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SoilR (version 1.2.107)

Models of Soil Organic Matter Decomposition

Description

Functions for modeling Soil Organic Matter decomposition in terrestrial ecosystems with linear and nonlinear systems of differential equations. The package implements models according to the compartmental system representation described in Sierra and others (2012) and Sierra and others (2014) .

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Install

install.packages('SoilR')

Monthly Downloads

355

Version

1.2.107

License

GPL-3

Maintainer

Carlos Sierra

Last Published

October 13th, 2023

Functions in SoilR (1.2.107)

BoundFc,character-method

automatic title
BoundFc-class

S4-class to represent atmospheric 14C concentration as scalar function of time.
BoundFc,missing-method

automatic title
AbsoluteFractionModern,BoundFc-method

automatic title
C14Atm_NH

Post-bomb atmospheric 14C fraction
ConstFc-class

S4 class representing a constant 14C fraction
AbsoluteFractionModern_from_Delta14C,matrix-method

Conversion of radiocarbon values
ConstInFluxes,ConstantInFluxList_by_PoolIndex,numeric-method

automatic title
AbsoluteFractionModern_from_Delta14C,numeric-method

Conversion of radiocarbon values, from Delta14C to absolute fraction modern
BoundLinDecompOp

Generic constructor for the class with the same name
BoundInFluxes

constructor for BoundInFluxes
BoundLinDecompOp,UnBoundLinDecompOp-method

A converter
BoundLinDecompOp-class

A S4 class to represent a linear compartmental operator defined on time interval
ConstInFluxes-class

S4 class for a constant influx vector
BoundLinDecompOp,ANY-method

Creates an object of class BoundLinDecompOp
ConstantInFluxRate_by_PoolName

Constructor for the class with the same name
ConstLinDecompOp,matrix,missing,missing,missing,missing-method

Constructor of object of ConstLinDecompOp class
C14Atm

Atmospheric 14C fraction
ConstInFluxes,numeric,ANY-method

automatic title
CenturyModel

Implementation of the Century model
Delta14C_from_AbsoluteFractionModern,matrix-method

Conversion of radiocarbon values
ConstFc

creates an object containing the initial values for the 14C fraction needed to create models in SoilR
ConstantInternalFluxRateList_by_PoolIndex,list-method

constructor from a normal list
InFluxList_by_PoolIndex

Generic constructor for the class with the same name
CenturyModel14

Implementation of a radiocarbon version of the Century model
GeneralPoolId,numeric-method

generic factory for this virtual class
ConstantInFlux_by_PoolName-class

class for a constant influx to a single pool identified by pool name
ConstantInternalFluxRateList_by_PoolIndex-class

Describes a list of flux rates.
GeneralDecompOp

A generic factory for subclasses of GeneralDecompOp
InFluxes,numeric-method

automatic title
AbsoluteFractionModern,ConstFc-method

automatic title
AbsoluteFractionModern

Conversion of radiocarbon values
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
ConstantInternalFluxRate_by_PoolName

Generic constructor for the class with the same name
GeneralDecompOp,matrix-method

automatic title
Delta14C_from_AbsoluteFractionModern

Conversion of radiocarbon values
ConstLinDecompOp

Generic constructor for the class with the same name
ConstLinDecompOpWithLinearScalarFactor

Generic constructor for the class with the same name
ConstantOutFluxRateList_by_PoolIndex,list-method

constructor from a normal list
InternalFlux_by_PoolIndex

Generic constructor for the class with the same name
ConstInFluxes

Constant input fluxes
ConstantInFluxList_by_PoolIndex-class

Subclass of list that is guaranteed to contain only elements of type ConstantInFlux_by_PoolIndex
BoundFc

Bound Fc object
ConstantInFluxRate_by_PoolIndex-class

Describes a flux rates.
ConstantInFluxList_by_PoolName-class

Subclass of list that is guaranteed to contain only elements of type ConstantInFlux_by_PoolName
ConstantInFluxRate_by_PoolName-class

Describes a flux rates.
ConstLinDecompOp_by_PoolName

Generic constructor for the class with the same name
GeneralNlModel

Use this function to create objects of class NlModel.
InFluxes,ConstantInFluxList_by_PoolIndex-method

automatic title
OutFlux_by_PoolIndex-class

S4 class for a single out-flux with source pool index
ConstantInFluxList_by_PoolIndex,list-method

constructor from a normal list
ConstantInFluxList_by_PoolName

Generic constructor for the class with the same name
ConstantInternalFluxRate_by_PoolIndex-class

