Man pages for SoilR
Models of Soil Organic Matter Decomposition

AbsoluteFractionModernautomatic title
AbsoluteFractionModern-BoundFc-methodautomatic title
AbsoluteFractionModern-ConstFc-methodautomatic title
AbsoluteFractionModern_from_Delta14Cconversion
AbsoluteFractionModern_from_Delta14C-matrix-methodautomatic title
AbsoluteFractionModern_from_Delta14C-numeric-methodautomatic title
add_plotautomatic title
add_plot-TimeMap-methodautomatic title
as.character-TimeMap-methodautomatic title
as.numeric-InFluxList_by_PoolName-methodConvert to a numeric vector with the pool names as names
as.numeric-InternalFlux_by_PoolName-methodConvert to a numeric value with name of the form 'a->b'
as.numeric-InternalFluxList_by_PoolName-methodConvert to a numeric vector with names of the form 'a->b'
as.numeric-OutFluxList_by_PoolName-methodConvert to a numeric vector with the pool names as names
availableParticlePropertiesautomatic title
availableParticleProperties-MCSim-methodautomatic title
availableParticleSetsautomatic title
availableParticleSets-MCSim-methodautomatic title
availableResidentSetsautomatic title
availableResidentSets-MCSim-methodautomatic title
AWBmodelImplementation of the microbial model AWB (Allison,...
bacwaveModelImplementation of the microbial model Bacwave (bacterial...
bind.C14curvesBinding of pre- and post-bomb Delta14C curves
BoundFcautomatic title
BoundFc-character-methodautomatic title
BoundFc-classS4-class to represent atmospheric 14C concentration as scalar...
BoundFc-missing-methodautomatic title
BoundInFluxesconstructor for BoundInFluxes
BoundInFluxes-classautomatic title
BoundLinDecompOpGeneric constructor for the class with the same name
BoundLinDecompOp-ANY-methodautomatic title
BoundLinDecompOp-classA S4 class to represent a linear compartmental operator...
BoundLinDecompOp-UnBoundLinDecompOp-methodA converter
by_PoolIndexautomatic title
by_PoolIndex-ConstantInFluxRate_by_PoolName-ANY-ANY-methodnew object with the source pool id converted to a PoolIndex...
by_PoolIndex-ConstantInternalFluxRate_by_PoolName-ANY-ANY-methodnew object with the source pool id converted to a PoolName if...
by_PoolIndex-ConstantInternalFluxRateList_by_PoolName-ANY-ANY-methodconvert to a list indexed by pool names
by_PoolIndex-ConstantOutFluxRate_by_PoolName-ANY-ANY-methodnew object with the source pool id converted to a PoolIndex...
by_PoolIndex-ConstantOutFluxRateList_by_PoolName-ANY-ANY-methodconvert to a list indexed by pool names
by_PoolIndex-function-character-character-methodconvert a function f of to f_vec
by_PoolIndex-InFlux_by_PoolName-character-character-methodConvert the pool names to indices
by_PoolIndex-InFluxList_by_PoolName-character-character-methodTransform pool names to indices
by_PoolIndex-InternalFlux_by_PoolName-character-character-methodautomatic title
by_PoolIndex-InternalFluxList_by_PoolName-character-character-methodautomatic title
by_PoolIndex-OutFlux_by_PoolName-character-character-methodautomatic title
by_PoolIndex-OutFluxList_by_PoolName-character-character-methodautomatic title
by_PoolIndex-PoolConnection_by_PoolName-ANY-ANY-methodconstructor from strings of the form 'x->y' new object with...
by_PoolNameautomatic title
by_PoolName-ConstantInFlux_by_PoolIndex-methodnew object with the source pool id converted to a PoolIndex...
by_PoolName-ConstantInFluxList_by_PoolIndex-methodconvert to a list indexed by pool names
by_PoolName-ConstantInFluxRate_by_PoolIndex-methodnew object with the source pool id converted to a PoolIndex...
by_PoolName-ConstantInternalFluxRate_by_PoolIndex-methodnew object with the source pool id converted to a PoolIndex...
by_PoolName-ConstantInternalFluxRateList_by_PoolIndex-methodconvert to a list indexed by pool names
by_PoolName-ConstantOutFluxRate_by_PoolIndex-methodnew object with the source pool id converted to a PoolName if...
