Models of Soil Organic Matter Decomposition

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Documentation for package ‘SoilR’ version 1.2.107

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A B C D E F G H I L M N O P R S T U Y misc

SoilR-package SoilR

-- A --

AbsoluteFractionModern Conversion of radiocarbon values
AbsoluteFractionModern-method automatic title
AbsoluteFractionModern-method automatic title
AbsoluteFractionModern_from_Delta14C Conversion of radiocarbon values
AbsoluteFractionModern_from_Delta14C-method Conversion of radiocarbon values
AbsoluteFractionModern_from_Delta14C-method Conversion of radiocarbon values, from Delta14C to absolute fraction modern
add_plot Add elements to plot
add_plot-method automatic title
as.character-method automatic title
as.numeric-method Convert to a numeric vector with the pool names as names
as.numeric-method Convert to a numeric vector with names of the form 'a->b'
as.numeric-method Convert to a numeric value with name of the form 'a->b'
as.numeric-method Convert to a numeric vector with the pool names as names
availableParticleProperties Available particle properties
availableParticleProperties-method automatic title
availableParticleSets Available particle sets
availableParticleSets-method automatic title
availableResidentSets Available resident sets
availableResidentSets-method automatic title
AWBmodel Implementation of the microbial model AWB (Allison, Wallenstein, Bradford, 2010)

-- B --

bacwaveModel Implementation of the microbial model Bacwave (bacterial waves)
bind.C14curves Binding of pre- and post-bomb Delta14C curves
BoundFc Bound Fc object
BoundFc-class S4-class to represent atmospheric 14C concentration as scalar function of time.
BoundFc-method automatic title
BoundFc-method automatic title
BoundInFluxes constructor for BoundInFluxes
BoundInFluxes-class automatic title
BoundLinDecompOp Generic constructor for the class with the same name
BoundLinDecompOp-class A S4 class to represent a linear compartmental operator defined on time interval
BoundLinDecompOp-method Creates an object of class BoundLinDecompOp
BoundLinDecompOp-method A converter
by_PoolIndex automatic title
by_PoolIndex-method new object with the source pool id converted to a PoolIndex if necessary
by_PoolIndex-method convert to a list indexed by pool names
by_PoolIndex-method new object with the source pool id converted to a PoolName if necessary
by_PoolIndex-method convert to a list indexed by pool names
by_PoolIndex-method new object with the source pool id converted to a PoolIndex if necessary
by_PoolIndex-method Transform pool names to indices
by_PoolIndex-method Convert the pool names to indices
by_PoolIndex-method automatic title
by_PoolIndex-method automatic title
by_PoolIndex-method automatic title
by_PoolIndex-method automatic title
by_PoolIndex-method constructor from strings of the form 'x->y' new object with the source pool id and the destination pool id guaranteed to be of class PoolIndex
by_PoolIndex-method convert a function f of to f_vec
by_PoolName automatic title
by_PoolName-method convert to a list indexed by pool names
by_PoolName-method new object with the source pool id converted to a PoolIndex if necessary
by_PoolName-method new object with the source pool id converted to a PoolIndex if necessary
by_PoolName-method convert to a list indexed by pool names
by_PoolName-method convert to a list indexed by pool names
by_PoolName-method new object with the source pool id converted to a PoolName if necessary

