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SoilR (version 1.2.105)

Models of Soil Organic Matter Decomposition

Description

Functions for modeling Soil Organic Matter decomposition in terrestrial ecosystems with linear and nonlinear models.

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Version

Install

install.packages('SoilR')

Monthly Downloads

440

Version

1.2.105

License

GPL-3

Maintainer

Carlos Sierra

Last Published

January 23rd, 2022

Functions in SoilR (1.2.105)

AbsoluteFractionModern_from_Delta14C,matrix-method

automatic title

AbsoluteFractionModern

automatic title

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,ConstFc-method

automatic title

AbsoluteFractionModern_from_Delta14C

conversion

AWBmodel

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

AbsoluteFractionModern_from_Delta14C,numeric-method

Post-bomb atmospheric 14C fraction

ConstInFluxes

automatic title

CenturyModel

Implementation of the Century model

ConstInFluxes,ConstantInFluxList_by_PoolIndex,numeric-method

automatic title

BoundInFluxes-class

automatic title

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.

ConstantInFluxList_by_PoolIndex,ConstInFluxes-method

constructor from ConstInFluxes

ConstFc

creates an object containing the initial values for the 14C fraction needed to create models in SoilR

ConstantInFluxList_by_PoolIndex-class

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

ConstLinDecompOp,missing,ConstantInternalFluxRateList_by_PoolIndex,missing,numeric,missing-method

Constructor

BoundLinDecompOp

Generic constructor for the class with the same name

AbsoluteFractionModern,BoundFc-method

automatic title

C14Atm

Atmospheric 14C fraction

ConstantInFluxList_by_PoolIndex,list-method

constructor from a normal list

BoundLinDecompOp,ANY-method

automatic title

ConstLinDecompOp

Generic constructor for the class with the same name

BoundInFluxes

constructor for BoundInFluxes

ConstantInFluxRate_by_PoolName-class

Describes a flux rates.

ConstLinDecompOp,missing,missing,ConstantOutFluxRateList_by_PoolIndex,numeric,missing-method

Constructor

ConstLinDecompOp,matrix,missing,missing,missing,missing-method

Constructor

ConstantInternalFluxRateList_by_PoolIndex-class

Describes a list of flux rates.

ConstantInFluxList_by_PoolIndex,numeric-method

constructor from numeric vector

ConstLinDecompOp,missing,ConstantInternalFluxRateList_by_PoolName,ConstantOutFluxRateList_by_PoolName,missing,character-method

alternative Constructor with pool names

ConstantInternalFluxRateList_by_PoolIndex,list-method

constructor from a normal list

ConstantInFluxRate_by_PoolName

Constructor for the class with the same name

ConstantInternalFluxRateList_by_PoolName,list-method

Constructor from a normal list of fluxes

ConstantInternalFluxRateList_by_PoolName-class

Describes a list of flux rates.

CenturyModel14

Implementation of a radiocarbon version of the Century model

ConstFc-class

S4 class representing a constant ^14C fraction

ConstLinDecompOp_by_PoolName

Generic constructor for the class with the same name

ConstLinDecompOpWithLinearScalarFactor

Generic constructor for the class with the same name

ConstantInternalFluxRate_by_PoolIndex

Generic constructor for the class with the same name

ConstantInternalFluxRate_by_PoolName,character,character,missing,numeric-method

constructor with argument conversion

ConstantOutFluxRate_by_PoolName-class

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

ConstantOutFluxRateList_by_PoolIndex,list-method

constructor from a normal list

DecompOp-class

S4-class to represent compartmental operators

ConstLinDecompOp,missing,ConstantInternalFluxRateList_by_PoolIndex,ConstantOutFluxRateList_by_PoolIndex,numeric,missing-method

Constructor

GeneralDecompOp,matrix-method

automatic title

GeneralDecompOp

A generic factory for subclasses of GeneralDecompOp

ConstantInFluxRate_by_PoolIndex-class

Describes a flux rates.