S4 class representing a constant internal flux rate
ConstantOutFluxRate_by_PoolIndex

Generic constructor for the class with the same name
GeneralDecompOp,list-method

automatic title
DecompOp-class

S4-class to represent compartmental operators
BoundInFluxes-class

automatic title
ConstantInternalFluxRate_by_PoolIndex,numeric,numeric,missing,numeric-method

automatic title
ConstantInFlux_by_PoolIndex-class

class for a constant influx to a single pool identified by index
PoolIndex

Pool index
ConstantOutFluxRateList_by_PoolIndex-class

Describes a list of flux rates.
InFluxList_by_PoolName-class

Class for a list of influxes indexed by the names of the target pools
GeneralPoolId,character-method

automatic title
ConstantInFluxList_by_PoolIndex,ConstInFluxes-method

constructor from ConstInFluxes
Fc-class

automatic title
ScalarTimeMap,missing,missing,missing,numeric,numeric-method

constructor for data and times given as vectors
GeneralDecompOp,DecompOp-method

Pass through factory for objects of subclasses of DecompOp
InFluxes,StateIndependentInFluxList_by_PoolIndex-method

automatic title
GeneralDecompOp,TimeMap-method

automatic title
ConstantOutFluxRateList_by_PoolIndex

Generic constructor for the class with the same name
ConstantOutFluxRateList_by_PoolName-class

Describes a list of flux rates.
Model_14

general constructor for class Model_14
ConstantInternalFluxRateList_by_PoolIndex,numeric-method

automatic title
ConstantOutFluxRateList_by_PoolIndex,numeric-method

automatic title
GeneralModel

additional function to create Models
IntCal20

The IntCal20 northern hemisphere radiocarbon curve for the 0-55,000 yr BP period
UnBoundLinDecompOp

Generic constructor for the class with the same name
Graven2017

Compiled records of radicarbon in atmospheric CO2 for historical simulations in CMIP6
InFluxList_by_PoolIndex,list-method

constructor from a normal list after checking the elements
InternalFlux_by_PoolIndex,function,numeric,numeric,missing-method

constructor from an ordered pair of PoolIndex (integer like) objects and a function with vector argument
ConstantInternalFluxRate_by_PoolName,character,character,missing,numeric-method

constructor with argument conversion
InFluxes,InFluxes-method

automatic title
ICBMModel

Implementation of the Introductory Carbon Balance Model (ICBM)
ConstantInternalFluxRate_by_PoolName-class

S4-class to represent a constant internal flux rate with source and target indexed by name
ConstantInternalFluxRate_by_PoolName,missing,missing,character,numeric-method

constructor from strings of the form 'a->b'
example.2DBoundInFluxesFromFunction

example.2DBoundInFluxesFromFunction
ConstantInternalFluxRateList_by_PoolName,list-method

Constructor from a normal list of fluxes
ConstantOutFluxRate_by_PoolIndex,numeric,numeric-method

automatic title
InternalFluxList_by_PoolIndex-class

S4-class for a list of internal fluxes with source and destination pool inidices
PoolName

Pool name
UnBoundInFluxes,function-method

automatic title
ICBM_N

Implementation of the ICBM/N model
InternalFlux_by_PoolName,function,character,character,missing-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
StateIndependentInFluxList_by_PoolIndex

Generic constructor for the class with the same name
InFluxList_by_PoolName

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.
ScalarTimeMap,data.frame,missing,missing,missing,missing-method

constructor for data given as 2 column data.frame
ScalarTimeMap-class

S4 class for a scalar time dependent function on a finite time interval
ThreepSeriesModel14

Implementation of a three-pool C14 model with series structure
DecompositionOperator-class

automatic title
Delta14C_from_AbsoluteFractionModern,numeric-method

Conversion of radiocarbon values
ConstantInternalFluxRateList_by_PoolName

Generic constructor for the class with the same name
Delta14C,ConstFc-method

automatic title
PoolConnection_by_PoolIndex,missing,missing,character-method

constructor from strings of the form '1_to_2'
Model_by_PoolNames-class

A model run based on flux functions
InFlux

Generic constructor for the class with the same name
InFluxList_by_PoolName,list-method

constructor from a normal list
InFluxes,TimeMap-method

automatic title
Delta14C

Conversion of radiocarbon values
InternalFluxList_by_PoolIndex

Generic constructor for the class with the same name
ConstantOutFluxRateList_by_PoolName