by_PoolName-ConstantOutFluxRateList_by_PoolIndex-methodconvert to a list indexed by pool names
C14AtmAtmospheric 14C fraction
C14Atm_NHPost-bomb atmospheric 14C fraction
cash-NlModel-methodautomatic title
CenturyModelImplementation of the Century model
CenturyModel14Implementation of a radiocarbon version of the Century model
check_duplicate_pool_nameshelper function
check_id_lengthhelper function to check that the length of the argument is...
check_pool_idsautomatic title
check_pool_ids-PoolConnection_by_PoolIndex-integer-methodautomatic title
computeResultsautomatic title
computeResults-MCSim-methodautomatic title
ConstantInFlux_by_PoolIndex-classclass for a constant influx to a single pool identified by...
ConstantInFlux_by_PoolName-classclass for a constant influx to a single pool identified by...
ConstantInFluxList_by_PoolIndexGeneric constructor for the class with the same name
ConstantInFluxList_by_PoolIndex-classSubclass of list that is guaranteed to contain only elements...
ConstantInFluxList_by_PoolIndex-ConstInFluxes-methodconstructor from ConstInFluxes
ConstantInFluxList_by_PoolIndex-list-methodconstructor from a normal list
ConstantInFluxList_by_PoolIndex-numeric-methodconstructor from numeric vector
ConstantInFluxList_by_PoolNameGeneric constructor for the class with the same name
ConstantInFluxList_by_PoolName-classSubclass of list that is guaranteed to contain only elements...
ConstantInFluxRate_by_PoolIndex-classDescribes a flux rates.
ConstantInFluxRate_by_PoolNameConstructor for the class with the same name
ConstantInFluxRate_by_PoolName-classDescribes a flux rates.
ConstantInternalFluxRate_by_PoolIndexGeneric constructor for the class with the same name
ConstantInternalFluxRate_by_PoolIndex-classS4 class representing a constant internal flux rate
ConstantInternalFluxRate_by_PoolIndex-missing-missing-character-04a58139constructor from strings of the form '1_to_2'
ConstantInternalFluxRate_by_PoolIndex-numeric-numeric-missing-nu0ca778cfautomatic title
ConstantInternalFluxRate_by_PoolNameGeneric constructor for the class with the same name
ConstantInternalFluxRate_by_PoolName-character-character-missing4e76a719constructor with argument conversion
ConstantInternalFluxRate_by_PoolName-classS4-class to represent a constant internal flux rate with...
ConstantInternalFluxRate_by_PoolName-missing-missing-character-nabea446dconstructor from strings of the form 'a->b'
ConstantInternalFluxRateList_by_PoolIndexGeneric constructor for the class with the same name
ConstantInternalFluxRateList_by_PoolIndex-classDescribes a list of flux rates.
ConstantInternalFluxRateList_by_PoolIndex-list-methodconstructor from a normal list
ConstantInternalFluxRateList_by_PoolIndex-numeric-methodautomatic title
ConstantInternalFluxRateList_by_PoolNameGeneric constructor for the class with the same name
ConstantInternalFluxRateList_by_PoolName-classDescribes a list of flux rates.
ConstantInternalFluxRateList_by_PoolName-list-methodConstructor from a normal list of fluxes
ConstantOutFluxRate_by_PoolIndexGeneric constructor for the class with the same name
ConstantOutFluxRate_by_PoolIndex-classS4 Class to represent a single constant out-flux rate with...
ConstantOutFluxRate_by_PoolIndex-numeric-numeric-methodautomatic title
ConstantOutFluxRate_by_PoolName-classS4 Class to represent a single constant out-flux rate with...
ConstantOutFluxRateList_by_PoolIndexGeneric constructor for the class with the same name
ConstantOutFluxRateList_by_PoolIndex-classDescribes a list of flux rates.
ConstantOutFluxRateList_by_PoolIndex-list-methodconstructor from a normal list
ConstantOutFluxRateList_by_PoolIndex-numeric-methodautomatic title
ConstantOutFluxRateList_by_PoolNameGeneric constructor for the class with the same name
ConstantOutFluxRateList_by_PoolName-classDescribes a list of flux rates.
ConstantOutFluxRateList_by_PoolName-list-methodconstructor from a normal list
ConstantOutFluxRateList_by_PoolName-numeric-methodautomatic title
ConstFccreates an object containing the initial values for the 14C...
