type ConstantInFlux_by_PoolIndex | ConstantInFluxList_by_PoolIndex-class |
| constructor from ConstInFluxes | ConstantInFluxList_by_PoolIndex,ConstInFluxes-method |
| constructor from a normal list | ConstantInFluxList_by_PoolIndex,list-method |
| constructor from numeric vector | ConstantInFluxList_by_PoolIndex,numeric-method |
| Generic constructor for the class with the same name | ConstantInFluxList_by_PoolName |
| Subclass of list that is guaranteed to contain only elements of type ConstantInFlux_by_PoolName | ConstantInFluxList_by_PoolName-class |
| Describes a flux rates. | ConstantInFluxRate_by_PoolIndex-class |
| Constructor for the class with the same name | ConstantInFluxRate_by_PoolName |
| Describes a flux rates. | ConstantInFluxRate_by_PoolName-class |
| Generic constructor for the class with the same name | ConstantInternalFluxRate_by_PoolIndex |
| S4 class representing a constant internal flux rate | ConstantInternalFluxRate_by_PoolIndex-class |
| automatic title | ConstantInternalFluxRate_by_PoolIndex,numeric,numeric,missing,numeric-method |
| Generic constructor for the class with the same name | ConstantInternalFluxRate_by_PoolName |
| S4-class to represent a constant internal flux rate with source and target indexed by name | ConstantInternalFluxRate_by_PoolName-class |
| constructor with argument conversion | ConstantInternalFluxRate_by_PoolName,character,character,missing,numeric-method |
| constructor from strings of the form 'a->b' | ConstantInternalFluxRate_by_PoolName,missing,missing,character,numeric-method |
| Generic constructor for the class with the same name | ConstantInternalFluxRateList_by_PoolIndex |
| Describes a list of flux rates. | ConstantInternalFluxRateList_by_PoolIndex-class |
| constructor from a normal list | ConstantInternalFluxRateList_by_PoolIndex,list-method |
| automatic title | ConstantInternalFluxRateList_by_PoolIndex,numeric-method |
| Generic constructor for the class with the same name | ConstantInternalFluxRateList_by_PoolName |
| Describes a list of flux rates. | ConstantInternalFluxRateList_by_PoolName-class |
| Constructor from a normal list of fluxes | ConstantInternalFluxRateList_by_PoolName,list-method |
| Generic constructor for the class with the same name | ConstantOutFluxRate_by_PoolIndex |
| S4 Class to represent a single constant out-flux rate with the source pool specified by an index | ConstantOutFluxRate_by_PoolIndex-class |
| automatic title | ConstantOutFluxRate_by_PoolIndex,numeric,numeric-method |
| S4 Class to represent a single constant out-flux rate with the source pool specified by name | ConstantOutFluxRate_by_PoolName-class |
| Generic constructor for the class with the same name | ConstantOutFluxRateList_by_PoolIndex |
| Describes a list of flux rates. | ConstantOutFluxRateList_by_PoolIndex-class |
| constructor from a normal list | ConstantOutFluxRateList_by_PoolIndex,list-method |
| automatic title | ConstantOutFluxRateList_by_PoolIndex,numeric-method |
| Generic constructor for the class with the same name | ConstantOutFluxRateList_by_PoolName |
| Describes a list of flux rates. | ConstantOutFluxRateList_by_PoolName-class |
| constructor from a normal list | ConstantOutFluxRateList_by_PoolName,list-method |
| automatic title | ConstantOutFluxRateList_by_PoolName,numeric-method |
| creates an object containing the initial values for the 14C fraction needed to create models in SoilR | ConstFc |
| S4 class representing a constant 14C fraction | ConstFc-class |
| Constant input fluxes | ConstInFluxes |
| S4 class for a constant influx vector | ConstInFluxes-class |
| automatic title | ConstInFluxes,ConstantInFluxList_by_PoolIndex,numeric-method |
| automatic title | ConstInFluxes,numeric,ANY-method |
| Generic constructor for the class with the same name | ConstLinDecompOp |
| Generic constructor for the class with the same name | ConstLinDecompOp_by_PoolName |
| 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-class |
| Constructor of object of ConstLinDecompOp class | ConstLinDecompOp,matrix,missing,missing,missing,missing-method |
| Generic constructor for the class with the same name | ConstLinDecompOpWithLinearScalarFactor |
| 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 | ConstLinDecompOpWithLinearScalarFactor-class |
