{ "_id": "6a17fa41acfb0bcc41da9b85", "Package": "SoilR", "Title": "Models of Soil Organic Matter Decomposition", "Version": "1.2.107", "Date": "2023-10-13", "Author": "Carlos A. Sierra, Markus Mueller", "Maintainer": "Carlos A. Sierra ", "Description": "Functions for modeling Soil Organic Matter decomposition\nin terrestrial ecosystems with linear and nonlinear systems of\ndifferential equations. The package implements models according\nto the compartmental system representation described in Sierra\nand others (2012) and Sierra and\nothers (2014) .", "License": "GPL-3", "LazyData": "TRUE", "Collate": "setGlobalVariables.R setOldClasses.R genericFunctions.R\nS4ClassDefinitions.R TimeMap.R ScalarTimeMap.R PoolId.R\nPoolIndex.R PoolName.R InFlux_by_PoolIndex.R\nInFlux_by_PoolName.R OutFlux_by_PoolIndex.R\nOutFlux_by_PoolName.R InternalFlux_by_PoolIndex.R\nInternalFlux_by_PoolName.R PoolConnection_by_PoolIndex.R\nPoolConnection_by_PoolName.R ConstantInFluxRate_by_PoolIndex.R\nConstantInFluxRate_by_PoolName.R InFluxes.R ConstInFluxes.R\nConstantInFlux_by_PoolIndex.R\nConstantInternalFluxRate_by_PoolIndex.R\nConstantInternalFluxRate_by_PoolName.R\nConstantOutFluxRate_by_PoolIndex.R\nConstantOutFluxRate_by_PoolName.R InFluxList_by_PoolIndex.R\nInFluxList_by_PoolName.R\nStateIndependentInFluxList_by_PoolIndex.R\nStateDependentInFluxVector.R OutFluxList_by_PoolIndex.R\nOutFluxList_by_PoolName.R InternalFluxList_by_PoolIndex.R\nInternalFluxList_by_PoolName.R\nConstantInFluxList_by_PoolIndex.R\nConstantInternalFluxRateList_by_PoolIndex.R\nConstantInternalFluxRateList_by_PoolName.R\nConstantOutFluxRateList_by_PoolIndex.R\nConstantOutFluxRateList_by_PoolName.R Fc.R HelperFunctions.R\nBoundInFluxes.R deSolve.lsoda.wrapper.R\nRespirationCoefficients.R TransportDecompositionOperator.R\nSoilR.F0__deprecated_in_1.2.R MCSim.R DecompOp.R\nUnboundInflux.R UnBoundLinDecompOp.R BoundLinDecompOp.R\nUnBoundNonLinDecompOp.R\nDecompositionOperator_deprecated_in_1.2.R Model_by_PoolNames.R\nModel.R Model_14.R NlModel.R AutonomousLinearModel.R\nNonAutonomousLinearModel.R AWBmodel.R bacwaveModel.R\nbind.C14curves.R BoundFc.R CenturyModel.R ConstFc.R\nConstLinDecompOp.R ConstLinDecompOpWithLinearScaleFactor.R\nSymbolicModel_by_PoolName.R\nUnBoundNonLinDecompOp_by_PoolNames.R cycling.R euler.R\nexample.2DBoundInFluxesFromFunction.R\nexample.2DBoundLinDecompOpFromFunction.R\nexample.2DConstFC.Args.R example.2DConstInFluxesFromVector.R\nexample.2DGeneralDecompOpArgs.R example.2DInFluxes.Args.R\nexample.2DUnBoundLinDecompOp.R\nexample.BoundLinDecompOpFromFunction.R\nexample.ConstlinDecompOpFromMatrix.R\nexample.nestedTime2DMatrixList.R\nexample.nestedTime3DArrayList.R example.Time2DArrayList.R\nexample.Time3DArrayList.R example.TimeMapFromArray.R\nFcAtm_deprecated_in_1.2.R fT.Arrhenius.R fT.Century1.R\nfT.Century2.R fT.Daycent1.R fT.Daycent2.R fT.Demeter.R fT.KB.R\nfT.LandT.R fT.linear.R fT.Q10.R fT.RothC.R fT.Standcarb.R\nfunction.R fW.Candy.R fW.Century.R fW.Daycent1.R fW.Daycent2.R\nfW.Demeter.R fW.Gompertz.R fW.Moyano.R fW.RothC.R fW.Skopp.R\nfW.Standcarb.R GeneralModel.R GaudinskiModel14.R\nGeneralModel_14.R GeneralNlModel.R ICBMModel.R linesCPool.R\nlinMaker.R list.R listProduct.R makelink.R MeanAge.R MeanTT.R\nNpYdot.R OnepModel.R OnepModel14.R ParallelModel.R\nplotC14Pool.R plotCPool.R RothCModel.R SeriesLinearModel.R\nSeriesLinearModel14.R solver.R spectralNorm.R systemAge.R\nThreepairMMmodel.R ThreepFeedbackModel.R\nThreepFeedbackModel14.R ThreepParallelModel.R\nThreepParallelModel14.R