Models of Soil Organic Matter Decomposition


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Documentation for package ‘SoilR’ version 1.0-7

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

SoilR-package Models of Soil Organic Matter Decomposition

-- A --

AbsoluteFractionModern_from_Delta14C convert its argument to an Absolute Fraction Modern representation
AbsoluteFractionModern_from_Delta14C-method ~~ Methods for Function 'AbsoluteFractionModern_from_Delta14C' ~~
AbsoluteFractionModern_from_Delta14C-methods ~~ Methods for Function 'AbsoluteFractionModern_from_Delta14C' ~~
as.character creates a character representation of the object in question
as.character-method ~~ Methods for Function 'as.character' ~~
as.character-methods ~~ Methods for Function 'as.character' ~~

-- C --

C14Atm $^14C$ fraction in per mille
C14Atm_NH Post-bomb atmospheric 14C fraction

-- D --

Delta14C_from_AbsoluteFractionModern convert its argument from an Absolute Fraction Modern to a Delta14C representation
Delta14C_from_AbsoluteFractionModern-method ~~ Methods for Function 'Delta14C_from_AbsoluteFractionModern' ~~
Delta14C_from_AbsoluteFractionModern-methods ~~ Methods for Function 'Delta14C_from_AbsoluteFractionModern' ~~
deSolve.lsoda.wrapper deSolve lsoda wrapper

-- E --

eCO2 Soil CO2 efflux from incubation experiments

-- F --

FcAtm.from.Dataframe FcAtm from Dataframe
fT.Arrhenius Effects of temperature on decomposition rates according the Arrhenius equation
fT.Century1 Effects of temperature on decomposition rates according the the CENTURY model
fT.Century2 Effects of temperature on decomposition rates according the the CENTURY model
fT.Daycent1 Effects of temperature on decomposition rates according to the DAYCENT model
fT.Daycent2 Effects of temperature on decomposition rates according to the DAYCENT model
fT.Demeter effects of temperature on decomposition rates according to the DEMETER model
fT.KB Effects of temperature on decomposition rates according to a model proposed by M. Kirschbaum (1995)
fT.LandT Effects of temperature on decomposition rates according to a function proposed by Lloyd and Taylor (1994)
fT.linear Effects of temperature on decomposition rates according to a linear model
fT.Q10 Effects of temperature on decomposition rates according to a Q10 function
fT.RothC Effects of temperature on decomposition rates according to the functions included in the RothC model
fT.Standcarb effects of temperature on decomposition rates according to the StandCarb model
fW.Candy Effects of moisture on decomposition rates according to the Candy model
fW.Century Effects of moisture on decomposition rates according to the CENTURY model
fW.Daycent1 Effects of moisture on decomposition rates according to the DAYCENT model
fW.Daycent2 #Effects of moisture on decomposition rates according to the DAYCENT model
fW.Demeter Effects of moisture on decomposition rates according to the DEMETER model
fW.Gompertz Effects of moisture on decomposition rates according to the Gompertz function
fW.Moyano Effects of moisture on decomposition rates according to the function proposed by Moyano et al. (2013)
fW.RothC Effects of moisture on decomposition rates according to the RothC model
fW.Skopp Effects of moisture on decomposition rates according to the function proposed by Skopp et al. 1990
fW.Standcarb Effects of moisture on decomposition rates according to the StandCarb model

