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SoilR (version 1.1-23)

Models of Soil Organic Matter Decomposition

Description

This package contains functions for modeling Soil Organic Matter decomposition in terrestrial ecosystems.

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Version

Install

install.packages('SoilR')

Monthly Downloads

409

Version

1.1-23

License

GPL-3

Maintainer

Markus Mueller

Last Published

April 30th, 2014

Functions in SoilR (1.1-23)

as.character-methods

~~ Methods for Function as.character ~~

BoundFc_method__data.frame_missing_missing_missing_character_missing

constructor

fW.Standcarb

Effects of moisture on decomposition rates according to the StandCarb model

eCO2

Soil CO2 efflux from incubation experiments

BoundFc_method__function_numeric_numeric_numeric_character_missing

constructor

getTransitTimeDistributionDensity-methods

~~ Methods for Function getTransitTimeDistributionDensity ~~

getF14R-methods

~~ Methods for Function getF14R ~~

getReleaseFlux_method__Model

get the release rate for all pools

Yasso07Model

Implementation of the Yasso07 model

YassoModel

Implementation of the Yasso model.

getC-methods

~~ Methods for Function getC ~~

getTimeRange_method__BoundInFlux

time domain of the function

fT.linear

Effects of temperature on decomposition rates according to a linear model

fT.Daycent2

Effects of temperature on decomposition rates according to the DAYCENT model

fT.KB

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

getMeanTransitTime-methods

~~ Methods for Function getMeanTransitTime ~~

fW.Candy

Effects of moisture on decomposition rates according to the Candy model

getC_method__Model

getC method Model

BoundInFlux-class

Class "BoundInFlux"

fW.Daycent2

Effects of moisture on decomposition rates according to the DAYCENT model

getF14

Calculates the 14C fraction of all pools

getF14-methods

~~ Methods for Function getF14 ~~

getC14-methods

~~ Methods for Function getC14 ~~

BoundFc_method__data.frame_missing_missing_numeric_character_missing

constructor

getFunctionDefinition_method__ConstLinDecompOp

creates a constant timedependent function and returns it

initialize_method__Model_14

An internal constructor for Model_14 objects not recommended to be used directly in user code.

fW.Demeter

Effects of moisture on decomposition rates according to the DEMETER model

getFunctionDefinition_method__DecompositionOperator

getFunctionDefinition method DecompositionOperator

fT.Standcarb

Effects of temperature on decomposition rates according to the StandCarb model

print-methods

~~ Methods for Function print ~~

getAccumulatedRelease

Calculates the accumulated carbon release from the pools as a function of time

availableParticleSets-methods

~~ Methods for Function availableParticleSets ~~

fW.RothC

Effects of moisture on decomposition rates according to the RothC model

getF14_method__Model_14

radiocarbon

ConstFc

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

ConstLinDecompOp-class

Class "ConstLinDecompOp"

GeneralModel_14

A general constructor

getC14

Calculates the mass of radiocarbon (14C fraction times C stock) in all pools

getTransitTimeDistributionDensity

methods for transit time distributions

computeResults-methods

~~ Methods for Function computeResults ~~

bind.C14curves

Binding of pre- and post-bomb Delta14C curves

getC

Calculates the C content of the pools

IntCal09

Northern Hemisphere atmospheric radiocarbon for the pre-bomb period

getC14_method__Model_14

getC14 method Model 14

getTimeRange_method__ConstLinDecompOp

return an (infinite) time range since the operator is constant

fW.Century

Effects of moisture on decomposition rates according to the CENTURY model

plot_method__Model

plot method Model

as.character_method__TimeMap

convert TimeMap Objects to something printable.

initialize_method__BoundLinDecompOp

initialize called by (new)

