A B C D E F G H I L M O P R S T Y misc
| SoilR-package | Models of Soil Organic Matter Decomposition |
| AbsoluteFractionModern-method | ~~ Methods for Function 'AbsoluteFractionModern' ~~ |
| AbsoluteFractionModern-methods | ~~ Methods for Function 'AbsoluteFractionModern' ~~ |
| AbsoluteFractionModern_from_Delta14C | Converts its argument to an Absolute Fraction Modern representation |
| AbsoluteFractionModern_from_Delta14C-method | ~~ Methods for Function 'AbsoluteFractionModern_from_Delta14C' ~~ |
| AbsoluteFractionModern_from_Delta14C-methods | ~~ Methods for Function 'AbsoluteFractionModern_from_Delta14C' ~~ |
| AbsoluteFractionModern_from_Delta14C_method__matrix | Converts from Delta14C to Absolute Fraction Modern |
| AbsoluteFractionModern_from_Delta14C_method__numeric | Converts from Delta14C to Absolute Fraction Modern |
| AbsoluteFractionModern_method__BoundFc | convert to Absolute Fraction Normal values |
| as.character | creates a character representation of the object in question |
| as.character-method | ~~ Methods for Function 'as.character' ~~ |
| as.character-methods | ~~ Methods for Function 'as.character' ~~ |
| as.character_method__BoundInFlux | convert BoundInFlux Objects to something printable. |
| as.character_method__TimeMap | convert TimeMap Objects to something printable. |
| availableParticleProperties-method | ~~ Methods for Function 'availableParticleProperties' ~~ |
| availableParticleProperties-methods | ~~ Methods for Function 'availableParticleProperties' ~~ |
| availableParticleSets-method | ~~ Methods for Function 'availableParticleSets' ~~ |
| availableParticleSets-methods | ~~ Methods for Function 'availableParticleSets' ~~ |
| C14Atm | Atmospheric 14C fraction |
| C14Atm_NH | Post-bomb atmospheric 14C fraction |
| computeResults-method | ~~ Methods for Function 'computeResults' ~~ |
| computeResults-methods | ~~ Methods for Function 'computeResults' ~~ |
| ConstFc | creates an object containing the initial values for the 14C fraction needed to create models in SoilR |
| ConstLinDecompOp | Generic constructor |
| ConstLinDecompOp-class | Class '"ConstLinDecompOp"' |
| ConstLinDecompOp-method | ~~ Methods for Function 'ConstLinDecompOp' ~~ |
| ConstLinDecompOp-methods | ~~ Methods for Function 'ConstLinDecompOp' ~~ |
| ConstLinDecompOp_method__matrix | construct from matric |
| DecompOp-class | Class '"DecompOp"' |
| DecompOp-method | ~~ Methods for Function 'DecompOp' ~~ |
| DecompOp-methods | ~~ Methods for Function 'DecompOp' ~~ |
| DecompOp_method__DecompOp | pass through constructor |
| DecompOp_method__matrix | creates a ConstanDecompOp from a matrix |
| DecompOp_method__TimeMap | creates a BoundLinDecompOp from a TimeMap object |
| DecompositionOperator-class | Class '"DecompositionOperator"' |
| Delta14C-method | ~~ Methods for Function 'Delta14C' ~~ |
| Delta14C-methods | ~~ Methods for Function 'Delta14C' ~~ |
| Delta14C_from_AbsoluteFractionModern | Converts its argument from an Absolute Fraction Modern to a Delta14C representation |
| Delta14C_from_AbsoluteFractionModern-method | ~~ Methods for Function 'Delta14C_from_AbsoluteFractionModern' ~~ |
| Delta14C_from_AbsoluteFractionModern-methods | ~~ Methods for Function 'Delta14C_from_AbsoluteFractionModern' ~~ |
| Delta14C_from_AbsoluteFractionModern_method__matrix | Converts Absolute Fraction Modern values to Delta14C |
| Delta14C_from_AbsoluteFractionModern_method__numeric | Converts to Delta14C format |
| Delta14C_method__BoundFc | convert to Absolute Fraction Normal values |
| deSolve.lsoda.wrapper | deSolve lsoda wrapper |
| eCO2 | Soil CO2 efflux from incubation experiments |
| 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 |
| GaudinskiModel14 | Implementation of a the six-pool C14 model proposed by Gaudinski et al. 2000 |
| GeneralModel | A general constructor |
