 Home
 RForge
 SoilR: Models of Soil Organic Matter Decomposition
 212: generic constructor
generic constructor
Description
create a TimeMap object from different sources
Usage
1 
Arguments
map 

starttime 

endtime 

lag 

interpolation 
Author(s)
Carlos A. Sierra, Markus Mueller
Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker. Vote for new features on Trello.
 1: Converts from Delta14C to Absolute Fraction Modern
 10: ~~ Methods for Function 'availableParticleProperties' ~~
 100: ~~ Methods for Function 'getAccumulatedRelease' ~~
 100: ~~ Methods for Function 'getAccumulatedRelease' ~~
 101: Calculates the accumulated carbon release from the pools as a...
 101: Calculates the accumulated carbon release from the pools as a...
 102: getC14 method Model 14
 102: getC14 method Model 14
 103: ~~ Methods for Function 'getC14' ~~
 103: ~~ Methods for Function 'getC14' ~~
 104: Calculates the mass of radiocarbon (14C fraction times C...
 104: Calculates the mass of radiocarbon (14C fraction times C...
 105: getC method Model
 105: getC method Model
 106: ~~ Methods for Function 'getC' ~~
 107: Calculates the C content of the pools
 107: Calculates the C content of the pools
 108: ~~ Methods for Function 'getCumulativeC' ~~
 108: ~~ Methods for Function 'getCumulativeC' ~~
 109: ~~ Methods for Function 'getDecompOp' ~~
 109: ~~ Methods for Function 'getDecompOp' ~~
 11: ~~ Methods for Function 'availableParticleSets' ~~
 11: ~~ Methods for Function 'availableParticleSets' ~~
 110: ~~ Methods for Function 'getDotOut' ~~
 110: ~~ Methods for Function 'getDotOut' ~~
 111: read access to the models F14C variable
 111: read access to the models F14C variable
 112: ~~ Methods for Function 'getF14C' ~~
 112: ~~ Methods for Function 'getF14C' ~~
 113: Calculates the average radiocarbon fraction weighted by the...
 113: Calculates the average radiocarbon fraction weighted by the...
 114: radiocarbon
 114: radiocarbon
 115: ~~ Methods for Function 'getF14' ~~
 115: ~~ Methods for Function 'getF14' ~~
 116: Calculates the 14C fraction of all pools
 116: Calculates the 14C fraction of all pools
 117: average radiocarbon fraction weighted by carbonrelease
 117: average radiocarbon fraction weighted by carbonrelease
 118: ~~ Methods for Function 'getF14R' ~~
 118: ~~ Methods for Function 'getF14R' ~~
 119: Calculates the average radiocarbon fraction weighted by the...
 119: Calculates the average radiocarbon fraction weighted by the...
 12: ~~ Methods for Function 'availableResidentSets' ~~
 12: ~~ Methods for Function 'availableResidentSets' ~~
 120: extract the format string
 120: extract the format string
 121: ~~ Methods for Function 'getFormat' ~~
 121: ~~ Methods for Function 'getFormat' ~~
 122: creates a constant timedependent function and returns it
 122: creates a constant timedependent function and returns it
 123: getFunctionDefinition method DecompositionOperator
 123: getFunctionDefinition method DecompositionOperator
 124: ~~ Methods for Function 'getFunctionDefinition' ~~
 124: ~~ Methods for Function 'getFunctionDefinition' ~~
 125: getFunctionDefinition method TimeMap
 125: getFunctionDefinition method TimeMap
 126: getFunctionDefinition
 126: getFunctionDefinition
 127: ~~ Methods for Function 'getInFluxes' ~~
 127: ~~ Methods for Function 'getInFluxes' ~~
 128: ~~ Methods for Function 'getInitialValues' ~~
 128: ~~ Methods for Function 'getInitialValues' ~~
 129: compute the mean transit time
 129: compute the mean transit time
 13: Implementation of the microbial model AWB (Allison,...
 13: Implementation of the microbial model AWB (Allison,...
