Models of Soil Organic Matter Decomposition

1 | ~~ Methods for Function 'AbsoluteFractionModern' ~~ |

10 | constructor |

100 | Implementation of a two-pool C14 model with series structure |

101 | Implementation of the Yasso07 model |

102 | Implementation of the Yasso model. |

103 | ~~ Methods for Function 'as.character' ~~ |

104 | creates a character representation of the object in question |

105 | convert BoundInFlux Objects to something printable. |

106 | convert TimeMap Objects to something printable. |

107 | ~~ Methods for Function 'availableParticleProperties' ~~ |

108 | ~~ Methods for Function 'availableParticleSets' ~~ |

109 | Implementation of the microbial model Bacwave (bacterial... |

11 | constructor |

110 | Binding of pre- and post-bomb Delta14C curves |

111 | ~~ Methods for Function 'computeResults' ~~ |

112 | deSolve lsoda wrapper |

113 | Soil CO2 efflux from incubation experiments |

114 | Effects of temperature on decomposition rates according the... |

115 | Effects of temperature on decomposition rates according the... |

116 | Effects of temperature on decomposition rates according the... |

117 | Effects of temperature on decomposition rates according to... |

118 | Effects of temperature on decomposition rates according to... |

119 | Effects of temperature on decomposition rates according to... |

12 | constructor |

120 | Effects of temperature on decomposition rates according to a... |

121 | Effects of temperature on decomposition rates according to a... |

122 | Effects of temperature on decomposition rates according to a... |

123 | Effects of temperature on decomposition rates according to... |

124 | Effects of temperature on decomposition rates according to... |

125 | Effects of temperature on decomposition rates according to a... |

126 | Effects of moisture on decomposition rates according to the... |

127 | Effects of moisture on decomposition rates according to the... |

128 | Effects of moisture on decomposition rates according to the... |

129 | Effects of moisture on decomposition rates according to the... |

13 | constructor |

130 | Effects of moisture on decomposition rates according to the... |

131 | Effects of moisture on decomposition rates according to the... |

132 | Effects of moisture on decomposition rates according to the... |

133 | Effects of moisture on decomposition rates according to the... |

134 | Effects of moisture on decomposition rates according to the... |

135 | Effects of moisture on decomposition rates according to the... |

136 | ~~ Methods for Function 'getAccumulatedRelease' ~~ |

137 | Calculates the accumulated carbon release from the pools as a... |

138 | time integrals of release fluxes per pool |

139 | ~~ Methods for Function 'getC' ~~ |

14 | constructor |

140 | Calculates the C content of the pools |

141 | ~~ Methods for Function 'getC14' ~~ |

142 | Calculates the mass of radiocarbon (14C fraction times C... |

143 | getC14 method Model 14 |

144 | getC method Model |

145 | ~~ Methods for Function 'getDecompOp' ~~ |

146 | ~~ Methods for Function 'getDotOut' ~~ |

147 | ~~ Methods for Function 'getF14' ~~ |

148 | Calculates the 14C fraction of all pools |

149 | ~~ Methods for Function 'getF14C' ~~ |

15 | constructor |

150 | Calculates the average radiocarbon fraction weighted by the... |

151 | read access to the models F14C variable |

152 | ~~ Methods for Function 'getF14R' ~~ |

153 | Calculates the average radiocarbon fraction weighted by the... |

154 | average radiocarbon fraction weighted by carbonrelease |

155 | radiocarbon |

156 | ~~ Methods for Function 'getFormat' ~~ |

157 | extract the format string |

158 | ~~ Methods for Function 'getFunctionDefinition' ~~ |

159 | getFunctionDefinition |

16 | Class '"BoundInFlux"' |

160 | function definition |

161 | getFunctionDefinition method BoundInFlux |

162 | getFunctionDefinition method BoundLinDecompOp |

163 | creates a constant timedependent function and returns it |

164 | getFunctionDefinition method DecompositionOperator |

165 | getFunctionDefinition method TimeMap |

166 | ~~ Methods for Function 'getInFluxes' ~~ |

167 | ~~ Methods for Function 'getInitialValues' ~~ |

168 | ~~ Methods for Function 'getMeanTransitTime' ~~ |

169 | Access to the mean transit time |

17 | ~~ Methods for Function 'BoundInFlux' ~~ |

170 | compute 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' ~~ |

176 | Calculates the release of C from each pool |

177 | ~~ Methods for Function 'getReleaseFlux14' ~~ |

178 | Calculates the mass of radiocarbon in the release flux (14C... |

179 | 14C respiration rate for all pools |

18 | generic constructor |

180 | get the release rate for all pools |

181 | ~~ Methods for Function 'getTimeRange' ~~ |

182 | getTimeRange |

183 | ask for the boundaries of the underlying time interval |

184 | time domain of the function |

185 | ask for the boundaries of the underlying time interval |

186 | return an (infinite) time range since the operator is... |

187 | ask for the boundaries of the underlying time interval |

188 | ask for the boundaries of the underlying time interval |

189 | ~~ Methods for Function 'getTimes' ~~ |

19 | convert to BoundInFlux |

190 | Extracts the times argument |

191 | getTimes method Model |

192 | ~~ Methods for Function 'getTransferCoefficients' ~~ |

193 | ~~ Methods for Function 'getTransferMatrix' ~~ |

194 | ~~ Methods for Function 'getTransitTimeDistributionDensity'... |

