SoilR: Models of Soil Organic Matter Decomposition

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

Author
Carlos A. Sierra, Markus Mueller
Date of publication
2016-07-25 20:03:57
Maintainer
Markus Mueller <mamueller@bgc-jena.mpg.de>
License
GPL-3
Version
1.1-29

View on R-Forge

Man pages

1
Converts from Delta14C to Absolute Fraction Modern
10
~~ Methods for Function 'availableParticleProperties' ~~
100
~~ Methods for Function 'getAccumulatedRelease' ~~
101
Calculates the accumulated carbon release from the pools as a...
102
getC14 method Model 14
103
~~ Methods for Function 'getC14' ~~
104
Calculates the mass of radiocarbon (14C fraction times C...
105
getC method Model
106
~~ Methods for Function 'getC' ~~
107
Calculates the C content of the pools
108
~~ Methods for Function 'getCumulativeC' ~~
109
~~ Methods for Function 'getDecompOp' ~~
11
~~ Methods for Function 'availableParticleSets' ~~
110
~~ Methods for Function 'getDotOut' ~~
111
read access to the models F14C variable
112
~~ Methods for Function 'getF14C' ~~
113
Calculates the average radiocarbon fraction weighted by the...
114
radiocarbon
115
~~ Methods for Function 'getF14' ~~
116
Calculates the 14C fraction of all pools
117
average radiocarbon fraction weighted by carbonrelease
118
~~ Methods for Function 'getF14R' ~~
119
Calculates the average radiocarbon fraction weighted by the...
12
~~ Methods for Function 'availableResidentSets' ~~
120
extract the format string
121
~~ Methods for Function 'getFormat' ~~
122
creates a constant timedependent function and returns it
123
getFunctionDefinition method DecompositionOperator
124
~~ Methods for Function 'getFunctionDefinition' ~~
125
getFunctionDefinition method TimeMap
126
getFunctionDefinition
127
~~ Methods for Function 'getInFluxes' ~~
128
~~ Methods for Function 'getInitialValues' ~~
129
compute the mean transit time
13
Implementation of the microbial model AWB (Allison,...
130
~~ Methods for Function 'getMeanTransitTime' ~~
131
Access to the mean transit time
132
~~ Methods for Function 'getNumberOfPools' ~~
133
~~ Methods for Function 'getOutputFluxes' ~~
134
~~ Methods for Function 'getOutputReceivers' ~~
135
~~ Methods for Function 'getParticleMonteCarloSimulator' ~~
136
14C respiration rate for all pools
137
~~ Methods for Function 'getReleaseFlux14' ~~
138
Calculates the mass of radiocarbon in the release flux (14C...
139
get the release rate for all pools
14
Implementation of the microbial model Bacwave (bacterial...
140
~~ Methods for Function 'getReleaseFlux' ~~
141
Calculates the release of C from each pool
142
return an (infinite) time range since the operator is...
143
ask for the boundaries of the underlying time interval
144
~~ Methods for Function 'getTimeRange' ~~
145
ask for the boundaries of the underlying time interval
146
getTimeRange
147
getTimes method Model
148
~~ Methods for Function 'getTimes' ~~
149
Extracts the times argument
15
Binding of pre- and post-bomb Delta14C curves
150
~~ Methods for Function 'getTransferCoefficients' ~~
151
~~ Methods for Function 'getTransferMatrix' ~~
152
compute the TransitTimeDistributionDensity
153
~~ Methods for Function 'getTransitTimeDistributionDensity'...
154
methods for transit time distributions
155
~~ Methods for Function 'getValues' ~~
156
Delta14C in soil CO2 efflux from Harvard Forest
157
Atmospheric radiocarbon for the period 1950-2010 from Hua et...
158
Implementation of the Introductory Carbon Balance Model...
159
Class '"InFlux"'
16
Class '"BoundFc"'
160
pass through constructor
161
~~ Methods for Function 'InFlux' ~~
162
create a BoundInFlux from a TimeMap object
163
internal constructor (new)
164
internal constructor
165
initialize called by (new)
166
An internal constructor for 'Model_14' objects not...
167
internal constructor for Model objects
168
~~ Methods for Function 'initialize' ~~
169
initialize called by (new)
17
constructor
170
Northern Hemisphere atmospheric radiocarbon for the pre-bomb...
171
Atmospheric radiocarbon for the 0-50,000 yr BP period
172
Add lines with the output of 'getC14', 'getC', or...