Generic constructor for the class with the same name
PoolConnection_by_PoolIndex,ANY,ANY,missing-method

constructor from an ordered pair of PoolId objects
OutFlux

Generic constructor for the class with the same name
ConstantInFluxList_by_PoolIndex,numeric-method

constructor from numeric vector
InternalFlux_by_PoolName,function,missing,missing,character-method

automatic title
ConstantInFluxList_by_PoolIndex

Generic constructor for the class with the same name
fT.Daycent1

Effects of temperature on decomposition rates according to the DAYCENT model
MCSim-class

Experimental Class for a Monte Carlo Simulation of particles leaving the pool
ConstantInternalFluxRateList_by_PoolIndex

Generic constructor for the class with the same name
GeneralPoolId

General pool Id
OutFluxList_by_PoolIndex-class

A list of outfluxes
ConstantInternalFluxRateList_by_PoolName-class

Describes a list of flux rates.
Model_by_PoolNames

Constructor for Model_by_PoolNames
InFluxList_by_PoolIndex-class

Describes a list of flux rates.
by_PoolName,ConstantInFluxList_by_PoolIndex-method

convert to a list indexed by pool names
GeneralDecompOp,function-method

automatic title
InFluxes

A generic factory for subclasses of InFluxes
PoolIndex,numeric-method

construct from number
OutFluxList_by_PoolIndex

Generic constructor for the class with the same name
InFlux_by_PoolName

Generic constructor for an influx to a single pool from an ordered pair of PoolName (string like) and function objects
ConstantInternalFluxRate_by_PoolIndex

Generic constructor for the class with the same name
ConstantOutFluxRateList_by_PoolName,list-method

constructor from a normal list
InternalFlux_by_PoolName-class

S4-class for a single internal flux with source and destination pools specified by name
TimeMap,missing,missing,missing,numeric,matrix-method

automatic title
TimeMap,function,missing,missing,missing,missing-method

manual constructor for just a function
ConstantOutFluxRateList_by_PoolName,numeric-method

automatic title
Hua2021

Atmospheric radiocarbon for the period 1950-2019 from Hua et al. (2021)
cycling

Cycling analysis of compartmental matrices
InternalFlux_by_PoolName

Generic constructor for the class with the same name
ConstantOutFluxRate_by_PoolName-class

S4 Class to represent a single constant out-flux rate with the source pool specified by name
InternalFluxList_by_PoolName-class

S4-class for a list of internal fluxes with indexed by (source and destination pool) names
HarvardForest14CO2

Delta14C in soil CO2 efflux from Harvard Forest
InFlux_by_PoolIndex-class

S4 class for the influx to a single pool identified by the index
ThreepParallelModel

Implementation of a three pool model with parallel structure
Yasso07Model

Implementation of the Yasso07 model
TimeMap,data.frame,missing,missing,missing,missing-method

automatic title
PoolIndex,PoolIndex-method

pass through constructor fron an object of the same class
Delta14C,BoundFc-method

automatic title
ConstantOutFluxRate_by_PoolIndex-class

S4 Class to represent a single constant out-flux rate with the source pool specified by an index
InternalFluxList_by_PoolName,list-method

constructor from a normal list
GeneralModel_14

create objects of class Model_14
ThreepFeedbackModel

Implementation of a three pool model with feedback structure
example.nestedTime2DMatrixList

create an example nested list that can be
FcAtm.from.Dataframe

FcAtm.from.Dataframe
TimeMap,missing,missing,missing,numeric,list-method

automatic title
Model

Constructor for class Model
OutFlux_by_PoolIndex,function,numeric-method

constructor from a PoolIndex (integer like) objects and a function with vector argument
InternalFluxList_by_PoolName

Generic constructor for the class with the same name
OutFlux_by_PoolIndex

Generic constructor for the class with the same name
SeriesLinearModel

General m-pool linear model with series structure
PoolName,PoolIndex-method

convert to string like object
availableResidentSets

Available resident sets
OutFluxList_by_PoolIndex,list-method

constructor from a normal list
InFluxes-class

A virtual S4-class representing (different subclasses) of in-fluxes to the system
availableParticleProperties

