API for SoilR
Models of Soil Organic Matter Decomposition

Global functions
$,NlModel-method	Man page
AWBmodel	Man page
AbsoluteFractionModern	Man page
AbsoluteFractionModern,BoundFc-method	Man page
AbsoluteFractionModern,ConstFc-method	Man page
AbsoluteFractionModern_from_Delta14C	Man page
AbsoluteFractionModern_from_Delta14C,matrix-method	Man page
AbsoluteFractionModern_from_Delta14C,numeric-method	Man page
BoundFc	Man page
BoundFc,character-method	Man page
BoundFc,missing-method	Man page
BoundFc-class	Man page
BoundInFluxes	Man page
BoundInFluxes-class	Man page
BoundLinDecompOp	Man page
BoundLinDecompOp,ANY-method	Man page
BoundLinDecompOp,UnBoundLinDecompOp-method	Man page
BoundLinDecompOp-class	Man page
C14Atm	Man page
C14Atm_NH	Man page
CallWithPlotVars	Source code
CenturyModel	Man page
CenturyModel14	Man page
ConstFc	Man page
ConstFc-class	Man page
ConstInFluxes	Man page
ConstInFluxes,ConstantInFluxList_by_PoolIndex,numeric-method	Man page
ConstInFluxes,numeric,ANY-method	Man page
ConstInFluxes-class	Man page
ConstLinDecompOp	Man page
ConstLinDecompOp,matrix,missing,missing,missing,missing-method	Man page
ConstLinDecompOp-class	Man page
ConstLinDecompOpWithLinearScalarFactor	Man page
ConstLinDecompOpWithLinearScalarFactor-class	Man page
ConstLinDecompOp_by_PoolName	Man page
ConstantInFluxList_by_PoolIndex	Man page
ConstantInFluxList_by_PoolIndex,ConstInFluxes-method	Man page
ConstantInFluxList_by_PoolIndex,list-method	Man page
ConstantInFluxList_by_PoolIndex,numeric-method	Man page
ConstantInFluxList_by_PoolIndex-class	Man page
ConstantInFluxList_by_PoolName	Man page
ConstantInFluxList_by_PoolName-class	Man page
ConstantInFluxRate_by_PoolIndex	Source code
ConstantInFluxRate_by_PoolIndex-class	Man page
ConstantInFluxRate_by_PoolName	Man page Source code Source code Source code Source code
ConstantInFluxRate_by_PoolName-class	Man page
ConstantInFlux_by_PoolIndex	Source code
ConstantInFlux_by_PoolIndex-class	Man page
ConstantInFlux_by_PoolName-class	Man page
ConstantInternalFluxRateList_by_PoolIndex	Man page
ConstantInternalFluxRateList_by_PoolIndex,list-method	Man page
ConstantInternalFluxRateList_by_PoolIndex,numeric-method	Man page
ConstantInternalFluxRateList_by_PoolIndex-class	Man page
ConstantInternalFluxRateList_by_PoolName	Man page
ConstantInternalFluxRateList_by_PoolName,list-method	Man page
ConstantInternalFluxRateList_by_PoolName-class	Man page
ConstantInternalFluxRate_by_PoolIndex	Man page
ConstantInternalFluxRate_by_PoolIndex,numeric,numeric,missing,nu	Man page
ConstantInternalFluxRate_by_PoolIndex-class	Man page
ConstantInternalFluxRate_by_PoolName	Man page
ConstantInternalFluxRate_by_PoolName,character,character,missing	Man page
ConstantInternalFluxRate_by_PoolName,missing,missing,character,n	Man page
ConstantInternalFluxRate_by_PoolName-class	Man page
ConstantOutFluxRateList_by_PoolIndex	Man page
ConstantOutFluxRateList_by_PoolIndex,list-method	Man page
ConstantOutFluxRateList_by_PoolIndex,numeric-method	Man page
ConstantOutFluxRateList_by_PoolIndex-class	Man page
ConstantOutFluxRateList_by_PoolName	Man page
ConstantOutFluxRateList_by_PoolName,list-method	Man page
ConstantOutFluxRateList_by_PoolName,numeric-method	Man page
ConstantOutFluxRateList_by_PoolName-class	Man page
ConstantOutFluxRate_by_PoolIndex	Man page
ConstantOutFluxRate_by_PoolIndex,numeric,numeric-method	Man page