173
Class '"Model_14"'
174
~~ Methods for Function 'Model_14' ~~
175
A general constructor
176
Class '"Model"'
177
general constructor for class Model
178
~~ Methods for Function 'Model' ~~
179
A general constructor
18
constructor
180
Implementation of a one-pool C14 model
181
Implementation of a one pool model
182
ParallelModel
183
Plots the output of 'getF14' for each pool over time
184
Plots the output of 'getC' or 'getReleaseFlux' for each pool...
185
not yet implemented method to plot an overview of several...
186
~~ Methods for Function 'plot' ~~
187
not yet implemented method to print an overview of several...
188
~~ Methods for Function 'print' ~~
189
helper function to compute respiration coefficients
19
constructor
190
Implementation of the RothCModel
191
General m-pool linear C14 model with series structure
192
General m-pool linear model with series structure
193
show method Model
194
~~ Methods for Function 'show' ~~
195
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("SoilR")}
196
summary method Model
197
~~ Methods for Function 'summary' ~~
198
System and pool age for compartment models
199
Implementation of a 6-pool Michaelis-Menten model
2
Converts from Delta14C to Absolute Fraction Modern
20
constructor
200
Implementation of a three-pool C14 model with feedback...
201
Implementation of a three pool model with feedback structure
202
Implementation of a three-pool C14 model with parallel...
203
Implementation of a three pool model with parallel structure
204
Implementation of a three-pool C14 model with series...
205
Implementation of a three pool model with series structure
206
Class '"TimeMap"'
207
TimeMap from Dataframe
208
constructor
209
constructor
21
constructor
210
~~ Methods for Function 'TimeMap' ~~
211
deprecated constructor of the class TimeMap.
212
generic constructor
213
Transit times for compartment models
214
Estimation of the turnover time from a soil radiocarbon...
215
Implementation of a two-pool C14 model with feedback...
216
Implementation of a two pool model with feedback structure
217
Implementation of a two-pool Michaelis-Menten model
218
Implementation of a two-pool C14 model with parallel...
219
Implementation of a linear two pool model with parallel...
22
constructor
220
Implementation of a two-pool C14 model with series structure
221
Implementation of a two pool model with series structure
222
Implementation of the Yasso07 model
223
Implementation of the Yasso model.
224
(experimenta) partially overload [ ] for models
225
~~ Methods for Function '[' ~~
226
~~ Methods for Function '[[<-' ~~
227
~~ Methods for Function '[[' ~~
228
~~ Methods for Function '$' ~~
23
~~ Methods for Function 'BoundFc' ~~
24
generic constructor
25
Class '"BoundInFlux"'
26
constructor
27
constructor
28
constructor
29
constructor
3
~~ Methods for Function...
30
~~ Methods for Function 'BoundInFlux' ~~
31
convert to BoundInFlux
32
generic constructor
33
Class '"BoundLinDecompOp"'
34
convert a ConstLinDecompOp to a BoundLinDecompOp
35
a constructor
36
a constructor
37
~~ Methods for Function 'BoundLinDecompOp' ~~
38
create a BoundLinDecompOp from a TimeMap
39
Generic constructor
4
Converts its argument to an Absolute Fraction Modern...
40
Post-bomb atmospheric 14C fraction
41
Atmospheric 14C fraction
42
Implementation of the Century model
43
~~ Methods for Function 'computeResults' ~~
44
creates an object containing the initial values for the 14C...
45
Class '"ConstLinDecompOp"'
46
construct from matric
47
~~ Methods for Function 'ConstLinDecompOp' ~~
48
Generic constructor
49
Class '"DecompOp"'
5
convert to Absolute Fraction Normal values
50
pass through constructor
51
creates a ConstanDecompOp from a matrix
52
~~ Methods for Function 'DecompOp' ~~
53
creates a BoundLinDecompOp from a TimeMap object
54
Class '"DecompositionOperator"'
55
Converts Absolute Fraction Modern values to Delta14C
56
Converts to Delta14C format
57
~~ Methods for Function...
58
Converts its argument from an Absolute Fraction Modern to a...
59
convert to Absolute Fraction Normal values
6
~~ Methods for Function 'AbsoluteFractionModern' ~~
60
~~ Methods for Function 'Delta14C' ~~
61
deSolve lsoda wrapper
62
Soil CO2 efflux from an incubation experiment
63
~~ Methods for Function 'fromDataFrame' ~~
64
assemble the objects components
65
Effects of temperature on decomposition rates according the...