195 | methods for transit time distributions |

196 | compute the TransitTimeDistributionDensity |

197 | ~~ Methods for Function 'getValues' ~~ |

198 | ~~ Methods for Function 'initialize' ~~ |

199 | internal constructor (new) |

2 | ~~ Methods for Function... |

20 | constructor |

200 | internal constructor |

201 | initialize called by (new) |

202 | internal constructor |

203 | initialize called by (new) |

204 | internal constructor for Model objects |

205 | An internal constructor for 'Model_14' objects not... |

206 | initialize called by (new) |

207 | Add lines with the output of 'getC14', 'getC', or... |

208 | ~~ Methods for Function 'plot' ~~ |

209 | Plots the output of 'getC14' for each pool over time |

21 | constructor |

210 | Plots the output of 'getC' or 'getReleaseFlux' for each pool... |

211 | plot method Model |

212 | ~~ Methods for Function 'print' ~~ |

213 | print method Model |

214 | ~~ Methods for Function 'show' ~~ |

215 | show method Model |

216 | ~~ Methods for Function 'summary' ~~ |

217 | summary method Model |

218 | Estimation of the turnover time from a soil radiocarbon... |

219 | ~~ Methods for Function '$' ~~ |

22 | constructor |

220 | ~~ Methods for Function '[' ~~ |

221 | ~~ Methods for Function '[[' ~~ |

222 | ~~ Methods for Function '[[<-' ~~ |

223 | (experimenta) partially overload [ ] for models |

23 | constructor |

24 | Class '"BoundLinDecompOp"' |

25 | ~~ Methods for Function 'BoundLinDecompOp' ~~ |

26 | Generic constructor |

27 | convert a ConstLinDecompOp to a BoundLinDecompOp |

28 | create a BoundLinDecompOp from a TimeMap |

29 | a constructor |

3 | Converts its argument to an Absolute Fraction Modern... |

30 | a constructor |

31 | Atmospheric 14C fraction |

32 | Post-bomb atmospheric 14C fraction |

33 | creates an object containing the initial values for the 14C... |

34 | Class '"ConstLinDecompOp"' |

35 | ~~ Methods for Function 'ConstLinDecompOp' ~~ |

36 | Generic constructor |

37 | construct from matric |

38 | Class '"DecompOp"' |

39 | ~~ Methods for Function 'DecompOp' ~~ |

4 | Converts from Delta14C to Absolute Fraction Modern |

40 | pass through constructor |

41 | creates a BoundLinDecompOp from a TimeMap object |

42 | creates a ConstanDecompOp from a matrix |

43 | Class '"DecompositionOperator"' |

44 | ~~ Methods for Function 'Delta14C' ~~ |

45 | ~~ Methods for Function... |

46 | Converts its argument from an Absolute Fraction Modern to a... |

47 | Converts Absolute Fraction Modern values to Delta14C |

48 | Converts to Delta14C format |

49 | convert to Absolute Fraction Normal values |

5 | Converts from Delta14C to Absolute Fraction Modern |

50 | Implementation of a the six-pool C14 model proposed by... |

51 | ~~ Methods for Function 'GeneralModel' ~~ |

52 | A general constructor |

53 | ~~ Methods for Function 'GeneralModel_14' ~~ |

54 | A general constructor |

55 | a constructor for class Model |

56 | a constructor for class Model_14 |

57 | a constructor for class Model <- 14 |

58 | a constructor for class Model_ 14 |

59 | a constructor for class Model |

6 | convert to Absolute Fraction Normal values |

60 | a constructor for class Model |

61 | a constructor for class Model |

62 | Delta14C in soil CO2 efflux from Harvard Forest |

63 | Atmospheric radiocarbon for the period 1950-2010 from Hua et... |

64 | Implementation of the Introductory Carbon Balance Model... |

65 | Class '"InFlux"' |

66 | ~~ Methods for Function 'InFlux' ~~ |

67 | pass through constructor |

68 | create a BoundInFlux from a TimeMap object |

69 | Northern Hemisphere atmospheric radiocarbon for the pre-bomb... |

7 | Class '"BoundFc"' |

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

71 | Class '"Model"' |

72 | ~~ Methods for Function 'Model' ~~ |

73 | A general constructor |

74 | Class '"Model_14"' |

75 | ~~ Methods for Function 'Model_14' ~~ |

76 | A general constructor |

77 | general constructor for class Model |

78 | Implementation of a one pool model |

79 | Implementation of a one-pool C14 model |

8 | ~~ Methods for Function 'BoundFc' ~~ |

80 | ParallelModel |

81 | helper function to compute respiration coefficients |

82 | Implementation of the RothCModel |

83 | Models of Soil Organic Matter Decomposition |

84 | Implementation of a three pool model with feedback structure |

85 | Implementation of a three-pool C14 model with feedback... |

86 | Implementation of a three pool model with parallel structure |

87 | Implementation of a three-pool C14 model with parallel... |

88 | Implementation of a three pool model with series structure |

89 | Implementation of a three-pool C14 model with series... |

9 | generic constructor |

90 | Implementation of a 6-pool Michaelis-Menten model |

91 | Class '"TimeMap"' |

92 | TimeMap from Dataframe |

93 | basic constructor of the class TimeMap. |

94 | Implementation of a two pool model with feedback structure |

95 | Implementation of a two-pool C14 model with feedback... |

96 | Implementation of a two-pool Michaelis-Menten model |

97 | Implementation of a two pool model with parallel structure |

98 | Implementation of a two-pool C14 model with parallel... |

99 | Implementation of a two pool model with series structure |

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 incubation experiments |

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 |

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