Models of Soil Organic Matter Decomposition

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 | Models of Soil Organic Matter Decomposition |

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 |

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