Available particle properties
PoolConnection_by_PoolName,ANY,ANY,missing-method

constructor from an ordered pair of PoolName objects
by_PoolIndex,OutFluxList_by_PoolName,character,character-method

automatic title
TwopParallelModel14

Implementation of a two-pool C14 model with parallel structure
Hua2013

Atmospheric radiocarbon for the period 1950-2010 from Hua et al. (2013)
UnBoundLinDecompOp-class

An S4 class to represent a linear nonautonomous compartmental matrix
PoolConnection_by_PoolIndex-class

Objects that have a source and a destination described by integer like objects ( of class PoolIndex)
getConstantCompartmentalMatrix,ConstLinDecompOpWithLinearScalarFactor-method

automatic title
PoolIndex,PoolName-method

convert to number like object
InternalFluxList_by_PoolIndex,list-method

Constructor from a normal list after checking the elements
OutFluxList_by_PoolName

Generic constructor for the class with the same name
GaudinskiModel14

Implementation of a the six-pool C14 model proposed by Gaudinski et al. 2000
UnBoundNonLinDecompOp_by_PoolNames

Generic constructor for the class with the same name
PoolName,PoolName-method

pass through constructor fron an object of the same class
StateIndependentInFluxList_by_PoolName

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
PoolIndex,character-method

construct from number string like '1' or '3'
TimeMap,list,missing,missing,missing,missing-method

automatic title
InFlux_by_PoolIndex,function,numeric-method

Constructor from an ordered pair of PoolIndex (integer like) objects
as.character,TimeMap-method

automatic title
OnepModel

Implementation of a one pool model
OnepModel14

Implementation of a one-pool C14 model
InFluxes,function-method

automatic title
OutFlux_by_PoolName,function,character-method

constructor from a PoolName (integer like) object and a function
PoolId-class

common class for pool ids
example.2DConstInFluxesFromVector

2D example for constant Influx
TimeMap,TimeMap,ANY,ANY,ANY,ANY-method

automatic title
OutFluxList_by_PoolName-class

S4 class for a list of out-fluxes indexed by source pool name
InFlux_by_PoolIndex

Generic constructor for the class with the same name
InFluxes,list-method

automatic title
StateIndependentInFluxList_by_PoolIndex-class

Subclass of list that is guaranteed to contain only elements of type StateIndependentInFlux_by_PoolIndex
NlModel-class

deprecated class for a non-linear model run.
TimeMap,missing,missing,missing,numeric,array-method

automatic title
Model-class

S4 class representing a model run
InFlux_by_PoolName-class

S4 class for the influx to a single pool identified by the name
RespirationCoefficients

helper function to compute respiration coefficients
ThreepSeriesModel

Implementation of a three pool model with series structure
ThreepairMMmodel

Implementation of a 6-pool Michaelis-Menten model
StateIndependentInFluxList_by_PoolIndex,list-method

constructor from a normal list
as.numeric,InFluxList_by_PoolName-method

Convert to a numeric vector with the pool names as names
IntCal09

Northern Hemisphere atmospheric radiocarbon for the pre-bomb period
UnBoundNonLinDecompOp-class

An S4 class to represent a nonlinear nonautonomous compartmental matrix
entropyRatePerTime

Entropy rate per time
example.Time2DArrayList

create an example TimeMap from 2D array
PoolIndex-class

S4 class for pool indices
InFlux_by_PoolName,function,character-method

Constructor from an ordered pair of PoolName (string like) and function objects
fW.Demeter

Effects of moisture on decomposition rates according to the DEMETER model
TimeRangeIntersection

The time interval where both functions are defined
OutFluxList_by_PoolName,list-method

constructor from a normal list
TwopMMmodel

Implementation of a two-pool Michaelis-Menten model
TwopParallelModel

Implementation of a linear two pool model with parallel structure
getConstLinDecompOp

Constant linear decomposition operator
ScalarTimeMap,missing,missing,missing,missing,numeric-method

special case for a time map from a constant
by_PoolIndex,PoolConnection_by_PoolName,ANY,ANY-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
RothCModel

Implementation of the RothCModel
by_PoolIndex,InFlux_by_PoolName,character,character-method

Convert the pool names to indices
IntCal13

Atmospheric radiocarbon for the 0-50,000 yr BP period
SoilR.F0.new

deprecated function that used to create an object of class SoilR.F0
PoolConnection_by_PoolIndex

Pool connection by pool index
PoolName,character-method

construct from string with checks
as.numeric,InternalFluxList_by_PoolName-method

Convert to a numeric vector with names of the form 'a->b'
SHCal20

The SHCal20 southern hemisphere radiocarbon curve for the 0-55,000 yr BP period
PoolConnection_by_PoolName