| GeneralModel-method | ~~ Methods for Function 'GeneralModel' ~~ |
| GeneralModel-methods | ~~ Methods for Function 'GeneralModel' ~~ |
| GeneralModel_14 | A general constructor |
| GeneralModel_14-method | ~~ Methods for Function 'GeneralModel_14' ~~ |
| GeneralModel_14-methods | ~~ Methods for Function 'GeneralModel_14' ~~ |
| GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_missing_missing_missing_logical | a constructor for class Model |
| GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_function_logical | a constructor for class Model_14 |
| GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_function_missing | a constructor for class Model <- 14 |
| GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_missing_logical | a constructor for class Model_ 14 |
| GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_missing_missing | a constructor for class Model |
| GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_missing_ANY_numeric_missing_missing_missing | a constructor for class Model |
| GeneralModel_method__numeric_ANY_numeric | a constructor for class Model |
| getAccumulatedRelease | Calculates the accumulated carbon release from the pools as a function of time |
| getAccumulatedRelease-method | ~~ Methods for Function 'getAccumulatedRelease' ~~ |
| getAccumulatedRelease-methods | ~~ Methods for Function 'getAccumulatedRelease' ~~ |
| getAccumulatedRelease_method__Model | time integrals of release fluxes per pool |
| getC | Calculates the C content of the pools |
| getC-method | ~~ Methods for Function 'getC' ~~ |
| getC-methods | ~~ Methods for Function 'getC' ~~ |
| getC14 | Calculates the mass of radiocarbon (14C fraction times C stock) in all pools |
| getC14-method | ~~ Methods for Function 'getC14' ~~ |
| getC14-methods | ~~ Methods for Function 'getC14' ~~ |
| getC14_method__Model_14 | getC14 method Model 14 |
| getC_method__Model | getC method Model |
| getDecompOp-method | ~~ Methods for Function 'getDecompOp' ~~ |
| getDecompOp-methods | ~~ Methods for Function 'getDecompOp' ~~ |
| getDotOut-method | ~~ Methods for Function 'getDotOut' ~~ |
| getDotOut-methods | ~~ Methods for Function 'getDotOut' ~~ |
| getF14 | Calculates the 14C fraction of all pools |
| getF14-method | ~~ Methods for Function 'getF14' ~~ |
| getF14-methods | ~~ Methods for Function 'getF14' ~~ |
| getF14C | Calculates the average radiocarbon fraction weighted by the mass of carbon |
| getF14C-method | ~~ Methods for Function 'getF14C' ~~ |
| getF14C-methods | ~~ Methods for Function 'getF14C' ~~ |
| getF14C_method__Model_14 | read access to the models F14C variable |
| getF14R | Calculates the average radiocarbon fraction weighted by the amount of carbon release |
| getF14R-method | ~~ Methods for Function 'getF14R' ~~ |
| getF14R-methods | ~~ Methods for Function 'getF14R' ~~ |
| getF14R_method__Model_14 | average radiocarbon fraction weighted by carbonrelease |
| getF14_method__Model_14 | radiocarbon |
| getFormat-method | ~~ Methods for Function 'getFormat' ~~ |
| getFormat-methods | ~~ Methods for Function 'getFormat' ~~ |
| getFormat_method__BoundFc | extract the format string |
| getFunctionDefinition | getFunctionDefinition |
| getFunctionDefinition-method | ~~ Methods for Function 'getFunctionDefinition' ~~ |
| getFunctionDefinition-methods | ~~ Methods for Function 'getFunctionDefinition' ~~ |
| getFunctionDefinition_method__BoundFc | function definition |
| getFunctionDefinition_method__BoundInFlux | getFunctionDefinition method BoundInFlux |
| getFunctionDefinition_method__BoundLinDecompOp | getFunctionDefinition method BoundLinDecompOp |
| getFunctionDefinition_method__ConstLinDecompOp | creates a constant timedependent function and returns it |
| getFunctionDefinition_method__DecompositionOperator | getFunctionDefinition method DecompositionOperator |