-- C --

C14Atm Atmospheric 14C fraction
C14Atm_NH Post-bomb atmospheric 14C fraction
CenturyModel Implementation of the Century model
CenturyModel14 Implementation of a radiocarbon version of the Century model
check_duplicate_pool_names helper function
check_id_length helper function to check that the length of the argument is exactly 1
check_pool_ids Check pool ids
check_pool_ids-method automatic title
computeResults Computes results
computeResults-method automatic title
ConstantInFluxList_by_PoolIndex Generic constructor for the class with the same name
ConstantInFluxList_by_PoolIndex-class Subclass of list that is guaranteed to contain only elements of type ConstantInFlux_by_PoolIndex
ConstantInFluxList_by_PoolIndex-method constructor from ConstInFluxes
ConstantInFluxList_by_PoolIndex-method constructor from a normal list
ConstantInFluxList_by_PoolIndex-method constructor from numeric vector
ConstantInFluxList_by_PoolName Generic constructor for the class with the same name
ConstantInFluxList_by_PoolName-class Subclass of list that is guaranteed to contain only elements of type ConstantInFlux_by_PoolName
ConstantInFluxRate_by_PoolIndex-class Describes a flux rates.
ConstantInFluxRate_by_PoolName Constructor for the class with the same name
ConstantInFluxRate_by_PoolName-class Describes a flux rates.
ConstantInFlux_by_PoolIndex-class class for a constant influx to a single pool identified by index
ConstantInFlux_by_PoolName-class class for a constant influx to a single pool identified by pool name
ConstantInternalFluxRateList_by_PoolIndex Generic constructor for the class with the same name
ConstantInternalFluxRateList_by_PoolIndex-class Describes a list of flux rates.
ConstantInternalFluxRateList_by_PoolIndex-method constructor from a normal list
ConstantInternalFluxRateList_by_PoolIndex-method automatic title
ConstantInternalFluxRateList_by_PoolName Generic constructor for the class with the same name
ConstantInternalFluxRateList_by_PoolName-class Describes a list of flux rates.
ConstantInternalFluxRateList_by_PoolName-method Constructor from a normal list of fluxes
ConstantInternalFluxRate_by_PoolIndex Generic constructor for the class with the same name
ConstantInternalFluxRate_by_PoolIndex-class S4 class representing a constant internal flux rate
ConstantInternalFluxRate_by_PoolIndex-method automatic title
ConstantInternalFluxRate_by_PoolName Generic constructor for the class with the same name
ConstantInternalFluxRate_by_PoolName-class S4-class to represent a constant internal flux rate with source and target indexed by name
ConstantInternalFluxRate_by_PoolName-method constructor with argument conversion
ConstantInternalFluxRate_by_PoolName-method constructor from strings of the form 'a->b'
ConstantOutFluxRateList_by_PoolIndex Generic constructor for the class with the same name
ConstantOutFluxRateList_by_PoolIndex-class Describes a list of flux rates.
ConstantOutFluxRateList_by_PoolIndex-method constructor from a normal list
ConstantOutFluxRateList_by_PoolIndex-method automatic title
ConstantOutFluxRateList_by_PoolName Generic constructor for the class with the same name
ConstantOutFluxRateList_by_PoolName-class Describes a list of flux rates.
ConstantOutFluxRateList_by_PoolName-method constructor from a normal list
ConstantOutFluxRateList_by_PoolName-method automatic title
ConstantOutFluxRate_by_PoolIndex Generic constructor for the class with the same name
ConstantOutFluxRate_by_PoolIndex-class S4 Class to represent a single constant out-flux rate with the source pool specified by an index
ConstantOutFluxRate_by_PoolIndex-method automatic title
ConstantOutFluxRate_by_PoolName-class S4 Class to represent a single constant out-flux rate with the source pool specified by name
ConstFc creates an object containing the initial values for the 14C fraction needed to create models in SoilR
ConstFc-class S4 class representing a constant 14C fraction
ConstInFluxes Constant input fluxes
ConstInFluxes-class S4 class for a constant influx vector
ConstInFluxes-method automatic title
ConstInFluxes-method automatic title
ConstLinDecompOp Generic constructor for the class with the same name
ConstLinDecompOp-class A class to represent a constant (=nonautonomous,linear) compartmental matrix or equivalently a combination of ordered constant internal flux rates and constant out flux rates.
ConstLinDecompOp-method Constructor of object of ConstLinDecompOp class
ConstLinDecompOpWithLinearScalarFactor Generic constructor for the class with the same name
ConstLinDecompOpWithLinearScalarFactor-class A class to represent a constant (=nonautonomous,linear) compartmental matrix with a time dependent (linear) scalar pre factor This is a special case of a linear compartmental operator/matrix
ConstLinDecompOp_by_PoolName Generic constructor for the class with the same name
cycling Cycling analysis of compartmental matrices

-- D --

DecompOp-class S4-class to represent compartmental operators
DecompositionOperator-class automatic title
Delta14C Conversion of radiocarbon values
Delta14C-method automatic title
Delta14C-method automatic title
Delta14C_from_AbsoluteFractionModern Conversion of radiocarbon values
Delta14C_from_AbsoluteFractionModern-method Conversion of radiocarbon values
Delta14C_from_AbsoluteFractionModern-method Conversion of radiocarbon values
deSolve.lsoda.wrapper deSolve.lsoda.wrapper