ConstLinDecompOpWithLinearScalarFactor,matrix,missing,missing,missing,ScalarTimeMap-method

convert names of vectors or lists to class ConstantOutFluxRate convert names of vectors or lists to class ConstantInternalFluxRate

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

ConstantInFluxList_by_PoolName

Generic constructor for the class with the same name

ConstantInternalFluxRate_by_PoolIndex,missing,missing,character,numeric-method

constructor from strings of the form '1_to_2'

ConstantInternalFluxRate_by_PoolIndex,numeric,numeric,missing,numeric-method

automatic title

BoundLinDecompOp,UnBoundLinDecompOp-method

A converter

ConstantInFluxList_by_PoolIndex

Generic constructor for the class with the same name

ConstantInternalFluxRateList_by_PoolIndex,numeric-method

automatic title

ConstantInFluxList_by_PoolName-class

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

ConstantInternalFluxRateList_by_PoolName

Generic constructor for the class with the same name

ConstantOutFluxRateList_by_PoolIndex

Generic constructor for the class with the same name

ConstantOutFluxRateList_by_PoolName-class

Describes a list of flux rates.

ConstantInternalFluxRateList_by_PoolIndex

Generic constructor for the class with the same name

ConstInFluxes-class

S4 class for a constant influx vector

ConstInFluxes,numeric,ANY-method

automatic title

BoundLinDecompOp-class

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

Delta14C_from_AbsoluteFractionModern,matrix-method

automatic title

ConstantInternalFluxRate_by_PoolIndex-class

S4 class representing a constant internal flux rate

ConstantOutFluxRateList_by_PoolName

Generic constructor for the class with the same name

Delta14C_from_AbsoluteFractionModern,numeric-method

automatic title

InFlux_by_PoolIndex-class

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

ConstantOutFluxRate_by_PoolIndex-class

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

Delta14C_from_AbsoluteFractionModern

automatic title

GeneralPoolId

automatic title

GeneralPoolId,numeric-method

generic factory for this virtual class

ICBM_N

Implementation of the ICBM/N model

Fc-class

automatic title

InternalFlux_by_PoolIndex-class

S4-class for a single internal flux with source and destination pools specified by indices

InFluxes,StateIndependentInFluxList_by_PoolIndex-method

automatic title

InFluxes,TimeMap-method

automatic title

InFlux_by_PoolIndex,function,numeric-method

constructor from an ordered pair of PoolIndex (integer like) objects

ConstantInternalFluxRate_by_PoolName-class

S4-class to represent a constant internal flux rate with source and target indexed by name

InternalFlux_by_PoolIndex,function,numeric,numeric,missing-method

constructor from an ordered pair of PoolIndex (integer like) objects and a function with vector argument

ConstantOutFluxRateList_by_PoolIndex,numeric-method

automatic title

ConstantInFlux_by_PoolName-class

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

ConstantInFlux_by_PoolIndex-class

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

InFlux

Generic constructor for the class with the same name

GeneralModel

additional function to create Models

InFluxes,ConstantInFluxList_by_PoolIndex-method

automatic title

Hua2013

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

ICBMModel

Implementation of the Introductory Carbon Balance Model (ICBM)

GeneralModel_14

create objects of class Model_14

InFluxes,InFluxes-method

automatic title

Model_by_PoolNames,SymbolicModel_by_PoolNames,numeric,missing,numeric,missing,missing,missing,missing,missing-method

Create a model(run) described by fluxes

Model_by_PoolNames-class

A model run based on flux functions

OutFluxList_by_PoolIndex

Generic constructor for the class with the same name

ConstantOutFluxRateList_by_PoolIndex-class

Describes a list of flux rates.