ConstFc-classS4 class representing a constant ^14C fraction
ConstInFluxesautomatic title
ConstInFluxes-classS4 class for a constant influx vector
ConstInFluxes-ConstantInFluxList_by_PoolIndex-numeric-methodautomatic title
ConstInFluxes-numeric-ANY-methodautomatic title
ConstLinDecompOpGeneric constructor for the class with the same name
ConstLinDecompOp_by_PoolNameGeneric constructor for the class with the same name
ConstLinDecompOp-classA class to represent a constant (=nonautonomous,linear)...
ConstLinDecompOp-matrix-missing-missing-missing-missing-methodConstructor
ConstLinDecompOp-missing-ConstantInternalFluxRateList_by_PoolInd637fbcafConstructor
ConstLinDecompOp-missing-ConstantInternalFluxRateList_by_PoolIndfec8276dConstructor
ConstLinDecompOp-missing-ConstantInternalFluxRateList_by_PoolNam6d81aaa9alternative Constructor with pool names
ConstLinDecompOp-missing-missing-ConstantOutFluxRateList_by_Pooleee52cd9Constructor
ConstLinDecompOpWithLinearScalarFactorGeneric constructor for the class with the same name
ConstLinDecompOpWithLinearScalarFactor-classA class to represent a constant (=nonautonomous,linear)...
ConstLinDecompOpWithLinearScalarFactor-matrix-missing-missing-mi02dcc78econvert names of vectors or lists to class...
cyclingCycling analysis of compartmental matrices
DecompOp-classS4-class to represent compartmental operators
DecompositionOperator-classautomatic title
Delta14Cautomatic title
Delta14C-BoundFc-methodautomatic title
Delta14C-ConstFc-methodautomatic title
Delta14C_from_AbsoluteFractionModernautomatic title
Delta14C_from_AbsoluteFractionModern-matrix-methodautomatic title
Delta14C_from_AbsoluteFractionModern-numeric-methodautomatic title
deSolve.lsoda.wrapperdeSolve.lsoda.wrapper
eCO2Soil CO2 efflux from an incubation experiment
entropyRatePerJumpEntropy rate per jump
entropyRatePerTimeEntropy rate per time
eulereuler
example.2DBoundInFluxesFromFunctionexample.2DBoundInFluxesFromFunction
example.2DBoundLinDecompOpFromFunctionexample.2DBoundLinDecompOpFromFunction
example.2DConstFc.Argsexample.2DConstFc.Args
example.2DConstInFluxesFromVector2D example for constant Influx
example.2DGeneralDecompOpArgsexample.2DGeneralDecompOpArgs
example.2DInFluxes.Argsexample.2DInFluxes.Args
example.2DUnBoundLinDecompOpFromFunctionexample.2DUnBoundLinDecompOpFromFunction
example.ConstlinDecompOpFromMatrixexample.ConstlinDecompOpFromMatrix
example.nestedTime2DMatrixListcreate an example nested list that can be
example.Time2DArrayListcreate an example TimeMap from 2D array
example.Time3DArrayListcreate an example TimeFrame from 3D array
example.TimeMapFromArraycreate an example TimeFrame from 3D array
FcAtm.from.DataframeFcAtm.from.Dataframe
Fc-classautomatic title
from_integer_flux_lists_with_defaultshelper function
fT.ArrheniusEffects of temperature on decomposition rates according the...
fT.Century1Effects of temperature on decomposition rates according the...
fT.Century2Effects of temperature on decomposition rates according the...
fT.Daycent1Effects of temperature on decomposition rates according to...
fT.Daycent2Effects of temperature on decomposition rates according to...
fT.DemeterEffects of temperature on decomposition rates according to...
fT.KBEffects of temperature on decomposition rates according to a...
fT.LandTEffects of temperature on decomposition rates according to a...
fT.linearEffects of temperature on decomposition rates according to a...
fT.Q10Effects of temperature on decomposition rates according to a...
fT.RothCEffects of temperature on decomposition rates according to...
fT.StandcarbEffects of temperature on decomposition rates according to...
fW.CandyEffects of moisture on decomposition rates according to the...
fW.CenturyEffects of moisture on decomposition rates according to the...
fW.Daycent1Effects of moisture on decomposition rates according to the...
fW.Daycent2Effects of moisture on decomposition rates according to the...
fW.DemeterEffects of moisture on decomposition rates according to the...
fW.GompertzEffects of moisture on decomposition rates according to the...
fW.MoyanoEffects of moisture on decomposition rates according to the...
fW.RothCEffects of moisture on decomposition rates according to the...
fW.SkoppEffects of moisture on decomposition rates according to the...
fW.StandcarbEffects of moisture on decomposition rates according to the...