 130: ~~ Methods for Function 'getMeanTransitTime' ~~
 130: ~~ Methods for Function 'getMeanTransitTime' ~~
 131: Access to the mean transit time
 131: Access to the mean transit time
 132: ~~ Methods for Function 'getNumberOfPools' ~~
 132: ~~ Methods for Function 'getNumberOfPools' ~~
 133: ~~ Methods for Function 'getOutputFluxes' ~~
 133: ~~ Methods for Function 'getOutputFluxes' ~~
 134: ~~ Methods for Function 'getOutputReceivers' ~~
 134: ~~ Methods for Function 'getOutputReceivers' ~~
 135: ~~ Methods for Function 'getParticleMonteCarloSimulator' ~~
 135: ~~ Methods for Function 'getParticleMonteCarloSimulator' ~~
 136: 14C respiration rate for all pools
 136: 14C respiration rate for all pools
 137: ~~ Methods for Function 'getReleaseFlux14' ~~
 137: ~~ Methods for Function 'getReleaseFlux14' ~~
 138: Calculates the mass of radiocarbon in the release flux (14C...
 138: Calculates the mass of radiocarbon in the release flux (14C...
 139: get the release rate for all pools
 139: get the release rate for all pools
 14: Implementation of the microbial model Bacwave (bacterial...
 14: Implementation of the microbial model Bacwave (bacterial...
 140: ~~ Methods for Function 'getReleaseFlux' ~~
 140: ~~ Methods for Function 'getReleaseFlux' ~~
 141: Calculates the release of C from each pool
 141: Calculates the release of C from each pool
 142: return an (infinite) time range since the operator is...
 142: return an (infinite) time range since the operator is...
 143: ask for the boundaries of the underlying time interval
 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
 145: ask for the boundaries of the underlying time interval
 146: getTimeRange
 146: getTimeRange
 147: getTimes method Model
 147: getTimes method Model
 148: ~~ Methods for Function 'getTimes' ~~
 148: ~~ Methods for Function 'getTimes' ~~
 149: Extracts the times argument
 149: Extracts the times argument
 15: Binding of pre and postbomb Delta14C curves
 15: Binding of pre and postbomb Delta14C curves
 150: ~~ Methods for Function 'getTransferCoefficients' ~~
 150: ~~ Methods for Function 'getTransferCoefficients' ~~
 151: ~~ Methods for Function 'getTransferMatrix' ~~
 151: ~~ Methods for Function 'getTransferMatrix' ~~
 152: compute the TransitTimeDistributionDensity
 152: compute the TransitTimeDistributionDensity
 153: ~~ Methods for Function 'getTransitTimeDistributionDensity'...
 153: ~~ Methods for Function 'getTransitTimeDistributionDensity'...
 154: methods for transit time distributions
 154: methods for transit time distributions
 155: ~~ Methods for Function 'getValues' ~~
 155: ~~ Methods for Function 'getValues' ~~
 156: Delta14C in soil CO2 efflux from Harvard Forest
 156: Delta14C in soil CO2 efflux from Harvard Forest
 157: Atmospheric radiocarbon for the period 19502010 from Hua et...
 157: Atmospheric radiocarbon for the period 19502010 from Hua et...
 158: Implementation of the Introductory Carbon Balance Model...
 158: Implementation of the Introductory Carbon Balance Model...
 159: Class '"InFlux"'
 16: Class '"BoundFc"'
 16: Class '"BoundFc"'
 160: pass through constructor
 160: pass through constructor
 161: ~~ Methods for Function 'InFlux' ~~
 161: ~~ Methods for Function 'InFlux' ~~
 162: create a BoundInFlux from a TimeMap object
 162: create a BoundInFlux from a TimeMap object
 163: internal constructor (new)
 163: internal constructor (new)
 164: internal constructor
 164: internal constructor
 165: initialize called by (new)
 165: initialize called by (new)
 166: An internal constructor for 'Model_14' objects not...
 166: An internal constructor for 'Model_14' objects not...
 167: internal constructor for Model objects
 167: internal constructor for Model objects
 168: ~~ Methods for Function 'initialize' ~~
 168: ~~ Methods for Function 'initialize' ~~
 169: initialize called by (new)
 17: constructor
 17: constructor
 170: Northern Hemisphere atmospheric radiocarbon for the prebomb...
 170: Northern Hemisphere atmospheric radiocarbon for the prebomb...
 171: Atmospheric radiocarbon for the 050,000 yr BP period
 171: Atmospheric radiocarbon for the 050,000 yr BP period
 172: Add lines with the output of 'getC14', 'getC', or...
 172: Add lines with the output of 'getC14', 'getC', or...