BoundFc_method__data.frame_missing_missing_numeric_character_function

constructor

SoilR-package

Models of Soil Organic Matter Decomposition

getInFluxes-methods

~~ Methods for Function getInFluxes ~~

getReleaseFlux14

Calculates the mass of radiocarbon in the release flux (14C fraction times release flux)

getReleaseFlux14_method__Model_14

14C respiration rate for all pools

fT.Century1

Effects of temperature on decomposition rates according the the CENTURY model

BoundFc_method__function_numeric_numeric_missing_character_missing

constructor

fT.Demeter

Effects of temperature on decomposition rates according to the DEMETER model

BoundFc_method__data.frame_missing_missing_missing_character_function

constructor

getNumberOfPools-methods

~~ Methods for Function getNumberOfPools ~~

getAccumulatedRelease-methods

~~ Methods for Function getAccumulatedRelease ~~

getTimeRange

fT.Daycent1

Effects of temperature on decomposition rates according to the DAYCENT model

AbsoluteFractionModern_method__BoundFc

convert to Absolute Fraction Normal values

AbsoluteFractionModern_from_Delta14C-methods

~~ Methods for Function AbsoluteFractionModern_from_Delta14C ~~

plotC14Pool

Plots the output of getC14 for each pool over time

getFunctionDefinition_method__BoundLinDecompOp

getFunctionDefinition method BoundLinDecompOp

TwopSeriesModel14

Implementation of a two-pool C14 model with series structure

fT.RothC

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

getParticleMonteCarloSimulator-methods

~~ Methods for Function getParticleMonteCarloSimulator ~~

getInitialValues-methods

~~ Methods for Function getInitialValues ~~

as.character

creates a character representation of the object in question

getFunctionDefinition-methods

~~ Methods for Function getFunctionDefinition ~~

getFunctionDefinition_method__TimeMap

getFunctionDefinition method TimeMap

initialize_method__DecompositionOperator

initialize called by (new)

plotCPool

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

getOutputReceivers-methods

~~ Methods for Function getOutputReceivers ~~

AbsoluteFractionModern-methods

~~ Methods for Function AbsoluteFractionModern ~~

GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_function_missing

a constructor for class Model <- 14

fT.Century2

Effects of temperature on decomposition rates according the the CENTURY model

getF14C-methods

~~ Methods for Function getF14C ~~

getTimes-methods

~~ Methods for Function getTimes ~~

fW.Daycent1

Effects of moisture on decomposition rates according to the DAYCENT model

deSolve.lsoda.wrapper

deSolve lsoda wrapper

DecompOp_method__TimeMap

creates a BoundLinDecompOp from a TimeMap object

GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_missing_missing_missing_logical

a constructor for class Model

BoundLinDecompOp_method__ConstLinDecompOp

convert a ConstLinDecompOp to a BoundLinDecompOp

ConstLinDecompOp

Generic constructor

BoundInFlux_method__TimeMap_missing_missing_missing_missing

convert to BoundInFlux

BoundInFlux_method__data.frame_missing_missing_missing_missing

constructor

ThreepParallelModel

Implementation of a three pool model with parallel structure

getReleaseFlux14-methods

~~ Methods for Function getReleaseFlux14 ~~

GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_missing_missing

a constructor for class Model

getTimeRange_method__BoundLinDecompOp

ask for the boundaries of the underlying time interval

getDecompOp-methods

~~ Methods for Function getDecompOp ~~

initialize-methods

~~ Methods for Function initialize ~~

getFunctionDefinition

getOutputFluxes-methods

~~ Methods for Function getOutputFluxes ~~

Model_method__numeric_ANY_numeric

general constructor for class Model

DecompOp_method__DecompOp

pass through constructor

GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_missing_logical

a constructor for class Model_ 14

TimeMap.new

basic constructor of the class TimeMap.

