Man pages for SoilR
Models of Soil Organic Matter Decomposition
| AbsoluteFractionModern | automatic title |
| AbsoluteFractionModern-BoundFc-method | automatic title |
| AbsoluteFractionModern-ConstFc-method | automatic title |
| AbsoluteFractionModern_from_Delta14C | conversion |
| AbsoluteFractionModern_from_Delta14C-matrix-method | automatic title |
| AbsoluteFractionModern_from_Delta14C-numeric-method | automatic title |
| add_plot | automatic title |
| 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-InternalFlux_by_PoolName-method | Convert to a numeric value with name of the form 'a->b' |
| as.numeric-InternalFluxList_by_PoolName-method | Convert to a numeric vector with names of the form 'a->b' |
| as.numeric-OutFluxList_by_PoolName-method | Convert to a numeric vector with the pool names as names |
| availableParticleProperties | automatic title |
| availableParticleProperties-MCSim-method | automatic title |
| availableParticleSets | automatic title |
| availableParticleSets-MCSim-method | automatic title |
| availableResidentSets | automatic title |
| availableResidentSets-MCSim-method | automatic title |
| AWBmodel | Implementation of the microbial model AWB (Allison,... |
| bacwaveModel | Implementation of the microbial model Bacwave (bacterial... |
| bind.C14curves | Binding of pre- and post-bomb Delta14C curves |
| BoundFc | automatic title |
| BoundFc-character-method | automatic title |
| BoundFc-class | S4-class to represent atmospheric 14C concentration as scalar... |
| BoundFc-missing-method | automatic title |
| BoundInFluxes | constructor for BoundInFluxes |
| BoundInFluxes-class | automatic title |
| BoundLinDecompOp | Generic constructor for the class with the same name |
| BoundLinDecompOp-ANY-method | automatic title |
| BoundLinDecompOp-class | A S4 class to represent a linear compartmental operator... |
| BoundLinDecompOp-UnBoundLinDecompOp-method | A converter |
| by_PoolIndex | automatic title |
| by_PoolIndex-ConstantInFluxRate_by_PoolName-ANY-ANY-method | new object with the source pool id converted to a PoolIndex... |
| by_PoolIndex-ConstantInternalFluxRate_by_PoolName-ANY-ANY-method | new object with the source pool id converted to a PoolName if... |
| by_PoolIndex-ConstantInternalFluxRateList_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... |
| by_PoolIndex-ConstantOutFluxRateList_by_PoolName-ANY-ANY-method | convert to a list indexed by pool names |
| by_PoolIndex-function-character-character-method | convert a function f of to f_vec |
| by_PoolIndex-InFlux_by_PoolName-character-character-method | Convert the pool names to indices |
| by_PoolIndex-InFluxList_by_PoolName-character-character-method | Transform pool names to indices |
| 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 | automatic title |
| by_PoolIndex-PoolConnection_by_PoolName-ANY-ANY-method | constructor from strings of the form 'x->y' new object with... |
| by_PoolName | automatic title |
| by_PoolName-ConstantInFlux_by_PoolIndex-method | new object with the source pool id converted to a PoolIndex... |
| 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... |
| by_PoolName-ConstantInternalFluxRate_by_PoolIndex-method | new object with the source pool id converted to a PoolIndex... |
| by_PoolName-ConstantInternalFluxRateList_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... |
| by_PoolName-ConstantOutFluxRateList_by_PoolIndex-method | convert to a list indexed by pool names |
| C14Atm | Atmospheric 14C fraction |
| C14Atm_NH | Post-bomb atmospheric 14C fraction |
| cash-NlModel-method | automatic title |
| 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... |
| check_pool_ids | automatic title |
| check_pool_ids-PoolConnection_by_PoolIndex-integer-method | automatic title |
| computeResults | automatic title |
| computeResults-MCSim-method | automatic title |
| ConstantInFlux_by_PoolIndex-class | class for a constant influx to a single pool identified by... |
| ConstantInFlux_by_PoolName-class | class for a constant influx to a single pool identified by... |
| 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... |
| 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_PoolName | Generic constructor for the class with the same name |
| ConstantInFluxList_by_PoolName-class | Subclass of list that is guaranteed to contain only elements... |