 173: Class '"Model_14"'
 173: Class '"Model_14"'
 174: ~~ Methods for Function 'Model_14' ~~
 174: ~~ Methods for Function 'Model_14' ~~
 175: A general constructor
 175: A general constructor
 176: Class '"Model"'
 176: Class '"Model"'
 177: general constructor for class Model
 177: general constructor for class Model
 178: ~~ Methods for Function 'Model' ~~
 178: ~~ Methods for Function 'Model' ~~
 179: A general constructor
 179: A general constructor
 18: constructor
 18: constructor
 180: Implementation of a onepool C14 model
 180: Implementation of a onepool C14 model
 181: Implementation of a one pool model
 181: Implementation of a one pool model
 182: ParallelModel
 182: ParallelModel
 183: Plots the output of 'getF14' for each pool over time
 183: Plots the output of 'getF14' for each pool over time
 184: Plots the output of 'getC' or 'getReleaseFlux' for each pool...
 184: Plots the output of 'getC' or 'getReleaseFlux' for each pool...
 185: not yet implemented method to plot an overview of several...
 185: not yet implemented method to plot an overview of several...
 186: ~~ Methods for Function 'plot' ~~
 186: ~~ Methods for Function 'plot' ~~
 187: not yet implemented method to print an overview of several...
 187: not yet implemented method to print an overview of several...
 188: ~~ Methods for Function 'print' ~~
 189: helper function to compute respiration coefficients
 189: helper function to compute respiration coefficients
 19: constructor
 19: constructor
 190: Implementation of the RothCModel
 190: Implementation of the RothCModel
 191: General mpool linear C14 model with series structure
 191: General mpool linear C14 model with series structure
 192: General mpool linear model with series structure
 192: General mpool linear model with series structure
 193: show method Model
 193: show method Model
 194: ~~ Methods for Function 'show' ~~
 194: ~~ Methods for Function 'show' ~~
 195: \Sexpr[results=rd,stage=build]{tools:::Rd_package_title("SoilR")}
 195: \packageTitleSoilR
 196: summary method Model
 196: summary method Model
 197: ~~ Methods for Function 'summary' ~~
 197: ~~ Methods for Function 'summary' ~~
 198: System and pool age for compartment models
 198: System and pool age for compartment models
 199: Implementation of a 6pool MichaelisMenten model
 199: Implementation of a 6pool MichaelisMenten model
 2: Converts from Delta14C to Absolute Fraction Modern
 2: Converts from Delta14C to Absolute Fraction Modern
 20: constructor
 20: constructor
 200: Implementation of a threepool C14 model with feedback...
 200: Implementation of a threepool C14 model with feedback...
 201: Implementation of a three pool model with feedback structure
 201: Implementation of a three pool model with feedback structure
 202: Implementation of a threepool C14 model with parallel...
 202: Implementation of a threepool C14 model with parallel...
 203: Implementation of a three pool model with parallel structure
 203: Implementation of a three pool model with parallel structure
 204: Implementation of a threepool C14 model with series...
 204: Implementation of a threepool C14 model with series...
 205: Implementation of a three pool model with series structure
 205: Implementation of a three pool model with series structure
 206: Class '"TimeMap"'
 206: Class '"TimeMap"'
 207: TimeMap from Dataframe
 207: TimeMap from Dataframe
 208: constructor
 208: constructor
 209: constructor
 209: constructor
 21: constructor
 21: constructor
 210: ~~ Methods for Function 'TimeMap' ~~
 210: ~~ Methods for Function 'TimeMap' ~~
 211: deprecated constructor of the class TimeMap.
 211: deprecated constructor of the class TimeMap.
 212: generic constructor
 212: generic constructor
 213: Transit times for compartment models
 213: Transit times for compartment models
 214: Estimation of the turnover time from a soil radiocarbon...
 214: Estimation of the turnover time from a soil radiocarbon...
 215: Implementation of a twopool C14 model with feedback...
 215: Implementation of a twopool C14 model with feedback...
 216: Implementation of a two pool model with feedback structure
 216: Implementation of a two pool model with feedback structure
 217: Implementation of a twopool MichaelisMenten model
 217: Implementation of a twopool MichaelisMenten model
 218: Implementation of a twopool C14 model with parallel...
 218: Implementation of a twopool C14 model with parallel...
 219: Implementation of a linear two pool model with parallel...
 219: Implementation of a linear two pool model with parallel...