ThreepSeriesModel.R\nThreepSeriesModel14.R transitTime.R tupelList.R turnoverFit.R\nmakeListInstance.R pe.R pp.R plotPoolGraphFromTupleLists.R\ncheckTargetClassOfElements.R TimeRangeIntersection.R\nTwopFeedbackModel.R TwopFeedbackModel14.R TwopMMmodel.R\nTwopParallelModel.R TwopParallelModel14.R TwopSeriesModel.R\nTwopSeriesModel14.R vecFuncMaker.R warnings.R Yasso07Model.R\nscalarFuncMaker.R apply_to_state_and_time.R YassoModel.R\nC14Atm_NH.R C14Atm.R Hua2013.R IntCal09.R IntCal13.R\nGraven2017.R IntCal20.R SHCal20.R incubation_experiment.R\nHarvardForest14CO2.R getTransferMatrix.R SoilR-package.R\nIVP_maker.R ydot_maker.R ICBM_N.R linearScalarModel.R\nCenturyModel14.R pathEntropy.R entropyRatePerJump.R\nentropyRatePerTime.R Hua2021.R", "RoxygenNote": "7.2.3.9000", "Encoding": "UTF-8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-28 08:13:50 UTC", "User": "root" }, "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://crlsierra.r-universe.dev", "Date/Publication": "2023-10-13 14:31:33 UTC", "RemoteUrl": "https://github.com/cran/SoilR", "RemoteRef": "HEAD", "RemoteSha": "6d63c04336e3ce208a804462828bab40cebf5c99", "MD5sum": "63a88f8675c0d2f74cccf87b3d12b53a", "_user": "crlsierra", "_type": "src", "_file": "SoilR_1.2.107.tar.gz", "_fileid": "427b55a832a44fa07edf14c8ddd1f08d47c34fb3a7bc74e7fcac52f73fba1576", "_filesize": 1659694, "_sha256": "427b55a832a44fa07edf14c8ddd1f08d47c34fb3a7bc74e7fcac52f73fba1576", "_created": "2026-05-28T08:13:50.000Z", "_published": "2026-05-28T08:18:09.525Z", "_distro": "noble", "_jobs": [ { "job": 78250700577, "time": 154, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7260975682" }, { "job": 78250700441, "time": 166, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7260979475" }, { "job": 78250700420, "time": 190, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7260978166" }, { "job": 78250700486, "time": 179, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7260975493" }, { "job": 78250009456, "time": 266, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7260926355" }, { "job": 78250700422, "time": 105, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7260960500" }, { "job": 78250700442, "time": 150, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7260974197" }, { "job": 78250700528, "time": 141, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7260971568" }, { "job": 78250700471, "time": 154, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7260975442" } ], "_buildurl": "https://github.com/r-universe/crlsierra/actions/runs/26562866143", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/SoilR", "_commit": { "id": "6d63c04336e3ce208a804462828bab40cebf5c99", "author": "Carlos A. Sierra ", "committer": "cran-robot ", "message": "version 1.2.107\n", "time": 1697207493 }, "_maintainer": { "name": "Carlos A. Sierra", "email": "csierra@bgc-jena.mpg.de", "login": "crlsierra", "description": "", "uuid": 9167269 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "role": "Depends" }, { "package": "deSolve", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "igraph", "role": "Imports" }, { "package": "assertthat", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "expm", "role": "Imports" }, { "package": "sets", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "FME", "role": "Suggests" }, { "package": "lattice", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "getopt", "role": "Suggests" }, { "package": "tinytex", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 