| Cycling analysis of compartmental matrices | cycling |
| S4-class to represent compartmental operators | DecompOp-class |
| automatic title | DecompositionOperator-class |
| Conversion of radiocarbon values | Delta14C |
| Conversion of radiocarbon values | Delta14C_from_AbsoluteFractionModern |
| Conversion of radiocarbon values | Delta14C_from_AbsoluteFractionModern,matrix-method |
| Conversion of radiocarbon values | Delta14C_from_AbsoluteFractionModern,numeric-method |
| automatic title | Delta14C,BoundFc-method |
| automatic title | Delta14C,ConstFc-method |
| deSolve.lsoda.wrapper | deSolve.lsoda.wrapper |
| Soil CO2 efflux from an incubation experiment | eCO2 |
| Entropy rate per jump | entropyRatePerJump |
| Entropy rate per time | entropyRatePerTime |
| euler | euler |
| example.2DBoundInFluxesFromFunction | example.2DBoundInFluxesFromFunction |
| example.2DBoundLinDecompOpFromFunction | example.2DBoundLinDecompOpFromFunction |
| example.2DConstFc.Args | example.2DConstFc.Args |
| 2D example for constant Influx | example.2DConstInFluxesFromVector |
| example.2DGeneralDecompOpArgs | example.2DGeneralDecompOpArgs |
| example.2DInFluxes.Args | example.2DInFluxes.Args |
| example.2DUnBoundLinDecompOpFromFunction | example.2DUnBoundLinDecompOpFromFunction |
| example.ConstlinDecompOpFromMatrix | example.ConstlinDecompOpFromMatrix |
| create an example nested list that can be | example.nestedTime2DMatrixList |
| create an example TimeMap from 2D array | example.Time2DArrayList |
| create an example TimeFrame from 3D array | example.Time3DArrayList |
| create an example TimeFrame from 3D array | example.TimeMapFromArray |
| automatic title | Fc-class |
| FcAtm.from.Dataframe | FcAtm.from.Dataframe |
| Effects of temperature on decomposition rates according the Arrhenius equation | fT.Arrhenius |
| Effects of temperature on decomposition rates according the the CENTURY model | fT.Century1 |
| Effects of temperature on decomposition rates according the the CENTURY model | fT.Century2 |
| Effects of temperature on decomposition rates according to the DAYCENT 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 DEMETER model | fT.Demeter |
| Effects of temperature on decomposition rates according to a model proposed by M. Kirschbaum (1995) | fT.KB |
| Effects of temperature on decomposition rates according to a function proposed by Lloyd and Taylor (1994) | fT.LandT |
| Effects of temperature on decomposition rates according to a linear model | fT.linear |
| Effects of temperature on decomposition rates according to a Q10 function | fT.Q10 |
| Effects of temperature on decomposition rates according to the functions included in the RothC model | fT.RothC |
| Effects of temperature on decomposition rates according to the StandCarb model | fT.Standcarb |
| Effects of moisture on decomposition rates according to the Candy model | fW.Candy |
| Effects of moisture on decomposition rates according to the CENTURY model | fW.Century |
| Effects of moisture on decomposition rates according to the DAYCENT 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 DEMETER model | fW.Demeter |
| Effects of moisture on decomposition rates according to the Gompertz function | fW.Gompertz |
| Effects of moisture on decomposition rates according to the function proposed by Moyano et al. (2013) | fW.Moyano |
| Effects of moisture on decomposition rates according to the RothC model | fW.RothC |
| Effects of moisture on decomposition rates according to the function proposed by Skopp et al. 1990 | fW.Skopp |
| Effects of moisture on decomposition rates according to the StandCarb model | fW.Standcarb |
| Implementation of a the six-pool C14 model proposed by Gaudinski et al. 2000 | GaudinskiModel14 |
| A generic factory for subclasses of GeneralDecompOp | GeneralDecompOp |
| Pass through factory for objects of subclasses of DecompOp | GeneralDecompOp,DecompOp-method |
| automatic title | GeneralDecompOp,function-method |
| automatic title | GeneralDecompOp,list-method |
| automatic title | GeneralDecompOp,matrix-method |
| automatic title | GeneralDecompOp,TimeMap-method |
| additional function to create Models | GeneralModel |
| create objects of class Model_14 | GeneralModel_14 |
| Use this function to create objects of class NlModel. | GeneralNlModel |