| 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. |
| 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-missing-missing-character-04a58139 | constructor from strings of the form '1_to_2' |
| ConstantInternalFluxRate_by_PoolIndex-numeric-numeric-missing-nu0ca778cf | automatic title |
| ConstantInternalFluxRate_by_PoolName | Generic constructor for the class with the same name |
| ConstantInternalFluxRate_by_PoolName-character-character-missing4e76a719 | constructor with argument conversion |
| ConstantInternalFluxRate_by_PoolName-class | S4-class to represent a constant internal flux rate with... |
| ConstantInternalFluxRate_by_PoolName-missing-missing-character-nabea446d | constructor from strings of the form 'a->b' |
| 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-list-method | constructor from a normal list |
| ConstantInternalFluxRateList_by_PoolIndex-numeric-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-list-method | Constructor from a normal list of fluxes |
| 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... |
| ConstantOutFluxRate_by_PoolIndex-numeric-numeric-method | automatic title |
| ConstantOutFluxRate_by_PoolName-class | S4 Class to represent a single constant out-flux rate with... |
| 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-list-method | constructor from a normal list |
| ConstantOutFluxRateList_by_PoolIndex-numeric-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-list-method | constructor from a normal list |
| ConstantOutFluxRateList_by_PoolName-numeric-method | automatic title |
| ConstFc | creates an object containing the initial values for the 14C... |
| ConstFc-class | S4 class representing a constant ^14C fraction |
| ConstInFluxes | automatic title |
| ConstInFluxes-class | S4 class for a constant influx vector |
| ConstInFluxes-ConstantInFluxList_by_PoolIndex-numeric-method | automatic title |
| ConstInFluxes-numeric-ANY-method | automatic title |
| ConstLinDecompOp | Generic constructor for the class with the same name |
| ConstLinDecompOp_by_PoolName | Generic constructor for the class with the same name |
| ConstLinDecompOp-class | A class to represent a constant (=nonautonomous,linear)... |
| ConstLinDecompOp-matrix-missing-missing-missing-missing-method | Constructor |
| ConstLinDecompOp-missing-ConstantInternalFluxRateList_by_PoolInd637fbcaf | Constructor |
| ConstLinDecompOp-missing-ConstantInternalFluxRateList_by_PoolIndfec8276d | Constructor |
| ConstLinDecompOp-missing-ConstantInternalFluxRateList_by_PoolNam6d81aaa9 | alternative Constructor with pool names |
| ConstLinDecompOp-missing-missing-ConstantOutFluxRateList_by_Pooleee52cd9 | Constructor |
| ConstLinDecompOpWithLinearScalarFactor | Generic constructor for the class with the same name |
| ConstLinDecompOpWithLinearScalarFactor-class | A class to represent a constant (=nonautonomous,linear)... |
| ConstLinDecompOpWithLinearScalarFactor-matrix-missing-missing-mi02dcc78e | convert names of vectors or lists to class... |
| cycling | Cycling analysis of compartmental matrices |
| DecompOp-class | S4-class to represent compartmental operators |
| DecompositionOperator-class | automatic title |
| Delta14C | automatic title |
| Delta14C-BoundFc-method | automatic title |
| Delta14C-ConstFc-method | automatic title |
| Delta14C_from_AbsoluteFractionModern | automatic title |
| Delta14C_from_AbsoluteFractionModern-matrix-method | automatic title |
| Delta14C_from_AbsoluteFractionModern-numeric-method | automatic title |
| 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.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 |
| FcAtm.from.Dataframe | FcAtm.from.Dataframe |
| Fc-class | automatic title |
| from_integer_flux_lists_with_defaults | helper function |
| fT.Arrhenius | Effects of temperature on decomposition rates according the... |
| fT.Century1 | Effects of temperature on decomposition rates according the... |
| fT.Century2 | Effects of temperature on decomposition rates according the... |
| fT.Daycent1 | Effects of temperature on decomposition rates according to... |
| fT.Daycent2 | Effects of temperature on decomposition rates according to... |
| fT.Demeter | Effects of temperature on decomposition rates according to... |
| fT.KB | Effects of temperature on decomposition rates according to a... |