6, "_contributors": [ { "user": "mamueller", "count": 5, "uuid": 1119037 }, { "user": "crlsierra", "count": 3, "uuid": 9167269 } ], "_userbio": { "uuid": 9167269, "type": "user", "name": "Carlos A. Sierra" }, "_downloads": { "count": 317, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SoilR" }, "_searchresults": 188, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/SoilR.html", "manual.pdf" ], "_realowner": "crlsierra", "_cranurl": false, "_releases": [ { "version": "1.0-0", "date": "2012-04-01" }, { "version": "1.0-2", "date": "2012-07-20" }, { "version": "1.0-3", "date": "2012-07-25" }, { "version": "1.0-7", "date": "2013-10-10" }, { "version": "1.1-23", "date": "2014-04-30" }, { "version": "1.2.105", "date": "2022-01-23" }, { "version": "1.2.106", "date": "2023-10-12" }, { "version": "1.2.107", "date": "2023-10-13" } ], "_exports": [ "AbsoluteFractionModern_from_Delta14C", "add_plot", "AWBmodel", "bacwaveModel", "bind.C14curves", "BoundFc", "BoundInFluxes", "BoundLinDecompOp", "by_PoolIndex", "CenturyModel", "CenturyModel14", "ConstantInternalFluxRateList_by_PoolIndex", "ConstantOutFluxRateList_by_PoolIndex", "ConstFc", "ConstInFluxes", "ConstLinDecompOp", "cycling", "Delta14C", "Delta14C_from_AbsoluteFractionModern", "deSolve.lsoda.wrapper", "entropyRatePerJump", "entropyRatePerTime", "euler", "example.2DBoundInFluxesFromFunction", "example.2DBoundLinDecompOpFromFunction", "example.2DConstFc.Args", "example.2DConstInFluxesFromVector", "example.2DGeneralDecompOpArgs", "example.2DInFluxes.Args", "example.2DUnBoundLinDecompOpFromFunction", "example.ConstlinDecompOpFromMatrix", "example.nestedTime2DMatrixList", "example.Time2DArrayList", "example.Time3DArrayList", "example.TimeMapFromArray", "FcAtm.from.Dataframe", "fT.Arrhenius", "fT.Century1", "fT.Century2", "fT.Daycent1", "fT.Daycent2", "fT.Demeter", "fT.KB", "fT.LandT", "fT.linear", "fT.Q10", "fT.RothC", "fT.Standcarb", "fW.Candy", "fW.Century", "fW.Daycent1", "fW.Daycent2", "fW.Demeter", "fW.Gompertz", "fW.Moyano", "fW.RothC", "fW.Skopp", "fW.Standcarb", "GaudinskiModel14", "GeneralDecompOp", "GeneralModel", "GeneralModel_14", "GeneralNlModel", "getAccumulatedRelease", "getC", "getC14", "getCompartmentalMatrixFunc", "getDecompOp", "getF14", "getF14C", "getF14R", "getFunctionDefinition", "getMeanTransitTime", "getReleaseFlux", "getReleaseFlux14", "getSolution", "getTimeRange", "getTimes", "getTransferMatrixFunc", "getTransitTimeDistributionDensity", "ICBM_N", "ICBMModel", "InFluxes", "linearScalarModel", "linesCPool", "listProduct", "Model", "Model_14", "Model_by_PoolNames", "OnepModel", "OnepModel14", "ParallelModel", "pathEntropy", "plot", "plotC14Pool", "plotCPool", "plotPoolGraph", "plotPoolGraphFromTupleLists", "PoolIndex", "RespirationCoefficients", "RothCModel", "SeriesLinearModel", "SeriesLinearModel14", "SoilR.F0.new", "state_variable_names", "systemAge", "ThreepairMMmodel", "ThreepFeedbackModel", "ThreepFeedbackModel14", "ThreepParallelModel", "ThreepParallelModel14", "ThreepSeriesModel", "ThreepSeriesModel14", "TimeMap", "TimeMap.from.Dataframe", "TimeMap.new", "transitTime", "turnoverFit", "TwopFeedbackModel", "TwopFeedbackModel14", "TwopMMmodel", "TwopParallelModel", "TwopParallelModel14", "TwopSeriesModel", "TwopSeriesModel14", "UnBoundLinDecompOp", "UnBoundNonLinDecompOp", "Yasso07Model", "YassoModel" ], "_datasets": [ { "name": "C14Atm", "title": "Atmospheric 14C fraction", "object": "C14Atm", "class": [ "data.frame" ], "fields": [ "V1", "V2" ], "rows": 108, "table": true, "tojson": true }, { "name": "C14Atm_NH", "title": "Post-bomb atmospheric 14C fraction", "object": "C14Atm_NH", "class": [ "data.frame" ], "fields": [ "YEAR", "Atmosphere" ], "rows": 111, "table": true, "tojson": true }, { "name": "eCO2", "title": "Soil CO2 efflux from an incubation experiment", "object": "eCO2", "class": [ "data.frame" ], "fields": [ "Days", "eCO2mean", "eCO2sd" ], "rows": 18, "table": true, "tojson": true }, { "name": "Graven2017", "title": "Compiled records of radicarbon in atmospheric CO2 for historical simulations in CMIP6", "object": "Graven2017", "class": [ "data.frame" ], "fields": [ "Year.AD", "NH", "Tropics", "SH" ], "rows": 166, "table": true, "tojson": true }, { "name": "HarvardForest14CO2", "title": "Delta14C in soil CO2 efflux from Harvard Forest", "object": "HarvardForest14CO2", "class": [ "data.frame" ], "fields": [ "Year", "D14C", "Site" ], "rows": 173, "table": true, "tojson": true }, { "name": "Hua2013", "title": "Atmospheric radiocarbon for the period 1950-2010 from Hua et al. (2013)", "object": "Hua2013", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "Hua2021", "title": "Atmospheric radiocarbon for the period 1950-2019 from Hua et al. (2021)", "object": "Hua2021", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "incubation_experiment", "title": "Soil CO2 efflux from an incubation experiment, along with the soil mass and carbon concentration measurements.", "object": "incubation_experiment", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "IntCal09", "title": "Northern Hemisphere atmospheric radiocarbon for the pre-bomb period", "object": "IntCal09", "class": [ "data.frame" ], "fields": [ "CAL.BP", "C14.age", "Error", "Delta.14C", "Sigma" ], "rows": 3522, "table": true, "tojson": true }, { "name": "IntCal13", "title": "Atmospheric radiocarbon for the 0-50,000 yr BP period", "object": "IntCal13", "class": [ "data.frame" ], "fields": [ "CAL.BP", "C14.age", "Error", "Delta.14C", "Sigma" ], "rows": 5141, "table": true, "tojson": true }, { "name": "IntCal20", "title": "The IntCal20 northern hemisphere radiocarbon curve for the 0-55,000 yr BP period", "object": "IntCal20", "class": [ "data.frame" ], "fields": [ "CAL.BP", "C14.age", "Sigma.C14.age", "Delta.14C", "Sigma.Delta.14C" ], "rows": 9501, "table": true, "tojson": true }, { "name": "SHCal20", "title": "The SHCal20 southern hemisphere radiocarbon curve for the 0-55,000 yr BP period", "object": "SHCal20", "class": [ "data.frame" ], "fields": [ "CAL.BP", "C14.age", "Sigma.C14.age", "Delta.14C", "Sigma.Delta.14C" ], "rows": 9501, "table": true, "tojson": true } ], "_help": [ { "page": "SoilR-package", "title": "SoilR", "topics": [ "SoilR-package" ] }, { "page": "sub-Model-character-missing-missing-method", "title": "Experimentally overloaded index operator", "topics": [ "[,Model,character,missing,missing-method" ] }, { "page": "sub-NlModel-character-ANY-ANY-method", "title": "automatic title", "topics": [ "[,NlModel,character,ANY,ANY-method" ] }, { "page": "sub-sub-MCSim-method", "title": "automatic title", "topics": [ "[[,MCSim-method" ] }, { "page": "sub-subset-MCSim-method", "title": "automatic title", "topics": [ "[[<-,MCSim-method" ] }, { "page": "cash-NlModel-method", "title": "automatic title", "topics": [ "$,NlModel-method" ] }, { "page": "AbsoluteFractionModern", "title": "Conversion of radiocarbon values", "topics": [ "AbsoluteFractionModern" ] }, { "page": "AbsoluteFractionModern_from_Delta14C", "title": "Conversion