Man pages for SoilR
Models of Soil Organic Matter Decomposition

1~~ Methods for Function 'AbsoluteFractionModern' ~~
10constructor
100Implementation of a two-pool C14 model with series structure
101Implementation of the Yasso07 model
102Implementation of the Yasso model.
103~~ Methods for Function 'as.character' ~~
104creates a character representation of the object in question
105convert BoundInFlux Objects to something printable.
106convert TimeMap Objects to something printable.
107~~ Methods for Function 'availableParticleProperties' ~~
108~~ Methods for Function 'availableParticleSets' ~~
109Implementation of the microbial model Bacwave (bacterial...
11constructor
110Binding of pre- and post-bomb Delta14C curves
111~~ Methods for Function 'computeResults' ~~
112deSolve lsoda wrapper
113Soil CO2 efflux from incubation experiments
114Effects of temperature on decomposition rates according the...
115Effects of temperature on decomposition rates according the...
116Effects of temperature on decomposition rates according the...
117Effects of temperature on decomposition rates according to...
118Effects of temperature on decomposition rates according to...
119Effects of temperature on decomposition rates according to...
12constructor
120Effects of temperature on decomposition rates according to a...
121Effects of temperature on decomposition rates according to a...
122Effects of temperature on decomposition rates according to a...
123Effects of temperature on decomposition rates according to...
124Effects of temperature on decomposition rates according to...
125Effects of temperature on decomposition rates according to a...
126Effects of moisture on decomposition rates according to the...
127Effects of moisture on decomposition rates according to the...
128Effects of moisture on decomposition rates according to the...
129Effects of moisture on decomposition rates according to the...
13constructor
130Effects of moisture on decomposition rates according to the...
131Effects of moisture on decomposition rates according to the...
132Effects of moisture on decomposition rates according to the...
133Effects of moisture on decomposition rates according to the...
134Effects of moisture on decomposition rates according to the...
135Effects of moisture on decomposition rates according to the...
136~~ Methods for Function 'getAccumulatedRelease' ~~
137Calculates the accumulated carbon release from the pools as a...
138time integrals of release fluxes per pool
139~~ Methods for Function 'getC' ~~
14constructor
140Calculates the C content of the pools
141~~ Methods for Function 'getC14' ~~
142Calculates the mass of radiocarbon (14C fraction times C...
143getC14 method Model 14
144getC method Model
145~~ Methods for Function 'getDecompOp' ~~
146~~ Methods for Function 'getDotOut' ~~
147~~ Methods for Function 'getF14' ~~
148Calculates the 14C fraction of all pools
149~~ Methods for Function 'getF14C' ~~
15constructor
150Calculates the average radiocarbon fraction weighted by the...
151read access to the models F14C variable
152~~ Methods for Function 'getF14R' ~~
153Calculates the average radiocarbon fraction weighted by the...
154average radiocarbon fraction weighted by carbonrelease
155radiocarbon
156~~ Methods for Function 'getFormat' ~~
157extract the format string
158~~ Methods for Function 'getFunctionDefinition' ~~
159getFunctionDefinition
16Class '"BoundInFlux"'
160function definition
161getFunctionDefinition method BoundInFlux
162getFunctionDefinition method BoundLinDecompOp
163creates a constant timedependent function and returns it
164getFunctionDefinition method DecompositionOperator
165getFunctionDefinition method TimeMap
166~~ Methods for Function 'getInFluxes' ~~
167~~ Methods for Function 'getInitialValues' ~~
168~~ Methods for Function 'getMeanTransitTime' ~~
169Access to the mean transit time
17~~ Methods for Function 'BoundInFlux' ~~
170compute the mean transit time
171~~ Methods for Function 'getNumberOfPools' ~~
172~~ Methods for Function 'getOutputFluxes' ~~
173~~ Methods for Function 'getOutputReceivers' ~~
174~~ Methods for Function 'getParticleMonteCarloSimulator' ~~
175~~ Methods for Function 'getReleaseFlux' ~~
176Calculates the release of C from each pool
177~~ Methods for Function 'getReleaseFlux14' ~~
178Calculates the mass of radiocarbon in the release flux (14C...
17914C respiration rate for all pools
18generic constructor
180get the release rate for all pools
181~~ Methods for Function 'getTimeRange' ~~
182getTimeRange
183ask for the boundaries of the underlying time interval
184time domain of the function
185ask for the boundaries of the underlying time interval
186return an (infinite) time range since the operator is...
187ask for the boundaries of the underlying time interval
188ask for the boundaries of the underlying time interval
189~~ Methods for Function 'getTimes' ~~
19convert to BoundInFlux
190Extracts the times argument
191getTimes method Model
192~~ Methods for Function 'getTransferCoefficients' ~~
193~~ Methods for Function 'getTransferMatrix' ~~
194~~ Methods for Function 'getTransitTimeDistributionDensity'...
195methods for transit time distributions
196compute the TransitTimeDistributionDensity
197~~ Methods for Function 'getValues' ~~
198~~ Methods for Function 'initialize' ~~
199internal constructor (new)
2~~ Methods for Function...