| General pool Id | GeneralPoolId |
| automatic title | GeneralPoolId,character-method |
| generic factory for this virtual class | GeneralPoolId,numeric-method |
| Accumulated release flux out of the pools | getAccumulatedRelease |
| Compute the time integral of the relaese fluxes over time | getAccumulatedRelease,Model-method |
| Calculates the content of the pools | getC |
| Pool Contents for all times | getC,Model_by_PoolNames-method |
| Pool Contents for all times | getC,Model-method |
| Pool Contents for all times | getC,NlModel-method |
| Generic that yields the 14C content for all pools and all times | getC14 |
| automatic title | getC14,Model_14-method |
| Compartmental matrix function | getCompartmentalMatrixFunc |
| automatic title | getCompartmentalMatrixFunc,BoundLinDecompOp-method |
| Compartmental matrix function | getCompartmentalMatrixFunc,ConstLinDecompOp-method |
| automatic title | getCompartmentalMatrixFunc,TransportDecompositionOperator-method |
| Extract the matrix valued function of time and state vector for the compartmental matrix | getCompartmentalMatrixFunc,UnBoundNonLinDecompOp-method |
| Constant compartmental matrix | getConstantCompartmentalMatrix |
| Constant compartmental matrix | getConstantCompartmentalMatrix,ConstLinDecompOp-method |
| automatic title | getConstantCompartmentalMatrix,ConstLinDecompOpWithLinearScalarFactor-method |
| Input flux vector | getConstantInFluxVector |
| automatic title | getConstantInFluxVector,ConstInFluxes-method |
| Constant internal flux rate list by pool index | getConstantInternalFluxRateList_by_PoolIndex |
| Constant internal flux rate list by pool index | getConstantInternalFluxRateList_by_PoolIndex,ConstLinDecompOp-method |
| Constant out flux rate list by pool index | getConstantOutFluxRateList_by_PoolIndex |
| Constant out flux rate list by pool index | getConstantOutFluxRateList_by_PoolIndex,ConstLinDecompOp-method |
| Constant linear decomposition operator | getConstLinDecompOp |
| automatic title | getConstLinDecompOp,ConstLinDecompOpWithLinearScalarFactor-method |
| Cummulative pool contents | getCumulativeC |
| automatic title | getCumulativeC,NlModel-method |
| Decomposition operator of a model | getDecompOp |
| Extract the Compartmental Operator | getDecompOp,Model-method |
| Extract the Compartmental Operator | getDecompOp,NlModel-method |
| Dot out | getDotOut |
| automatic title | getDotOut,TransportDecompositionOperator-method |
| Generic that yields the 14C fraction for the content all pools and all times | getF14 |
| automatic title | getF14,Model_14-method |
| Generic that yields the 14C fraction for the cumulative content of all pools and all times | getF14C |
| automatic title | getF14C,Model_14-method |
| Generic that yields the 14C fraction for the release flux of all pools and all times | getF14R |
| automatic title | getF14R,Model_14-method |
| Get format of SoilR object | getFormat |
| automatic title | getFormat,Fc-method |
| Function definition of SoilR model | getFunctionDefinition |
| automatic title | getFunctionDefinition,ConstInFluxes-method |
| Function describing an object of class ConstLinDecompOp | getFunctionDefinition,ConstLinDecompOp-method |
| convert names of vectors or lists to class ConstantOutFluxRate convert names of vectors or lists to class ConstantInternalFluxRate helper function | getFunctionDefinition,ConstLinDecompOpWithLinearScalarFactor-method |
| automatic title | 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 |
| Extracts the time dependent matrix valued function (compartmental matrix) | getFunctionDefinition,UnBoundLinDecompOp-method |
| Extract the influxes | getInFluxes |
| Extract the InFluxes as provided during creation of the model | getInFluxes,Model-method |
| automatic title | getInFluxes,NlModel-method |
| Initial values of SoilR object | getInitialValues |
| automatic title | getInitialValues,NlModel-method |
| Linear scale factor | getLinearScaleFactor |
| automatic title | getLinearScaleFactor,ConstLinDecompOpWithLinearScalarFactor-method |
| Mean transit time for SoilR objects | getMeanTransitTime |
| Mean transit time obtained through a numerical simulation. It produces an estimate with numerical errors. We recommend to use the function transitTime instead. | getMeanTransitTime,ConstLinDecompOp-method |