Pool connection by pool name
TransportDecompositionOperator-class

automatic title
OutFlux_by_PoolName-class

S4 class for a single out-flux with source pool name
ScalarTimeMap,function,missing,missing,missing,missing-method

manual constructor for just a function
getMeanTransitTime

Mean transit time for SoilR objects
TwopSeriesModel14

Implementation of a two-pool C14 model with series structure
availableParticleSets,MCSim-method

automatic title
by_PoolIndex,ConstantInFluxRate_by_PoolName,ANY,ANY-method

new object with the source pool id converted to a PoolIndex if necessary
by_PoolName

automatic title
Model_14-class

S4-class to represent a 14C model run
UnBoundInFluxes-class

automatic title
check_id_length

helper function to check that the length of the argument is exactly 1
getF14C,Model_14-method

automatic title
StateIndependentInFlux_by_PoolIndex-class

Constructor for the class with the same name
$,NlModel-method

automatic title
getF14

Generic that yields the 14C fraction for the content all pools and all times
print,NlModel-method

automatic title
check_pool_ids

Check pool ids
getC,Model-method

Pool Contents for all times
TimeMap-class

S4 class for a time dependent function
OutFlux_by_PoolName

Generic constructor for the class with the same name
ThreepParallelModel14

Implementation of a three-pool C14 model with parallel structure
availableParticleProperties,MCSim-method

automatic title
ParallelModel

models for unconnected pools
SeriesLinearModel14

General m-pool linear C14 model with series structure
availableResidentSets,MCSim-method

automatic title
by_PoolIndex,OutFlux_by_PoolName,character,character-method

automatic title
getF14C

Generic that yields the 14C fraction for the cumulative content of all pools and all times
YassoModel

Implementation of the Yasso model.
by_PoolIndex,InternalFlux_by_PoolName,character,character-method

automatic title
euler

euler
getConstLinDecompOp,ConstLinDecompOpWithLinearScalarFactor-method

automatic title
ScalarTimeMap,function,numeric,numeric,missing,missing-method

manual constructor for a function and an interval
fT.linear

Effects of temperature on decomposition rates according to a linear model
deSolve.lsoda.wrapper

deSolve.lsoda.wrapper
pathEntropy

Path Entropy
ScalarTimeMap

Constructor for ScalarTimeMap-class
state_variable_names

determine the minimum set of statevariables
UnBoundNonLinDecompOp

Generic constructor for the class with the same name
PoolConnection_by_PoolName-class

Objects that have a source and a destination determined by a string like object of class PoolName
TimeMap.new

deprecated constructor of the class TimeMap.
TimeMap,function,numeric,numeric,missing,missing-method

manual constructor for a function and an interval
StateDependentInFluxVector-class

Input vector that is a function of the pool contenst and time
bacwaveModel

Implementation of the microbial model Bacwave (bacterial waves)
fT.Century1

Effects of temperature on decomposition rates according the the CENTURY model
fT.Standcarb

Effects of temperature on decomposition rates according to the StandCarb model
UnBoundInFluxes

Unbound input fluxes
example.Time3DArrayList

create an example TimeFrame from 3D array
ThreepFeedbackModel14

Implementation of a three-pool C14 model with feedback structure
bind.C14curves

Binding of pre- and post-bomb Delta14C curves
getAccumulatedRelease

Accumulated release flux out of the pools
TimeMap.from.Dataframe

TimeMap.from.Dataframe
example.TimeMapFromArray

create an example TimeFrame from 3D array
TwopFeedbackModel

Implementation of a two pool model with feedback structure
listProduct

tensor product of lists
UnBoundLinDecompOp,function-method

Generic constructor for the class with the same name
TwopFeedbackModel14

Implementation of a two-pool C14 model with feedback structure
example.2DGeneralDecompOpArgs

example.2DGeneralDecompOpArgs
getFunctionDefinition,ConstLinDecompOpWithLinearScalarFactor-method

convert names of vectors or lists to class ConstantOutFluxRate convert names of vectors or lists to class ConstantInternalFluxRate helper function
fW.Gompertz

Effects of moisture on decomposition rates according to the Gompertz function
getRightHandSideOfODE,Model-method

