SoilR: Models of Soil Organic Matter Decomposition

This package contains functions for modeling Soil Organic Matter decomposition in terrestrial ecosystems.

AuthorCarlos A. Sierra <csierra@bgc-jena.mpg.de>, Markus Mueller <mamueller@bgc-jena.mpg.de>
Date of publication2014-04-30 18:53:34
MaintainerMarkus Mueller <mamueller@bgc-jena.mpg.de>
LicenseGPL-3
Version1.1-23

View on CRAN

Man pages

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

Functions

AbsoluteFractionModern,BoundFc-method Man page
AbsoluteFractionModern,ConstFc-method Man page
AbsoluteFractionModern_from_Delta14C Man page
AbsoluteFractionModern_from_Delta14C,matrix-method Man page
AbsoluteFractionModern_from_Delta14C_method__matrix Man page
AbsoluteFractionModern_from_Delta14C_method__numeric Man page
AbsoluteFractionModern_from_Delta14C-methods Man page
AbsoluteFractionModern_from_Delta14C,numeric-method Man page
AbsoluteFractionModern_method__BoundFc Man page
AbsoluteFractionModern-methods Man page
as.character Man page
as.character Man page
as.character,BoundInFlux-method Man page
as.character,MCSim-method Man page
as.character_method__BoundInFlux Man page
as.character-methods Man page
as.character_method__TimeMap Man page
as.character,TimeMap-method Man page
availableParticleProperties,MCSim-method Man page
availableParticleProperties-methods Man page
availableParticleSets,MCSim-method Man page
availableParticleSets-methods Man page
bacwaveModel Man page
bind.C14curves Man page
BoundFc Man page
BoundFc-class Man page
BoundFc,data.frame,missing,missing,missing,character,function-me Man page
BoundFc,data.frame,missing,missing,missing,character,missing-met Man page
BoundFc,data.frame,missing,missing,numeric,character,function-me Man page
BoundFc,data.frame,missing,missing,numeric,character,missing-met Man page
BoundFc,function,numeric,numeric,missing,character,missing-metho Man page
BoundFc,function,numeric,numeric,numeric,character,missing-metho Man page
BoundFc_method__data.frame_missing_missing_missing_character_fun Man page
BoundFc_method__data.frame_missing_missing_missing_character_mis Man page
BoundFc_method__data.frame_missing_missing_numeric_character_fun Man page
BoundFc_method__data.frame_missing_missing_numeric_character_mis Man page
BoundFc_method__function_numeric_numeric_missing_character_missi Man page
BoundFc_method__function_numeric_numeric_numeric_character_missi Man page
BoundFc-methods Man page
BoundInFlux Man page
BoundInFlux-class Man page
BoundInFlux,data.frame,missing,missing,missing,missing-method Man page
BoundInFlux,data.frame,missing,missing,numeric,function-method Man page
BoundInFlux,function,numeric,numeric,missing,missing-method Man page
BoundInFlux,function,numeric,numeric,numeric,missing-method Man page
BoundInFlux_method__data.frame_missing_missing_missing_missing Man page
BoundInFlux_method__data.frame_missing_missing_numeric_function Man page
BoundInFlux_method__function_numeric_numeric_missing_missing Man page
BoundInFlux_method__function_numeric_numeric_numeric_missing Man page
BoundInFlux-methods Man page
BoundInFlux_method__TimeMap_missing_missing_missing_missing Man page
BoundInFlux,TimeMap,missing,missing,missing,missing-method Man page
BoundLinDecompOp Man page
BoundLinDecompOp-class Man page
BoundLinDecompOp,ConstLinDecompOp,ANY,ANY,ANY-method Man page