| Number of pools in a model | getNumberOfPools |
| automatic title | getNumberOfPools,MCSim-method |
| automatic title | getNumberOfPools,NlModel-method |
| automatic title | getNumberOfPools,TransportDecompositionOperator-method |
| Generic Function to obtain the fluxes out of of the pools | getOutputFluxes |
| automatic title | getOutputFluxes,NlModel-method |
| Pools receiving outputs from other pools | getOutputReceivers |
| automatic title | getOutputReceivers,TransportDecompositionOperator,numeric-method |
| automatic title | getParticleMonteCarloSimulator |
| automatic title | getParticleMonteCarloSimulator,NlModel-method |
| Generic Function to obtain the vector of release fluxes out of the pools for all times. | getReleaseFlux |
| automatic title | getReleaseFlux,Model_by_PoolNames-method |
| The release fluxes [content]/[time] for all pools. | getReleaseFlux,Model-method |
| automatic title | getReleaseFlux,NlModel-method |
| Generic that yields the 14C fraction in the release flux | getReleaseFlux14 |
| automatic title | getReleaseFlux14,Model_14-method |
| Right hand side of ODE of a SoilR model | getRightHandSideOfODE |
| Provide the (vector valued) derivative of the stocks with respect to time | getRightHandSideOfODE,Model_by_PoolNames-method |
| Derivative of the state variables as function | getRightHandSideOfODE,Model-method |
| Calculates all stocks all fluxes to ,in and out of the compartment system and also their integrals over time | getSolution |
| All Fluxes and stocks for all times | getSolution,Model_by_PoolNames-method |
| Time range of a model simulation | getTimeRange |
| automatic title | getTimeRange,ConstInFluxes-method |
| Time range of a simulation described in an object of class ConstLinDecompOp | getTimeRange,ConstLinDecompOp-method |
| automatic title | getTimeRange,ConstLinDecompOpWithLinearScalarFactor-method |
| automatic title | getTimeRange,DecompositionOperator-method |
| The time interval where the function is defined | getTimeRange,TimeMap-method |
| automatic title | getTimeRange,UnBoundInFluxes-method |
| Extracts the time interval for which the function is valid. | getTimeRange,UnBoundLinDecompOp-method |
| Time vector of SoilR object | getTimes |
| Extract the times vector | getTimes,Model_by_PoolNames-method |
| Extract the times vector | getTimes,Model-method |
| automatic title | getTimes,NlModel-method |
| Transfer coefficients | getTransferCoefficients |
| automatic title | getTransferCoefficients,NlModel-method |
| automatic title | getTransferCoefficients,TransportDecompositionOperator-method |
| deprecated, use getTransferMatrixFunc instead | getTransferMatrix |
| Transfer matrix function | getTransferMatrixFunc |
| automatic title | getTransferMatrixFunc,TransportDecompositionOperator-method |
| Transit time distribution for SoilR objects | getTransitTimeDistributionDensity |
| Transit time distribution obtained through a numerical simulation. It introduces numerical errors. We recommend to use the function transitTime instead | getTransitTimeDistributionDensity,ConstLinDecompOp-method |
| Get values of SoilR object | getValues |
| automatic title | getValues,ConstFc-method |
| Compiled records of radicarbon in atmospheric CO2 for historical simulations in CMIP6 | Graven2017 |
| Delta14C in soil CO2 efflux from Harvard Forest | HarvardForest14CO2 |
| Atmospheric radiocarbon for the period 1950-2010 from Hua et al. (2013) | Hua2013 |
| Atmospheric radiocarbon for the period 1950-2019 from Hua et al. (2021) | Hua2021 |
| Implementation of the ICBM/N model | ICBM_N |
| Implementation of the Introductory Carbon Balance Model (ICBM) | ICBMModel |
| Soil CO2 efflux from an incubation experiment, along with the soil mass and carbon concentration measurements. | incubation_experiment |
| Generic constructor for the class with the same name | InFlux |
| Generic constructor for the class with the same name | InFlux_by_PoolIndex |
| S4 class for the influx to a single pool identified by the index | InFlux_by_PoolIndex-class |
| Constructor from an ordered pair of PoolIndex (integer like) objects | InFlux_by_PoolIndex,function,numeric-method |
| Generic constructor for an influx to a single pool from an ordered pair of PoolName (string like) and function objects | InFlux_by_PoolName |