Derivative of the state variables as function
PoolName-class

class for pool-name-strings
getTimeRange

Time range of a model simulation
getConstantInternalFluxRateList_by_PoolIndex

Constant internal flux rate list by pool index
getTimeRange,UnBoundLinDecompOp-method

Extracts the time interval for which the function is valid.
add_plot

Add elements to plot
by_PoolIndex,InFluxList_by_PoolName,character,character-method

Transform pool names to indices
getConstantOutFluxRateList_by_PoolIndex

Constant out flux rate list by pool index
check_duplicate_pool_names

helper function
fT.Q10

Effects of temperature on decomposition rates according to a Q10 function
by_PoolName,ConstantInternalFluxRateList_by_PoolIndex-method

convert to a list indexed by pool names
computeResults

Computes results
TimeMap,missing,missing,missing,numeric,numeric-method

automatic title
getCumulativeC,NlModel-method

automatic title
by_PoolName,ConstantInFluxRate_by_PoolIndex-method

new object with the source pool id converted to a PoolIndex if necessary
getOutputReceivers

Pools receiving outputs from other pools
by_PoolName,ConstantInFlux_by_PoolIndex-method

new object with the source pool id converted to a PoolIndex if necessary
by_PoolIndex,function,character,character-method

convert a function f of to f_vec
UnBoundNonLinDecompOp_by_PoolNames-class

An S4 class to represent the of nonlinear nonautonomous compartmental system independently of the order of state variables
predefinedModels

PREDEFINED MODELS
example.2DBoundLinDecompOpFromFunction

example.2DBoundLinDecompOpFromFunction
by_PoolIndex,ConstantInternalFluxRateList_by_PoolName,ANY,ANY-method

convert to a list indexed by pool names
fT.Century2

Effects of temperature on decomposition rates according the the CENTURY model
getParticleMonteCarloSimulator,NlModel-method

automatic title
computeResults,MCSim-method

automatic title
fW.Skopp

Effects of moisture on decomposition rates according to the function proposed by Skopp et al. 1990
getInitialValues

Initial values of SoilR object
by_PoolIndex

automatic title
getLinearScaleFactor

Linear scale factor
fT.Demeter

Effects of temperature on decomposition rates according to the DEMETER model
SoilR-package

SoilR
getNumberOfPools

Number of pools in a model
example.2DConstFc.Args

example.2DConstFc.Args
getReleaseFlux14

Generic that yields the 14C fraction in the release flux
getFunctionDefinition,DecompositionOperator-method

automatic title
by_PoolName,ConstantOutFluxRate_by_PoolIndex-method

new object with the source pool id converted to a PoolName if necessary
add_plot,TimeMap-method

automatic title
SymbolicModel_by_PoolNames-class

A symbolic model description based on flux functions
fT.LandT

Effects of temperature on decomposition rates according to a function proposed by Lloyd and Taylor (1994)
fW.Daycent1

Effects of moisture on decomposition rates according to the DAYCENT model
getFunctionDefinition,InFluxList_by_PoolIndex-method

automatic title
getCompartmentalMatrixFunc,ConstLinDecompOp-method

Compartmental matrix function
getFunctionDefinition,StateDependentInFluxVector-method

automatic title
getOutputFluxes,NlModel-method

automatic title
TimeMap

Constructor for TimeMap-class
UnBoundNonLinDecompOp,function,missing,missing,missing-method

Constructor for the class with the same name
TwopSeriesModel

Implementation of a two pool model with series structure
initialize,Model_14-method

Internal method to supervise creation of objects of this class
by_PoolIndex,ConstantOutFluxRate_by_PoolName,ANY,ANY-method

new object with the source pool id converted to a PoolIndex if necessary
getFormat,Fc-method

automatic title
getCompartmentalMatrixFunc,BoundLinDecompOp-method

automatic title
fT.RothC

Effects of temperature on decomposition rates according to the functions included in the RothC model
getTimes,NlModel-method

automatic title
availableParticleSets

Available particle sets
fT.Arrhenius

Effects of temperature on decomposition rates according the Arrhenius equation
getTransitTimeDistributionDensity,ConstLinDecompOp-method

Transit time distribution obtained through a numerical simulation. It introduces numerical errors. We recommend to use the function transitTime instead
check_pool_ids,PoolConnection_by_PoolIndex,integer-method

automatic title
[,Model,character,missing,missing-method

Experimentally overloaded index operator
fW.Standcarb

Effects of moisture on decomposition rates according to the StandCarb model
getConstantInFluxVector

