Models of Soil Organic Matter Decomposition
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Documentation for package ‘SoilR’ version 1.2.107
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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 |