 22: constructor
 220: Implementation of a twopool C14 model with series structure
 220: Implementation of a twopool C14 model with series structure
 221: Implementation of a two pool model with series structure
 221: Implementation of a two pool model with series structure
 222: Implementation of the Yasso07 model
 222: Implementation of the Yasso07 model
 223: Implementation of the Yasso model.
 223: Implementation of the Yasso model.
 224: (experimenta) partially overload [ ] for models
 224: (experimenta) partially overload [ ] for models
 225: ~~ Methods for Function '[' ~~
 225: ~~ Methods for Function '[' ~~
 226: ~~ Methods for Function '[[<' ~~
 226: ~~ Methods for Function '[[<' ~~
 227: ~~ Methods for Function '[[' ~~
 227: ~~ Methods for Function '[[' ~~
 228: ~~ Methods for Function '$' ~~
 228: ~~ Methods for Function '$' ~~
 23: ~~ Methods for Function 'BoundFc' ~~
 23: ~~ Methods for Function 'BoundFc' ~~
 24: generic constructor
 24: generic constructor
 25: Class '"BoundInFlux"'
 25: Class '"BoundInFlux"'
 26: constructor
 26: constructor
 27: constructor
 27: constructor
 28: constructor
 28: constructor
 29: constructor
 29: constructor
 3: ~~ Methods for Function...
 3: ~~ Methods for Function...
 30: ~~ Methods for Function 'BoundInFlux' ~~
 30: ~~ Methods for Function 'BoundInFlux' ~~
 31: convert to BoundInFlux
 31: convert to BoundInFlux
 32: generic constructor
 32: generic constructor
 33: Class '"BoundLinDecompOp"'
 33: Class '"BoundLinDecompOp"'
 34: convert a ConstLinDecompOp to a BoundLinDecompOp
 34: convert a ConstLinDecompOp to a BoundLinDecompOp
 35: a constructor
 35: a constructor
 36: a constructor
 36: a constructor
 37: ~~ Methods for Function 'BoundLinDecompOp' ~~
 37: ~~ Methods for Function 'BoundLinDecompOp' ~~
 38: create a BoundLinDecompOp from a TimeMap
 38: create a BoundLinDecompOp from a TimeMap
 39: Generic constructor
 39: Generic constructor
 4: Converts its argument to an Absolute Fraction Modern...
 4: Converts its argument to an Absolute Fraction Modern...
 40: Postbomb atmospheric 14C fraction
 40: Postbomb atmospheric 14C fraction
 41: Atmospheric 14C fraction
 41: Atmospheric 14C fraction
 42: Implementation of the Century model
 42: Implementation of the Century model
 43: ~~ Methods for Function 'computeResults' ~~
 43: ~~ Methods for Function 'computeResults' ~~
 44: creates an object containing the initial values for the 14C...
 44: creates an object containing the initial values for the 14C...
 45: Class '"ConstLinDecompOp"'
 45: Class '"ConstLinDecompOp"'
 46: construct from matric
 46: construct from matric
 47: ~~ Methods for Function 'ConstLinDecompOp' ~~
 47: ~~ Methods for Function 'ConstLinDecompOp' ~~
 48: Generic constructor
 48: Generic constructor
 49: Class '"DecompOp"'
 49: Class '"DecompOp"'
 5: convert to Absolute Fraction Normal values
 5: convert to Absolute Fraction Normal values
 50: pass through constructor
 50: pass through constructor
 51: creates a ConstanDecompOp from a matrix
 51: creates a ConstanDecompOp from a matrix
 52: ~~ Methods for Function 'DecompOp' ~~
 52: ~~ Methods for Function 'DecompOp' ~~
 53: creates a BoundLinDecompOp from a TimeMap object
 53: creates a BoundLinDecompOp from a TimeMap object
 54: Class '"DecompositionOperator"'
 54: Class '"DecompositionOperator"'
 55: Converts Absolute Fraction Modern values to Delta14C
 55: Converts Absolute Fraction Modern values to Delta14C
 56: Converts to Delta14C format
 56: Converts to Delta14C format
 57: ~~ Methods for Function...
 57: ~~ Methods for Function...
 58: Converts its argument from an Absolute Fraction Modern to a...
 58: Converts its argument from an Absolute Fraction Modern to a...
