Models of Soil Organic Matter Decomposition


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Documentation for package ‘SoilR’ version 1.1-23

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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