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**SoilR**: Models of Soil Organic Matter Decomposition**218**: Estimation of the turnover time from a soil radiocarbon...

# Estimation of the turnover time from a soil radiocarbon sample.

### Description

This function finds the best possible value of turnover time from a soil radiocarbon sample assuming a one pool model and annual litter inputs.

### Usage

1 2 | ```
turnoverFit(obsC14, obsyr, In, C0 = 0, yr0 = 1900, Zone = "NHZone2",
plot = TRUE)
``` |

### Arguments

`obsC14` |
a scalar with the observed radiocarbon value in Delta14C of the soil sample. |

`obsyr` |
a scalar with the year in which the soil sample was taken. |

`In` |
a scalar or data.frame with the annual amount of litter inputs to the soil. |

`C0` |
a scalar with the initial amount of carbon stored at the begning of the simulation. |

`yr0` |
The year at which simulations will start. |

`Zone` |
the hemispheric zone of atmospheric radiocarbon. Possible values are NHZone1: northern hemisphere zone 1, NHZone2: northern hemisphere zone 2, NHZone3: northern hemisphere zone 3, SHZone12: southern hemisphere zones 1 and 2, SHZone3: southern hemisphere zone 3. See |

`plot` |
logical. Should the function produce a plot? |

### Details

This algorithm takes the observed values and a given amount of litter inputs, runs `OnepModel14`

, calculates the squared difference between predictions and observations, and uses `optimize`

to find the minimum difference.
If the turnover time is relatively short (< 50 yrs), it is safe to assume C0=0 because the soil will reach steady state within the simulation time. However, for longer turnover times it is recommended to use a value of C0 close to the steady state value.

### Value

A scalar with the value of the turnover time that minimizes the difference between the prediction of a one pool model and the observed radiocarbon value.

### Author(s)

Carlos A. Sierra <csierra@bgc-jena.mpg.de>, Markus Mueller <mamueller@bgc-jena.mpg.de>

### Examples

1 2 3 4 5 6 7 | ```
## Not run:
# Calculate the turnover time for a sample from a temperate forest soil
turnoverFit(obsC14=115.22, obsyr=2004.5, C0=2800, yr0=1900,
In=473, Zone="NHZone2")
## End(Not run)
``` |

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- 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