BoundLinDecompOp,function,numeric,numeric,missing-method Man page
BoundLinDecompOp,function,numeric,numeric,numeric-method Man page
BoundLinDecompOp_method__ConstLinDecompOp Man page
BoundLinDecompOp_method__function_numeric_numeric_missing Man page
BoundLinDecompOp_method__function_numeric_numeric_numeric Man page
BoundLinDecompOp-methods Man page
BoundLinDecompOp_method__TimeMap_missing_missing_missing Man page
BoundLinDecompOp,TimeMap,missing,missing,missing-method Man page
C14Atm Man page
C14Atm Man page
C14Atm_NH Man page
C14Atm_NH Man page
computeResults,MCSim-method Man page
computeResults-methods Man page
computeResults,NlModel-method Man page
ConstFc Man page
ConstLinDecompOp Man page
ConstLinDecompOp-class Man page
ConstLinDecompOp,matrix-method Man page
ConstLinDecompOp_method__matrix Man page
ConstLinDecompOp-methods Man page
DecompOp-class Man page
DecompOp,DecompOp-method Man page
DecompOp,matrix-method Man page
DecompOp_method__DecompOp Man page
DecompOp_method__matrix Man page
DecompOp-methods Man page
DecompOp_method__TimeMap Man page
DecompOp,TimeMap-method Man page
DecompositionOperator-class Man page
Delta14C,BoundFc-method Man page
Delta14C,ConstFc-method Man page
Delta14C_from_AbsoluteFractionModern Man page
Delta14C_from_AbsoluteFractionModern,matrix-method Man page
Delta14C_from_AbsoluteFractionModern_method__matrix Man page
Delta14C_from_AbsoluteFractionModern_method__numeric Man page
Delta14C_from_AbsoluteFractionModern-methods Man page
Delta14C_from_AbsoluteFractionModern,numeric-method Man page
Delta14C_method__BoundFc Man page
Delta14C-methods Man page
deSolve.lsoda.wrapper Man page
eCO2 Man page
eCO2 Man page
fT.Arrhenius Man page
fT.Century1 Man page
fT.Century2 Man page
fT.Daycent1 Man page
fT.Daycent2 Man page
fT.Demeter Man page
fT.KB Man page
fT.LandT Man page
fT.linear Man page
fT.Q10 Man page
fT.RothC Man page
fT.Standcarb Man page
fW.Candy Man page
fW.Century Man page
fW.Daycent1 Man page
fW.Daycent2 Man page
fW.Demeter Man page
fW.Gompertz Man page
fW.Moyano Man page
fW.RothC Man page
fW.Skopp Man page
fW.Standcarb Man page
GaudinskiModel14 Man page
GeneralModel Man page
GeneralModel_14 Man page
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_ Man page
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_ Man page
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_ Man page
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_ Man page
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_ANY_missing_ Man page
GeneralModel_14_method__numeric_ANY_numeric_ANY_ANY_missing_ANY_ Man page
GeneralModel_14-methods Man page
GeneralModel_14,numeric,ANY,numeric,ANY,ANY,ANY,missing,missing, Man page
GeneralModel_14,numeric,ANY,numeric,ANY,ANY,ANY,missing,numeric, Man page
GeneralModel_14,numeric,ANY,numeric,ANY,ANY,ANY,missing,numeric, Man page
GeneralModel_14,numeric,ANY,numeric,ANY,ANY,ANY,missing,numeric, Man page
GeneralModel_14,numeric,ANY,numeric,ANY,ANY,ANY,missing,numeric, Man page
GeneralModel_14,numeric,ANY,numeric,ANY,ANY,missing,ANY,numeric, Man page
GeneralModel_method__numeric_ANY_numeric Man page
GeneralModel-methods Man page
GeneralModel,numeric,ANY,numeric-method Man page
getAccumulatedRelease Man page
getAccumulatedRelease_method__Model Man page
getAccumulatedRelease-methods Man page