66
Effects of temperature on decomposition rates according the...
67
Effects of temperature on decomposition rates according the...
68
Effects of temperature on decomposition rates according to...
69
Effects of temperature on decomposition rates according to...
7
~~ Methods for Function 'as.character' ~~
70
Effects of temperature on decomposition rates according to...
71
Effects of temperature on decomposition rates according to a...
72
Effects of temperature on decomposition rates according to a...
73
Effects of temperature on decomposition rates according to a...
74
Effects of temperature on decomposition rates according to a...
75
Effects of temperature on decomposition rates according to...
76
Effects of temperature on decomposition rates according to...
77
Effects of moisture on decomposition rates according to the...
78
Effects of moisture on decomposition rates according to the...
79
Effects of moisture on decomposition rates according to the...
8
convert TimeMap Objects to something printable.
80
Effects of moisture on decomposition rates according to the...
81
Effects of moisture on decomposition rates according to the...
82
Effects of moisture on decomposition rates according to the...
83
Effects of moisture on decomposition rates according to the...
84
Effects of moisture on decomposition rates according to the...
85
Effects of moisture on decomposition rates according to the...
86
Effects of moisture on decomposition rates according to the...
87
Implementation of a the six-pool C14 model proposed by...
88
a constructor for class Model
89
a constructor for class Model_14
9
creates a character representation of the object in question
90
a constructor for class Model <- 14
91
a constructor for class Model_ 14
92
a constructor for class Model
93
a constructor for class Model
94
~~ Methods for Function 'GeneralModel_14' ~~
95
A general constructor
96
a constructor for class Model
97
~~ Methods for Function 'GeneralModel' ~~
98
A general constructor
99
time integrals of release fluxes per pool
manMan/as.character
creates a character representation of the object in question
manMan/C14Atm
Atmospheric 14C fraction
manMan/C14Atm_NH
Post-bomb atmospheric 14C fraction
manMan/eCO2
Soil CO2 efflux from an incubation experiment
manMan/HarvardForest14CO2
Delta14C in soil CO2 efflux from Harvard Forest
manMan/Hua2013
Atmospheric radiocarbon for the period 1950-2010 from Hua et...
manMan/IntCal09
Northern Hemisphere atmospheric radiocarbon for the pre-bomb...
manMan/IntCal13
Atmospheric radiocarbon for the 0-50,000 yr BP period

Files in this package

SoilR/DESCRIPTION
SoilR/NAMESPACE
SoilR/NEWS
SoilR/R
SoilR/R/1_GenericFunctions.R
SoilR/R/1_HelperFunctions.R
SoilR/R/1_TimeMap.R
SoilR/R/2_InFlux.R
SoilR/R/3_BoundInFlux.R
SoilR/R/3_RespirationCoefficients.R
SoilR/R/3_TransportDecompositionOperator.R
SoilR/R/3_deSolve.lsoda.wrapper.R
SoilR/R/4_NlModel.R
SoilR/R/4_SoilR.F0__deprecated_in_1.2.R
SoilR/R/5_MCSim.R