-- E --

eCO2 Soil CO2 efflux from an incubation experiment
entropyRatePerJump Entropy rate per jump
entropyRatePerTime Entropy rate per time
euler euler
example.2DBoundInFluxesFromFunction example.2DBoundInFluxesFromFunction
example.2DBoundLinDecompOpFromFunction example.2DBoundLinDecompOpFromFunction
example.2DConstFc.Args example.2DConstFc.Args
example.2DConstInFluxesFromVector 2D example for constant Influx
example.2DGeneralDecompOpArgs example.2DGeneralDecompOpArgs
example.2DInFluxes.Args example.2DInFluxes.Args
example.2DUnBoundLinDecompOpFromFunction example.2DUnBoundLinDecompOpFromFunction
example.ConstlinDecompOpFromMatrix example.ConstlinDecompOpFromMatrix
example.nestedTime2DMatrixList create an example nested list that can be
example.Time2DArrayList create an example TimeMap from 2D array
example.Time3DArrayList create an example TimeFrame from 3D array
example.TimeMapFromArray create an example TimeFrame from 3D array

-- F --

Fc-class automatic title
FcAtm.from.Dataframe FcAtm.from.Dataframe
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
GeneralDecompOp A generic factory for subclasses of GeneralDecompOp
GeneralDecompOp-method Pass through factory for objects of subclasses of DecompOp
GeneralDecompOp-method automatic title
GeneralDecompOp-method automatic title
GeneralDecompOp-method automatic title
GeneralDecompOp-method automatic title
GeneralModel additional function to create Models
GeneralModel_14 create objects of class Model_14
GeneralNlModel Use this function to create objects of class NlModel.
GeneralPoolId General pool Id
GeneralPoolId-method automatic title
GeneralPoolId-method generic factory for this virtual class
getAccumulatedRelease Accumulated release flux out of the pools
getAccumulatedRelease-method Compute the time integral of the relaese fluxes over time
getC Calculates the content of the pools
getC-method Pool Contents for all times
getC-method Pool Contents for all times
getC-method Pool Contents for all times
getC14 Generic that yields the 14C content for all pools and all times
getC14-method automatic title
getCompartmentalMatrixFunc Compartmental matrix function
getCompartmentalMatrixFunc-method automatic title
getCompartmentalMatrixFunc-method Compartmental matrix function
getCompartmentalMatrixFunc-method automatic title
getCompartmentalMatrixFunc-method Extract the matrix valued function of time and state vector for the compartmental matrix
getConstantCompartmentalMatrix Constant compartmental matrix
getConstantCompartmentalMatrix-method Constant compartmental matrix
getConstantCompartmentalMatrix-method automatic title
getConstantInFluxVector Input flux vector
getConstantInFluxVector-method automatic title
getConstantInternalFluxRateList_by_PoolIndex Constant internal flux rate list by pool index
getConstantInternalFluxRateList_by_PoolIndex-method Constant internal flux rate list by pool index
getConstantOutFluxRateList_by_PoolIndex Constant out flux rate list by pool index
getConstantOutFluxRateList_by_PoolIndex-method Constant out flux rate list by pool index
getConstLinDecompOp Constant linear decomposition operator
getConstLinDecompOp-method automatic title
getCumulativeC Cummulative pool contents
getCumulativeC-method automatic title
getDecompOp Decomposition operator of a model
getDecompOp-method Extract the Compartmental Operator
getDecompOp-method Extract the Compartmental Operator
getDotOut Dot out
getDotOut-method automatic title
getF14 Generic that yields the 14C fraction for the content all pools and all times
getF14-method automatic title
getF14C Generic that yields the 14C fraction for the cumulative content of all pools and all times
getF14C-method automatic title
getF14R Generic that yields the 14C fraction for the release flux of all pools and all times
getF14R-method automatic title
getFormat Get format of SoilR object
getFormat-method automatic title