of radiocarbon values", "topics": [ "AbsoluteFractionModern_from_Delta14C" ] }, { "page": "AbsoluteFractionModern_from_Delta14C-matrix-method", "title": "Conversion of radiocarbon values", "topics": [ "AbsoluteFractionModern_from_Delta14C,matrix-method" ] }, { "page": "AbsoluteFractionModern_from_Delta14C-numeric-method", "title": "Conversion of radiocarbon values, from Delta14C to absolute fraction modern", "topics": [ "AbsoluteFractionModern_from_Delta14C,numeric-method" ] }, { "page": "AbsoluteFractionModern-BoundFc-method", "title": "automatic title", "topics": [ "AbsoluteFractionModern,BoundFc-method" ] }, { "page": "AbsoluteFractionModern-ConstFc-method", "title": "automatic title", "topics": [ "AbsoluteFractionModern,ConstFc-method" ] }, { "page": "add_plot", "title": "Add elements to plot", "topics": [ "add_plot" ] }, { "page": "add_plot-TimeMap-method", "title": "automatic title", "topics": [ "add_plot,TimeMap-method" ] }, { "page": "as.character-TimeMap-method", "title": "automatic title", "topics": [ "as.character,TimeMap-method" ] }, { "page": "as.numeric-InFluxList_by_PoolName-method", "title": "Convert to a numeric vector with the pool names as names", "topics": [ "as.numeric,InFluxList_by_PoolName-method" ] }, { "page": "as.numeric-InternalFlux_by_PoolName-method", "title": "Convert to a numeric value with name of the form 'a->b'", "topics": [ "as.numeric,InternalFlux_by_PoolName-method" ] }, { "page": "as.numeric-InternalFluxList_by_PoolName-method", "title": "Convert to a numeric vector with names of the form 'a->b'", "topics": [ "as.numeric,InternalFluxList_by_PoolName-method" ] }, { "page": "as.numeric-OutFluxList_by_PoolName-method", "title": "Convert to a numeric vector with the pool names as names", "topics": [ "as.numeric,OutFluxList_by_PoolName-method" ] }, { "page": "availableParticleProperties", "title": "Available particle properties", "topics": [ "availableParticleProperties" ] }, { "page": "availableParticleProperties-MCSim-method", "title": "automatic title", "topics": [ "availableParticleProperties,MCSim-method" ] }, { "page": "availableParticleSets", "title": "Available particle sets", "topics": [ "availableParticleSets" ] }, { "page": "availableParticleSets-MCSim-method", "title": "automatic title", "topics": [ "availableParticleSets,MCSim-method" ] }, { "page": "availableResidentSets", "title": "Available resident sets", "topics": [ "availableResidentSets" ] }, { "page": "availableResidentSets-MCSim-method", "title": "automatic title", "topics": [ "availableResidentSets,MCSim-method" ] }, { "page": "AWBmodel", "title": "Implementation of the microbial model AWB (Allison, Wallenstein, Bradford, 2010)", "topics": [ "AWBmodel" ] }, { "page": "bacwaveModel", "title": "Implementation of the microbial model Bacwave (bacterial waves)", "topics": [ "bacwaveModel" ] }, { "page": "bind.C14curves", "title": "Binding of pre- and post-bomb Delta14C curves", "topics": [ "bind.C14curves" ] }, { "page": "BoundFc", "title": "Bound Fc object", "topics": [ "BoundFc" ] }, { "page": "BoundFc-class", "title": "S4-class to represent atmospheric 14C concentration as scalar function of time.", "topics": [ "BoundFc-class" ] }, { "page": "BoundFc-character-method", "title": "automatic title", "topics": [ "BoundFc,character-method" ] }, { "page": "BoundFc-missing-method", "title": "automatic title", "topics": [ "BoundFc,missing-method" ] }, { "page": "BoundInFluxes", "title": "constructor for BoundInFluxes", "topics": [ "BoundInFluxes" ] }, { "page": "BoundInFluxes-class", "title": "automatic title", "topics": [ "BoundInFluxes-class" ] }, { "page": "BoundLinDecompOp", "title": "Generic constructor for the class with the same name", "topics": [ "BoundLinDecompOp" ] }, { "page": "BoundLinDecompOp-class", "title": "A S4 class to represent a linear compartmental operator defined on time interval", "topics": [ "BoundLinDecompOp-class" ] }, { "page": "BoundLinDecompOp-ANY-method", "title": "Creates an object of class BoundLinDecompOp", "topics": [ "BoundLinDecompOp,ANY-method" ] }, { "page": "BoundLinDecompOp-UnBoundLinDecompOp-method", "title": "A converter", "topics": [ "BoundLinDecompOp,UnBoundLinDecompOp-method" ] }, { "page": "by_PoolIndex", "title": "automatic title", "topics": [ "by_PoolIndex" ] }, { "page": "by_PoolIndex-ConstantInFluxRate_by_PoolName-ANY-ANY-method", "title": "new object with the source pool id converted to a PoolIndex if necessary", "topics": [ "by_PoolIndex,ConstantInFluxRate_by_PoolName,ANY,ANY-method" ] }, { "page": "by_PoolIndex-ConstantInternalFluxRate_by_PoolName-ANY-ANY-method", "title": "new object with the source pool id converted to a PoolName if necessary", "topics": [ "by_PoolIndex,ConstantInternalFluxRate_by_PoolName,ANY,ANY-method" ] }, { "page": "by_PoolIndex-ConstantInternalFluxRateList_by_PoolName-ANY-ANY-method", "title": "convert to a list indexed by pool names", "topics": [ "by_PoolIndex,ConstantInternalFluxRateList_by_PoolName,ANY,ANY-method" ] }, { "page": "by_PoolIndex-ConstantOutFluxRate_by_PoolName-ANY-ANY-method", "title": "new object with the source pool id converted to a PoolIndex if necessary", "topics": [ "by_PoolIndex,ConstantOutFluxRate_by_PoolName,ANY,ANY-method" ] }, { "page": "by_PoolIndex-ConstantOutFluxRateList_by_PoolName-ANY-ANY-method", "title": "convert to a list indexed by pool names", "topics": [ "by_PoolIndex,ConstantOutFluxRateList_by_PoolName,ANY,ANY-method" ] }, { "page": "by_PoolIndex-function-character-character-method", "title": "convert a function f of to f_vec", "topics": [ "by_PoolIndex,function,character,character-method" ] }, { "page": "by_PoolIndex-InFlux_by_PoolName-character-character-method", "title": "Convert the pool names to indices", "topics": [ "by_PoolIndex,InFlux_by_PoolName,character,character-method" ] }, { "page": "by_PoolIndex-InFluxList_by_PoolName-character-character-method", "title": "Transform pool names to indices", "topics": [ "by_PoolIndex,InFluxList_by_PoolName,character,character-method" ] }, { "page": "by_PoolIndex-InternalFlux_by_PoolName-character-character-method", "title": "automatic title", "topics": [ "by_PoolIndex,InternalFlux_by_PoolName,character,character-method" ] }, { "page": "by_PoolIndex-InternalFluxList_by_PoolName-character-character-method", "title": "automatic title", "topics": [ "by_PoolIndex,InternalFluxList_by_PoolName,character,character-method" ] }, { "page": "by_PoolIndex-OutFlux_by_PoolName-character-character-method", "title": "automatic title", "topics": [ "by_PoolIndex,OutFlux_by_PoolName,character,character-method" ] }, { "page": "by_PoolIndex-OutFluxList_by_PoolName-character-character-method", "title": "automatic title", "topics": [ "by_PoolIndex,OutFluxList_by_PoolName,character,character-method" ] }, { "page": "by_PoolIndex-PoolConnection_by_PoolName-ANY-ANY-method", "title": "constructor from strings of the form 'x->y' new object with the source pool id and the destination pool id guaranteed to be of class