ConstantInternalFluxRate_by_PoolName

Generic constructor for the class with the same name

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

OutFluxList_by_PoolName-class

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

InFlux_by_PoolName-class

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

InFlux_by_PoolIndex

Generic constructor for the class with the same name

ParallelModel

models for unconnected pools

ConstantOutFluxRate_by_PoolIndex,numeric,numeric-method

automatic title

Delta14C

automatic title

Delta14C,BoundFc-method

automatic title

Delta14C,ConstFc-method

automatic title

DecompositionOperator-class

automatic title

InternalFlux_by_PoolName,function,missing,missing,character-method

automatic title

PoolIndex,PoolIndex-method

pass through constructor fron an object of the same class

PoolId-class

common class for pool ids

ConstantOutFluxRate_by_PoolIndex

Generic constructor for the class with the same name

PoolConnection_by_PoolIndex,ANY,ANY,missing-method

constructor from an ordered pair of PoolId objects

PoolConnection_by_PoolIndex

automatic title

GeneralDecompOp,function-method

automatic title

SymbolicModel_by_PoolNames-class

A symbolic model description based on flux functions

ScalarTimeMap,missing,missing,missing,numeric,numeric-method

constructor for data and times given as vectors

ScalarTimeMap

Constructor for ScalarTimeMap-class

IntCal13

Atmospheric radiocarbon for the 0-50,000 yr BP period

FcAtm.from.Dataframe

GeneralNlModel

Use this function to create objects of class NlModel.

GaudinskiModel14

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

GeneralPoolId,character-method

automatic title

ConstantInternalFluxRate_by_PoolName,missing,missing,character,numeric-method

constructor from strings of the form 'a->b'

ConstantOutFluxRateList_by_PoolName,list-method

constructor from a normal list

ThreepFeedbackModel

Implementation of a three pool model with feedback structure

InternalFlux_by_PoolIndex

Generic constructor for the class with the same name

IntCal20

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

GeneralDecompOp,list-method

automatic title

InternalFlux_by_PoolName-class

S4-class for a single internal flux with source and destination pools specified by name

Model

Constructor for class Model

Model-class

S4 class representing a model run

TimeMap,data.frame,missing,missing,missing,missing-method

automatic title

ConstantOutFluxRateList_by_PoolName,numeric-method

automatic title

OnepModel

Implementation of a one pool model

NlModel-class

deprecated class for a non-linear model run.

PoolConnection_by_PoolName,ANY,ANY,missing-method

constructor from an ordered pair of PoolName objects

PoolIndex-class

S4 class for pool indices

TimeMap,function,missing,missing,missing,missing-method

manual constructor for just a function

PoolIndex,numeric-method

construct from number

SoilR.F0.new

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

SoilR-package

SoilR

TimeMap,TimeMap,ANY,ANY,ANY,ANY-method

automatic title

TimeMap,function,numeric,numeric,missing,missing-method

manual constructor for a function and an interval

TimeMap-class

S4 class for a time dependent function

TimeMap.new

deprecated constructor of the class TimeMap.

TwopSeriesModel

Implementation of a two pool model with series structure

TimeRangeIntersection

The time interval where both functions are defined

TimeMap,list,missing,missing,missing,missing-method

automatic title

TwopSeriesModel14

Implementation of a two-pool C14 model with series structure

InFluxList_by_PoolIndex-class

Describes a list of flux rates.

InFluxList_by_PoolName,list-method

constructor from a normal list

InFluxList_by_PoolIndex,list-method

constructor from a normal list

OutFlux_by_PoolIndex-class

S4 class for a single out-flux with source pool index

UnBoundNonLinDecompOp,function,missing,missing,missing,ANY,ANY,ANY-method

Constructor for the class with the same name

TwopParallelModel

Implementation of a linear two pool model with parallel structure

UnBoundNonLinDecompOp-class

An S4 class to represent a nonlinear nonautonomous compartmental matrix

as.numeric,InternalFlux_by_PoolName-method

Convert to a numeric value with name of the form 'a->b'

as.numeric,OutFluxList_by_PoolName-method

Convert to a numeric vector with the pool names as names

TwopParallelModel14

Implementation of a two-pool C14 model with parallel structure

GeneralDecompOp,DecompOp-method

Pass through factory for objects of subclasses of DecompOp

OutFlux_by_PoolIndex,function,numeric-method

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

InFluxList_by_PoolIndex

Generic constructor for the class with the same name

GeneralDecompOp,TimeMap-method

automatic title

Graven2017

Compiled records of radicarbon in atmospheric CO2 for historical simulations in CMIP6