getAccumulatedRelease,Model-method Man page
getC Man page
getC14 Man page
getC14_method__Model_14 Man page
getC14-methods Man page
getC14,Model_14-method Man page
getC_method__Model Man page
getC-methods Man page
getC,Model-method Man page
getC,NlModel-method Man page
getDecompOp-methods Man page
getDecompOp,NlModel-method Man page
getDotOut-methods Man page
getDotOut,TransportDecompositionOperator-method Man page
getF14 Man page
getF14C Man page
getF14C_method__Model_14 Man page
getF14C-methods Man page
getF14C,Model_14-method Man page
getF14_method__Model_14 Man page
getF14-methods Man page
getF14,Model_14-method Man page
getF14R Man page
getF14R_method__Model_14 Man page
getF14R-methods Man page
getF14R,Model_14-method Man page
getFormat,BoundFc-method Man page
getFormat,ConstFc-method Man page
getFormat_method__BoundFc Man page
getFormat-methods Man page
getFunctionDefinition Man page
getFunctionDefinition,BoundFc-method Man page
getFunctionDefinition,BoundInFlux-method Man page
getFunctionDefinition,BoundLinDecompOp-method Man page
getFunctionDefinition,ConstLinDecompOp-method Man page
getFunctionDefinition,DecompositionOperator-method Man page
getFunctionDefinition_method__BoundFc Man page
getFunctionDefinition_method__BoundInFlux Man page
getFunctionDefinition_method__BoundLinDecompOp Man page
getFunctionDefinition_method__ConstLinDecompOp Man page
getFunctionDefinition_method__DecompositionOperator Man page
getFunctionDefinition-methods Man page
getFunctionDefinition_method__TimeMap Man page
getFunctionDefinition,TimeMap-method Man page
getFunctionDefinition,TransportDecompositionOperator-method Man page
getInFluxes-methods Man page
getInFluxes,NlModel-method Man page
getInitialValues-methods Man page
getInitialValues,NlModel-method Man page
getMeanTransitTime Man page
getMeanTransitTime,ConstLinDecompOp-method Man page
getMeanTransitTime_method__ConstLinDecompOp Man page
getMeanTransitTime-methods Man page
getNumberOfPools-methods Man page
getNumberOfPools,NlModel-method Man page
getNumberOfPools,TransportDecompositionOperator-method Man page
getOutputFluxes-methods Man page
getOutputFluxes,NlModel-method Man page
getOutputReceivers-methods Man page
getOutputReceivers,TransportDecompositionOperator,numeric-method Man page
getParticleMonteCarloSimulator-methods Man page
getParticleMonteCarloSimulator,NlModel-method Man page
getReleaseFlux Man page
getReleaseFlux14 Man page
getReleaseFlux14_method__Model_14 Man page
getReleaseFlux14-methods Man page
getReleaseFlux14,Model_14-method Man page
getReleaseFlux_method__Model Man page
getReleaseFlux-methods Man page
getReleaseFlux,Model-method Man page
getTimeRange Man page
getTimeRange,BoundFc-method Man page
getTimeRange,BoundInFlux-method Man page
getTimeRange,BoundLinDecompOp-method Man page
getTimeRange,ConstLinDecompOp-method Man page
getTimeRange,DecompositionOperator-method Man page
getTimeRange_method__BoundFc Man page
getTimeRange_method__BoundInFlux Man page
getTimeRange_method__BoundLinDecompOp Man page
getTimeRange_method__ConstLinDecompOp Man page
getTimeRange_method__DecompositionOperator Man page
getTimeRange-methods Man page
getTimeRange_method__TimeMap Man page
getTimeRange,TimeMap-method Man page
getTimeRange,TransportDecompositionOperator-method Man page
getTimes Man page
getTimes_method__Model Man page
getTimes-methods Man page