ConstantOutFluxRate_by_PoolIndex-class	Man page
ConstantOutFluxRate_by_PoolName	Source code
ConstantOutFluxRate_by_PoolName-class	Man page
DecompOp-class	Man page
DecompositionOperator-class	Man page
Delta14C	Man page
Delta14C,BoundFc-method	Man page
Delta14C,ConstFc-method	Man page
Delta14C_from_AbsoluteFractionModern	Man page
Delta14C_from_AbsoluteFractionModern,matrix-method	Man page
Delta14C_from_AbsoluteFractionModern,numeric-method	Man page
Fc-class	Man page
FcAtm.from.Dataframe	Man page
GaudinskiModel14	Man page
GeneralDecompOp	Man page
GeneralDecompOp,DecompOp-method	Man page
GeneralDecompOp,TimeMap-method	Man page
GeneralDecompOp,function-method	Man page
GeneralDecompOp,list-method	Man page
GeneralDecompOp,matrix-method	Man page
GeneralModel	Man page Source code
GeneralModel_14	Man page
GeneralNlModel	Man page
GeneralPoolId	Man page
GeneralPoolId,character-method	Man page
GeneralPoolId,numeric-method	Man page
Graven2017	Man page
HarvardForest14CO2	Man page
Hua2013	Man page
Hua2021	Man page
ICBMModel	Man page
ICBM_N	Man page Source code
IVP_maker	Source code
InFlux	Man page
InFluxList_by_PoolIndex	Man page
InFluxList_by_PoolIndex,list-method	Man page
InFluxList_by_PoolIndex-class	Man page
InFluxList_by_PoolName	Man page
InFluxList_by_PoolName,list-method	Man page
InFluxList_by_PoolName-class	Man page
InFlux_by_PoolIndex	Man page
InFlux_by_PoolIndex,function,numeric-method	Man page
InFlux_by_PoolIndex-class	Man page
InFlux_by_PoolName	Man page
InFlux_by_PoolName,function,character-method	Man page
InFlux_by_PoolName-class	Man page
InFluxes	Man page
InFluxes,ConstantInFluxList_by_PoolIndex-method	Man page
InFluxes,InFluxes-method	Man page
InFluxes,StateIndependentInFluxList_by_PoolIndex-method	Man page
InFluxes,TimeMap-method	Man page
InFluxes,function-method	Man page
InFluxes,list-method	Man page
InFluxes,numeric-method	Man page
InFluxes-class	Man page
IntCal09	Man page
IntCal13	Man page
IntCal20	Man page
InternalFluxList_by_PoolIndex	Man page
InternalFluxList_by_PoolIndex,list-method	Man page
InternalFluxList_by_PoolIndex-class	Man page
InternalFluxList_by_PoolName	Man page
InternalFluxList_by_PoolName,list-method	Man page
InternalFluxList_by_PoolName-class	Man page
InternalFlux_by_PoolIndex	Man page
InternalFlux_by_PoolIndex,function,numeric,numeric,missing-metho	Man page
InternalFlux_by_PoolIndex-class	Man page
InternalFlux_by_PoolName	Man page
InternalFlux_by_PoolName,function,character,character,missing-me	Man page
InternalFlux_by_PoolName,function,missing,missing,character-meth	Man page
InternalFlux_by_PoolName-class	Man page
MCSim-class	Man page
Model	Man page Source code
Model-class	Man page
Model_14	Man page
Model_14-class	Man page
Model_by_PoolNames	Man page
Model_by_PoolNames-class	Man page
NlModel-class	Man page
OnepModel	Man page
OnepModel14	Man page
OutFlux	Man page
OutFluxList_by_PoolIndex	Man page
OutFluxList_by_PoolIndex,list-method	Man page
OutFluxList_by_PoolIndex-class	Man page
OutFluxList_by_PoolName	Man page
OutFluxList_by_PoolName,list-method	Man page
OutFluxList_by_PoolName-class	Man page
OutFlux_by_PoolIndex	Man page
OutFlux_by_PoolIndex,function,numeric-method	Man page
OutFlux_by_PoolIndex-class	Man page
OutFlux_by_PoolName	Man page
OutFlux_by_PoolName,function,character-method	Man page
OutFlux_by_PoolName-class	Man page
ParallelModel	Man page
PoolConnection_by_PoolIndex	Man page