| fT.LandT | Effects of temperature on decomposition rates according to a... |
| fT.linear | Effects of temperature on decomposition rates according to a... |
| fT.Q10 | Effects of temperature on decomposition rates according to a... |
| fT.RothC | Effects of temperature on decomposition rates according to... |
| fT.Standcarb | Effects of temperature on decomposition rates according to... |
| fW.Candy | Effects of moisture on decomposition rates according to the... |
| fW.Century | Effects of moisture on decomposition rates according to the... |
| fW.Daycent1 | Effects of moisture on decomposition rates according to the... |
| fW.Daycent2 | Effects of moisture on decomposition rates according to the... |
| fW.Demeter | Effects of moisture on decomposition rates according to the... |
| fW.Gompertz | Effects of moisture on decomposition rates according to the... |
| fW.Moyano | Effects of moisture on decomposition rates according to the... |
| fW.RothC | Effects of moisture on decomposition rates according to the... |
| fW.Skopp | Effects of moisture on decomposition rates according to the... |
| fW.Standcarb | Effects of moisture on decomposition rates according to the... |
| GaudinskiModel14 | Implementation of a the six-pool C14 model proposed by... |
| GeneralDecompOp | A generic factory for subclasses of GeneralDecompOp |
| GeneralDecompOp-DecompOp-method | Pass through factory for objects of subclasses of DecompOp |
| GeneralDecompOp-function-method | automatic title |
| GeneralDecompOp-list-method | automatic title |
| GeneralDecompOp-matrix-method | automatic title |
| GeneralDecompOp-TimeMap-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 | automatic title |
| GeneralPoolId-character-method | automatic title |
| GeneralPoolId-numeric-method | generic factory for this virtual class |
| getAccumulatedRelease | automatic title |
| getAccumulatedRelease-Model-method | Compute the time integral of the relaese fluxes over time |
| getC | Calculates the content of the pools |
| getC14 | Generic that yields the ^14C content for all pools and all... |
| getC14-Model_14-method | automatic title |
| getC-Model_by_PoolNames-method | Pool Contents for all times |
| getC-Model-method | Pool Contents for all times |
| getC-NlModel-method | Pool Contents for all times |
| getCompartmentalMatrixFunc | automatic title |
| getCompartmentalMatrixFunc-BoundLinDecompOp-ANY-ANY-method | automatic title |
| getCompartmentalMatrixFunc-ConstLinDecompOp-ANY-ANY-method | automatic title |
| getCompartmentalMatrixFunc-TransportDecompositionOperator-ANY-ANY-method | automatic title |
| getCompartmentalMatrixFunc-UnBoundNonLinDecompOp-ANY-ANY-method | Extract the matrix valued function of time and state vector... |
| getCompartmentalMatrixFunc-UnBoundNonLinDecompOp_by_PoolNames-chf19f8c91 | Compartmental Matrix as function of the state vector and time |
| getConstantCompartmentalMatrix | automatic title |
| getConstantCompartmentalMatrix-ConstLinDecompOp-method | automatic title |
| getConstantCompartmentalMatrix-ConstLinDecompOpWithLinearScalarF13f9803d | automatic title |
| getConstantInFluxVector | automatic title |
| getConstantInFluxVector-ConstInFluxes-method | automatic title |
| getConstantInternalFluxRateList_by_PoolIndex | automatic title |
| getConstantInternalFluxRateList_by_PoolIndex-ConstLinDecompOp-method | automatic title |
| getConstantOutFluxRateList_by_PoolIndex | automatic title |
| getConstantOutFluxRateList_by_PoolIndex-ConstLinDecompOp-method | automatic title |
| getConstLinDecompOp | automatic title |
| getConstLinDecompOp-ConstLinDecompOpWithLinearScalarFactor-method | automatic title |
| getCumulativeC | automatic title |
| getCumulativeC-NlModel-method | automatic title |
| getDecompOp | automatic title |
| getDecompOp-Model-method | Extract the Compartmental Operator |
| getDecompOp-NlModel-method | Extract the Compartmental Operator |
| getDotOut | automatic title |
| getDotOut-TransportDecompositionOperator-method | automatic title |
| getF14 | Generic that yields the ^14C fraction for the content all... |
| getF14C | Generic that yields the ^14C fraction for the cumulative... |
| getF14C-Model_14-method | automatic title |
| getF14-Model_14-method | automatic title |
| getF14R | Generic that yields the ^14C fraction for the release flux of... |