getTimes,Model-method Man page
getTimes,NlModel-method Man page
getTransferCoefficients-methods Man page
getTransferCoefficients,NlModel-method Man page
getTransferCoefficients,TransportDecompositionOperator-method Man page
getTransferMatrix-methods Man page
getTransferMatrix,TransportDecompositionOperator-method Man page
getTransitTimeDistributionDensity Man page
getTransitTimeDistributionDensity,ConstLinDecompOp-method Man page
getTransitTimeDistributionDensity_method__ConstLinDecompOp Man page
getTransitTimeDistributionDensity-methods Man page
getValues,ConstFc-method Man page
getValues-methods Man page
HarvardForest14CO2 Man page
HarvardForest14CO2 Man page
Hua2013 Man page
Hua2013 Man page
ICBMModel Man page
InFlux-class Man page
InFlux,InFlux-method Man page
InFlux_method__InFlux Man page
InFlux-methods Man page
InFlux_method__TimeMap Man page
InFlux,TimeMap-method Man page
initialize,BoundFc-method Man page
initialize,BoundInFlux-method Man page
initialize,BoundLinDecompOp-method Man page
initialize,ConstFc-method Man page
initialize,ConstLinDecompOp-method Man page
initialize,DecompositionOperator-method Man page
initialize,MCSim-method Man page
initialize_method__BoundFc Man page
initialize_method__BoundInFlux Man page
initialize_method__BoundLinDecompOp Man page
initialize_method__ConstLinDecompOp Man page
initialize_method__DecompositionOperator Man page
initialize_method__Model Man page
initialize_method__Model_14 Man page
initialize-methods Man page
initialize_method__TimeMap Man page
initialize,Model_14-method Man page
initialize,Model-method Man page
initialize,NlModel-method Man page
initialize,TimeMap-method Man page
initialize,TransportDecompositionOperator-method Man page
IntCal09 Man page
IntCal09 Man page
IntCal13 Man page
IntCal13 Man page
linesCPool Man page
[[<-,MCSim-method Man page
[[,MCSim-method Man page
[_method__Model_character Man page
[-methods Man page
[[<--methods Man page
[[-methods Man page
$-methods Man page
Model Man page
Model_14 Man page
Model_14-class Man page
Model_14-methods Man page
Model_14,numeric,ANY,numeric,ConstFc,ANY,ANY,numeric,function,lo Man page
Model_14,numeric,ANY,numeric,ConstFc,ANY,ANY,numeric,missing,log Man page
[,Model,character-method Man page
Model-class Man page
Model_method__numeric_ANY_numeric Man page
Model-methods Man page
Model,numeric,ANY,numeric-method Man page
[,NlModel,character-method Man page
$,NlModel-method Man page
OnepModel Man page
OnepModel14 Man page
ParallelModel Man page
plot,ANY-method Man page
plotC14Pool Man page
plotCPool Man page
plot,MCSim-method Man page
plot_method__Model Man page
plot-methods Man page
plot,Model-method Man page
plot,NlModel-method Man page
print,ANY-method Man page
print_method__Model Man page
print-methods Man page
print,Model-method Man page
print,NlModel-method Man page
RespirationCoefficients Man page
RothCModel Man page
show_method__Model Man page
show-methods Man page
show,Model-method Man page
show,NlModel-method Man page
SoilR Man page
SoilR-package Man page
summary,ANY-method Man page
summary_method__Model Man page
summary-methods Man page
summary,Model-method Man page
summary,NlModel-method Man page
ThreepairMMmodel Man page
ThreepFeedbackModel Man page
ThreepFeedbackModel14 Man page
ThreepParallelModel Man page
ThreepParallelModel14 Man page