SoilR/R/6_DecopmOp.R
SoilR/R/7_BoundLinDecompOp.R
SoilR/R/7_DecompositionOperator_deprecated_in_1.2.R
SoilR/R/7_Model.R
SoilR/R/AWBmodel.R
SoilR/R/BoundFc.R
SoilR/R/CenturyModel.R
SoilR/R/ConstFc.R
SoilR/R/ConstantDecompositionOperator.R
SoilR/R/FcAtm_deprecated_in_1.2.R
SoilR/R/GaudinskiModel14.R
SoilR/R/GeneralModelMethods.R
SoilR/R/GeneralModel_14Methods.R
SoilR/R/GeneralNlModel.R
SoilR/R/ICBMModel.R
SoilR/R/MeanAge.R
SoilR/R/MeanTT.R
SoilR/R/Model_14.R
SoilR/R/NpYdot.R
SoilR/R/OnepModel.R
SoilR/R/OnepModel14.R
SoilR/R/ParallelModel.R
SoilR/R/RothCModel.R
SoilR/R/SeriesLinearModel.R
SoilR/R/SeriesLinearModel14.R
SoilR/R/SoilR.euler.R
SoilR/R/ThreepFeedbackModel.R
SoilR/R/ThreepFeedbackModel14.R
SoilR/R/ThreepParallelModel.R
SoilR/R/ThreepParallelModel14.R
SoilR/R/ThreepSeriesModel.R
SoilR/R/ThreepSeriesModel14.R
SoilR/R/ThreepairMMmodel.R
SoilR/R/TwopFeedbackModel.R
SoilR/R/TwopFeedbackModel14.R
SoilR/R/TwopMMmodel.R
SoilR/R/TwopParallelModel.R
SoilR/R/TwopParallelModel14.R
SoilR/R/TwopSeriesModel.R
SoilR/R/TwopSeriesModel14.R
SoilR/R/Yasso07Model.R
SoilR/R/YassoModel.R
SoilR/R/bacwaveModel.R
SoilR/R/bind.C14curves.R
SoilR/R/fT.Arrhenius.R
SoilR/R/fT.Century1.R
SoilR/R/fT.Century2.R
SoilR/R/fT.Daycent1.R
SoilR/R/fT.Daycent2.R
SoilR/R/fT.Demeter.R
SoilR/R/fT.KB.R
SoilR/R/fT.LandT.R
SoilR/R/fT.Q10.R
SoilR/R/fT.RothC.R
SoilR/R/fT.Standcarb.R
SoilR/R/fT.linear.R
SoilR/R/fW.Candy.R
SoilR/R/fW.Century.R
SoilR/R/fW.Daycent1.R
SoilR/R/fW.Daycent2.R
SoilR/R/fW.Demeter.R
SoilR/R/fW.Gompertz.R
SoilR/R/fW.Moyano.R
SoilR/R/fW.RothC.R
SoilR/R/fW.Skopp.R
SoilR/R/fW.Standcarb.R
SoilR/R/linMaker.R
SoilR/R/linesCPool.R
SoilR/R/plotC14Pool.R
SoilR/R/plotCPool.R
SoilR/R/solver.R
SoilR/R/spectralNorm.R
SoilR/R/supported14CFractionFormats.R
SoilR/R/systemAge.R
SoilR/R/testhelpers.R
SoilR/R/transitTime.R
SoilR/R/turnoverFit.R
SoilR/R/vecFuncMaker.R
SoilR/R/warnings.R
SoilR/build
SoilR/build/partial.rdb
SoilR/build/vignette.rds
SoilR/data
SoilR/data/C14Atm.rda
SoilR/data/C14Atm_NH.rda
SoilR/data/HarvardForest14CO2.rda
SoilR/data/Hua2013.rda
SoilR/data/IntCal09.rda
SoilR/data/IntCal13.rda
SoilR/data/eCO2.rda
SoilR/inst
SoilR/inst/CITATION
SoilR/inst/doc
SoilR/inst/doc/GeneralModel.R
SoilR/inst/doc/GeneralModel.Rnw
SoilR/inst/doc/GeneralModel.pdf
SoilR/inst/doc/ParameterEstimation.R
SoilR/inst/doc/ParameterEstimation.Rnw
SoilR/inst/doc/ParameterEstimation.pdf
SoilR/inst/extdata
SoilR/inst/extdata/inputFluxForVignetteGeneralModel
SoilR/inst/extdata/inputFluxForVignetteGeneralModelShort
SoilR/inst/tests
SoilR/inst/tests/GlobalEmissions.csv
SoilR/inst/tests/Rtest.R
SoilR/inst/tests/addHeader.sh
SoilR/inst/tests/all.R
SoilR/inst/tests/c14test.R
SoilR/inst/tests/cRtest.sh
SoilR/inst/tests/csall.sh
SoilR/inst/tests/doubleExp.R
SoilR/inst/tests/exall.R
SoilR/inst/tests/example.GeneralModel_14.R
SoilR/inst/tests/example.getC.R
SoilR/inst/tests/example.getF14R_method__Model_14.R
SoilR/inst/tests/example.getReleaseFlux14_method__Model_14.R