GaudinskiModel14Implementation of a the six-pool C14 model proposed by...
GeneralDecompOpA generic factory for subclasses of GeneralDecompOp
GeneralDecompOp-DecompOp-methodPass through factory for objects of subclasses of DecompOp
GeneralDecompOp-function-methodautomatic title
GeneralDecompOp-list-methodautomatic title
GeneralDecompOp-matrix-methodautomatic title
GeneralDecompOp-TimeMap-methodautomatic title
GeneralModeladditional function to create Models
GeneralModel_14create objects of class Model_14
GeneralNlModelUse this function to create objects of class NlModel.
GeneralPoolIdautomatic title
GeneralPoolId-character-methodautomatic title
GeneralPoolId-numeric-methodgeneric factory for this virtual class
getAccumulatedReleaseautomatic title
getAccumulatedRelease-Model-methodCompute the time integral of the relaese fluxes over time
getCCalculates the content of the pools
getC14Generic that yields the ^14C content for all pools and all...
getC14-Model_14-methodautomatic title
getC-Model_by_PoolNames-methodPool Contents for all times
getC-Model-methodPool Contents for all times
getC-NlModel-methodPool Contents for all times
getCompartmentalMatrixFuncautomatic title
getCompartmentalMatrixFunc-BoundLinDecompOp-ANY-ANY-methodautomatic title
getCompartmentalMatrixFunc-ConstLinDecompOp-ANY-ANY-methodautomatic title
getCompartmentalMatrixFunc-TransportDecompositionOperator-ANY-ANY-methodautomatic title
getCompartmentalMatrixFunc-UnBoundNonLinDecompOp-ANY-ANY-methodExtract the matrix valued function of time and state vector...
getCompartmentalMatrixFunc-UnBoundNonLinDecompOp_by_PoolNames-chf19f8c91Compartmental Matrix as function of the state vector and time
getConstantCompartmentalMatrixautomatic title
getConstantCompartmentalMatrix-ConstLinDecompOp-methodautomatic title
getConstantCompartmentalMatrix-ConstLinDecompOpWithLinearScalarF13f9803dautomatic title
getConstantInFluxVectorautomatic title
getConstantInFluxVector-ConstInFluxes-methodautomatic title
getConstantInternalFluxRateList_by_PoolIndexautomatic title
getConstantInternalFluxRateList_by_PoolIndex-ConstLinDecompOp-methodautomatic title
getConstantOutFluxRateList_by_PoolIndexautomatic title
getConstantOutFluxRateList_by_PoolIndex-ConstLinDecompOp-methodautomatic title
getConstLinDecompOpautomatic title
getConstLinDecompOp-ConstLinDecompOpWithLinearScalarFactor-methodautomatic title
getCumulativeCautomatic title
getCumulativeC-NlModel-methodautomatic title
getDecompOpautomatic title
getDecompOp-Model-methodExtract the Compartmental Operator
getDecompOp-NlModel-methodExtract the Compartmental Operator
getDotOutautomatic title
getDotOut-TransportDecompositionOperator-methodautomatic title
getF14Generic that yields the ^14C fraction for the content all...
getF14CGeneric that yields the ^14C fraction for the cumulative...
getF14C-Model_14-methodautomatic title
getF14-Model_14-methodautomatic title
getF14RGeneric that yields the ^14C fraction for the release flux of...
getF14R-Model_14-methodautomatic title
getFormatautomatic title
getFormat-Fc-methodautomatic title
getFunctionDefinitionautomatic title
getFunctionDefinition-ConstInFluxes-methodautomatic title
getFunctionDefinition-ConstLinDecompOp-methodautomatic title
getFunctionDefinition-ConstLinDecompOpWithLinearScalarFactor-methodhelper function
getFunctionDefinition-DecompositionOperator-methodautomatic title
getFunctionDefinition-InFluxList_by_PoolIndex-methodautomatic title
getFunctionDefinition-InFluxList_by_PoolName-methodautomatic title
getFunctionDefinition-StateDependentInFluxVector-methodautomatic title
getFunctionDefinition-TimeMap-methodautomatic title
getFunctionDefinition-TransportDecompositionOperator-methodautomatic title
getFunctionDefinition-UnBoundInFluxes-methodautomatic title
getFunctionDefinition-UnBoundLinDecompOp-methodExtracts the time dependent matrix valued function...