PoolConnection_by_PoolIndex,missing,missing,character-method

constructor from strings of the form '1_to_2'

PoolConnection_by_PoolIndex-class

Objects that have a source and a destination described by integer like objects ( of class PoolIndex)

InFluxes

A generic factory for subclasses of InFluxes

IntCal09

Northern Hemisphere atmospheric radiocarbon for the pre-bomb period

InFluxList_by_PoolName

Generic constructor for the class with the same name

UnBoundLinDecompOp,function-method

Generic constructor for the class with the same name

UnBoundLinDecompOp

Generic constructor for the class with the same name

InternalFluxList_by_PoolName,list-method

constructor from a normal list

InFluxList_by_PoolName-class

Class for a list of influxes indexed by the names of the target pools

InFlux_by_PoolName,function,character-method

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

PoolName-class

class for pool-name-strings

PoolName

automatic title

InternalFluxList_by_PoolName

Generic constructor for the class with the same name

HarvardForest14CO2

Delta14C in soil CO2 efflux from Harvard Forest

add_plot,TimeMap-method

automatic title

availableParticleSets

automatic title

YassoModel

Implementation of the Yasso model.

availableParticleSets,MCSim-method

S4-class to represent a ^14C model run

OnepModel14

Implementation of a one-pool C14 model

ScalarTimeMap,function,numeric,numeric,missing,missing-method

manual constructor for a function and an interval

OutFluxList_by_PoolName

Generic constructor for the class with the same name

PoolName,PoolName-method

pass through constructor fron an object of the same class

PoolName,character-method

construct from string with checks

OutFlux

Generic constructor for the class with the same name

Model_14

general constructor for class Model_14

by_PoolName,ConstantOutFluxRate_by_PoolIndex-method

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

OutFluxList_by_PoolName,list-method

constructor from a normal list

SHCal20

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

InFlux_by_PoolName

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

ScalarTimeMap-class

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

InFluxes,function-method

automatic title

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

InternalFluxList_by_PoolName-class

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

OutFlux_by_PoolName,function,character-method

constructor from a PoolName (integer like) object and a function

InternalFluxList_by_PoolIndex

Generic constructor for the class with the same name

OutFluxList_by_PoolIndex-class

A list of outfluxes

by_PoolName

automatic title

ScalarTimeMap,missing,missing,missing,missing,numeric-method

special case for a time map from a constant

StateDependentInFluxVector-class

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

euler

StateIndependentInFluxList_by_PoolIndex,list-method

constructor from a normal list

TimeMap

Constructor for TimeMap-class

TransportDecompositionOperator-class

automatic title

TimeMap.from.Dataframe

StateIndependentInFluxList_by_PoolIndex-class

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

TwopFeedbackModel

Implementation of a two pool model with feedback structure

by_PoolIndex,OutFluxList_by_PoolName,character,character-method

automatic title

by_PoolName,ConstantInternalFluxRate_by_PoolIndex-method

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

by_PoolIndex,InternalFlux_by_PoolName,character,character-method

automatic title

InFluxes,numeric-method

UnBoundLinDecompOp-class

An S4 class to represent a linear nonautonomous compartmental matrix

as.character,TimeMap-method

automatic title

bind.C14curves

Binding of pre- and post-bomb Delta14C curves

bacwaveModel

Implementation of the microbial model Bacwave (bacterial waves)