BoundLinDecompOp_method__function_numeric_numeric_missing

a constructor

[[-methods

~~ Methods for Function [[ ~~

DecompOp-class

Class "DecompOp"

getFunctionDefinition_method__BoundFc

function definition

TimeMap.from.Dataframe

TimeMap from Dataframe

InFlux_method__InFlux

pass through constructor

[[<--methods

~~ Methods for Function [[<- ~~

show-methods

~~ Methods for Function show ~~

bacwaveModel

Implementation of the microbial model Bacwave (bacterial waves)

TimeMap-class

Class "TimeMap"

DecompositionOperator-class

Class "DecompositionOperator"

GaudinskiModel14

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

getFormat_method__BoundFc

extract the format string

Hua2013

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

getTimes_method__Model

getTimes method Model

getTimeRange_method__BoundFc

ask for the boundaries of the underlying time interval

BoundLinDecompOp_method__function_numeric_numeric_numeric

a constructor

AbsoluteFractionModern_from_Delta14C_method__numeric

Converts from Delta14C to Absolute Fraction Modern

OnepModel

Implementation of a one pool model

TwopSeriesModel

Implementation of a two pool model with series structure

C14Atm_NH

Post-bomb atmospheric 14C fraction

getMeanTransitTime

Access to the mean transit time

initialize_method__BoundFc

internal constructor (new)

fW.Skopp

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

RespirationCoefficients

helper function to compute respiration coefficients

getReleaseFlux

Calculates the release of C from each pool

[_method__Model_character

(experimenta) partially overload [ ] for models

initialize_method__TimeMap

initialize called by (new)

linesCPool

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

getTransferMatrix-methods

~~ Methods for Function getTransferMatrix ~~

print_method__Model

print method Model

fW.Gompertz

Effects of moisture on decomposition rates according to the Gompertz function

getF14C_method__Model_14

read access to the models F14C variable

Model_14-class

Class "Model_14"

Delta14C_from_AbsoluteFractionModern_method__numeric

Converts to Delta14C format

initialize_method__ConstLinDecompOp

internal constructor

AbsoluteFractionModern_from_Delta14C_method__matrix

Converts from Delta14C to Absolute Fraction Modern

plot-methods

~~ Methods for Function plot ~~

TwopMMmodel

Implementation of a two-pool Michaelis-Menten model

BoundLinDecompOp-class

Class "BoundLinDecompOp"

[-methods

~~ Methods for Function [ ~~

getReleaseFlux-methods

~~ Methods for Function getReleaseFlux ~~

BoundFc-methods

~~ Methods for Function BoundFc ~~

BoundInFlux_method__data.frame_missing_missing_numeric_function

constructor

initialize_method__BoundInFlux

internal constructor

getFormat-methods

~~ Methods for Function getFormat ~~

Delta14C_from_AbsoluteFractionModern-methods

~~ Methods for Function Delta14C_from_AbsoluteFractionModern ~~

GeneralModel

A general constructor

fT.Arrhenius

Effects of temperature on decomposition rates according the Arrhenius equation

getDotOut-methods

~~ Methods for Function getDotOut ~~

BoundInFlux

generic constructor

initialize_method__Model

internal constructor for Model objects

BoundInFlux_method__function_numeric_numeric_numeric_missing

constructor

getTimeRange-methods

~~ Methods for Function getTimeRange ~~

availableParticleProperties-methods

~~ Methods for Function availableParticleProperties ~~

Model-class

Class "Model"

getFunctionDefinition_method__BoundInFlux

getFunctionDefinition method BoundInFlux

HarvardForest14CO2

Delta14C in soil CO2 efflux from Harvard Forest

ThreepParallelModel14

Implementation of a three-pool C14 model with parallel structure

Delta14C_from_AbsoluteFractionModern

Converts its argument from an Absolute Fraction Modern to a Delta14C representation

getTimes

Extracts the times argument

getF14C

Calculates the average radiocarbon fraction weighted by the mass of carbon

ThreepFeedbackModel14

Implementation of a three-pool C14 model with feedback structure

TwopFeedbackModel

Implementation of a two pool model with feedback structure

getTransferCoefficients-methods

~~ Methods for Function getTransferCoefficients ~~

show_method__Model

show method Model

DecompOp-methods

~~ Methods for Function DecompOp ~~

IntCal13

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

as.character_method__BoundInFlux

convert BoundInFlux Objects to something printable.

