# Models of Soil Organic Matter Decomposition

## Documentation for package ‘SoilR’ version 1.1-23

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## Help Pages

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

## -- A --

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' ~~

## -- B --

bacwaveModel | Implementation of the microbial model Bacwave (bacterial waves)
bind.C14curves | Binding of pre- and post-bomb Delta14C curves
BoundFc | generic constructor
BoundFc-class | Class '"BoundFc"'
BoundFc-method | ~~ Methods for Function 'BoundFc' ~~
BoundFc-methods | ~~ Methods for Function 'BoundFc' ~~
BoundFc_method__data.frame_missing_missing_missing_character_function | constructor
BoundFc_method__data.frame_missing_missing_missing_character_missing | constructor
BoundFc_method__data.frame_missing_missing_numeric_character_function | constructor
BoundFc_method__data.frame_missing_missing_numeric_character_missing | constructor
BoundFc_method__function_numeric_numeric_missing_character_missing | constructor
BoundFc_method__function_numeric_numeric_numeric_character_missing | constructor
BoundInFlux | generic constructor
BoundInFlux-class | Class '"BoundInFlux"'
BoundInFlux-method | ~~ Methods for Function 'BoundInFlux' ~~
BoundInFlux-methods | ~~ Methods for Function 'BoundInFlux' ~~
BoundInFlux_method__data.frame_missing_missing_missing_missing | constructor
BoundInFlux_method__data.frame_missing_missing_numeric_function | constructor
BoundInFlux_method__function_numeric_numeric_missing_missing | constructor
BoundInFlux_method__function_numeric_numeric_numeric_missing | constructor
BoundInFlux_method__TimeMap_missing_missing_missing_missing | convert to BoundInFlux
BoundLinDecompOp | Generic constructor
BoundLinDecompOp-class | Class '"BoundLinDecompOp"'
BoundLinDecompOp-method | ~~ Methods for Function 'BoundLinDecompOp' ~~
BoundLinDecompOp-methods | ~~ Methods for Function 'BoundLinDecompOp' ~~
BoundLinDecompOp_method__ConstLinDecompOp | convert a ConstLinDecompOp to a BoundLinDecompOp
BoundLinDecompOp_method__function_numeric_numeric_missing | a constructor
BoundLinDecompOp_method__function_numeric_numeric_numeric | a constructor
BoundLinDecompOp_method__TimeMap_missing_missing_missing | create a BoundLinDecompOp from a TimeMap

## -- C --

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

## -- D --

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

## -- E --

eCO2 | Soil CO2 efflux from incubation experiments

## -- F --

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
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' ~~

## -- H --

HarvardForest14CO2 | Delta14C in soil CO2 efflux from Harvard Forest
Hua2013 | Atmospheric radiocarbon for the period 1950-2010 from Hua et al. (2013)

## -- I --

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

## -- L --

linesCPool | Add lines with the output of 'getC14', 'getC', or 'getReleaseFlux' to an existing plot

## -- M --

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

## -- O --

OnepModel | Implementation of a one pool model
OnepModel14 | Implementation of a one-pool C14 model

## -- P --

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

## -- R --

RespirationCoefficients | helper function to compute respiration coefficients
RothCModel | Implementation of the RothCModel

## -- S --

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

## -- 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-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

## -- Y --

Yasso07Model | Implementation of the Yasso07 model
YassoModel | Implementation of the Yasso model.

## -- misc --

$-method | ~~ Methods for Function '$' ~~
$-methods | ~~ Methods for Function '$' ~~
[-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