SoilR1.2.107 package

Convert the pool names to indices

Transform pool names to indices

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constructor from strings of the form 'x->y' new object with the source...

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

convert to a list indexed by pool names

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

convert to a list indexed by pool names

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

convert to a list indexed by pool names

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Implementation of the Century model

Implementation of a radiocarbon version of the Century model

helper function

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

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Check pool ids

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Computes results

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

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

Subclass of list that is guaranteed to contain only elements of type C...

constructor from ConstInFluxes

constructor from a normal list

constructor from numeric vector

Generic constructor for the class with the same name

Subclass of list that is guaranteed to contain only elements of type C...

Generic constructor for the class with the same name

Describes a flux rates.

Extract the times vector

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Time vector of SoilR object

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Transfer coefficients

deprecated, use getTransferMatrixFunc instead

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Transfer matrix function

Transit time distribution obtained through a numerical simulation. It ...

Transit time distribution for SoilR objects

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Get values of SoilR object

Implementation of the ICBM/N model

Implementation of the Introductory Carbon Balance Model (ICBM)

Generic constructor for the class with the same name

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

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

Generic constructor for the class with the same name

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

Constructor from an ordered pair of PoolName (string like) and functio...

Generic constructor for an influx to a single pool from an ordered pai...

A virtual S4-class representing (different subclasses) of in-fluxes to...

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A generic factory for subclasses of InFluxes

Describes a list of flux rates.

constructor from a normal list after checking the elements

Generic constructor for the class with the same name

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

constructor from a normal list

Generic constructor for the class with the same name

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Internal method to supervise creation of objects of this class

Internal method to supervise creation of objects of this class

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S4-class for a single internal flux with source and destination pools ...

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

Generic constructor for the class with the same name

S4-class for a single internal flux with source and destination pools ...

constructor from an ordered pair of PoolName (string like) objects and...

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Generic constructor for the class with the same name

S4-class for a list of internal fluxes with source and destination poo...

Constructor from a normal list after checking the elements

Generic constructor for the class with the same name

S4-class for a list of internal fluxes with indexed by (source and des...

constructor from a normal list

Generic constructor for the class with the same name

Extract the times vector

Calculates all stocks all fluxes to ,in and out of the compartment sys...

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Time range of a simulation described in an object of class ConstLinDec...

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The time interval where the function is defined

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Extracts the time interval for which the function is valid.

Time range of a model simulation

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Conversion of radiocarbon values

Conversion of radiocarbon values

Conversion of radiocarbon values, from Delta14C to absolute fraction m...

Conversion of radiocarbon values

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Add elements to plot

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Convert to a numeric vector with the pool names as names

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

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

Convert to a numeric vector with the pool names as names

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Available particle properties

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Available particle sets

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Available resident sets

Implementation of the microbial model AWB (Allison, Wallenstein, Bradf...

Implementation of the microbial model Bacwave (bacterial waves)

Binding of pre- and post-bomb Delta14C curves

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S4-class to represent atmospheric 14C concentration as scalar function...

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Bound Fc object

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constructor for BoundInFluxes

Creates an object of class BoundLinDecompOp

A S4 class to represent a linear compartmental operator defined on tim...

A converter

Generic constructor for the class with the same name

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

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

convert to a list indexed by pool names

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

convert to a list indexed by pool names

convert a function f of to f_vec

Describes a flux rates.

Constructor for the class with the same name

S4 class representing a constant internal flux rate

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Generic constructor for the class with the same name

constructor with argument conversion

S4-class to represent a constant internal flux rate with source and ta...

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

Generic constructor for the class with the same name

Describes a list of flux rates.

constructor from a normal list

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Generic constructor for the class with the same name

Describes a list of flux rates.

Constructor from a normal list of fluxes

Generic constructor for the class with the same name

S4 Class to represent a single constant out-flux rate with the source ...

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Generic constructor for the class with the same name

S4 Class to represent a single constant out-flux rate with the source ...

Describes a list of flux rates.

constructor from a normal list

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Generic constructor for the class with the same name

Describes a list of flux rates.

constructor from a normal list

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Generic constructor for the class with the same name

S4 class representing a constant 14C fraction

creates an object containing the initial values for the 14C fraction n...