ThreepSeriesModel Man page
ThreepSeriesModel14 Man page
TimeMap-class Man page
TimeMap.from.Dataframe Man page
TimeMap.new Man page
turnoverFit Man page
TwopFeedbackModel Man page
TwopFeedbackModel14 Man page
TwopMMmodel Man page
TwopParallelModel Man page
TwopParallelModel14 Man page
TwopSeriesModel Man page
TwopSeriesModel14 Man page
Yasso07Model Man page
YassoModel Man page

Files

SoilR
SoilR/inst
SoilR/inst/CITATION
SoilR/inst/tests
SoilR/inst/tests/proto.MCSimulatorTest.R
SoilR/inst/tests/runit.TwopSerial_MCSim.R
SoilR/inst/tests/protected
SoilR/inst/tests/protected/runit.SoilRPaper1.R
SoilR/inst/tests/protected/runit.LowVerticalRatesPaper.R
SoilR/inst/tests/Rplots.pdf
SoilR/inst/tests/runit.automatic.TwopParallel_ZeroInput.pdf
SoilR/inst/tests/runit.automatic.OnePool_C14_ZeroDecay_Zero_c14.pdf
SoilR/inst/tests/runit.MeanAge3.R
SoilR/inst/tests/example.GeneralModel_14.R
SoilR/inst/tests/runit.MeanAge.pdf
SoilR/inst/tests/FeM2.R
SoilR/inst/tests/runit.operators.R
SoilR/inst/tests/runit.Interfaces.R
SoilR/inst/tests/runit.automatic.TwopParallel_ZeroDecayInputOnly.pdf
SoilR/inst/tests/runit.formatConversion.R
SoilR/inst/tests/runit.SoilRPaper1.R
SoilR/inst/tests/example.getReleaseFlux14_method__Model_14.R
SoilR/inst/tests/runit.ThreepSerial_linear_vs_nonlinear.pdf
SoilR/inst/tests/tex.log
SoilR/inst/tests/runit.automatic.OnePool_C14_ZeroDecay_Zero_c14_fromDelta14C.pdf
SoilR/inst/tests/functions.pyc
SoilR/inst/tests/runit.test.NlModel.R
SoilR/inst/tests/runit.automatic.op.pdf
SoilR/inst/tests/runit.ThreepSerialFeedback_linear_vs_nonlinear.pdf
SoilR/inst/tests/runit.BackwardTransferTime.R
SoilR/inst/tests/TestNp.R
SoilR/inst/tests/runit.BackwardTransferTime.pdf
SoilR/inst/tests/Manzoniexample.pyc
SoilR/inst/tests/ExampleTestSuite.R
SoilR/inst/tests/csall.sh
SoilR/inst/tests/runit.MeanAge3.pdf.orig
SoilR/inst/tests/runit.MeanAge.Densities.pdf
SoilR/inst/tests/runit.DeprecationWarnings.R
SoilR/inst/tests/GlobalEmissions.csv
SoilR/inst/tests/runit.TimeReversedSolution.R
SoilR/inst/tests/cRtest.sh
SoilR/inst/tests/runit.LinearDecompositionOperator.R
SoilR/inst/tests/runit.test.TimeMap.R
SoilR/inst/tests/ThreepParallelAnalytical.R
SoilR/inst/tests/all.R
SoilR/inst/tests/example.getF14R_method__Model_14.R
SoilR/inst/tests/runit.automatic.OnePool_C14_equalDecay_ZeroInput_c14.pdf
SoilR/inst/tests/c14test.R
SoilR/inst/tests/runit.automatic.FourpSerial_1.pdf
SoilR/inst/tests/C14exampleFromDelta14C.pyc
SoilR/inst/tests/package.test.manual.index
SoilR/inst/tests/addHeader.sh
SoilR/inst/tests/test.paramest.R
SoilR/inst/tests/runit.MeanAge2.pdf
SoilR/inst/tests/example.initialize_method__Model_14.R
SoilR/inst/tests/sall.R
SoilR/inst/tests/package.manual.help.R
SoilR/inst/tests/example.getTimeRange_method__TimeMap.R
SoilR/inst/tests/runit.automatic.OnePool_C14_equalDecay_ZeroInput_c14_fromDelta14C.pdf
SoilR/inst/tests/runit.automatic.TwoPool_C14_equalDecay_ZeroInput_c14_fromDelta14C.pdf
SoilR/inst/tests/runit.ThreepSerialFeedback_linear_vs_nonlinear.R
SoilR/inst/tests/tasklist_proto.R
SoilR/inst/tests/runit.MeanAge3.pdf
SoilR/inst/tests/dialog-warning.wav
SoilR/inst/tests/runit.automatic.OnePool_C14_ZeroDecay_constantInputrate_c14_fromDelta14C.pdf
SoilR/inst/tests/runit.test.SoilRF0.R
SoilR/inst/tests/runit.MeanAgeImpuls.pdf
SoilR/inst/tests/runit.automatic.OnePool_C14_ZeroDecay_constantInputrate_c14.pdf