getFunctionDefinition Function definition of SoilR model
getFunctionDefinition-method automatic title
getFunctionDefinition-method Function describing an object of class ConstLinDecompOp
getFunctionDefinition-method convert names of vectors or lists to class ConstantOutFluxRate convert names of vectors or lists to class ConstantInternalFluxRate helper function
getFunctionDefinition-method automatic title
getFunctionDefinition-method automatic title
getFunctionDefinition-method automatic title
getFunctionDefinition-method automatic title
getFunctionDefinition-method automatic title
getFunctionDefinition-method automatic title
getFunctionDefinition-method automatic title
getFunctionDefinition-method Extracts the time dependent matrix valued function (compartmental matrix)
getInFluxes Extract the influxes
getInFluxes-method Extract the InFluxes as provided during creation of the model
getInFluxes-method automatic title
getInitialValues Initial values of SoilR object
getInitialValues-method automatic title
getLinearScaleFactor Linear scale factor
getLinearScaleFactor-method automatic title
getMeanTransitTime Mean transit time for SoilR objects
getMeanTransitTime-method Mean transit time obtained through a numerical simulation. It produces an estimate with numerical errors. We recommend to use the function transitTime instead.
getNumberOfPools Number of pools in a model
getNumberOfPools-method automatic title
getNumberOfPools-method automatic title
getNumberOfPools-method automatic title
getOutputFluxes Generic Function to obtain the fluxes out of of the pools
getOutputFluxes-method automatic title
getOutputReceivers Pools receiving outputs from other pools
getOutputReceivers-method automatic title
getParticleMonteCarloSimulator automatic title
getParticleMonteCarloSimulator-method automatic title
getReleaseFlux Generic Function to obtain the vector of release fluxes out of the pools for all times.
getReleaseFlux-method The release fluxes [content]/[time] for all pools.
getReleaseFlux-method automatic title
getReleaseFlux-method automatic title
getReleaseFlux14 Generic that yields the 14C fraction in the release flux
getReleaseFlux14-method automatic title
getRightHandSideOfODE Right hand side of ODE of a SoilR model
getRightHandSideOfODE-method Derivative of the state variables as function
getRightHandSideOfODE-method Provide the (vector valued) derivative of the stocks with respect to time
getSolution Calculates all stocks all fluxes to ,in and out of the compartment system and also their integrals over time
getSolution-method All Fluxes and stocks for all times
getTimeRange Time range of a model simulation
getTimeRange-method automatic title
getTimeRange-method Time range of a simulation described in an object of class ConstLinDecompOp
getTimeRange-method automatic title
getTimeRange-method automatic title
getTimeRange-method The time interval where the function is defined
getTimeRange-method automatic title
getTimeRange-method Extracts the time interval for which the function is valid.
getTimes Time vector of SoilR object
getTimes-method Extract the times vector
getTimes-method Extract the times vector
getTimes-method automatic title
getTransferCoefficients Transfer coefficients
getTransferCoefficients-method automatic title
getTransferCoefficients-method automatic title
getTransferMatrix deprecated, use getTransferMatrixFunc instead
getTransferMatrixFunc Transfer matrix function
getTransferMatrixFunc-method automatic title
getTransitTimeDistributionDensity Transit time distribution for SoilR objects
getTransitTimeDistributionDensity-method Transit time distribution obtained through a numerical simulation. It introduces numerical errors. We recommend to use the function transitTime instead
getValues Get values of SoilR object
getValues-method automatic title
Graven2017 Compiled records of radicarbon in atmospheric CO2 for historical simulations in CMIP6