| S4 class for the influx to a single pool identified by the name | InFlux_by_PoolName-class |
| Constructor from an ordered pair of PoolName (string like) and function objects | InFlux_by_PoolName,function,character-method |
| A generic factory for subclasses of InFluxes | InFluxes |
| A virtual S4-class representing (different subclasses) of in-fluxes to the system | InFluxes-class |
| automatic title | InFluxes,ConstantInFluxList_by_PoolIndex-method |
| automatic title | InFluxes,function-method |
| automatic title | InFluxes,InFluxes-method |
| automatic title | InFluxes,list-method |
| automatic title | InFluxes,numeric-method |
| automatic title | InFluxes,StateIndependentInFluxList_by_PoolIndex-method |
| automatic title | InFluxes,TimeMap-method |
| Generic constructor for the class with the same name | InFluxList_by_PoolIndex |
| Describes a list of flux rates. | InFluxList_by_PoolIndex-class |
| constructor from a normal list after checking the elements | InFluxList_by_PoolIndex,list-method |
| Generic constructor for the class with the same name | InFluxList_by_PoolName |
| Class for a list of influxes indexed by the names of the target pools | InFluxList_by_PoolName-class |
| constructor from a normal list | InFluxList_by_PoolName,list-method |
| automatic title | initialize,ConstLinDecompOp-method |
| automatic title | initialize,DecompositionOperator-method |
| automatic title | initialize,MCSim-method |
| Internal method to supervise creation of objects of this class | initialize,Model_14-method |
| automatic title | initialize,Model_by_PoolNames-method |
| Internal method to supervise creation of objects of this class | initialize,Model-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 |
| Northern Hemisphere atmospheric radiocarbon for the pre-bomb period | IntCal09 |
| Atmospheric radiocarbon for the 0-50,000 yr BP period | IntCal13 |
| The IntCal20 northern hemisphere radiocarbon curve for the 0-55,000 yr BP period | IntCal20 |
| Generic constructor for the class with the same name | InternalFlux_by_PoolIndex |
| S4-class for a single internal flux with source and destination pools specified by indices | InternalFlux_by_PoolIndex-class |
| constructor from an ordered pair of PoolIndex (integer like) objects and a function with vector argument | InternalFlux_by_PoolIndex,function,numeric,numeric,missing-method |
| Generic constructor for the class with the same name | InternalFlux_by_PoolName |
| S4-class for a single internal flux with source and destination pools specified by name | InternalFlux_by_PoolName-class |
| 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,character,character,missing-method |
| automatic title | InternalFlux_by_PoolName,function,missing,missing,character-method |
| Generic constructor for the class with the same name | InternalFluxList_by_PoolIndex |
| S4-class for a list of internal fluxes with source and destination pool inidices | InternalFluxList_by_PoolIndex-class |
| Constructor from a normal list after checking the elements | InternalFluxList_by_PoolIndex,list-method |
| Generic constructor for the class with the same name | InternalFluxList_by_PoolName |
| S4-class for a list of internal fluxes with indexed by (source and destination pool) names | InternalFluxList_by_PoolName-class |
| constructor from a normal list | InternalFluxList_by_PoolName,list-method |
| Implementation of a general model for linear non-autonomous systems with scalar modifiers | linearScalarModel |
| Add lines with the output of 'getC14', 'getC', or 'getReleaseFlux' to an existing plot | linesCPool |
| tensor product of lists | listProduct |
| Experimental Class for a Monte Carlo Simulation of particles leaving the pool | MCSim-class |
| Constructor for class Model | Model |
| general constructor for class Model_14 | Model_14 |
| S4-class to represent a 14C model run | Model_14-class |
| Constructor for 'Model_by_PoolNames' | Model_by_PoolNames |
| A model run based on flux functions | Model_by_PoolNames-class |
| S4 class representing a model run | Model-class |
| deprecated class for a non-linear model run. | NlModel-class |
| Implementation of a one pool model | OnepModel |
| Implementation of a one-pool C14 model | OnepModel14 |