AbsoluteFractionModern_from_Delta14C

Converts its argument to an Absolute Fraction Modern representation

ConstLinDecompOp-methods

~~ Methods for Function ConstLinDecompOp ~~

DecompOp_method__matrix

creates a ConstanDecompOp from a matrix

ThreepFeedbackModel

Implementation of a three pool model with feedback structure

RothCModel

Implementation of the RothCModel

GeneralModel-methods

~~ Methods for Function GeneralModel ~~

getTimeRange_method__DecompositionOperator

ask for the boundaries of the underlying time interval

Model_14-methods

~~ Methods for Function Model_14 ~~

Delta14C-methods

~~ Methods for Function Delta14C ~~

fW.Moyano

Effects of moisture on decomposition rates according to the function proposed by Moyano et al. (2013)

Model

A general constructor

GeneralModel_method__numeric_ANY_numeric

a constructor for class Model

ThreepSeriesModel14

Implementation of a three-pool C14 model with series structure

BoundFc-class

Class "BoundFc"

Delta14C_from_AbsoluteFractionModern_method__matrix

Converts Absolute Fraction Modern values to Delta14C

InFlux_method__TimeMap

create a BoundInFlux from a TimeMap object

getF14R

Calculates the average radiocarbon fraction weighted by the amount of carbon release

C14Atm

Atmospheric 14C fraction

GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_numeric_missing_function_logical

a constructor for class Model_14

TwopFeedbackModel14

Implementation of a two-pool C14 model with feedback structure

getAccumulatedRelease_method__Model

time integrals of release fluxes per pool

ThreepairMMmodel

Implementation of a 6-pool Michaelis-Menten model

TwopParallelModel

Implementation of a two pool model with parallel structure

ICBMModel

Implementation of the Introductory Carbon Balance Model (ICBM)

BoundFc

generic constructor

OnepModel14

Implementation of a one-pool C14 model

ThreepSeriesModel

Implementation of a three pool model with series structure

Model_14

A general constructor

summary_method__Model

summary method Model

GeneralModel_14-methods

~~ Methods for Function GeneralModel_14 ~~

TwopParallelModel14

Implementation of a two-pool C14 model with parallel structure

InFlux-methods

~~ Methods for Function InFlux ~~

BoundLinDecompOp_method__TimeMap_missing_missing_missing

create a BoundLinDecompOp from a TimeMap

BoundInFlux-methods

~~ Methods for Function BoundInFlux ~~

fT.Q10

Effects of temperature on decomposition rates according to a Q10 function

getMeanTransitTime_method__ConstLinDecompOp

compute the mean transit time

fT.LandT

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

getF14R_method__Model_14

average radiocarbon fraction weighted by carbonrelease

getTimeRange_method__TimeMap

ask for the boundaries of the underlying time interval

getValues-methods

~~ Methods for Function getValues ~~

BoundInFlux_method__function_numeric_numeric_missing_missing

constructor

getTransitTimeDistributionDensity_method__ConstLinDecompOp

compute the TransitTimeDistributionDensity

BoundLinDecompOp

Generic constructor

summary-methods

~~ Methods for Function summary ~~

turnoverFit

Estimation of the turnover time from a soil radiocarbon sample.

Delta14C_method__BoundFc

convert to Absolute Fraction Normal values

$-methods

~~ Methods for Function $ ~~

BoundLinDecompOp-methods

~~ Methods for Function BoundLinDecompOp ~~

InFlux-class

Class "InFlux"

Model-methods

~~ Methods for Function Model ~~

GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_missing_ANY_numeric_missing_missing_missing

a constructor for class Model

ParallelModel

ConstLinDecompOp_method__matrix

construct from matric