SoilR/inst/tests/runit.automatic.ThreepSerial_2.pdf
SoilR/inst/tests/C14example.pyc
SoilR/inst/tests/runit.ThreepSerial_linear_vs_nonlinear.R
SoilR/inst/tests/runit.automatic.ThreepSerial_1.pdf
SoilR/inst/tests/TwopParallelAnalytical.R
SoilR/inst/tests/runit.nonlinear.R
SoilR/inst/tests/runit.TwopSerial_linear_vs_nonlinear.R
SoilR/inst/tests/runit.test.Model_14.R
SoilR/inst/tests/runit.automatic.TwoPool_C14_equalDecay_ZeroInput_c14.pdf
SoilR/inst/tests/runit.check.pass.R
SoilR/inst/tests/example.initialize_method__Model.R
SoilR/inst/tests/runit.NonlinearAtmosphericModelLong.pdf
SoilR/inst/tests/Rtest.R
SoilR/inst/tests/runit.MeanAge2.R
SoilR/inst/tests/exall.R
SoilR/inst/tests/runit.NonlinearAtmosphericModelMeanAge.pdf
SoilR/inst/tests/runit.automatic.TwopFeedback.pdf
SoilR/inst/tests/prolog.R
SoilR/inst/tests/runit.2TwopSerial_linear_vs_nonlinear.R
SoilR/inst/tests/runit.ThreepFeedback_MCSim.R
SoilR/inst/tests/runit.test.Conversion.R
SoilR/inst/tests/makePlots.R
SoilR/inst/tests/Rexample.pyc
SoilR/inst/tests/testhelpers.R
SoilR/inst/tests/runit.BoundFc.R
SoilR/inst/tests/runit.test.Conversion.pdf
SoilR/inst/tests/runit.NonlinearAtmosphericModel.R
SoilR/inst/tests/runit.MeanAge.R
SoilR/inst/tests/runit.automatic.ThreepFeedback_1.pdf
SoilR/inst/tests/runit.automatic.TwopParallel_constantInput.pdf
SoilR/inst/tests/runit.testNumberOfPools.R
SoilR/inst/tests/fme.f90
SoilR/inst/tests/runit.test.TimeReversedSolution.pdf
SoilR/inst/tests/runit.manuel.Manzoni.op.R
SoilR/inst/tests/runit.test.checkSizes.R
SoilR/inst/tests/automatic
SoilR/inst/tests/automatic/runit.ThreepSerial_2.R
SoilR/inst/tests/automatic/runit.Manzoni.TwopFeedback.R
SoilR/inst/tests/automatic/runit.c14_fromDelta14C.TwoPool_C14_equalDecay_ZeroInput.R
SoilR/inst/tests/automatic/testmaker.py
SoilR/inst/tests/automatic/runit.ThreepSerial_1.R
SoilR/inst/tests/automatic/runit.OnePool_C14_ZeroDecay_Zero.R
SoilR/inst/tests/automatic/runit.c14_fromDelta14C.OnePool_C14_ZeroDecay_Zero.R
SoilR/inst/tests/automatic/Rexample.py
SoilR/inst/tests/automatic/runit.OnePool_C14_ZeroDecay_constantInputrate.R
SoilR/inst/tests/automatic/runit.c14_fromDelta14C.OnePool_C14_ZeroDecay_constantInputrate.R
SoilR/inst/tests/automatic/Manzoniexample.py
SoilR/inst/tests/automatic/mmtestmaker.py
SoilR/inst/tests/automatic/runit.TwopParallel_constantInput.R
SoilR/inst/tests/automatic/runit.TwopParallel_ZeroDecayInputOnly.R
SoilR/inst/tests/automatic/runit.OnePool_C14_equalDecay_ZeroInput.R
SoilR/inst/tests/automatic/functions.py
SoilR/inst/tests/automatic/runit.TwopParallel_ZeroInput.R
SoilR/inst/tests/automatic/RexampleWithTransfer.py
SoilR/inst/tests/automatic/runit.ThreepFeedback_1.R
SoilR/inst/tests/automatic/C14exampleFromDelta14C.py
SoilR/inst/tests/automatic/runit.TwoPool_C14_equalDecay_ZeroInput.R
SoilR/inst/tests/automatic/runit.FourpSerial_1.R
SoilR/inst/tests/automatic/runit.c14_fromDelta14C.OnePool_C14_equalDecay_ZeroInput.R
SoilR/inst/tests/automatic/C14example.py
SoilR/inst/tests/automatic/runit.Manzoni.op.R
SoilR/inst/tests/example.getC.R
SoilR/inst/tests/example.getReleaseFlux_method__Model.R
SoilR/inst/tests/runit.test.Model.R
SoilR/inst/tests/tryCatch.R
SoilR/inst/extdata
SoilR/inst/extdata/inputFluxForVignetteGeneralModelShort
SoilR/inst/extdata/inputFluxForVignetteGeneralModel
SoilR/inst/doc