PoolConnection_by_PoolIndex,ANY,ANY,missing-method	Man page
PoolConnection_by_PoolIndex,missing,missing,character-method	Man page
PoolConnection_by_PoolIndex-class	Man page
PoolConnection_by_PoolName	Man page
PoolConnection_by_PoolName,ANY,ANY,missing-method	Man page
PoolConnection_by_PoolName-class	Man page
PoolId-class	Man page
PoolIndex	Man page
PoolIndex,PoolIndex-method	Man page
PoolIndex,PoolName-method	Man page
PoolIndex,character-method	Man page
PoolIndex,numeric-method	Man page
PoolIndex-class	Man page
PoolName	Man page
PoolName,PoolIndex-method	Man page
PoolName,PoolName-method	Man page
PoolName,character-method	Man page
PoolName-class	Man page
RespirationCoefficients	Man page
RothCModel	Man page
SHCal20	Man page
ScalarTimeMap	Man page
ScalarTimeMap,data.frame,missing,missing,missing,missing-method	Man page
ScalarTimeMap,function,missing,missing,missing,missing-method	Man page
ScalarTimeMap,function,numeric,numeric,missing,missing-method	Man page
ScalarTimeMap,missing,missing,missing,missing,numeric-method	Man page
ScalarTimeMap,missing,missing,missing,numeric,numeric-method	Man page
ScalarTimeMap-class	Man page
SeriesLinearModel	Man page
SeriesLinearModel14	Man page
SoilR-package	Man page
SoilR.F0.new	Man page
StateDependentInFluxVector	Man page
StateDependentInFluxVector-class	Man page
StateIndependentInFluxList_by_PoolIndex	Man page
StateIndependentInFluxList_by_PoolIndex,list-method	Man page
StateIndependentInFluxList_by_PoolIndex-class	Man page
StateIndependentInFluxList_by_PoolName	Man page
StateIndependentInFlux_by_PoolIndex	Man page
StateIndependentInFlux_by_PoolIndex-class	Man page
SymbolicModel_by_PoolNames	Man page
SymbolicModel_by_PoolNames-class	Man page
ThreepFeedbackModel	Man page
ThreepFeedbackModel14	Man page
ThreepParallelModel	Man page
ThreepParallelModel14	Man page
ThreepSeriesModel	Man page
ThreepSeriesModel14	Man page
ThreepairMMmodel	Man page
TimeMap	Man page
TimeMap,TimeMap,ANY,ANY,ANY,ANY-method	Man page
TimeMap,data.frame,missing,missing,missing,missing-method	Man page
TimeMap,function,missing,missing,missing,missing-method	Man page
TimeMap,function,numeric,numeric,missing,missing-method	Man page
TimeMap,list,missing,missing,missing,missing-method	Man page
TimeMap,missing,missing,missing,numeric,array-method	Man page
TimeMap,missing,missing,missing,numeric,list-method	Man page
TimeMap,missing,missing,missing,numeric,matrix-method	Man page
TimeMap,missing,missing,missing,numeric,numeric-method	Man page
TimeMap-class	Man page
TimeMap.from.Dataframe	Man page
TimeMap.new	Man page
TimeRangeIntersection	Man page Source code
TransportDecompositionOperator-class	Man page
TwopFeedbackModel	Man page
TwopFeedbackModel14	Man page
TwopMMmodel	Man page
TwopParallelModel	Man page
TwopParallelModel14	Man page
TwopSeriesModel	Man page
TwopSeriesModel14	Man page
UnBoundInFluxes	Man page
UnBoundInFluxes,function-method	Man page
UnBoundInFluxes-class	Man page
UnBoundLinDecompOp	Man page
UnBoundLinDecompOp,function-method	Man page
UnBoundLinDecompOp-class	Man page
UnBoundNonLinDecompOp	Man page
UnBoundNonLinDecompOp,function,missing,missing,missing-method	Man page
UnBoundNonLinDecompOp,missing,vector,vector,numeric-method	Man page
UnBoundNonLinDecompOp-class	Man page
UnBoundNonLinDecompOp_by_PoolNames	Man page
UnBoundNonLinDecompOp_by_PoolNames-class	Man page
WarningConstFc	Source code
Yasso07Model	Man page