example.TimeMapFromArray

create an example TimeFrame from 3D array

example.2DBoundInFluxesFromFunction

example.Time3DArrayList

create an example TimeFrame from 3D array

fT.Demeter

Effects of temperature on decomposition rates according to the DEMETER model

by_PoolName,ConstantOutFluxRateList_by_PoolIndex-method

convert to a list indexed by pool names

$,NlModel-method

automatic title

by_PoolIndex,ConstantInternalFluxRate_by_PoolName,ANY,ANY-method

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

OutFlux_by_PoolName

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

StateIndependentInFluxList_by_PoolIndex

Generic constructor for the class with the same name

PoolIndex,PoolName-method

convert to number like object

by_PoolName,ConstantInFluxList_by_PoolIndex-method

convert to a list indexed by pool names

by_PoolIndex,ConstantOutFluxRateList_by_PoolName,ANY,ANY-method

convert to a list indexed by pool names

by_PoolName,ConstantInFluxRate_by_PoolIndex-method

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

fW.RothC

Effects of moisture on decomposition rates according to the RothC model

fT.KB

Effects of temperature on decomposition rates according to a model proposed by M. Kirschbaum (1995)

deSolve.lsoda.wrapper

eCO2

Soil CO2 efflux from an incubation experiment

example.2DUnBoundLinDecompOpFromFunction

example.2DInFluxes.Args

InternalFluxList_by_PoolIndex,list-method

constructor from a normal list

fT.linear

Effects of temperature on decomposition rates according to a linear model

ThreepSeriesModel14

Implementation of a three-pool C14 model with series structure

check_duplicate_pool_names

helper function

PoolIndex,character-method

construct from number string like '1' or '3'

InternalFlux_by_PoolName

Generic constructor for the class with the same name

entropyRatePerJump

Entropy rate per jump

UnBoundNonLinDecompOp,missing,missing,missing,missing,character,character,UnBoundNonLinDecompOp_by_PoolNames-method

convert to Indexed version

TwopFeedbackModel14

Implementation of a two-pool C14 model with feedback structure

ThreepairMMmodel

Implementation of a 6-pool Michaelis-Menten model

TwopMMmodel

Implementation of a two-pool Michaelis-Menten model

fT.LandT

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

entropyRatePerTime

Entropy rate per time

UnBoundNonLinDecompOp_by_PoolNames-class

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

UnBoundNonLinDecompOp,missing,vector,vector,numeric,ANY,ANY,ANY-method

Constructor for the class with the same name

UnBoundNonLinDecompOp_by_PoolNames

Generic constructor for the class with the same name

fW.Candy

Effects of moisture on decomposition rates according to the Candy model

availableParticleProperties,MCSim-method

automatic title

by_PoolIndex,InFlux_by_PoolName,character,character-method

Convert the pool names to indices

availableParticleProperties

automatic title

by_PoolIndex,InternalFluxList_by_PoolName,character,character-method

automatic title

fW.Skopp

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

getCompartmentalMatrixFunc,BoundLinDecompOp,ANY,ANY-method

automatic title

getCompartmentalMatrixFunc,ConstLinDecompOp,ANY,ANY-method

automatic title

MCSim-class

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

getConstantCompartmentalMatrix

automatic title

fW.Daycent2

Effects of moisture on decomposition rates according to the DAYCENT model

OutFlux_by_PoolIndex

Generic constructor for the class with the same name

OutFlux_by_PoolName-class

S4 class for a single out-flux with source pool name

Model_by_PoolNames

Constructor for Model_by_PoolNames

Model_by_PoolNames,missing,numeric,UnBoundNonLinDecompOp_by_PoolNames,numeric,InFluxList_by_PoolName,missing,missing,missing,missing-method