getInFluxesExtract the influxes
getInFluxes-Model-methodExtract the InFluxes as provided during creation of the model
getInFluxes-NlModel-methodautomatic title
getInitialValuesautomatic title
getInitialValues-NlModel-methodautomatic title
getLinearScaleFactorautomatic title
getLinearScaleFactor-ConstLinDecompOpWithLinearScalarFactor-methodautomatic title
getMeanTransitTimeautomatic title
getMeanTransitTime-ConstLinDecompOp-methodautomatic title
getNumberOfPoolsautomatic title
getNumberOfPools-MCSim-methodautomatic title
getNumberOfPools-NlModel-methodautomatic title
getNumberOfPools-TransportDecompositionOperator-methodautomatic title
getOutputFluxesGeneric Function to obtain the fluxes out of of the pools
getOutputFluxes-NlModel-methodautomatic title
getOutputReceiversautomatic title
getOutputReceivers-TransportDecompositionOperator-numeric-methodautomatic title
getParticleMonteCarloSimulatorautomatic title
getParticleMonteCarloSimulator-NlModel-methodautomatic title
getReleaseFluxGeneric Function to obtain the vector of release fluxes out...
getReleaseFlux14automatic title
getReleaseFlux14-Model_14-methodautomatic title
getReleaseFlux-Model_by_PoolNames-methodautomatic title
getReleaseFlux-Model-methodThe release fluxes [content]/[time] for all pools.
getReleaseFlux-NlModel-methodautomatic title
getRightHandSideOfODEautomatic title
getRightHandSideOfODE-Model_by_PoolNames-methodProvide the (vector valued) derivative of the stocks with...
getRightHandSideOfODE-Model-methodDerivative of the state variables as function
getSolutionCalculates all stocks all fluxes to ,in and out of the...
getSolution-Model_by_PoolNames-methodAll Fluxes and stocks for all times
getTimeRangeautomatic title
getTimeRange-ConstInFluxes-methodautomatic title
getTimeRange-ConstLinDecompOp-methodautomatic title
getTimeRange-ConstLinDecompOpWithLinearScalarFactor-methodautomatic title
getTimeRange-DecompositionOperator-methodautomatic title
getTimeRange-TimeMap-methodThe time interval where the function is defined
getTimeRange-UnBoundInFluxes-methodautomatic title
getTimeRange-UnBoundLinDecompOp-methodExtracts the time interval for which the function is valid.
getTimesautomatic title
getTimes-Model_by_PoolNames-methodExtract the times vector
getTimes-Model-methodExtract the times vector
getTimes-NlModel-methodautomatic title
getTransferCoefficientsautomatic title
getTransferCoefficients-NlModel-methodautomatic title
getTransferCoefficients-TransportDecompositionOperator-methodautomatic title
getTransferMatrixdeprecated, use getTransferMatrixFunc instead
getTransferMatrixFuncautomatic title
getTransferMatrixFunc-TransportDecompositionOperator-methodautomatic title
getTransitTimeDistributionDensityautomatic title
getTransitTimeDistributionDensity-ConstLinDecompOp-methodautomatic title
getValuesautomatic title
getValues-ConstFc-methodautomatic title
Graven2017Compiled records of radicarbon in atmospheric CO2 for...
HarvardForest14CO2Delta14C in soil CO2 efflux from Harvard Forest
Hua2013Atmospheric radiocarbon for the period 1950-2010 from Hua et...
ICBMModelImplementation of the Introductory Carbon Balance Model...
ICBM_NImplementation of the ICBM/N model
incubation_experimentSoil CO2 efflux from an incubation experiment, along with the...
InFluxGeneric constructor for the class with the same name
InFlux_by_PoolIndexGeneric constructor for the class with the same name
InFlux_by_PoolIndex-classS4 class for the influx to a single pool identified by the...
InFlux_by_PoolIndex-function-numeric-methodconstructor from an ordered pair of PoolIndex (integer like)...