YassoModel	Man page
[,Model,character,missing,missing-method	Man page
[,NlModel,character,ANY,ANY-method	Man page
[[,MCSim-method	Man page
[[<-,MCSim-method	Man page
add_plot	Man page
add_plot,TimeMap-method	Man page
allElementsAreOfClass	Source code
apply_to_state_vec_and_time	Source code
arrFuncMaker	Source code
as.character,TimeMap-method	Man page
as.numeric,InFluxList_by_PoolName-method	Man page
as.numeric,InternalFluxList_by_PoolName-method	Man page
as.numeric,InternalFlux_by_PoolName-method	Man page
as.numeric,OutFluxList_by_PoolName-method	Man page
availableParticleProperties	Man page
availableParticleProperties,MCSim-method	Man page
availableParticleSets	Man page
availableParticleSets,MCSim-method	Man page
availableResidentSets	Man page
availableResidentSets,MCSim-method	Man page
bacwaveModel	Man page
bind.C14curves	Man page
by_PoolIndex	Man page
by_PoolIndex,ConstantInFluxRate_by_PoolName,ANY,ANY-method	Man page
by_PoolIndex,ConstantInternalFluxRateList_by_PoolName,ANY,ANY-me	Man page
by_PoolIndex,ConstantInternalFluxRate_by_PoolName,ANY,ANY-method	Man page
by_PoolIndex,ConstantOutFluxRateList_by_PoolName,ANY,ANY-method	Man page
by_PoolIndex,ConstantOutFluxRate_by_PoolName,ANY,ANY-method	Man page
by_PoolIndex,InFluxList_by_PoolName,character,character-method	Man page
by_PoolIndex,InFlux_by_PoolName,character,character-method	Man page
by_PoolIndex,InternalFluxList_by_PoolName,character,character-me	Man page
by_PoolIndex,InternalFlux_by_PoolName,character,character-method	Man page
by_PoolIndex,OutFluxList_by_PoolName,character,character-method	Man page
by_PoolIndex,OutFlux_by_PoolName,character,character-method	Man page
by_PoolIndex,PoolConnection_by_PoolName,ANY,ANY-method	Man page
by_PoolIndex,function,character,character-method	Man page
by_PoolName	Man page
by_PoolName,ConstantInFluxList_by_PoolIndex-method	Man page
by_PoolName,ConstantInFluxRate_by_PoolIndex-method	Man page
by_PoolName,ConstantInFlux_by_PoolIndex-method	Man page
by_PoolName,ConstantInternalFluxRateList_by_PoolIndex-method	Man page
by_PoolName,ConstantOutFluxRateList_by_PoolIndex-method	Man page
by_PoolName,ConstantOutFluxRate_by_PoolIndex-method	Man page
checkTargetClassOfElements	Source code
check_duplicate_pool_names	Man page Source code
check_id_length	Man page Source code
check_pool_ids	Man page
check_pool_ids,PoolConnection_by_PoolIndex,integer-method	Man page
computeResults	Man page
computeResults,MCSim-method	Man page
correctnessOfBoundDecompOp	Source code
correctnessOfModel	Source code
correctnessOfModel_by_PoolNames	Source code
cycling	Man page
deSolve.lsoda.wrapper	Man page Source code
eCO2	Man page
entropyRatePerJump	Man page Source code
entropyRatePerTime	Man page Source code
errorPlotC	Source code
euler	Man page
example.2DBoundInFluxesFromFunction	Man page
example.2DBoundLinDecompOpFromFunction	Man page
example.2DConstFc.Args	Man page
example.2DConstInFluxesFromVector	Man page
example.2DGeneralDecompOpArgs	Man page Source code
example.2DInFluxes.Args	Man page Source code
example.2DUnBoundLinDecompOpFromFunction	Man page
example.ConstlinDecompOpFromMatrix	Man page Source code
example.Time2DArrayList	Man page
example.Time3DArrayList	Man page
example.TimeMapFromArray	Man page
example.nestedTime2DMatrixList	Man page
fT.Arrhenius	Man page
fT.Century1	Man page
fT.Century2	Man page
fT.Daycent1	Man page
fT.Daycent2	Man page