Create a model(run) described by fluxes

fT.Q10

Effects of temperature on decomposition rates according to a Q10 function

getConstantInFluxVector,ConstInFluxes-method

automatic title

getDecompOp,NlModel-method

Extract the Compartmental Operator

by_PoolIndex,OutFlux_by_PoolName,character,character-method

automatic title

PoolName,PoolIndex-method

convert to string like object

RothCModel

Implementation of the RothCModel

PoolConnection_by_PoolName

automatic title

PoolConnection_by_PoolName-class

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

RespirationCoefficients

helper function to compute respiration coefficients

fW.Demeter

Effects of moisture on decomposition rates according to the DEMETER model

getC,Model-method

Pool Contents for all times

getC,Model_by_PoolNames-method

Pool Contents for all times

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

check_id_length

helper function to check that the length of the argument is exactly 1

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

constructor for data given as 2 column data.frame

SeriesLinearModel

General m-pool linear model with series structure

check_pool_ids,PoolConnection_by_PoolIndex,integer-method

automatic title

SeriesLinearModel14

General m-pool linear C14 model with series structure

getF14R,Model_14-method

automatic title

getF14R

Generic that yields the ^14C fraction for the release flux of all pools and all times

ScalarTimeMap,function,missing,missing,missing,missing-method

manual constructor for just a function

ThreepSeriesModel

Implementation of a three pool model with series structure

ThreepParallelModel14

Implementation of a three-pool C14 model with parallel structure

example.nestedTime2DMatrixList

create an example nested list that can be

fW.Century

Effects of moisture on decomposition rates according to the CENTURY model

fT.Arrhenius

Effects of temperature on decomposition rates according the Arrhenius equation

getFunctionDefinition,InFluxList_by_PoolIndex-method

automatic title

getFunctionDefinition,ConstInFluxes-method

automatic title

TimeMap,missing,missing,missing,numeric,list-method

automatic title

TimeMap,missing,missing,missing,numeric,array-method

automatic title

UnBoundInFluxes-class

automatic title

as.numeric,InFluxList_by_PoolName-method

Convert to a numeric vector with the pool names as names

as.numeric,InternalFluxList_by_PoolName-method

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

availableResidentSets,MCSim-method

automatic title

UnBoundInFluxes,function-method

automatic title

availableResidentSets

automatic title

by_PoolIndex

automatic title

by_PoolIndex,ConstantInternalFluxRateList_by_PoolName,ANY,ANY-method

convert to a list indexed by pool names

by_PoolIndex,ConstantInFluxRate_by_PoolName,ANY,ANY-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