| Generic constructor for the class with the same name | OutFlux |
| Generic constructor for the class with the same name | OutFlux_by_PoolIndex |
| S4 class for a single out-flux with source pool index | OutFlux_by_PoolIndex-class |
| constructor from a PoolIndex (integer like) objects and a function with vector argument | OutFlux_by_PoolIndex,function,numeric-method |
| Generic constructor for the class with the same name | OutFlux_by_PoolName |
| S4 class for a single out-flux with source pool name | OutFlux_by_PoolName-class |
| constructor from a PoolName (integer like) object and a function | OutFlux_by_PoolName,function,character-method |
| Generic constructor for the class with the same name | OutFluxList_by_PoolIndex |
| A list of outfluxes | OutFluxList_by_PoolIndex-class |
| constructor from a normal list | OutFluxList_by_PoolIndex,list-method |
| Generic constructor for the class with the same name | OutFluxList_by_PoolName |
| S4 class for a list of out-fluxes indexed by source pool name | OutFluxList_by_PoolName-class |
| constructor from a normal list | OutFluxList_by_PoolName,list-method |
| models for unconnected pools | ParallelModel |
| Path Entropy | pathEntropy |
| automatic title | plot,MCSim-method |
| Plot the graph of pool connections | plot,Model_by_PoolNames-method |
| Create an overview plot | plot,Model-method |
| automatic title | plot,NlModel-method |
| automatic title | plot,TimeMap-method |
| Plots the output of 'getF14' for each pool over time | plotC14Pool |
| Plots the output of 'getC' or 'getReleaseFlux' for each pool over time | plotCPool |
| Generic plotter | plotPoolGraph |
| Plot the graph of pool connections | plotPoolGraph,SymbolicModel_by_PoolNames-method |
| Helper function to draw connectivity graphs | plotPoolGraphFromTupleLists |
| Pool connection by pool index | PoolConnection_by_PoolIndex |
| Objects that have a source and a destination described by integer like objects ( of class PoolIndex) | PoolConnection_by_PoolIndex-class |
| constructor from an ordered pair of PoolId objects | PoolConnection_by_PoolIndex,ANY,ANY,missing-method |
| constructor from strings of the form '1_to_2' | PoolConnection_by_PoolIndex,missing,missing,character-method |
| Pool connection by pool name | PoolConnection_by_PoolName |
| Objects that have a source and a destination determined by a string like object of class PoolName | PoolConnection_by_PoolName-class |
| constructor from an ordered pair of PoolName objects | PoolConnection_by_PoolName,ANY,ANY,missing-method |
| common class for pool ids | PoolId-class |
| Pool index | PoolIndex |
| S4 class for pool indices | PoolIndex-class |
| construct from number string like '1' or '3' | PoolIndex,character-method |
| construct from number | PoolIndex,numeric-method |
| pass through constructor fron an object of the same class | PoolIndex,PoolIndex-method |
| convert to number like object | PoolIndex,PoolName-method |
| Pool name | PoolName |
| class for pool-name-strings | PoolName-class |
| construct from string with checks | PoolName,character-method |
| convert to string like object | PoolName,PoolIndex-method |
| pass through constructor fron an object of the same class | PoolName,PoolName-method |
| PREDEFINED MODELS | predefinedModels |
| automatic title | print,NlModel-method |
| helper function to compute respiration coefficients | RespirationCoefficients |
| Implementation of the RothCModel | RothCModel |
| Constructor for 'ScalarTimeMap-class' | ScalarTimeMap |
| S4 class for a scalar time dependent function on a finite time interval | ScalarTimeMap-class |
| constructor for data given as 2 column data.frame | ScalarTimeMap,data.frame,missing,missing,missing,missing-method |
| manual constructor for just a function | ScalarTimeMap,function,missing,missing,missing,missing-method |
| manual constructor for a function and an interval | ScalarTimeMap,function,numeric,numeric,missing,missing-method |
| special case for a time map from a constant | ScalarTimeMap,missing,missing,missing,missing,numeric-method |
| constructor for data and times given as vectors | ScalarTimeMap,missing,missing,missing,numeric,numeric-method |
| General m-pool linear model with series structure | SeriesLinearModel |
| General m-pool linear C14 model with series structure | SeriesLinearModel14 |