SoilR/inst/doc/ParameterEstimation.pdf
SoilR/inst/doc/GeneralModel.R
SoilR/inst/doc/ParameterEstimation.Rnw
SoilR/inst/doc/ParameterEstimation.R
SoilR/inst/doc/GeneralModel.Rnw
SoilR/inst/doc/GeneralModel.pdf
SoilR/NAMESPACE
SoilR/NEWS
SoilR/data
SoilR/data/IntCal09.rda
SoilR/data/C14Atm.rda
SoilR/data/C14Atm_NH.rda
SoilR/data/Hua2013.rda
SoilR/data/IntCal13.rda
SoilR/data/eCO2.rda
SoilR/data/HarvardForest14CO2.rda
SoilR/R
SoilR/R/GaudinskiModel14.R SoilR/R/1_helperFunctions.R SoilR/R/TwopSeriesModel.R SoilR/R/fW.RothC.R SoilR/R/2_TimeMap_deprecated_in_1.2.R SoilR/R/bacwaveModel.R SoilR/R/fW.Daycent2.R SoilR/R/GeneralNlModel.R SoilR/R/fT.Century1.R SoilR/R/ThreepFeedbackModel.R SoilR/R/fW.Moyano.R SoilR/R/fW.Century.R SoilR/R/supported14CFractionFormats.R SoilR/R/TwopSeriesModel14.R SoilR/R/ParallelModel.R SoilR/R/2_InFlux.R SoilR/R/TwopParallelModel.R SoilR/R/ThreepParallelModel.R SoilR/R/5_MCSim.R SoilR/R/MeanAge.R SoilR/R/fT.KB.R SoilR/R/fT.Daycent2.R SoilR/R/3_deSolve.lsoda.wrapper.R SoilR/R/GeneralModel_14Methods.R SoilR/R/fT.RothC.R SoilR/R/fT.Standcarb.R SoilR/R/fT.Demeter.R SoilR/R/turnoverFit.R SoilR/R/fT.linear.R SoilR/R/Model.R SoilR/R/ThreepSeriesModel.R SoilR/R/warnings.R SoilR/R/YassoModel.R SoilR/R/fW.Standcarb.R SoilR/R/OnepModel.R SoilR/R/OnepModel14.R SoilR/R/linesCPool.R SoilR/R/6_DecopmOp.R SoilR/R/ConstantDecompositionOperator.R SoilR/R/solver.R SoilR/R/ThreepFeedbackModel14.R SoilR/R/3_BoundInFlux.R SoilR/R/TwopFeedbackModel.R SoilR/R/ICBMModel.R SoilR/R/plotCPool.R SoilR/R/fW.Demeter.R SoilR/R/TwopParallelModel14.R SoilR/R/7_DecompositionOperator_deprecated_in_1.2.R SoilR/R/7_BoundLinDecompOp.R SoilR/R/FcAtm_deprecated_in_1.2.R SoilR/R/ThreepParallelModel14.R SoilR/R/vecFuncMaker.R SoilR/R/fT.Daycent1.R SoilR/R/Yasso07Model.R SoilR/R/fW.Gompertz.R SoilR/R/TwopFeedbackModel14.R SoilR/R/fT.Century2.R SoilR/R/fW.Candy.R SoilR/R/bind.C14curves.R SoilR/R/fW.Daycent1.R SoilR/R/4_SoilR.F0__deprecated_in_1.2.R SoilR/R/fT.Arrhenius.R SoilR/R/GeneralModelMethods.R SoilR/R/RothCModel.R SoilR/R/plotC14Pool.R SoilR/R/ConstFc.R SoilR/R/testhelpers.R SoilR/R/1_genericFunctions.R SoilR/R/fW.Skopp.R SoilR/R/NpYdot.R SoilR/R/SoilR.euler.R SoilR/R/3_RespirationCoefficients.R SoilR/R/ThreepSeriesModel14.R SoilR/R/fT.LandT.R SoilR/R/BoundFc.R SoilR/R/linMaker.R SoilR/R/MeanTT.R SoilR/R/fT.Q10.R SoilR/R/4_NlModel.R SoilR/R/ThreepairMMmodel.R SoilR/R/Model_14.R SoilR/R/TwopMMmodel.R SoilR/R/spectralNorm.R SoilR/R/3_TransportDecompositionOperator.R
SoilR/vignettes
SoilR/vignettes/ParameterEstimation.Rnw
SoilR/vignettes/GeneralModel.Rnw
SoilR/MD5
SoilR/build
SoilR/build/vignette.rds
SoilR/DESCRIPTION
SoilR/man
SoilR/man/115.Rd SoilR/man/117.Rd SoilR/man/38.Rd SoilR/man/162.Rd SoilR/man/39.Rd SoilR/man/47.Rd SoilR/man/140.Rd SoilR/man/217.Rd SoilR/man/63.Rd SoilR/man/126.Rd SoilR/man/100.Rd SoilR/man/133.Rd SoilR/man/222.Rd SoilR/man/138.Rd SoilR/man/118.Rd SoilR/man/123.Rd SoilR/man/167.Rd SoilR/man/56.Rd SoilR/man/159.Rd SoilR/man/66.Rd SoilR/man/6.Rd SoilR/man/36.Rd SoilR/man/124.Rd SoilR/man/104.Rd SoilR/man/110.Rd SoilR/man/54.Rd SoilR/man/92.Rd SoilR/man/30.Rd SoilR/man/70.Rd SoilR/man/99.Rd SoilR/man/94.Rd SoilR/man/198.Rd SoilR/man/42.Rd SoilR/man/132.Rd SoilR/man/67.Rd SoilR/man/211.Rd SoilR/man/23.Rd SoilR/man/48.Rd SoilR/man/11.Rd SoilR/man/197.Rd