| getF14R-Model_14-method | automatic title |
| getFormat | automatic title |
| getFormat-Fc-method | automatic title |
| getFunctionDefinition | automatic title |
| getFunctionDefinition-ConstInFluxes-method | automatic title |
| getFunctionDefinition-ConstLinDecompOp-method | automatic title |
| getFunctionDefinition-ConstLinDecompOpWithLinearScalarFactor-method | 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... |
| getInFluxes | Extract the influxes |
| getInFluxes-Model-method | Extract the InFluxes as provided during creation of the model |
| getInFluxes-NlModel-method | automatic title |
| getInitialValues | automatic title |
| getInitialValues-NlModel-method | automatic title |
| getLinearScaleFactor | automatic title |
| getLinearScaleFactor-ConstLinDecompOpWithLinearScalarFactor-method | automatic title |
| getMeanTransitTime | automatic title |
| getMeanTransitTime-ConstLinDecompOp-method | automatic title |
| getNumberOfPools | automatic title |
| 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 | automatic title |
| 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... |
| getReleaseFlux14 | automatic title |
| getReleaseFlux14-Model_14-method | automatic title |
| getReleaseFlux-Model_by_PoolNames-method | automatic title |
| getReleaseFlux-Model-method | The release fluxes [content]/[time] for all pools. |
| getReleaseFlux-NlModel-method | automatic title |
| getRightHandSideOfODE | automatic title |
| getRightHandSideOfODE-Model_by_PoolNames-method | Provide the (vector valued) derivative of the stocks with... |
| getRightHandSideOfODE-Model-method | Derivative of the state variables as function |
| getSolution | Calculates all stocks all fluxes to ,in and out of the... |
| getSolution-Model_by_PoolNames-method | All Fluxes and stocks for all times |
| getTimeRange | automatic title |
| getTimeRange-ConstInFluxes-method | automatic title |
| getTimeRange-ConstLinDecompOp-method | automatic title |
| 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 | automatic title |
| getTimes-Model_by_PoolNames-method | Extract the times vector |
| getTimes-Model-method | Extract the times vector |
| getTimes-NlModel-method | automatic title |
| getTransferCoefficients | automatic title |
| getTransferCoefficients-NlModel-method | automatic title |
| getTransferCoefficients-TransportDecompositionOperator-method | automatic title |
| getTransferMatrix | deprecated, use getTransferMatrixFunc instead |
| getTransferMatrixFunc | automatic title |
| getTransferMatrixFunc-TransportDecompositionOperator-method | automatic title |
| getTransitTimeDistributionDensity | automatic title |
| getTransitTimeDistributionDensity-ConstLinDecompOp-method | automatic title |
| getValues | automatic title |
| getValues-ConstFc-method | automatic title |
| Graven2017 | Compiled records of radicarbon in atmospheric CO2 for... |
| HarvardForest14CO2 | Delta14C in soil CO2 efflux from Harvard Forest |
| Hua2013 | Atmospheric radiocarbon for the period 1950-2010 from Hua et... |
| ICBMModel | Implementation of the Introductory Carbon Balance Model... |
| ICBM_N | Implementation of the ICBM/N model |
| incubation_experiment | Soil CO2 efflux from an incubation experiment, along with the... |
| InFlux | Generic constructor for the class with the same name |
| 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... |
| InFlux_by_PoolIndex-function-numeric-method | constructor from an ordered pair of PoolIndex (integer like)... |
| InFlux_by_PoolName | Generic constructor for an influx to a single pool from an... |
| InFlux_by_PoolName-class | S4 class for the influx to a single pool identified by the... |
| InFlux_by_PoolName-function-character-method | Constructor from an ordered pair of PoolName (string like)... |
| InFluxes | A generic factory for subclasses of InFluxes |
| InFluxes-class | A virtual S4-class representing (different subclasses) of... |
| 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 | 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-list-method | constructor from a normal list |
| 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... |
| InFluxList_by_PoolName-list-method | constructor from a normal list |
| initialize-ConstLinDecompOp-method | automatic title |
| initialize-DecompositionOperator-method | automatic title |