fW.Daycent1

Effects of moisture on decomposition rates according to the DAYCENT model

computeResults

automatic title

getFunctionDefinition,ConstLinDecompOp-method

automatic title

from_integer_flux_lists_with_defaults

helper function

getAccumulatedRelease,Model-method

Compute the time integral of the relaese fluxes over time

fW.Standcarb

Effects of moisture on decomposition rates according to the StandCarb model

cycling

Cycling analysis of compartmental matrices

getConstLinDecompOp

automatic title

getAccumulatedRelease

automatic title

getInFluxes,Model-method

Extract the InFluxes as provided during creation of the model

getFunctionDefinition,InFluxList_by_PoolName-method

automatic title

getConstLinDecompOp,ConstLinDecompOpWithLinearScalarFactor-method

automatic title

getInFluxes,NlModel-method

automatic title

getC14,Model_14-method

automatic title

example.2DGeneralDecompOpArgs

example.2DConstInFluxesFromVector

2D example for constant Influx

getConstantOutFluxRateList_by_PoolIndex

automatic title

getDotOut,TransportDecompositionOperator-method

automatic title

getFunctionDefinition,ConstLinDecompOpWithLinearScalarFactor-method

helper function

getCumulativeC,NlModel-method

automatic title

getDotOut

automatic title

getFunctionDefinition,DecompositionOperator-method

StateIndependentInFluxList_by_PoolName

Generic constructor for the class with the same name

getC14

Generic that yields the ^14C content for all pools and all times

getOutputFluxes,NlModel-method

automatic title

getNumberOfPools,MCSim-method

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

getLinearScaleFactor,ConstLinDecompOpWithLinearScalarFactor-method

automatic title

StateIndependentInFlux_by_PoolIndex-class

Constructor for the class with the same name

fT.Century1

Effects of temperature on decomposition rates according the the CENTURY model

getConstantCompartmentalMatrix,ConstLinDecompOp-method

automatic title

getMeanTransitTime,ConstLinDecompOp-method

automatic title

getTimes

automatic title

getTimeRange,TimeMap-method

The time interval where the function is defined

getReleaseFlux14,Model_14-method

automatic title

turnoverFit

Estimation of the turnover time from a radiocarbon sample.

getTimes,NlModel-method

automatic title

getTimeRange,UnBoundInFluxes-method

automatic title

getOutputFluxes

Generic Function to obtain the fluxes out of of the pools

getOutputReceivers,TransportDecompositionOperator,numeric-method

automatic title

getRightHandSideOfODE

automatic title

getConstantCompartmentalMatrix,ConstLinDecompOpWithLinearScalarFactor-method

automatic title

TimeMap,missing,missing,missing,numeric,numeric-method

automatic title

Yasso07Model

Implementation of the Yasso07 model

UnBoundNonLinDecompOp_by_PoolNames,InternalFluxList_by_PoolName,OutFluxList_by_PoolName,character-method

A flux and pool name based representation of a possibly nonlinear and nonautonomous Compartmental Matrix

ThreepParallelModel

Implementation of a three pool model with parallel structure

by_PoolIndex,ConstantOutFluxRate_by_PoolName,ANY,ANY-method

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

ThreepFeedbackModel14

Implementation of a three-pool C14 model with feedback structure

UnBoundNonLinDecompOp

Generic constructor for the class with the same name

WangThreePoolNonAutonomous_sym

A non-autonomous version of the original Wang 3 pool model

TimeMap,missing,missing,missing,numeric,matrix-method

automatic title

getParticleMonteCarloSimulator

automatic title

getConstantInFluxVector

automatic title

getReleaseFlux,Model-method

The release fluxes $\frac{[content]}{[time]}$ for all pools.

getRightHandSideOfODE,Model_by_PoolNames-method

Provide the (vector valued) derivative of the stocks with respect to time

fT.Standcarb

Effects of temperature on decomposition rates according to the StandCarb model

fT.Century2

Effects of temperature on decomposition rates according the the CENTURY 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)

getCompartmentalMatrixFunc,UnBoundNonLinDecompOp_by_PoolNames,character,character-method

Compartmental Matrix as function of the state vector and time

fT.RothC

Effects of temperature on decomposition rates according to the functions included in the RothC model