| getFunctionDefinition_method__TimeMap | getFunctionDefinition method TimeMap |
| getInFluxes-method | ~~ Methods for Function 'getInFluxes' ~~ |
| getInFluxes-methods | ~~ Methods for Function 'getInFluxes' ~~ |
| getInitialValues-method | ~~ Methods for Function 'getInitialValues' ~~ |
| getInitialValues-methods | ~~ Methods for Function 'getInitialValues' ~~ |
| getMeanTransitTime | Access to the mean transit time |
| getMeanTransitTime-method | ~~ Methods for Function 'getMeanTransitTime' ~~ |
| getMeanTransitTime-methods | ~~ Methods for Function 'getMeanTransitTime' ~~ |
| getMeanTransitTime_method__ConstLinDecompOp | compute the mean transit time |
| getNumberOfPools-method | ~~ Methods for Function 'getNumberOfPools' ~~ |
| getNumberOfPools-methods | ~~ Methods for Function 'getNumberOfPools' ~~ |
| getOutputFluxes-method | ~~ Methods for Function 'getOutputFluxes' ~~ |
| getOutputFluxes-methods | ~~ Methods for Function 'getOutputFluxes' ~~ |
| getOutputReceivers-method | ~~ Methods for Function 'getOutputReceivers' ~~ |
| getOutputReceivers-methods | ~~ Methods for Function 'getOutputReceivers' ~~ |
| getParticleMonteCarloSimulator-method | ~~ Methods for Function 'getParticleMonteCarloSimulator' ~~ |
| getParticleMonteCarloSimulator-methods | ~~ Methods for Function 'getParticleMonteCarloSimulator' ~~ |
| getReleaseFlux | Calculates the release of C from each pool |
| getReleaseFlux-method | ~~ Methods for Function 'getReleaseFlux' ~~ |
| getReleaseFlux-methods | ~~ Methods for Function 'getReleaseFlux' ~~ |
| getReleaseFlux14 | Calculates the mass of radiocarbon in the release flux (14C fraction times release flux) |
| getReleaseFlux14-method | ~~ Methods for Function 'getReleaseFlux14' ~~ |
| getReleaseFlux14-methods | ~~ Methods for Function 'getReleaseFlux14' ~~ |
| getReleaseFlux14_method__Model_14 | 14C respiration rate for all pools |
| getReleaseFlux_method__Model | get the release rate for all pools |
| getTimeRange | getTimeRange |
| getTimeRange-method | ~~ Methods for Function 'getTimeRange' ~~ |
| getTimeRange-methods | ~~ Methods for Function 'getTimeRange' ~~ |
| getTimeRange_method__BoundFc | ask for the boundaries of the underlying time interval |
| getTimeRange_method__BoundInFlux | time domain of the function |
| getTimeRange_method__BoundLinDecompOp | ask for the boundaries of the underlying time interval |
| getTimeRange_method__ConstLinDecompOp | return an (infinite) time range since the operator is constant |
| getTimeRange_method__DecompositionOperator | ask for the boundaries of the underlying time interval |
| getTimeRange_method__TimeMap | ask for the boundaries of the underlying time interval |
| getTimes | Extracts the times argument |
| getTimes-method | ~~ Methods for Function 'getTimes' ~~ |
| getTimes-methods | ~~ Methods for Function 'getTimes' ~~ |
| getTimes_method__Model | getTimes method Model |
| getTransferCoefficients-method | ~~ Methods for Function 'getTransferCoefficients' ~~ |
| getTransferCoefficients-methods | ~~ Methods for Function 'getTransferCoefficients' ~~ |
| getTransferMatrix-method | ~~ Methods for Function 'getTransferMatrix' ~~ |
| getTransferMatrix-methods | ~~ Methods for Function 'getTransferMatrix' ~~ |
| getTransitTimeDistributionDensity | methods for transit time distributions |
| getTransitTimeDistributionDensity-method | ~~ Methods for Function 'getTransitTimeDistributionDensity' ~~ |
| getTransitTimeDistributionDensity-methods | ~~ Methods for Function 'getTransitTimeDistributionDensity' ~~ |
| getTransitTimeDistributionDensity_method__ConstLinDecompOp | compute the TransitTimeDistributionDensity |
| getValues-method | ~~ Methods for Function 'getValues' ~~ |
| getValues-methods | ~~ Methods for Function 'getValues' ~~ |
| HarvardForest14CO2 | Delta14C in soil CO2 efflux from Harvard Forest |