| initialize-MCSim-method | automatic title |
| initialize-Model_14-method | Internal method to supervise creation of objects of this... |
| initialize-Model_by_PoolNames-method | automatic title |
| initialize-Model-method | Internal method to supervise creation of objects of this... |
| 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 |
| IntCal09 | Northern Hemisphere atmospheric radiocarbon for the pre-bomb... |
| IntCal13 | Atmospheric radiocarbon for the 0-50,000 yr BP period |
| IntCal20 | The IntCal20 northern hemisphere radiocarbon curve for the... |
| 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... |
| InternalFlux_by_PoolIndex-function-numeric-numeric-missing-method | constructor from an ordered pair of PoolIndex (integer like)... |
| 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... |
| InternalFlux_by_PoolName-function-character-character-missing-method | constructor from an ordered pair of PoolName (string like)... |
| InternalFlux_by_PoolName-function-missing-missing-character-method | automatic title |
| 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... |
| InternalFluxList_by_PoolIndex-list-method | constructor from a normal list |
| 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... |
| InternalFluxList_by_PoolName-list-method | constructor from a normal list |
| linearScalarModel | Implementation of a general model for linear non-autonomous... |
| linesCPool | Add lines with the output of 'getC14', 'getC', or... |
| listProduct | tensor product of lists |
| MCSim-class | Experimental Class for a Monte Carlo Simulation of particles... |
| Model | Constructor for class Model |
| 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 |
| Model_by_PoolNames-missing-numeric-UnBoundNonLinDecompOp_by_Poole522475a | Create a model(run) described by fluxes |
| Model_by_PoolNames-SymbolicModel_by_PoolNames-numeric-missing-nu37a011e6 | Create a model(run) described by fluxes |
| Model-class | S4 class representing a model run |
| NlModel-class | deprecated class for a non-linear model run. |
| no_outflux_warning | helper function |
| 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 |
| 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-function-numeric-method | constructor from a PoolIndex (integer like) objects and a... |
| 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-function-character-method | constructor from a PoolName (integer like) object and a... |
| OutFluxList_by_PoolIndex | Generic constructor for the class with the same name |
| OutFluxList_by_PoolIndex-class | A list of outfluxes |
| OutFluxList_by_PoolIndex-list-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-list-method | constructor from a normal list |
| ParallelModel | models for unconnected pools |
| pathEntropy | Path Entropy |
| plotC14Pool | Plots the output of 'getF14' for each pool over time |
| plotCPool | Plots the output of 'getC' or 'getReleaseFlux' for each pool... |
| plot-MCSim-method | automatic title |
| plot-Model_by_PoolNames-method | Plot the graph of pool connections |
| plot-Model-method | Create an overview plot |
| plot-NlModel-method | automatic title |
| plotPoolGraph | Generic plotter |
| plotPoolGraphFromTupleLists | Helper function to draw connectivity graphs |
| plotPoolGraph-SymbolicModel_by_PoolNames-method | Plot the graph of pool connections |
| plot-TimeMap-method | automatic title |
| PoolConnection_by_PoolIndex | automatic title |
| PoolConnection_by_PoolIndex-ANY-ANY-missing-method | constructor from an ordered pair of PoolId objects |
| PoolConnection_by_PoolIndex-class | Objects that have a source and a destination described by... |
| PoolConnection_by_PoolIndex-missing-missing-character-method | constructor from strings of the form '1_to_2' |
| PoolConnection_by_PoolName | automatic title |
| 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... |
| PoolId-class | common class for pool ids |
| PoolIndex | automatic title |
| PoolIndex-character-method | construct from number string like '1' or '3' |
| PoolIndex-class | S4 class for pool indices |
| PoolIndex-numeric-method | construct from number |
| PoolIndex-PoolIndex-method | pass through constructor fron an object of the same class |
| PoolIndex-PoolName-method | convert to number like object |
| PoolName | automatic title |
| PoolName-character-method | construct from string with checks |