InFlux_by_PoolNameGeneric constructor for an influx to a single pool from an...
InFlux_by_PoolName-classS4 class for the influx to a single pool identified by the...
InFlux_by_PoolName-function-character-methodConstructor from an ordered pair of PoolName (string like)...
InFluxesA generic factory for subclasses of InFluxes
InFluxes-classA virtual S4-class representing (different subclasses) of...
InFluxes-ConstantInFluxList_by_PoolIndex-methodautomatic title
InFluxes-function-methodautomatic title
InFluxes-InFluxes-methodautomatic title
InFluxes-list-methodautomatic title
InFluxes-numeric-methodautomatic title
InFluxes-StateIndependentInFluxList_by_PoolIndex-methodautomatic title
InFluxes-TimeMap-methodautomatic title
InFluxList_by_PoolIndexGeneric constructor for the class with the same name
InFluxList_by_PoolIndex-classDescribes a list of flux rates.
InFluxList_by_PoolIndex-list-methodconstructor from a normal list
InFluxList_by_PoolNameGeneric constructor for the class with the same name
InFluxList_by_PoolName-classClass for a list of influxes indexed by the names of the...
InFluxList_by_PoolName-list-methodconstructor from a normal list
initialize-ConstLinDecompOp-methodautomatic title
initialize-DecompositionOperator-methodautomatic title
initialize-MCSim-methodautomatic title
initialize-Model_14-methodInternal method to supervise creation of objects of this...
initialize-Model_by_PoolNames-methodautomatic title
initialize-Model-methodInternal method to supervise creation of objects of this...
initialize-NlModel-methodautomatic title
initialize-TimeMap-methodautomatic title
initialize-TransportDecompositionOperator-methodautomatic title
initialize-UnBoundInFluxes-methodautomatic title
initialize-UnBoundLinDecompOp-methodautomatic title
IntCal09Northern Hemisphere atmospheric radiocarbon for the pre-bomb...
IntCal13Atmospheric radiocarbon for the 0-50,000 yr BP period
IntCal20The IntCal20 northern hemisphere radiocarbon curve for the...
InternalFlux_by_PoolIndexGeneric constructor for the class with the same name
InternalFlux_by_PoolIndex-classS4-class for a single internal flux with source and...
InternalFlux_by_PoolIndex-function-numeric-numeric-missing-methodconstructor from an ordered pair of PoolIndex (integer like)...
InternalFlux_by_PoolNameGeneric constructor for the class with the same name
InternalFlux_by_PoolName-classS4-class for a single internal flux with source and...
InternalFlux_by_PoolName-function-character-character-missing-methodconstructor from an ordered pair of PoolName (string like)...
InternalFlux_by_PoolName-function-missing-missing-character-methodautomatic title
InternalFluxList_by_PoolIndexGeneric constructor for the class with the same name
InternalFluxList_by_PoolIndex-classS4-class for a list of internal fluxes with source and...
InternalFluxList_by_PoolIndex-list-methodconstructor from a normal list
InternalFluxList_by_PoolNameGeneric constructor for the class with the same name
InternalFluxList_by_PoolName-classS4-class for a list of internal fluxes with indexed by...
InternalFluxList_by_PoolName-list-methodconstructor from a normal list
linearScalarModelImplementation of a general model for linear non-autonomous...
linesCPoolAdd lines with the output of 'getC14', 'getC', or...
listProducttensor product of lists
MCSim-classExperimental Class for a Monte Carlo Simulation of particles...
ModelConstructor for class Model
Model_14general constructor for class Model_14
Model_14-classS4-class to represent a ^14C model run
Model_by_PoolNamesConstructor for 'Model_by_PoolNames'
Model_by_PoolNames-classA model run based on flux functions
Model_by_PoolNames-missing-numeric-UnBoundNonLinDecompOp_by_Poole522475aCreate a model(run) described by fluxes
Model_by_PoolNames-SymbolicModel_by_PoolNames-numeric-missing-nu37a011e6Create a model(run) described by fluxes
Model-classS4 class representing a model run
NlModel-classdeprecated class for a non-linear model run.
no_outflux_warninghelper function
OnepModelImplementation of a one pool model
OnepModel14Implementation of a one-pool C14 model
OutFluxGeneric constructor for the class with the same name
OutFlux_by_PoolIndexGeneric constructor for the class with the same name
OutFlux_by_PoolIndex-classS4 class for a single out-flux with source pool index
OutFlux_by_PoolIndex-function-numeric-methodconstructor from a PoolIndex (integer like) objects and a...