fT.Demeter	Man page
fT.KB	Man page
fT.LandT	Man page
fT.Q10	Man page
fT.RothC	Man page
fT.Standcarb	Man page
fT.linear	Man page
fW.Candy	Man page
fW.Century	Man page
fW.Daycent1	Man page
fW.Daycent2	Man page
fW.Demeter	Man page
fW.Gompertz	Man page
fW.Moyano	Man page
fW.RothC	Man page
fW.Skopp	Man page
fW.Standcarb	Man page
flat_arr_TimeMap	Source code
fromToSplitter	Source code
from_integer_flux_lists_with_defaults	Man page Source code
getAccumulatedRelease	Man page
getAccumulatedRelease,Model-method	Man page
getC	Man page
getC,Model-method	Man page
getC,Model_by_PoolNames-method	Man page
getC,NlModel-method	Man page
getC14	Man page
getC14,Model_14-method	Man page
getCompartmentalMatrixFunc	Man page
getCompartmentalMatrixFunc,BoundLinDecompOp-method	Man page
getCompartmentalMatrixFunc,ConstLinDecompOp-method	Man page
getCompartmentalMatrixFunc,TransportDecompositionOperator-method	Man page
getCompartmentalMatrixFunc,UnBoundNonLinDecompOp-method	Man page
getConstLinDecompOp	Man page
getConstLinDecompOp,ConstLinDecompOpWithLinearScalarFactor-metho	Man page
getConstantCompartmentalMatrix	Man page
getConstantCompartmentalMatrix,ConstLinDecompOp-method	Man page
getConstantCompartmentalMatrix,ConstLinDecompOpWithLinearScalarF	Man page
getConstantInFluxVector	Man page
getConstantInFluxVector,ConstInFluxes-method	Man page
getConstantInternalFluxRateList_by_PoolIndex	Man page
getConstantInternalFluxRateList_by_PoolIndex,ConstLinDecompOp-me	Man page
getConstantOutFluxRateList_by_PoolIndex	Man page
getConstantOutFluxRateList_by_PoolIndex,ConstLinDecompOp-method	Man page
getCumulativeC	Man page
getCumulativeC,NlModel-method	Man page
getDecompOp	Man page
getDecompOp,Model-method	Man page
getDecompOp,NlModel-method	Man page
getDotOut	Man page
getDotOut,TransportDecompositionOperator-method	Man page
getF14	Man page
getF14,Model_14-method	Man page
getF14C	Man page
getF14C,Model_14-method	Man page
getF14R	Man page
getF14R,Model_14-method	Man page
getFormat	Man page
getFormat,Fc-method	Man page
getFunctionDefinition	Man page
getFunctionDefinition,ConstInFluxes-method	Man page
getFunctionDefinition,ConstLinDecompOp-method	Man page
getFunctionDefinition,ConstLinDecompOpWithLinearScalarFactor-met	Man page
getFunctionDefinition,DecompositionOperator-method	Man page
getFunctionDefinition,InFluxList_by_PoolIndex-method	Man page
getFunctionDefinition,InFluxList_by_PoolName-method	Man page
getFunctionDefinition,StateDependentInFluxVector-method	Man page
getFunctionDefinition,TimeMap-method	Man page
getFunctionDefinition,TransportDecompositionOperator-method	Man page
getFunctionDefinition,UnBoundInFluxes-method	Man page
getFunctionDefinition,UnBoundLinDecompOp-method	Man page
getInFluxes	Man page
getInFluxes,Model-method	Man page
getInFluxes,NlModel-method	Man page
getInitialValues	Man page
getInitialValues,NlModel-method	Man page
getLinearScaleFactor	Man page
getLinearScaleFactor,ConstLinDecompOpWithLinearScalarFactor-meth	Man page
getMeanTransitTime	Man page
getMeanTransitTime,ConstLinDecompOp-method	Man page
getNumberOfPools	Man page
getNumberOfPools,MCSim-method	Man page
getNumberOfPools,NlModel-method	Man page
getNumberOfPools,TransportDecompositionOperator-method	Man page
getOutputFluxes	Man page
getOutputFluxes,NlModel-method	Man page
getOutputReceivers	Man page
getOutputReceivers,TransportDecompositionOperator,numeric-method	Man page