| PoolName-class | class for pool-name-strings |
| PoolName-PoolIndex-method | convert to string like object |
| PoolName-PoolName-method | pass through constructor fron an object of the same class |
| predefinedModels | PREDEFINED MODELS |
| print-NlModel-method | automatic title |
| RespirationCoefficients | helper function to compute respiration coefficients |
| RothCModel | Implementation of the RothCModel |
| ScalarTimeMap | Constructor for 'ScalarTimeMap-class' |
| ScalarTimeMap-class | S4 class for a scalar time dependent function on a finite... |
| 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 |
| 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... |
| show-NlModel-method | automatic title |
| SoilR.F0.new | deprecated function that used to create an object of class... |
| SoilR-package | SoilR |
| StateDependentInFluxVector-class | Input vector that is a function of the pool contenst and time |
| StateIndependentInFlux_by_PoolIndex-class | Constructor for the class with the same name |
| 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... |
| StateIndependentInFluxList_by_PoolIndex-list-method | constructor from a normal list |
| StateIndependentInFluxList_by_PoolName | Generic constructor for the class with the same name |
| state_variable_names | determine the minimum set of statevariables |
| sub-Model-character-missing-missing-method | Experimentally overloaded index operator |
| sub-NlModel-character-ANY-ANY-method | automatic title |
| sub-sub-MCSim-method | automatic title |
| sub-subset-MCSim-method | automatic title |
| SymbolicModel_by_PoolNames-class | A symbolic model description based on flux functions |
| systemAge | System and pool age for constant compartment models |
| 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... |
| ThreepParallelModel | Implementation of a three pool model with parallel structure |
| ThreepParallelModel14 | Implementation of a three-pool C14 model with parallel... |
| ThreepSeriesModel | Implementation of a three pool model with series structure |
| ThreepSeriesModel14 | Implementation of a three-pool C14 model with series... |
| TimeMap | Constructor for 'TimeMap-class' |
| TimeMap-class | S4 class for a time dependent function |
| TimeMap-data.frame-missing-missing-missing-missing-method | automatic title |
| TimeMap.from.Dataframe | TimeMap.from.Dataframe |
| 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.new | deprecated constructor of the class TimeMap. |
| TimeMap-TimeMap-ANY-ANY-ANY-ANY-method | automatic title |
| 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... |
| TwopMMmodel | Implementation of a two-pool Michaelis-Menten model |
| TwopParallelModel | Implementation of a linear two pool model with parallel... |
| TwopParallelModel14 | Implementation of a two-pool C14 model with parallel... |
| TwopSeriesModel | Implementation of a two pool model with series structure |
| TwopSeriesModel14 | Implementation of a two-pool C14 model with series structure |
| UnBoundInFluxes | automatic title |
| UnBoundInFluxes-class | automatic title |
| UnBoundInFluxes-function-method | automatic title |
| UnBoundLinDecompOp | Generic constructor for the class with the same name |
| UnBoundLinDecompOp-class | An S4 class to represent a linear nonautonomous compartmental... |
| 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 | Generic constructor for the class with the same name |
| UnBoundNonLinDecompOp_by_PoolNames-class | An S4 class to represent the of nonlinear nonautonomous... |
| UnBoundNonLinDecompOp_by_PoolNames-InternalFluxList_by_PoolName-11a8362e | A flux and pool name based representation of a possibly... |
| UnBoundNonLinDecompOp-class | An S4 class to represent a nonlinear nonautonomous... |
| UnBoundNonLinDecompOp-function-missing-missing-missing-ANY-ANY-A4c673fb7 | Constructor for the class with the same name |
| UnBoundNonLinDecompOp-missing-missing-missing-missing-character-ee27243e | convert to Indexed version |
| UnBoundNonLinDecompOp-missing-vector-vector-numeric-ANY-ANY-ANY-method | Constructor for the class with the same name |
| WangThreePoolNonAutonomous_sym | A non-autonomous version of the original Wang 3 pool model |
| Yasso07Model | Implementation of the Yasso07 model |
| YassoModel | Implementation of the Yasso model. |