PoolIndex", "topics": [ "by_PoolIndex,PoolConnection_by_PoolName,ANY,ANY-method" ] }, { "page": "by_PoolName", "title": "automatic title", "topics": [ "by_PoolName" ] }, { "page": "by_PoolName-ConstantInFlux_by_PoolIndex-method", "title": "new object with the source pool id converted to a PoolIndex if necessary", "topics": [ "by_PoolName,ConstantInFlux_by_PoolIndex-method" ] }, { "page": "by_PoolName-ConstantInFluxList_by_PoolIndex-method", "title": "convert to a list indexed by pool names", "topics": [ "by_PoolName,ConstantInFluxList_by_PoolIndex-method" ] }, { "page": "by_PoolName-ConstantInFluxRate_by_PoolIndex-method", "title": "new object with the source pool id converted to a PoolIndex if necessary", "topics": [ "by_PoolName,ConstantInFluxRate_by_PoolIndex-method" ] }, { "page": "by_PoolName-ConstantInternalFluxRateList_by_PoolIndex-method", "title": "convert to a list indexed by pool names", "topics": [ "by_PoolName,ConstantInternalFluxRateList_by_PoolIndex-method" ] }, { "page": "by_PoolName-ConstantOutFluxRate_by_PoolIndex-method", "title": "new object with the source pool id converted to a PoolName if necessary", "topics": [ "by_PoolName,ConstantOutFluxRate_by_PoolIndex-method" ] }, { "page": "by_PoolName-ConstantOutFluxRateList_by_PoolIndex-method", "title": "convert to a list indexed by pool names", "topics": [ "by_PoolName,ConstantOutFluxRateList_by_PoolIndex-method" ] }, { "page": "C14Atm", "title": "Atmospheric 14C fraction", "topics": [ "C14Atm" ] }, { "page": "C14Atm_NH", "title": "Post-bomb atmospheric 14C fraction", "topics": [ "C14Atm_NH" ] }, { "page": "CenturyModel", "title": "Implementation of the Century model", "topics": [ "CenturyModel" ] }, { "page": "CenturyModel14", "title": "Implementation of a radiocarbon version of the Century model", "topics": [ "CenturyModel14" ] }, { "page": "check_duplicate_pool_names", "title": "helper function", "topics": [ "check_duplicate_pool_names" ] }, { "page": "check_id_length", "title": "helper function to check that the length of the argument is exactly 1", "topics": [ "check_id_length" ] }, { "page": "check_pool_ids", "title": "Check pool ids", "topics": [ "check_pool_ids" ] }, { "page": "check_pool_ids-PoolConnection_by_PoolIndex-integer-method", "title": "automatic title", "topics": [ "check_pool_ids,PoolConnection_by_PoolIndex,integer-method" ] }, { "page": "computeResults", "title": "Computes results", "topics": [ "computeResults" ] }, { "page": "computeResults-MCSim-method", "title": "automatic title", "topics": [ "computeResults,MCSim-method" ] }, { "page": "ConstantInFlux_by_PoolIndex-class", "title": "class for a constant influx to a single pool identified by index", "topics": [ "ConstantInFlux_by_PoolIndex-class" ] }, { "page": "ConstantInFlux_by_PoolName-class", "title": "class for a constant influx to a single pool identified by pool name", "topics": [ "ConstantInFlux_by_PoolName-class" ] }, { "page": "ConstantInFluxList_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "ConstantInFluxList_by_PoolIndex" ] }, { "page": "ConstantInFluxList_by_PoolIndex-class", "title": "Subclass of list that is guaranteed to contain only elements of type ConstantInFlux_by_PoolIndex", "topics": [ "ConstantInFluxList_by_PoolIndex-class" ] }, { "page": "ConstantInFluxList_by_PoolIndex-ConstInFluxes-method", "title": "constructor from ConstInFluxes", "topics": [ "ConstantInFluxList_by_PoolIndex,ConstInFluxes-method" ] }, { "page": "ConstantInFluxList_by_PoolIndex-list-method", "title": "constructor