OutFlux_by_PoolNameGeneric constructor for the class with the same name
OutFlux_by_PoolName-classS4 class for a single out-flux with source pool name
OutFlux_by_PoolName-function-character-methodconstructor from a PoolName (integer like) object and a...
OutFluxList_by_PoolIndexGeneric constructor for the class with the same name
OutFluxList_by_PoolIndex-classA list of outfluxes
OutFluxList_by_PoolIndex-list-methodconstructor from a normal list
OutFluxList_by_PoolNameGeneric constructor for the class with the same name
OutFluxList_by_PoolName-classS4 class for a list of out-fluxes indexed by source pool name
OutFluxList_by_PoolName-list-methodconstructor from a normal list
ParallelModelmodels for unconnected pools
pathEntropyPath Entropy
plotC14PoolPlots the output of 'getF14' for each pool over time
plotCPoolPlots the output of 'getC' or 'getReleaseFlux' for each pool...
plot-MCSim-methodautomatic title
plot-Model_by_PoolNames-methodPlot the graph of pool connections
plot-Model-methodCreate an overview plot
plot-NlModel-methodautomatic title
plotPoolGraphGeneric plotter
plotPoolGraphFromTupleListsHelper function to draw connectivity graphs
plotPoolGraph-SymbolicModel_by_PoolNames-methodPlot the graph of pool connections
plot-TimeMap-methodautomatic title
PoolConnection_by_PoolIndexautomatic title
PoolConnection_by_PoolIndex-ANY-ANY-missing-methodconstructor from an ordered pair of PoolId objects
PoolConnection_by_PoolIndex-classObjects that have a source and a destination described by...
PoolConnection_by_PoolIndex-missing-missing-character-methodconstructor from strings of the form '1_to_2'
PoolConnection_by_PoolNameautomatic title
PoolConnection_by_PoolName-ANY-ANY-missing-methodconstructor from an ordered pair of PoolName objects
PoolConnection_by_PoolName-classObjects that have a source and a destination determined by a...
PoolId-classcommon class for pool ids
PoolIndexautomatic title
PoolIndex-character-methodconstruct from number string like '1' or '3'
PoolIndex-classS4 class for pool indices
PoolIndex-numeric-methodconstruct from number
PoolIndex-PoolIndex-methodpass through constructor fron an object of the same class
PoolIndex-PoolName-methodconvert to number like object
PoolNameautomatic title
PoolName-character-methodconstruct from string with checks
PoolName-classclass for pool-name-strings
PoolName-PoolIndex-methodconvert to string like object
PoolName-PoolName-methodpass through constructor fron an object of the same class
predefinedModelsPREDEFINED MODELS
print-NlModel-methodautomatic title
RespirationCoefficientshelper function to compute respiration coefficients
RothCModelImplementation of the RothCModel
ScalarTimeMapConstructor for 'ScalarTimeMap-class'
ScalarTimeMap-classS4 class for a scalar time dependent function on a finite...
ScalarTimeMap-data.frame-missing-missing-missing-missing-methodconstructor for data given as 2 column data.frame
ScalarTimeMap-function-missing-missing-missing-missing-methodmanual constructor for just a function
ScalarTimeMap-function-numeric-numeric-missing-missing-methodmanual constructor for a function and an interval
ScalarTimeMap-missing-missing-missing-missing-numeric-methodspecial case for a time map from a constant
ScalarTimeMap-missing-missing-missing-numeric-numeric-methodconstructor for data and times given as vectors
SeriesLinearModelGeneral m-pool linear model with series structure
SeriesLinearModel14General m-pool linear C14 model with series structure
SHCal20The SHCal20 southern hemisphere radiocarbon curve for the...
show-NlModel-methodautomatic title
SoilR.F0.newdeprecated function that used to create an object of class...
SoilR-packageSoilR
StateDependentInFluxVector-classInput vector that is a function of the pool contenst and time
StateIndependentInFlux_by_PoolIndex-classConstructor for the class with the same name
StateIndependentInFluxList_by_PoolIndexGeneric constructor for the class with the same name
StateIndependentInFluxList_by_PoolIndex-classSubclass of list that is guaranteed to contain only elements...