-- H --

HarvardForest14CO2 Delta14C in soil CO2 efflux from Harvard Forest
Hua2013 Atmospheric radiocarbon for the period 1950-2010 from Hua et al. (2013)
Hua2021 Atmospheric radiocarbon for the period 1950-2019 from Hua et al. (2021)

-- I --

ICBMModel Implementation of the Introductory Carbon Balance Model (ICBM)
ICBM_N Implementation of the ICBM/N model
incubation_experiment Soil CO2 efflux from an incubation experiment, along with the soil mass and carbon concentration measurements.
InFlux Generic constructor for the class with the same name
InFluxes A generic factory for subclasses of InFluxes
InFluxes-class A virtual S4-class representing (different subclasses) of in-fluxes to the system
InFluxes-method automatic title
InFluxes-method automatic title
InFluxes-method automatic title
InFluxes-method automatic title
InFluxes-method automatic title
InFluxes-method automatic title
InFluxes-method automatic title
InFluxList_by_PoolIndex Generic constructor for the class with the same name
InFluxList_by_PoolIndex-class Describes a list of flux rates.
InFluxList_by_PoolIndex-method constructor from a normal list after checking the elements
InFluxList_by_PoolName Generic constructor for the class with the same name
InFluxList_by_PoolName-class Class for a list of influxes indexed by the names of the target pools
InFluxList_by_PoolName-method constructor from a normal list
InFlux_by_PoolIndex Generic constructor for the class with the same name
InFlux_by_PoolIndex-class S4 class for the influx to a single pool identified by the index
InFlux_by_PoolIndex-method Constructor from an ordered pair of PoolIndex (integer like) objects
InFlux_by_PoolName Generic constructor for an influx to a single pool from an ordered pair of PoolName (string like) and function objects
InFlux_by_PoolName-class S4 class for the influx to a single pool identified by the name
InFlux_by_PoolName-method Constructor from an ordered pair of PoolName (string like) and function objects
initialize-method automatic title
initialize-method automatic title
initialize-method automatic title
initialize-method Internal method to supervise creation of objects of this class
initialize-method Internal method to supervise creation of objects of this class
initialize-method automatic title
initialize-method automatic title
initialize-method automatic title
initialize-method automatic title
initialize-method automatic title
initialize-method automatic title
IntCal09 Northern Hemisphere atmospheric radiocarbon for the pre-bomb period
IntCal13 Atmospheric radiocarbon for the 0-50,000 yr BP period
IntCal20 The IntCal20 northern hemisphere radiocarbon curve for the 0-55,000 yr BP period
InternalFluxList_by_PoolIndex Generic constructor for the class with the same name
InternalFluxList_by_PoolIndex-class S4-class for a list of internal fluxes with source and destination pool inidices
InternalFluxList_by_PoolIndex-method Constructor from a normal list after checking the elements
InternalFluxList_by_PoolName Generic constructor for the class with the same name
InternalFluxList_by_PoolName-class S4-class for a list of internal fluxes with indexed by (source and destination pool) names
InternalFluxList_by_PoolName-method constructor from a normal list
InternalFlux_by_PoolIndex Generic constructor for the class with the same name
InternalFlux_by_PoolIndex-class S4-class for a single internal flux with source and destination pools specified by indices
InternalFlux_by_PoolIndex-method constructor from an ordered pair of PoolIndex (integer like) objects and a function with vector argument
InternalFlux_by_PoolName Generic constructor for the class with the same name
InternalFlux_by_PoolName-class S4-class for a single internal flux with source and destination pools specified by name
InternalFlux_by_PoolName-method constructor from an ordered pair of PoolName (string like) objects and a function with the set of formal argument names forming a subset of the state_variable_names
InternalFlux_by_PoolName-method automatic title

-- L --

linearScalarModel Implementation of a general model for linear non-autonomous systems with scalar modifiers
linesCPool Add lines with the output of 'getC14', 'getC', or 'getReleaseFlux' to an existing plot
listProduct tensor product of lists

-- M --

MCSim-class Experimental Class for a Monte Carlo Simulation of particles leaving the pool
Model Constructor for class Model
Model-class S4 class representing a model run
Model_14 general constructor for class Model_14
Model_14-class S4-class to represent a 14C model run
Model_by_PoolNames Constructor for 'Model_by_PoolNames'
Model_by_PoolNames-class A model run based on flux functions

-- N --

NlModel-class deprecated class for a non-linear model run.

-- O --

OnepModel Implementation of a one pool model
OnepModel14 Implementation of a one-pool C14 model
OutFlux Generic constructor for the class with the same name
OutFluxList_by_PoolIndex Generic constructor for the class with the same name
OutFluxList_by_PoolIndex-class A list of outfluxes
OutFluxList_by_PoolIndex-method constructor from a normal list
OutFluxList_by_PoolName Generic constructor for the class with the same name
OutFluxList_by_PoolName-class S4 class for a list of out-fluxes indexed by source pool name
OutFluxList_by_PoolName-method constructor from a normal list
OutFlux_by_PoolIndex Generic constructor for the class with the same name
OutFlux_by_PoolIndex-class S4 class for a single out-flux with source pool index
OutFlux_by_PoolIndex-method constructor from a PoolIndex (integer like) objects and a function with vector argument
OutFlux_by_PoolName Generic constructor for the class with the same name
OutFlux_by_PoolName-class S4 class for a single out-flux with source pool name
OutFlux_by_PoolName-method constructor from a PoolName (integer like) object and a function