20constructor
200internal constructor
201initialize called by (new)
202internal constructor
203initialize called by (new)
204internal constructor for Model objects
205An internal constructor for 'Model_14' objects not...
206initialize called by (new)
207Add lines with the output of 'getC14', 'getC', or...
208~~ Methods for Function 'plot' ~~
209Plots the output of 'getC14' for each pool over time
21constructor
210Plots the output of 'getC' or 'getReleaseFlux' for each pool...
211plot method Model
212~~ Methods for Function 'print' ~~
213print method Model
214~~ Methods for Function 'show' ~~
215show method Model
216~~ Methods for Function 'summary' ~~
217summary method Model
218Estimation of the turnover time from a soil radiocarbon...
219~~ Methods for Function '$' ~~
22constructor
220~~ Methods for Function '[' ~~
221~~ Methods for Function '[[' ~~
222~~ Methods for Function '[[<-' ~~
223(experimenta) partially overload [ ] for models
23constructor
24Class '"BoundLinDecompOp"'
25~~ Methods for Function 'BoundLinDecompOp' ~~
26Generic constructor
27convert a ConstLinDecompOp to a BoundLinDecompOp
28create a BoundLinDecompOp from a TimeMap
29a constructor
3Converts its argument to an Absolute Fraction Modern...
30a constructor
31Atmospheric 14C fraction
32Post-bomb atmospheric 14C fraction
33creates an object containing the initial values for the 14C...
34Class '"ConstLinDecompOp"'
35~~ Methods for Function 'ConstLinDecompOp' ~~
36Generic constructor
37construct from matric
38Class '"DecompOp"'
39~~ Methods for Function 'DecompOp' ~~
4Converts from Delta14C to Absolute Fraction Modern
40pass through constructor
41creates a BoundLinDecompOp from a TimeMap object
42creates a ConstanDecompOp from a matrix
43Class '"DecompositionOperator"'
44~~ Methods for Function 'Delta14C' ~~
45~~ Methods for Function...
46Converts its argument from an Absolute Fraction Modern to a...
47Converts Absolute Fraction Modern values to Delta14C
48Converts to Delta14C format
49convert to Absolute Fraction Normal values
5Converts from Delta14C to Absolute Fraction Modern
50Implementation of a the six-pool C14 model proposed by...
51~~ Methods for Function 'GeneralModel' ~~
52A general constructor
53~~ Methods for Function 'GeneralModel_14' ~~
54A general constructor
55a constructor for class Model
56a constructor for class Model_14
57a constructor for class Model <- 14
58a constructor for class Model_ 14
59a constructor for class Model
6convert to Absolute Fraction Normal values
60a constructor for class Model
61a constructor for class Model
62Delta14C in soil CO2 efflux from Harvard Forest
63Atmospheric radiocarbon for the period 1950-2010 from Hua et...
64Implementation of the Introductory Carbon Balance Model...
65Class '"InFlux"'
66~~ Methods for Function 'InFlux' ~~
67pass through constructor
68create a BoundInFlux from a TimeMap object
69Northern Hemisphere atmospheric radiocarbon for the pre-bomb...
7Class '"BoundFc"'
70Atmospheric radiocarbon for the 0-50,000 yr BP period
71Class '"Model"'
72~~ Methods for Function 'Model' ~~
73A general constructor
74Class '"Model_14"'
75~~ Methods for Function 'Model_14' ~~
76A general constructor
77general constructor for class Model
78Implementation of a one pool model
79Implementation of a one-pool C14 model
8~~ Methods for Function 'BoundFc' ~~
80ParallelModel
81helper function to compute respiration coefficients
82Implementation of the RothCModel
83Models of Soil Organic Matter Decomposition
84Implementation of a three pool model with feedback structure
85Implementation of a three-pool C14 model with feedback...
86Implementation of a three pool model with parallel structure
87Implementation of a three-pool C14 model with parallel...
88Implementation of a three pool model with series structure
89Implementation of a three-pool C14 model with series...
9generic constructor
90Implementation of a 6-pool Michaelis-Menten model
91Class '"TimeMap"'
92TimeMap from Dataframe
93basic constructor of the class TimeMap.
94Implementation of a two pool model with feedback structure
95Implementation of a two-pool C14 model with feedback...
96Implementation of a two-pool Michaelis-Menten model
97Implementation of a two pool model with parallel structure
98Implementation of a two-pool C14 model with parallel...
99Implementation of a two pool model with series structure
manMan/as.charactercreates a character representation of the object in question
manMan/C14AtmAtmospheric 14C fraction
manMan/C14Atm_NHPost-bomb atmospheric 14C fraction
manMan/eCO2Soil CO2 efflux from incubation experiments
manMan/HarvardForest14CO2Delta14C in soil CO2 efflux from Harvard Forest
manMan/Hua2013Atmospheric radiocarbon for the period 1950-2010 from Hua et...
manMan/IntCal09Northern Hemisphere atmospheric radiocarbon for the pre-bomb...
manMan/IntCal13Atmospheric radiocarbon for the 0-50,000 yr BP period
SoilR documentation built on May 29, 2017, 10:57 a.m.