-- G --

GaudinskiModel14 Implementation of a the six-pool C14 model proposed by Gaudinski et al. 2000
GeneralModel The most general costructor for class Model
GeneralModel_14 The most general costructor for class Model14
getAccumulatedRelease Calculates the accumulated carbon release from the pools as a function of time
getAccumulatedRelease-method ~~ Methods for Function 'getAccumulatedRelease' ~~
getAccumulatedRelease-methods ~~ Methods for Function 'getAccumulatedRelease' ~~
getC Calculates the C content of the pools
getC-method ~~ Methods for Function 'getC' ~~
getC-methods ~~ Methods for Function 'getC' ~~
getC14 access to the C content of the pools
getC14-method ~~ Methods for Function 'getC14' ~~
getC14-methods ~~ Methods for Function 'getC14' ~~
getF14 access to the C content of the pools
getF14-method ~~ Methods for Function 'getF14' ~~
getF14-methods ~~ Methods for Function 'getF14' ~~
getF14C access to the C release flux from the pools
getF14C-method ~~ Methods for Function 'getF14C' ~~
getF14C-methods ~~ Methods for Function 'getF14C' ~~
getF14R access to the C release flux from the pools
getF14R-method ~~ Methods for Function 'getF14R' ~~
getF14R-methods ~~ Methods for Function 'getF14R' ~~
getFunctionDefinition getFunctionDefinition
getFunctionDefinition-method ~~ Methods for Function 'getFunctionDefinition' ~~
getFunctionDefinition-methods ~~ Methods for Function 'getFunctionDefinition' ~~
getReleaseFlux Calculates the release of C from each pool
getReleaseFlux-method ~~ Methods for Function 'getReleaseFlux' ~~
getReleaseFlux-methods ~~ Methods for Function 'getReleaseFlux' ~~
getReleaseFlux14 access to the C content of the pools
getReleaseFlux14-method ~~ Methods for Function 'getReleaseFlux14' ~~
getReleaseFlux14-methods ~~ Methods for Function 'getReleaseFlux14' ~~
getTimeRange getTimeRange
getTimeRange-method ~~ Methods for Function 'getTimeRange' ~~
getTimeRange-methods ~~ Methods for Function 'getTimeRange' ~~
getTimes extract the times argumen
getTimes-method ~~ Methods for Function 'getTimes' ~~
getTimes-methods ~~ Methods for Function 'getTimes' ~~

-- H --

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

-- I --

ICBMModel Implementation of the Introductory Carbon Balance Model (ICBM)
IntCal09 Northern Hemisphere atmospheric radiocarbon for the pre-bomb period

-- L --

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

-- M --

Model Model
Model-class Model
Model_14 Model_14
Model_14-class Model_14

-- O --

OnepModel Implementation of a one pool model
OnepModel14 Implementation of a one-pool C14 model

-- P --

ParallelModel ParallelModel
plot-method ~~ Methods for Function 'plot' ~~
plot-methods ~~ Methods for Function 'plot' ~~
plotC14Pool Plots the output of 'getC14' for each pool over time
plotCPool Plots the output of 'getC' or 'getReleaseFlux' for each pool over time
print-method ~~ Methods for Function 'print' ~~
print-methods ~~ Methods for Function 'print' ~~

-- R --

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

-- S --

SoilR Models of Soil Organic Matter Decomposition
SoilR.F0.new creates an object containing the initial values for the 14C fraction needed to create models in SoilR
summary-method ~~ Methods for Function 'summary' ~~
summary-methods ~~ Methods for Function 'summary' ~~

-- T --

ThreepFeedbackModel Implementation of a three pool model with feedback structure
ThreepFeedbackModel14 Implementation of a three-pool C14 model with feedback structure
ThreepParallelModel Implementation of a three pool model with parallel structure
ThreepParallelModel14 Implementation of a three-pool C14 model with parallel structure
ThreepSeriesModel Implementation of a three pool model with series structure
ThreepSeriesModel14 Implementation of a three-pool C14 model with series structure
TimeMap TimeMap S4 class
TimeMap-class TimeMap S4 class
TimeMap.from.Dataframe TimeMap from Dataframe
TimeMap.new basic constructor of the class TimeMap.
TwopFeedbackModel Implementation of a two pool model with feedback structure
TwopFeedbackModel14 Implementation of a two-pool C14 model with feedback structure
TwopParallelModel Implementation of a two pool model with parallel structure
TwopParallelModel14 Implementation of a two-pool C14 model with parallel structure
TwopSeriesModel Implementation of a two pool model with series structure
TwopSeriesModel14 Implementation of a two-pool C14 model with series structure

-- misc --

$-method ~~ Methods for Function '$' ~~
$-methods ~~ Methods for Function '$' ~~
[-method Model
[-method ~~ Methods for Function '[' ~~
[-methods ~~ Methods for Function '[' ~~
[[-method ~~ Methods for Function '[[' ~~
[[-methods ~~ Methods for Function '[[' ~~
[[<--method ~~ Methods for Function '[[<-' ~~
[[<--methods ~~ Methods for Function '[[<-' ~~