-- P --

ParallelModel models for unconnected pools
pathEntropy Path Entropy
plot-method automatic title
plot-method Create an overview plot
plot-method Plot the graph of pool connections
plot-method automatic title
plot-method automatic title
plotC14Pool Plots the output of 'getF14' for each pool over time
plotCPool Plots the output of 'getC' or 'getReleaseFlux' for each pool over time
plotPoolGraph Generic plotter
plotPoolGraph-method Plot the graph of pool connections
plotPoolGraphFromTupleLists Helper function to draw connectivity graphs
PoolConnection_by_PoolIndex Pool connection by pool index
PoolConnection_by_PoolIndex-class Objects that have a source and a destination described by integer like objects ( of class PoolIndex)
PoolConnection_by_PoolIndex-method constructor from an ordered pair of PoolId objects
PoolConnection_by_PoolIndex-method constructor from strings of the form '1_to_2'
PoolConnection_by_PoolName Pool connection by pool name
PoolConnection_by_PoolName-class Objects that have a source and a destination determined by a string like object of class PoolName
PoolConnection_by_PoolName-method constructor from an ordered pair of PoolName objects
PoolId-class common class for pool ids
PoolIndex Pool index
PoolIndex-class S4 class for pool indices
PoolIndex-method pass through constructor fron an object of the same class
PoolIndex-method convert to number like object
PoolIndex-method construct from number string like '1' or '3'
PoolIndex-method construct from number
PoolName Pool name
PoolName-class class for pool-name-strings
PoolName-method convert to string like object
PoolName-method pass through constructor fron an object of the same class
PoolName-method construct from string with checks
predefinedModels PREDEFINED MODELS
print-method automatic title

-- R --

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

-- S --

ScalarTimeMap Constructor for 'ScalarTimeMap-class'
ScalarTimeMap-class S4 class for a scalar time dependent function on a finite time interval
ScalarTimeMap-method constructor for data given as 2 column data.frame
ScalarTimeMap-method manual constructor for just a function
ScalarTimeMap-method manual constructor for a function and an interval
ScalarTimeMap-method special case for a time map from a constant
ScalarTimeMap-method constructor for data and times given as vectors
SeriesLinearModel General m-pool linear model with series structure
SeriesLinearModel14 General m-pool linear C14 model with series structure
SHCal20 The SHCal20 southern hemisphere radiocarbon curve for the 0-55,000 yr BP period
show-method automatic title
SoilR.F0.new deprecated function that used to create an object of class SoilR.F0
StateDependentInFluxVector Input vector that is a function of the pool contenst and time
StateDependentInFluxVector-class Input vector that is a function of the pool contenst and time
StateIndependentInFluxList_by_PoolIndex Generic constructor for the class with the same name
StateIndependentInFluxList_by_PoolIndex-class Subclass of list that is guaranteed to contain only elements of type StateIndependentInFlux_by_PoolIndex
StateIndependentInFluxList_by_PoolIndex-method constructor from a normal list
StateIndependentInFluxList_by_PoolName Generic constructor for the class with the same name
StateIndependentInFlux_by_PoolIndex Constructor for the class with the same name
StateIndependentInFlux_by_PoolIndex-class Constructor for the class with the same name
state_variable_names determine the minimum set of statevariables
SymbolicModel_by_PoolNames A symbolic model description based on flux functions
SymbolicModel_by_PoolNames-class A symbolic model description based on flux functions
systemAge System and pool age for constant compartment models

-- 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 Constructor for 'TimeMap-class'
TimeMap-class S4 class for a time dependent function
TimeMap-method automatic title
TimeMap-method automatic title
TimeMap-method manual constructor for just a function
TimeMap-method manual constructor for a function and an interval
TimeMap-method automatic title
TimeMap-method automatic title
TimeMap-method automatic title
TimeMap-method automatic title
TimeMap-method automatic title
TimeMap.from.Dataframe TimeMap.from.Dataframe
TimeMap.new deprecated constructor of the class TimeMap.
TimeRangeIntersection The time interval where both functions are defined
transitTime Transit times for compartment models
TransportDecompositionOperator-class automatic title
turnoverFit Estimation of the turnover time from a 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 linear 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

-- U --

UnBoundInFluxes Unbound input fluxes
UnBoundInFluxes-class automatic title
UnBoundInFluxes-method automatic title
UnBoundLinDecompOp Generic constructor for the class with the same name
UnBoundLinDecompOp-class An S4 class to represent a linear nonautonomous compartmental matrix
UnBoundLinDecompOp-method Generic constructor for the class with the same name
UnBoundNonLinDecompOp Generic constructor for the class with the same name
UnBoundNonLinDecompOp-class An S4 class to represent a nonlinear nonautonomous compartmental matrix
UnBoundNonLinDecompOp-method Constructor for the class with the same name
UnBoundNonLinDecompOp-method Constructor for the class with the same name
UnBoundNonLinDecompOp_by_PoolNames Generic constructor for the class with the same name
UnBoundNonLinDecompOp_by_PoolNames-class An S4 class to represent the of nonlinear nonautonomous compartmental system independently of the order of state variables

-- Y --

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

-- misc --

$-method automatic title
[-method Experimentally overloaded index operator
[-method automatic title
[[-method automatic title
[[<--method automatic title