getParticleMonteCarloSimulator	Man page
getParticleMonteCarloSimulator,NlModel-method	Man page
getRecipient	Source code Source code
getRecipientIndex	Source code
getRecipientName	Source code
getReleaseFlux	Man page
getReleaseFlux,Model-method	Man page
getReleaseFlux,Model_by_PoolNames-method	Man page
getReleaseFlux,NlModel-method	Man page
getReleaseFlux14	Man page
getReleaseFlux14,Model_14-method	Man page
getRightHandSideOfODE	Man page
getRightHandSideOfODE,Model-method	Man page
getRightHandSideOfODE,Model_by_PoolNames-method	Man page
getSender	Source code Source code
getSenderIndex	Source code
getSenderName	Source code
getSingleCol	Source code
getSolution	Man page
getSolution,Model_by_PoolNames-method	Man page
getTimeRange	Man page
getTimeRange,ConstInFluxes-method	Man page
getTimeRange,ConstLinDecompOp-method	Man page
getTimeRange,ConstLinDecompOpWithLinearScalarFactor-method	Man page
getTimeRange,DecompositionOperator-method	Man page
getTimeRange,TimeMap-method	Man page
getTimeRange,UnBoundInFluxes-method	Man page
getTimeRange,UnBoundLinDecompOp-method	Man page
getTimes	Man page
getTimes,Model-method	Man page
getTimes,Model_by_PoolNames-method	Man page
getTimes,NlModel-method	Man page
getTransferCoefficients	Man page
getTransferCoefficients,NlModel-method	Man page
getTransferCoefficients,TransportDecompositionOperator-method	Man page
getTransferMatrix	Man page Source code
getTransferMatrixFunc	Man page
getTransferMatrixFunc,TransportDecompositionOperator-method	Man page
getTransitTimeDistributionDensity	Man page
getTransitTimeDistributionDensity,ConstLinDecompOp-method	Man page
getValues	Man page
getValues,ConstFc-method	Man page
incubation_experiment	Man page
initialize,ConstLinDecompOp-method	Man page
initialize,DecompositionOperator-method	Man page
initialize,MCSim-method	Man page
initialize,Model-method	Man page
initialize,Model_14-method	Man page
initialize,Model_by_PoolNames-method	Man page
initialize,NlModel-method	Man page
initialize,TimeMap-method	Man page
initialize,TransportDecompositionOperator-method	Man page
initialize,UnBoundInFluxes-method	Man page
initialize,UnBoundLinDecompOp-method	Man page
is.negative	Source code Source code
key	Source code
leaveKey	Source code
linearScalarModel	Man page
linesCPool	Man page
listProduct	Man page
listProduct_append	Source code
listProduct_append_2D	Source code
makeListInstance	Source code
makelink	Source code
no_outflux_warning	Man page Source code
non_zero_rates	Source code
pathEntropy	Man page Source code
pe	Source code
plot,MCSim-method	Man page
plot,Model-method	Man page
plot,Model_by_PoolNames-method	Man page
plot,NlModel-method	Man page
plot,TimeMap-method	Man page
plotAll	Source code
plotC14Pool	Man page
plotCPool	Man page
plotCoordSystem	Source code
plotPoolGraph	Man page
plotPoolGraph,SymbolicModel_by_PoolNames-method	Man page
plotPoolGraphFromTupleLists	Man page Source code
plotTrajectories	Source code
pp	Source code
predefinedModels	Man page
print,NlModel-method	Man page
res2fun	Source code
rightArrowSplitter	Source code
scalarFuncMaker	Source code
show,NlModel-method	Man page
spectralNorm	Source code
src_to_dest_parts	Source code
src_to_dest_string	Source code
state_variable_names	Man page
stockKey	Source code
systemAge	Man page
transitTime	Man page
tupelize	Source code
tupels	Source code
turnoverFit	Man page
ydot_maker	Source code