SoilR/man/216.Rd SoilR/man/173.Rd SoilR/man/93.Rd SoilR/man/134.Rd SoilR/man/165.Rd SoilR/man/203.Rd SoilR/man/180.Rd SoilR/man/35.Rd SoilR/man/50.Rd SoilR/man/24.Rd SoilR/man/223.Rd SoilR/man/13.Rd SoilR/man/3.Rd SoilR/man/200.Rd SoilR/man/172.Rd SoilR/man/71.Rd SoilR/man/178.Rd SoilR/man/183.Rd SoilR/man/169.Rd SoilR/man/163.Rd SoilR/man/43.Rd SoilR/man/179.Rd SoilR/man/31.Rd SoilR/man/58.Rd SoilR/man/219.Rd SoilR/man/111.Rd SoilR/man/49.Rd SoilR/man/57.Rd SoilR/man/221.Rd SoilR/man/14.Rd SoilR/man/129.Rd SoilR/man/208.Rd SoilR/man/176.Rd SoilR/man/214.Rd SoilR/man/150.Rd SoilR/man/51.Rd SoilR/man/154.Rd SoilR/man/19.Rd SoilR/man/44.Rd SoilR/man/164.Rd SoilR/man/147.Rd SoilR/man/119.Rd SoilR/man/174.Rd SoilR/man/20.Rd SoilR/man/107.Rd SoilR/man/88.Rd SoilR/man/4.Rd SoilR/man/81.Rd
SoilR/man/manMan
SoilR/man/manMan/Hua2013.Rd
SoilR/man/manMan/as.character.Rd
SoilR/man/manMan/eCO2.Rd
SoilR/man/manMan/C14Atm_NH.Rd
SoilR/man/manMan/IntCal09.Rd
SoilR/man/manMan/C14Atm.Rd
SoilR/man/manMan/HarvardForest14CO2.Rd
SoilR/man/manMan/IntCal13.Rd
SoilR/man/151.Rd SoilR/man/201.Rd SoilR/man/155.Rd SoilR/man/146.Rd SoilR/man/5.Rd SoilR/man/218.Rd SoilR/man/75.Rd SoilR/man/152.Rd SoilR/man/80.Rd SoilR/man/161.Rd SoilR/man/10.Rd SoilR/man/16.Rd SoilR/man/98.Rd SoilR/man/25.Rd SoilR/man/168.Rd SoilR/man/131.Rd SoilR/man/83.Rd SoilR/man/26.Rd SoilR/man/187.Rd SoilR/man/32.Rd SoilR/man/171.Rd SoilR/man/62.Rd SoilR/man/78.Rd SoilR/man/130.Rd SoilR/man/209.Rd SoilR/man/113.Rd SoilR/man/84.Rd SoilR/man/9.Rd SoilR/man/158.Rd SoilR/man/136.Rd SoilR/man/105.Rd SoilR/man/77.Rd SoilR/man/40.Rd SoilR/man/29.Rd SoilR/man/181.Rd SoilR/man/52.Rd SoilR/man/96.Rd SoilR/man/109.Rd SoilR/man/143.Rd SoilR/man/212.Rd SoilR/man/177.Rd SoilR/man/135.Rd SoilR/man/1.Rd SoilR/man/166.Rd SoilR/man/59.Rd SoilR/man/82.Rd SoilR/man/89.Rd SoilR/man/127.Rd SoilR/man/184.Rd SoilR/man/91.Rd SoilR/man/194.Rd SoilR/man/60.Rd SoilR/man/182.Rd SoilR/man/101.Rd SoilR/man/121.Rd SoilR/man/122.Rd SoilR/man/116.Rd SoilR/man/21.Rd SoilR/man/53.Rd SoilR/man/7.Rd SoilR/man/202.Rd SoilR/man/144.Rd SoilR/man/79.Rd SoilR/man/74.Rd SoilR/man/106.Rd SoilR/man/114.Rd SoilR/man/191.Rd SoilR/man/108.Rd SoilR/man/157.Rd SoilR/man/220.Rd SoilR/man/195.Rd SoilR/man/45.Rd SoilR/man/86.Rd SoilR/man/213.Rd SoilR/man/103.Rd SoilR/man/160.Rd SoilR/man/204.Rd SoilR/man/192.Rd SoilR/man/97.Rd SoilR/man/137.Rd SoilR/man/206.Rd SoilR/man/112.Rd SoilR/man/22.Rd SoilR/man/55.Rd SoilR/man/90.Rd SoilR/man/207.Rd SoilR/man/153.Rd SoilR/man/190.Rd SoilR/man/186.Rd SoilR/man/95.Rd SoilR/man/68.Rd SoilR/man/17.Rd SoilR/man/156.Rd SoilR/man/8.Rd SoilR/man/18.Rd SoilR/man/73.Rd SoilR/man/125.Rd SoilR/man/34.Rd SoilR/man/210.Rd SoilR/man/33.Rd SoilR/man/148.Rd SoilR/man/149.Rd SoilR/man/15.Rd SoilR/man/199.Rd SoilR/man/27.Rd SoilR/man/170.Rd SoilR/man/65.Rd SoilR/man/128.Rd SoilR/man/120.Rd SoilR/man/139.Rd SoilR/man/76.Rd SoilR/man/185.Rd SoilR/man/2.Rd SoilR/man/72.Rd SoilR/man/189.Rd SoilR/man/69.Rd SoilR/man/141.Rd SoilR/man/196.Rd SoilR/man/12.Rd SoilR/man/85.Rd SoilR/man/205.Rd SoilR/man/215.Rd SoilR/man/46.Rd SoilR/man/142.Rd SoilR/man/188.Rd SoilR/man/145.Rd SoilR/man/175.Rd SoilR/man/102.Rd SoilR/man/87.Rd SoilR/man/64.Rd SoilR/man/41.Rd SoilR/man/37.Rd SoilR/man/61.Rd SoilR/man/193.Rd SoilR/man/28.Rd

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