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 |