 59: convert to Absolute Fraction Normal values
 59: convert to Absolute Fraction Normal values
 6: ~~ Methods for Function 'AbsoluteFractionModern' ~~
 6: ~~ Methods for Function 'AbsoluteFractionModern' ~~
 60: ~~ Methods for Function 'Delta14C' ~~
 60: ~~ Methods for Function 'Delta14C' ~~
 61: deSolve lsoda wrapper
 61: deSolve lsoda wrapper
 62: Soil CO2 efflux from an incubation experiment
 62: Soil CO2 efflux from an incubation experiment
 63: ~~ Methods for Function 'fromDataFrame' ~~
 63: ~~ Methods for Function 'fromDataFrame' ~~
 64: assemble the objects components
 64: assemble the objects components
 65: Effects of temperature on decomposition rates according the...
 65: Effects of temperature on decomposition rates according the...
 66: 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...
 67: Effects of temperature on decomposition rates according the...
 68: Effects of temperature on decomposition rates according to...
 68: Effects of temperature on decomposition rates according to...
 69: Effects of temperature on decomposition rates according to...
 69: Effects of temperature on decomposition rates according to...
 7: ~~ Methods for Function 'as.character' ~~
 7: ~~ Methods for Function 'as.character' ~~
 70: Effects of temperature on decomposition rates according to...
 70: Effects of temperature on decomposition rates according to...
 71: Effects of temperature on decomposition rates according to a...
 71: Effects of temperature on decomposition rates according to a...
 72: 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...
 73: Effects of temperature on decomposition rates according to a...
 74: 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...
 75: Effects of temperature on decomposition rates according to...
 76: 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...
 77: Effects of moisture on decomposition rates according to the...
 78: 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...
 79: Effects of moisture on decomposition rates according to the...
 8: convert TimeMap Objects to something printable.
 8: convert TimeMap Objects to something printable.
 80: Effects of moisture on decomposition rates according to the...
 80: Effects of moisture on decomposition rates according to the...
 81: 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...
 82: Effects of moisture on decomposition rates according to the...
 83: 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...
 84: Effects of moisture on decomposition rates according to the...
 85: 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...
 86: Effects of moisture on decomposition rates according to the...
 87: Implementation of a the sixpool C14 model proposed by...
 87: Implementation of a the sixpool C14 model proposed by...
 88: a constructor for class Model
 88: a constructor for class Model
 89: a constructor for class Model_14
 89: a constructor for class Model_14
 9: creates a character representation of the object in question
 9: creates a character representation of the object in question
 90: a constructor for class Model < 14
 90: a constructor for class Model < 14
 91: a constructor for class Model_ 14
 91: a constructor for class Model_ 14
 92: a constructor for class Model
 92: a constructor for class Model
 93: a constructor for class Model
 93: a constructor for class Model
 94: ~~ Methods for Function 'GeneralModel_14' ~~
 94: ~~ Methods for Function 'GeneralModel_14' ~~
 95: A general constructor
 95: A general constructor
 96: a constructor for class Model
 96: a constructor for class Model
 97: ~~ Methods for Function 'GeneralModel' ~~
 97: ~~ Methods for Function 'GeneralModel' ~~
 98: A general constructor
 98: A general constructor
 99: time integrals of release fluxes per pool
 99: time integrals of release fluxes per pool
 manMan/as.character: creates a character representation of the object in question
 manMan/as.character: creates a character representation of the object in question
 manMan/C14Atm: Atmospheric 14C fraction
 manMan/C14Atm: Atmospheric 14C fraction
 manMan/C14Atm_NH: Postbomb atmospheric 14C fraction
 manMan/eCO2: Soil CO2 efflux from an incubation experiment
 manMan/eCO2: Soil CO2 efflux from an incubation experiment
 manMan/HarvardForest14CO2: Delta14C in soil CO2 efflux from Harvard Forest
 manMan/HarvardForest14CO2: Delta14C in soil CO2 efflux from Harvard Forest
 manMan/Hua2013: Atmospheric radiocarbon for the period 19502010 from Hua et...
 manMan/Hua2013: Atmospheric radiocarbon for the period 19502010 from Hua et...
 manMan/IntCal09: Northern Hemisphere atmospheric radiocarbon for the prebomb...
 manMan/IntCal09: Northern Hemisphere atmospheric radiocarbon for the prebomb...
 manMan/IntCal13: Atmospheric radiocarbon for the 050,000 yr BP period
 manMan/IntCal13: Atmospheric radiocarbon for the 050,000 yr BP period