S4 class for a constant influx vector

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Constant input fluxes

A class to represent a constant (=nonautonomous,linear) compartmental ...

Constructor of object of ConstLinDecompOp class

Generic constructor for the class with the same name

Generic constructor for the class with the same name

A class to represent a constant (=nonautonomous,linear) compartmental ...

Generic constructor for the class with the same name

Cycling analysis of compartmental matrices

S4-class to represent compartmental operators

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Conversion of radiocarbon values

Conversion of radiocarbon values

Conversion of radiocarbon values

Conversion of radiocarbon values

deSolve.lsoda.wrapper

Entropy rate per jump

Entropy rate per time

euler

example.2DBoundInFluxesFromFunction

example.2DBoundLinDecompOpFromFunction

example.2DConstFc.Args

2D example for constant Influx

example.2DGeneralDecompOpArgs

example.2DInFluxes.Args

example.2DUnBoundLinDecompOpFromFunction

example.ConstlinDecompOpFromMatrix

create an example nested list that can be

create an example TimeMap from 2D array

create an example TimeFrame from 3D array

create an example TimeFrame from 3D array

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FcAtm.from.Dataframe

helper function

Effects of temperature on decomposition rates according the Arrhenius ...

Effects of temperature on decomposition rates according the the CENTUR...

Effects of temperature on decomposition rates according the the CENTUR...

Effects of temperature on decomposition rates according to the DAYCENT...

Effects of temperature on decomposition rates according to the DAYCENT...

Effects of temperature on decomposition rates according to the DEMETER...

Effects of temperature on decomposition rates according to a model pro...

Effects of temperature on decomposition rates according to a function ...

Effects of temperature on decomposition rates according to a linear mo...

Effects of temperature on decomposition rates according to a Q10 funct...

Effects of temperature on decomposition rates according to the functio...

Effects of temperature on decomposition rates according to the StandCa...

Effects of moisture on decomposition rates according to the Candy mode...

Effects of moisture on decomposition rates according to the CENTURY mo...

Effects of moisture on decomposition rates according to the DAYCENT mo...

Effects of moisture on decomposition rates according to the DAYCENT mo...

Effects of moisture on decomposition rates according to the DEMETER mo...

Effects of moisture on decomposition rates according to the Gompertz f...

Effects of moisture on decomposition rates according to the function p...

Effects of moisture on decomposition rates according to the RothC mode...

Effects of moisture on decomposition rates according to the function p...

Effects of moisture on decomposition rates according to the StandCarb ...

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

Pass through factory for objects of subclasses of DecompOp

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A generic factory for subclasses of GeneralDecompOp

additional function to create Models

create objects of class Model_14

Use this function to create objects of class NlModel.

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generic factory for this virtual class

General pool Id

Compute the time integral of the relaese fluxes over time

Accumulated release flux out of the pools

Pool Contents for all times

Pool Contents for all times

Pool Contents for all times

Calculates the content of the pools

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

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Compartmental matrix function

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Extract the matrix valued function of time and state vector for the co...

Compartmental matrix function

Constant compartmental matrix

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Constant compartmental matrix

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Input flux vector

Constant internal flux rate list by pool index

Constant internal flux rate list by pool index

Constant out flux rate list by pool index

Constant out flux rate list by pool index

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Constant linear decomposition operator

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Cummulative pool contents

Extract the Compartmental Operator

Extract the Compartmental Operator

Decomposition operator of a model

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Dot out

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

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Generic that yields the 14C fraction for the cumulative content of all...

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Generic that yields the 14C fraction for the release flux of all pools...

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Get format of SoilR object

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Function describing an object of class ConstLinDecompOp

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

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Extracts the time dependent matrix valued function (compartmental matr...

Function definition of SoilR model

Extract the InFluxes as provided during creation of the model

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Extract the influxes

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Initial values of SoilR object

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Linear scale factor

Mean transit time obtained through a numerical simulation. It produces...

Mean transit time for SoilR objects

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Number of pools in a model

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Generic Function to obtain the fluxes out of of the pools

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Pools receiving outputs from other pools

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The release fluxes $[content]/[time]$ for all pools.