Input flux vector
getDotOut

Dot out
example.2DInFluxes.Args

example.2DInFluxes.Args
getFormat

Get format of SoilR object
getDotOut,TransportDecompositionOperator-method

automatic title
UnBoundNonLinDecompOp,missing,vector,vector,numeric-method

Constructor for the class with the same name
getC,Model_by_PoolNames-method

Pool Contents for all times
getReleaseFlux,Model_by_PoolNames-method

automatic title
linearScalarModel

Implementation of a general model for linear non-autonomous systems with scalar modifiers
plotPoolGraphFromTupleLists

Helper function to draw connectivity graphs
fT.KB

Effects of temperature on decomposition rates according to a model proposed by M. Kirschbaum (1995)
getMeanTransitTime,ConstLinDecompOp-method

Mean transit time obtained through a numerical simulation. It produces an estimate with numerical errors. We recommend to use the function transitTime instead.
by_PoolIndex,ConstantOutFluxRateList_by_PoolName,ANY,ANY-method

convert to a list indexed by pool names
getC14

Generic that yields the 14C content for all pools and all times
initialize,ConstLinDecompOp-method

automatic title
by_PoolIndex,ConstantInternalFluxRate_by_PoolName,ANY,ANY-method

new object with the source pool id converted to a PoolName if necessary
getTimeRange,ConstInFluxes-method

automatic title
getFunctionDefinition,InFluxList_by_PoolName-method

automatic title
fW.Candy

Effects of moisture on decomposition rates according to the Candy model
by_PoolIndex,InternalFluxList_by_PoolName,character,character-method

automatic title
fW.Century

Effects of moisture on decomposition rates according to the CENTURY model
getTimes

Time vector of SoilR object
getConstantCompartmentalMatrix

Constant compartmental matrix
transitTime

Transit times for compartment models
getReleaseFlux

Generic Function to obtain the vector of release fluxes out of the pools for all times.
linesCPool

Add lines with the output of getC14, getC, or getReleaseFlux to an existing plot
getInFluxes

Extract the influxes
fW.Moyano

Effects of moisture on decomposition rates according to the function proposed by Moyano et al. (2013)
getNumberOfPools,MCSim-method

automatic title
fW.RothC

Effects of moisture on decomposition rates according to the RothC model
getC14,Model_14-method

automatic title
as.numeric,InternalFlux_by_PoolName-method

Convert to a numeric value with name of the form 'a->b'
getCompartmentalMatrixFunc,TransportDecompositionOperator-method

automatic title
as.numeric,OutFluxList_by_PoolName-method

Convert to a numeric vector with the pool names as names
fW.Daycent2

Effects of moisture on decomposition rates according to the DAYCENT model
plot,TimeMap-method

automatic title
getConstantCompartmentalMatrix,ConstLinDecompOp-method

Constant compartmental matrix
initialize,NlModel-method

automatic title
fT.Daycent2

Effects of temperature on decomposition rates according to the DAYCENT model
getTimeRange,DecompositionOperator-method

automatic title
no_outflux_warning

alternative Constructor with pool names helper function
incubation_experiment

Soil CO2 efflux from an incubation experiment, along with the soil mass and carbon concentration measurements.
getTransferCoefficients,NlModel-method

automatic title
getInitialValues,NlModel-method

automatic title
getFunctionDefinition,TransportDecompositionOperator-method

automatic title
getDecompOp,NlModel-method

Extract the Compartmental Operator
getFunctionDefinition,ConstInFluxes-method

automatic title
getReleaseFlux,NlModel-method

automatic title
getInFluxes,NlModel-method

automatic title
initialize,Model_by_PoolNames-method

automatic title
getTimeRange,ConstLinDecompOp-method

Time range of a simulation described in an object of class ConstLinDecompOp
from_integer_flux_lists_with_defaults

helper function
getFunctionDefinition,ConstLinDecompOp-method

Function describing an object of class ConstLinDecompOp
by_PoolName,ConstantOutFluxRateList_by_PoolIndex-method

convert to a list indexed by pool names
getRightHandSideOfODE

Right hand side of ODE of a SoilR model
getTransferCoefficients,TransportDecompositionOperator-method

automatic title
example.2DUnBoundLinDecompOpFromFunction

example.2DUnBoundLinDecompOpFromFunction
getF14,Model_14-method

automatic title
getCumulativeC

Cummulative pool contents
getConstantInternalFluxRateList_by_PoolIndex,ConstLinDecompOp-method

