Man pages for SoilR
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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