StateIndependentInFluxList_by_PoolIndex-list-methodconstructor from a normal list
StateIndependentInFluxList_by_PoolNameGeneric constructor for the class with the same name
state_variable_namesdetermine the minimum set of statevariables
sub-Model-character-missing-missing-methodExperimentally overloaded index operator
sub-NlModel-character-ANY-ANY-methodautomatic title
sub-sub-MCSim-methodautomatic title
sub-subset-MCSim-methodautomatic title
SymbolicModel_by_PoolNames-classA symbolic model description based on flux functions
systemAgeSystem and pool age for constant compartment models
ThreepairMMmodelImplementation of a 6-pool Michaelis-Menten model
ThreepFeedbackModelImplementation of a three pool model with feedback structure
ThreepFeedbackModel14Implementation of a three-pool C14 model with feedback...
ThreepParallelModelImplementation of a three pool model with parallel structure
ThreepParallelModel14Implementation of a three-pool C14 model with parallel...
ThreepSeriesModelImplementation of a three pool model with series structure
ThreepSeriesModel14Implementation of a three-pool C14 model with series...
TimeMapConstructor for 'TimeMap-class'
TimeMap-classS4 class for a time dependent function
TimeMap-data.frame-missing-missing-missing-missing-methodautomatic title
TimeMap.from.DataframeTimeMap.from.Dataframe
TimeMap-function-missing-missing-missing-missing-methodmanual constructor for just a function
TimeMap-function-numeric-numeric-missing-missing-methodmanual constructor for a function and an interval
TimeMap-list-missing-missing-missing-missing-methodautomatic title
TimeMap-missing-missing-missing-numeric-array-methodautomatic title
TimeMap-missing-missing-missing-numeric-list-methodautomatic title
TimeMap-missing-missing-missing-numeric-matrix-methodautomatic title
TimeMap-missing-missing-missing-numeric-numeric-methodautomatic title
TimeMap.newdeprecated constructor of the class TimeMap.
TimeMap-TimeMap-ANY-ANY-ANY-ANY-methodautomatic title
TimeRangeIntersectionThe time interval where both functions are defined
transitTimeTransit times for compartment models
TransportDecompositionOperator-classautomatic title
turnoverFitEstimation of the turnover time from a radiocarbon sample.
TwopFeedbackModelImplementation of a two pool model with feedback structure
TwopFeedbackModel14Implementation of a two-pool C14 model with feedback...
TwopMMmodelImplementation of a two-pool Michaelis-Menten model
TwopParallelModelImplementation of a linear two pool model with parallel...
TwopParallelModel14Implementation of a two-pool C14 model with parallel...
TwopSeriesModelImplementation of a two pool model with series structure
TwopSeriesModel14Implementation of a two-pool C14 model with series structure
UnBoundInFluxesautomatic title
UnBoundInFluxes-classautomatic title
UnBoundInFluxes-function-methodautomatic title
UnBoundLinDecompOpGeneric constructor for the class with the same name
UnBoundLinDecompOp-classAn S4 class to represent a linear nonautonomous compartmental...
UnBoundLinDecompOp-function-methodGeneric constructor for the class with the same name
UnBoundNonLinDecompOpGeneric constructor for the class with the same name
UnBoundNonLinDecompOp_by_PoolNamesGeneric constructor for the class with the same name
UnBoundNonLinDecompOp_by_PoolNames-classAn S4 class to represent the of nonlinear nonautonomous...
UnBoundNonLinDecompOp_by_PoolNames-InternalFluxList_by_PoolName-11a8362eA flux and pool name based representation of a possibly...
UnBoundNonLinDecompOp-classAn S4 class to represent a nonlinear nonautonomous...
UnBoundNonLinDecompOp-function-missing-missing-missing-ANY-ANY-A4c673fb7Constructor for the class with the same name
UnBoundNonLinDecompOp-missing-missing-missing-missing-character-ee27243econvert to Indexed version
UnBoundNonLinDecompOp-missing-vector-vector-numeric-ANY-ANY-ANY-methodConstructor for the class with the same name
WangThreePoolNonAutonomous_symA non-autonomous version of the original Wang 3 pool model
Yasso07ModelImplementation of the Yasso07 model
YassoModelImplementation of the Yasso model.
SoilR documentation built on Jan. 23, 2022, 5:07 p.m.