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Generic Function to obtain the vector of release fluxes out of the poo...

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Generic that yields the 14C fraction in the release flux

Derivative of the state variables as function

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

Right hand side of ODE of a SoilR model

All Fluxes and stocks for all times

Implementation of a general model for linear non-autonomous systems wi...

Add lines with the output of getC14, getC, or getReleaseFlux to ...

tensor product of lists

Experimental Class for a Monte Carlo Simulation of particles leaving t...

S4 class representing a model run

Constructor for class Model

S4-class to represent a 14C model run

general constructor for class Model_14

A model run based on flux functions

Constructor for Model_by_PoolNames

deprecated class for a non-linear model run.

alternative Constructor with pool names helper function

Implementation of a one pool model

Implementation of a one-pool C14 model

Generic constructor for the class with the same name

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

constructor from a PoolIndex (integer like) objects and a function wit...

Generic constructor for the class with the same name

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

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

Generic constructor for the class with the same name

A list of outfluxes

constructor from a normal list

Generic constructor for the class with the same name

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

constructor from a normal list

Generic constructor for the class with the same name

models for unconnected pools

Path Entropy

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Create an overview plot

Plot the graph of pool connections

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Plots the output of getF14 for each pool over time

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

Plot the graph of pool connections

Generic plotter

Helper function to draw connectivity graphs

constructor from an ordered pair of PoolId objects

Objects that have a source and a destination described by integer like...

constructor from strings of the form '1_to_2'

Pool connection by pool index

constructor from an ordered pair of PoolName objects

Objects that have a source and a destination determined by a string li...

Pool connection by pool name

common class for pool ids

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

S4 class for pool indices

construct from number

pass through constructor fron an object of the same class

convert to number like object

Pool index

construct from string with checks

class for pool-name-strings

convert to string like object

pass through constructor fron an object of the same class

Pool name

PREDEFINED MODELS

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helper function to compute respiration coefficients

Implementation of the RothCModel

S4 class for a scalar time dependent function on a finite time interva...

constructor for data given as 2 column data.frame

manual constructor for just a function

manual constructor for a function and an interval

special case for a time map from a constant

constructor for data and times given as vectors

Constructor for ScalarTimeMap-class

General m-pool linear model with series structure

General m-pool linear C14 model with series structure

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SoilR

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

determine the minimum set of statevariables

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

Constructor for the class with the same name

Subclass of list that is guaranteed to contain only elements of type S...

constructor from a normal list

Generic constructor for the class with the same name

Generic constructor for the class with the same name

Experimentally overloaded index operator

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A symbolic model description based on flux functions

System and pool age for constant compartment models

Implementation of a 6-pool Michaelis-Menten model

Implementation of a three pool model with feedback structure

Implementation of a three-pool C14 model with feedback structure

Implementation of a three pool model with parallel structure

Implementation of a three-pool C14 model with parallel structure

Implementation of a three pool model with series structure

Implementation of a three-pool C14 model with series structure

S4 class for a time dependent function

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manual constructor for just a function

manual constructor for a function and an interval

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TimeMap.from.Dataframe

deprecated constructor of the class TimeMap.

Constructor for TimeMap-class

The time interval where both functions are defined

Transit times for compartment models

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Estimation of the turnover time from a radiocarbon sample.

Implementation of a two pool model with feedback structure

Implementation of a two-pool C14 model with feedback structure

Implementation of a two-pool Michaelis-Menten model

Implementation of a linear two pool model with parallel structure

Implementation of a two-pool C14 model with parallel structure

Implementation of a two pool model with series structure

Implementation of a two-pool C14 model with series structure

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Unbound input fluxes

An S4 class to represent a linear nonautonomous compartmental matrix

Generic constructor for the class with the same name

Generic constructor for the class with the same name

An S4 class to represent a nonlinear nonautonomous compartmental matri...

Constructor for the class with the same name

Constructor for the class with the same name

Generic constructor for the class with the same name

An S4 class to represent the of nonlinear nonautonomous compartmental ...

Generic constructor for the class with the same name

Implementation of the Yasso07 model

Implementation of the Yasso model.