| The SHCal20 southern hemisphere radiocarbon curve for the 0-55,000 yr BP period | SHCal20 |
| automatic title | show,NlModel-method |
| deprecated function that used to create an object of class SoilR.F0 | SoilR.F0.new |
| determine the minimum set of statevariables | state_variable_names |
| Input vector that is a function of the pool contenst and time | StateDependentInFluxVector StateDependentInFluxVector-class |
| Constructor for the class with the same name | StateIndependentInFlux_by_PoolIndex StateIndependentInFlux_by_PoolIndex-class |
| Generic constructor for the class with the same name | StateIndependentInFluxList_by_PoolIndex |
| Subclass of list that is guaranteed to contain only elements of type StateIndependentInFlux_by_PoolIndex | StateIndependentInFluxList_by_PoolIndex-class |
| constructor from a normal list | StateIndependentInFluxList_by_PoolIndex,list-method |
| Generic constructor for the class with the same name | StateIndependentInFluxList_by_PoolName |
| A symbolic model description based on flux functions | SymbolicModel_by_PoolNames SymbolicModel_by_PoolNames-class |
| System and pool age for constant compartment models | systemAge |
| Implementation of a 6-pool Michaelis-Menten model | ThreepairMMmodel |
| Implementation of a three pool model with feedback structure | ThreepFeedbackModel |
| Implementation of a three-pool C14 model with feedback structure | ThreepFeedbackModel14 |
| Implementation of a three pool model with parallel structure | ThreepParallelModel |
| Implementation of a three-pool C14 model with parallel structure | ThreepParallelModel14 |
| Implementation of a three pool model with series structure | ThreepSeriesModel |
| Implementation of a three-pool C14 model with series structure | ThreepSeriesModel14 |
| Constructor for 'TimeMap-class' | TimeMap |
| S4 class for a time dependent function | TimeMap-class |
| automatic title | TimeMap,data.frame,missing,missing,missing,missing-method |
| manual constructor for just a function | TimeMap,function,missing,missing,missing,missing-method |
| manual constructor for a function and an interval | TimeMap,function,numeric,numeric,missing,missing-method |
| automatic title | 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,TimeMap,ANY,ANY,ANY,ANY-method |
| TimeMap.from.Dataframe | TimeMap.from.Dataframe |
| deprecated constructor of the class TimeMap. | TimeMap.new |
| The time interval where both functions are defined | TimeRangeIntersection |
| Transit times for compartment models | transitTime |
| automatic title | TransportDecompositionOperator-class |
| Estimation of the turnover time from a radiocarbon sample. | turnoverFit |
| Implementation of a two pool model with feedback structure | TwopFeedbackModel |
| Implementation of a two-pool C14 model with feedback structure | TwopFeedbackModel14 |
| Implementation of a two-pool Michaelis-Menten model | TwopMMmodel |
| Implementation of a linear two pool model with parallel structure | TwopParallelModel |
| Implementation of a two-pool C14 model with parallel structure | TwopParallelModel14 |
| Implementation of a two pool model with series structure | TwopSeriesModel |
| Implementation of a two-pool C14 model with series structure | TwopSeriesModel14 |
| Unbound input fluxes | UnBoundInFluxes |
| automatic title | UnBoundInFluxes-class |
| automatic title | UnBoundInFluxes,function-method |
| Generic constructor for the class with the same name | UnBoundLinDecompOp |
| An S4 class to represent a linear nonautonomous compartmental matrix | UnBoundLinDecompOp-class |
| Generic constructor for the class with the same name | UnBoundLinDecompOp,function-method |
| Generic constructor for the class with the same name | UnBoundNonLinDecompOp |
| Generic constructor for the class with the same name | UnBoundNonLinDecompOp_by_PoolNames |
| An S4 class to represent the of nonlinear nonautonomous compartmental system independently of the order of state variables | UnBoundNonLinDecompOp_by_PoolNames-class |
| An S4 class to represent a nonlinear nonautonomous compartmental matrix | UnBoundNonLinDecompOp-class |
| 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 |
| Implementation of the Yasso07 model | Yasso07Model |
| Implementation of the Yasso model. | YassoModel |