SoilR/inst/tests/example.getReleaseFlux_method__Model.R
SoilR/inst/tests/example.getTimeRange_method__TimeMap.R
SoilR/inst/tests/example.initialize_method__Model.R
SoilR/inst/tests/example.initialize_method__Model_14.R
SoilR/inst/tests/prolog.R
SoilR/inst/tests/runit.2TwopSerial_linear_vs_nonlinear.R
SoilR/inst/tests/runit.BackwardTransferTime.R
SoilR/inst/tests/runit.BoundFc.R
SoilR/inst/tests/runit.BoundLinDecomOp.R
SoilR/inst/tests/runit.Conversion.R
SoilR/inst/tests/runit.DeprecationWarnings.R
SoilR/inst/tests/runit.Interfaces.R
SoilR/inst/tests/runit.LinearDecompositionOperator.R
SoilR/inst/tests/runit.MeanAge.R
SoilR/inst/tests/runit.MeanAge2.R
SoilR/inst/tests/runit.MeanAge3.R
SoilR/inst/tests/runit.Model.R
SoilR/inst/tests/runit.Model_14.R
SoilR/inst/tests/runit.NlModel.R
SoilR/inst/tests/runit.NonlinearAtmosphericModel.R
SoilR/inst/tests/runit.SoilRF0.R
SoilR/inst/tests/runit.SoilRPaper1.R
SoilR/inst/tests/runit.ThreepFeedback_MCSim.R
SoilR/inst/tests/runit.ThreepSerialFeedback_linear_vs_nonlinear.R
SoilR/inst/tests/runit.ThreepSerial_linear_vs_nonlinear.R
SoilR/inst/tests/runit.TimeMap.R
SoilR/inst/tests/runit.TimeReversedSolution.R
SoilR/inst/tests/runit.TwopSerial_MCSim.R
SoilR/inst/tests/runit.TwopSerial_linear_vs_nonlinear.R
SoilR/inst/tests/runit.check.pass.R
SoilR/inst/tests/runit.formatConversion.R
SoilR/inst/tests/runit.manuel.Manzoni.op.R
SoilR/inst/tests/runit.nonlinear.R
SoilR/inst/tests/runit.operators.R
SoilR/inst/tests/runit.testNumberOfPools.R
SoilR/inst/tests/runit.turnoverFit.R
SoilR/inst/tests/sall.R
SoilR/inst/tests/single_test.R
SoilR/inst/tests/testhelpers.R
SoilR/man
SoilR/man/1.Rd
SoilR/man/10.Rd
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SoilR/man/48.Rd
SoilR/man/49.Rd
SoilR/man/5.Rd
SoilR/man/50.Rd
SoilR/man/51.Rd
SoilR/man/52.Rd
SoilR/man/53.Rd
SoilR/man/54.Rd
SoilR/man/55.Rd
SoilR/man/56.Rd
SoilR/man/57.Rd
SoilR/man/58.Rd
SoilR/man/59.Rd
SoilR/man/6.Rd
SoilR/man/60.Rd
SoilR/man/61.Rd
SoilR/man/62.Rd
SoilR/man/63.Rd
SoilR/man/64.Rd
SoilR/man/65.Rd
SoilR/man/66.Rd
SoilR/man/67.Rd
SoilR/man/68.Rd
SoilR/man/69.Rd
SoilR/man/7.Rd
SoilR/man/70.Rd
SoilR/man/71.Rd
SoilR/man/72.Rd
SoilR/man/73.Rd
SoilR/man/74.Rd
SoilR/man/75.Rd
SoilR/man/76.Rd
SoilR/man/77.Rd
SoilR/man/78.Rd
SoilR/man/79.Rd
SoilR/man/8.Rd
SoilR/man/80.Rd
SoilR/man/81.Rd
SoilR/man/82.Rd
SoilR/man/83.Rd
SoilR/man/84.Rd
SoilR/man/85.Rd
SoilR/man/86.Rd
SoilR/man/87.Rd
SoilR/man/88.Rd
SoilR/man/89.Rd
SoilR/man/9.Rd
SoilR/man/90.Rd
SoilR/man/91.Rd
SoilR/man/92.Rd
SoilR/man/93.Rd
SoilR/man/94.Rd
SoilR/man/95.Rd
SoilR/man/96.Rd
SoilR/man/97.Rd
SoilR/man/98.Rd
SoilR/man/99.Rd
SoilR/man/manMan
SoilR/man/manMan/C14Atm.Rd
SoilR/man/manMan/C14Atm_NH.Rd
SoilR/man/manMan/HarvardForest14CO2.Rd
SoilR/man/manMan/Hua2013.Rd
SoilR/man/manMan/IntCal09.Rd
SoilR/man/manMan/IntCal13.Rd
SoilR/man/manMan/as.character.Rd
SoilR/man/manMan/eCO2.Rd
SoilR/vignettes
SoilR/vignettes/GeneralModel.Rnw
SoilR/vignettes/ParameterEstimation.Rnw