Constant internal flux rate list by pool index
getDecompOp,Model-method

Extract the Compartmental Operator
getInFluxes,Model-method

Extract the InFluxes as provided during creation of the model
plot,Model-method

Create an overview plot
initialize,Model-method

Internal method to supervise creation of objects of this class
getOutputFluxes

Generic Function to obtain the fluxes out of of the pools
turnoverFit

Estimation of the turnover time from a radiocarbon sample.
getFunctionDefinition,UnBoundInFluxes-method

automatic title
getNumberOfPools,NlModel-method

automatic title
getConstantInFluxVector,ConstInFluxes-method

automatic title
getC,NlModel-method

Pool Contents for all times
getLinearScaleFactor,ConstLinDecompOpWithLinearScalarFactor-method

automatic title
getTimeRange,ConstLinDecompOpWithLinearScalarFactor-method

automatic title
getAccumulatedRelease,Model-method

Compute the time integral of the relaese fluxes over time
getNumberOfPools,TransportDecompositionOperator-method

automatic title
eCO2

Soil CO2 efflux from an incubation experiment
getTransferMatrix

deprecated, use getTransferMatrixFunc instead
entropyRatePerJump

Entropy rate per jump
getValues

Get values of SoilR object
getTimeRange,TimeMap-method

The time interval where the function is defined
getDecompOp

Decomposition operator of a model
initialize,DecompositionOperator-method

automatic title
initialize,UnBoundInFluxes-method

automatic title
initialize,MCSim-method

automatic title
getOutputReceivers,TransportDecompositionOperator,numeric-method

automatic title
example.ConstlinDecompOpFromMatrix

example.ConstlinDecompOpFromMatrix
getTimes,Model-method

Extract the times vector
getReleaseFlux14,Model_14-method

automatic title
plot,MCSim-method

automatic title
getFunctionDefinition,TimeMap-method

automatic title
getTransferCoefficients

Transfer coefficients
getSolution,Model_by_PoolNames-method

All Fluxes and stocks for all times
getTimeRange,UnBoundInFluxes-method

automatic title
getTransitTimeDistributionDensity

Transit time distribution for SoilR objects
getF14R,Model_14-method

automatic title
plot,Model_by_PoolNames-method

Plot the graph of pool connections
show,NlModel-method

automatic title
systemAge

System and pool age for constant compartment models
getC

Calculates the content of the pools
getCompartmentalMatrixFunc,UnBoundNonLinDecompOp-method

Extract the matrix valued function of time and state vector for the compartmental matrix
getFunctionDefinition

Function definition of SoilR model
plotC14Pool

Plots the output of getF14 for each pool over time
getRightHandSideOfODE,Model_by_PoolNames-method

Provide the (vector valued) derivative of the stocks with respect to time
getValues,ConstFc-method

automatic title
[[<-,MCSim-method

automatic title
getCompartmentalMatrixFunc

Compartmental matrix function
getF14R

Generic that yields the 14C fraction for the release flux of all pools and all times
getConstantOutFluxRateList_by_PoolIndex,ConstLinDecompOp-method

Constant out flux rate list by pool index
plotPoolGraph

Generic plotter
initialize,UnBoundLinDecompOp-method

automatic title
getParticleMonteCarloSimulator

automatic title
getFunctionDefinition,UnBoundLinDecompOp-method

Extracts the time dependent matrix valued function (compartmental matrix)
plot,NlModel-method

automatic title
getReleaseFlux,Model-method

The release fluxes \(\frac{[content]}{[time]}\) for all pools.
plotCPool

Plots the output of getC or getReleaseFlux for each pool over time
getTransferMatrixFunc

Transfer matrix function
getTransferMatrixFunc,TransportDecompositionOperator-method

automatic title
getSolution

Calculates all stocks all fluxes to ,in and out of the compartment system and also their integrals over time
initialize,TransportDecompositionOperator-method

automatic title
getTimes,Model_by_PoolNames-method

Extract the times vector
[[,MCSim-method

automatic title
initialize,TimeMap-method

automatic title
[,NlModel,character,ANY,ANY-method

automatic title
plotPoolGraph,SymbolicModel_by_PoolNames-method

Plot the graph of pool connections
AWBmodel

Implementation of the microbial model AWB (Allison, Wallenstein, Bradford, 2010)
AbsoluteFractionModern_from_Delta14C

Conversion of radiocarbon values