| Hua2013 | Atmospheric radiocarbon for the period 1950-2010 from Hua et al. (2013) |
| ICBMModel | Implementation of the Introductory Carbon Balance Model (ICBM) |
| InFlux-class | Class '"InFlux"' |
| InFlux-method | ~~ Methods for Function 'InFlux' ~~ |
| InFlux-methods | ~~ Methods for Function 'InFlux' ~~ |
| InFlux_method__InFlux | pass through constructor |
| InFlux_method__TimeMap | create a BoundInFlux from a TimeMap object |
| initialize-method | ~~ Methods for Function 'initialize' ~~ |
| initialize-methods | ~~ Methods for Function 'initialize' ~~ |
| initialize_method__BoundFc | internal constructor (new) |
| initialize_method__BoundInFlux | internal constructor |
| initialize_method__BoundLinDecompOp | initialize called by (new) |
| initialize_method__ConstLinDecompOp | internal constructor |
| initialize_method__DecompositionOperator | initialize called by (new) |
| initialize_method__Model | internal constructor for Model objects |
| initialize_method__Model_14 | An internal constructor for 'Model_14' objects not recommended to be used directly in user code. |
| initialize_method__TimeMap | initialize called by (new) |
| IntCal09 | Northern Hemisphere atmospheric radiocarbon for the pre-bomb period |
| IntCal13 | Atmospheric radiocarbon for the 0-50,000 yr BP period |
| linesCPool | Add lines with the output of 'getC14', 'getC', or 'getReleaseFlux' to an existing plot |
| Model | A general constructor |
| Model-class | Class '"Model"' |
| Model-method | ~~ Methods for Function 'Model' ~~ |
| Model-methods | ~~ Methods for Function 'Model' ~~ |
| Model_14 | A general constructor |
| Model_14-class | Class '"Model_14"' |
| Model_14-method | ~~ Methods for Function 'Model_14' ~~ |
| Model_14-methods | ~~ Methods for Function 'Model_14' ~~ |
| Model_method__numeric_ANY_numeric | general constructor for class Model |
| OnepModel | Implementation of a one pool model |
| OnepModel14 | Implementation of a one-pool C14 model |
| ParallelModel | ParallelModel |
| plot-method | ~~ Methods for Function 'plot' ~~ |
| plot-methods | ~~ Methods for Function 'plot' ~~ |
| plotC14Pool | Plots the output of 'getC14' for each pool over time |
| plotCPool | Plots the output of 'getC' or 'getReleaseFlux' for each pool over time |
| plot_method__Model | plot method Model |
| print-method | ~~ Methods for Function 'print' ~~ |
| print-methods | ~~ Methods for Function 'print' ~~ |
| print_method__Model | print method Model |
| RespirationCoefficients | helper function to compute respiration coefficients |
| RothCModel | Implementation of the RothCModel |
| show-method | ~~ Methods for Function 'show' ~~ |
| show-methods | ~~ Methods for Function 'show' ~~ |
| show_method__Model | show method Model |
| SoilR | Models of Soil Organic Matter Decomposition |
| summary-method | ~~ Methods for Function 'summary' ~~ |
| summary-methods | ~~ Methods for Function 'summary' ~~ |
| summary_method__Model | summary method Model |
| 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-class | Class '"TimeMap"' |
| TimeMap.from.Dataframe | TimeMap from Dataframe |
| TimeMap.new | basic constructor of the class TimeMap. |
| turnoverFit | Estimation of the turnover time from a soil 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 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 |
| Yasso07Model | Implementation of the Yasso07 model |
| YassoModel | Implementation of the Yasso model. |
| $-method | ~~ Methods for Function '$' ~~ |
| $-methods | ~~ Methods for Function '$' ~~ |
| [-method | ~~ Methods for Function '[' ~~ |
| [-methods | ~~ Methods for Function '[' ~~ |
| [[-method | ~~ Methods for Function '[[' ~~ |
| [[-methods | ~~ Methods for Function '[[' ~~ |
| [[<--method | ~~ Methods for Function '[[<-' ~~ |
| [[<--methods | ~~ Methods for Function '[[<-' ~~ |
| [_method__Model_character | (experimenta) partially overload [ ] for models |