getTransitTimeDistributionDensity,ConstLinDecompOp-method

automatic title

by_PoolIndex,InFluxList_by_PoolName,character,character-method

Transform pool names to indices

[[<-,MCSim-method

automatic title

getCompartmentalMatrixFunc

automatic title

getSolution

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

getTransferMatrixFunc

automatic title

getTransferMatrixFunc,TransportDecompositionOperator-method

automatic title

getSolution,Model_by_PoolNames-method

All Fluxes and stocks for all times

initialize,Model-method

Internal method to supervise creation of objects of this class

getTransitTimeDistributionDensity

automatic title

getFormat,Fc-method

automatic title

getConstantInternalFluxRateList_by_PoolIndex,ConstLinDecompOp-method

automatic title

getFormat

automatic title

initialize,UnBoundLinDecompOp-method

automatic title

[,NlModel,character,ANY,ANY-method

automatic title

getTimes,Model-method

Extract the times vector

getTimes,Model_by_PoolNames-method

Extract the times vector

initialize,Model_14-method

Internal method to supervise creation of objects of this class

initialize,NlModel-method

automatic title

initialize,Model_by_PoolNames-method

getValues,ConstFc-method

automatic title

getDecompOp,Model-method

Extract the Compartmental Operator

getNumberOfPools,NlModel-method

automatic title

initialize,TimeMap-method

automatic title

systemAge

System and pool age for constant compartment models

getNumberOfPools,TransportDecompositionOperator-method

automatic title

by_PoolName,ConstantInternalFluxRateList_by_PoolIndex-method

convert to a list indexed by pool names

check_pool_ids

automatic title

by_PoolName,ConstantInFlux_by_PoolIndex-method

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

getValues

automatic title

initialize,UnBoundInFluxes-method

automatic title

getTimeRange,ConstInFluxes-method

automatic title

getTimeRange,ConstLinDecompOp-method

automatic title

getF14,Model_14-method

automatic title

getF14

Generic that yields the ^14C fraction for the content all pools and all times

getTransferCoefficients,NlModel-method

automatic title

pathEntropy

Path Entropy

initialize,TransportDecompositionOperator-method

automatic title

plot,MCSim-method

automatic title

getFunctionDefinition,TimeMap-method

automatic title

getFunctionDefinition,StateDependentInFluxVector-method

automatic title

computeResults,MCSim-method

automatic title

plotPoolGraphFromTupleLists

Helper function to draw connectivity graphs

plot,TimeMap-method

automatic title

transitTime

Transit times for compartment models

example.2DConstFc.Args

example.ConstlinDecompOpFromMatrix

example.2DBoundLinDecompOpFromFunction

plotC14Pool

Plots the output of getF14 for each pool over time

predefinedModels

PREDEFINED MODELS

initialize,DecompositionOperator-method

automatic title

getTransferCoefficients,TransportDecompositionOperator-method

automatic title

getFunctionDefinition

automatic title

getFunctionDefinition,UnBoundLinDecompOp-method

Extracts the time dependent matrix valued function (compartmental matrix)

getParticleMonteCarloSimulator,NlModel-method

automatic title

example.Time2DArrayList

create an example TimeMap from 2D array

listProduct

tensor product of lists

no_outflux_warning

helper function

initialize,MCSim-method

automatic title

plot,Model_by_PoolNames-method

Plot the graph of pool connections

plot,Model-method

Create an overview plot

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

getC,NlModel-method

Pool Contents for all times

getRightHandSideOfODE,Model-method

Derivative of the state variables as function

getC

Calculates the content of the pools

plotCPool

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

[[,MCSim-method

automatic title

getTimeRange,UnBoundLinDecompOp-method

Extracts the time interval for which the function is valid.

getCompartmentalMatrixFunc,UnBoundNonLinDecompOp,ANY,ANY-method

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

getCompartmentalMatrixFunc,TransportDecompositionOperator,ANY,ANY-method

automatic title

getConstantInternalFluxRateList_by_PoolIndex

automatic title

getTimeRange

automatic title

initialize,ConstLinDecompOp-method

automatic title

incubation_experiment

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

state_variable_names

determine the minimum set of statevariables

getF14C,Model_14-method

automatic title

getConstantOutFluxRateList_by_PoolIndex,ConstLinDecompOp-method

automatic title

getReleaseFlux,Model_by_PoolNames-method

automatic title

getInFluxes

Extract the influxes

getFunctionDefinition,TransportDecompositionOperator-method

automatic title

getFunctionDefinition,UnBoundInFluxes-method

automatic title

getF14C

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

getInitialValues,NlModel-method

automatic title

getReleaseFlux,NlModel-method

automatic title

[,Model,character,missing,missing-method

Experimentally overloaded index operator

getTimeRange,ConstLinDecompOpWithLinearScalarFactor-method

automatic title

getTimeRange,DecompositionOperator-method

automatic title

getTransferCoefficients

automatic title

getTransferMatrix

deprecated, use getTransferMatrixFunc instead

plotPoolGraph

Generic plotter

linesCPool

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

linearScalarModel

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

plotPoolGraph,SymbolicModel_by_PoolNames-method

Plot the graph of pool connections