from a normal list", "topics": [ "ConstantInFluxList_by_PoolIndex,list-method" ] }, { "page": "ConstantInFluxList_by_PoolIndex-numeric-method", "title": "constructor from numeric vector", "topics": [ "ConstantInFluxList_by_PoolIndex,numeric-method" ] }, { "page": "ConstantInFluxList_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "ConstantInFluxList_by_PoolName" ] }, { "page": "ConstantInFluxList_by_PoolName-class", "title": "Subclass of list that is guaranteed to contain only elements of type ConstantInFlux_by_PoolName", "topics": [ "ConstantInFluxList_by_PoolName-class" ] }, { "page": "ConstantInFluxRate_by_PoolIndex-class", "title": "Describes a flux rates.", "topics": [ "ConstantInFluxRate_by_PoolIndex-class" ] }, { "page": "ConstantInFluxRate_by_PoolName", "title": "Constructor for the class with the same name", "topics": [ "ConstantInFluxRate_by_PoolName" ] }, { "page": "ConstantInFluxRate_by_PoolName-class", "title": "Describes a flux rates.", "topics": [ "ConstantInFluxRate_by_PoolName-class" ] }, { "page": "ConstantInternalFluxRate_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "ConstantInternalFluxRate_by_PoolIndex" ] }, { "page": "ConstantInternalFluxRate_by_PoolIndex-class", "title": "S4 class representing a constant internal flux rate", "topics": [ "ConstantInternalFluxRate_by_PoolIndex-class" ] }, { "page": "ConstantInternalFluxRate_by_PoolIndex-numeric-numeric-missing-numeric-method", "title": "automatic title", "topics": [ "ConstantInternalFluxRate_by_PoolIndex,numeric,numeric,missing,numeric-method" ] }, { "page": "ConstantInternalFluxRate_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "ConstantInternalFluxRate_by_PoolName" ] }, { "page": "ConstantInternalFluxRate_by_PoolName-class", "title": "S4-class to represent a constant internal flux rate with source and target indexed by name", "topics": [ "ConstantInternalFluxRate_by_PoolName-class" ] }, { "page": "ConstantInternalFluxRate_by_PoolName-character-character-missing-numeric-method", "title": "constructor with argument conversion", "topics": [ "ConstantInternalFluxRate_by_PoolName,character,character,missing,numeric-method" ] }, { "page": "ConstantInternalFluxRate_by_PoolName-missing-missing-character-numeric-method", "title": "constructor from strings of the form 'a->b'", "topics": [ "ConstantInternalFluxRate_by_PoolName,missing,missing,character,numeric-method" ] }, { "page": "ConstantInternalFluxRateList_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "ConstantInternalFluxRateList_by_PoolIndex" ] }, { "page": "ConstantInternalFluxRateList_by_PoolIndex-class", "title": "Describes a list of flux rates.", "topics": [ "ConstantInternalFluxRateList_by_PoolIndex-class" ] }, { "page": "ConstantInternalFluxRateList_by_PoolIndex-list-method", "title": "constructor from a normal list", "topics": [ "ConstantInternalFluxRateList_by_PoolIndex,list-method" ] }, { "page": "ConstantInternalFluxRateList_by_PoolIndex-numeric-method", "title": "automatic title", "topics": [ "ConstantInternalFluxRateList_by_PoolIndex,numeric-method" ] }, { "page": "ConstantInternalFluxRateList_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "ConstantInternalFluxRateList_by_PoolName" ] }, { "page": "ConstantInternalFluxRateList_by_PoolName-class", "title": "Describes a list of flux rates.", "topics": [ "ConstantInternalFluxRateList_by_PoolName-class" ] }, { "page": "ConstantInternalFluxRateList_by_PoolName-list-method", "title": "Constructor from a normal list of fluxes", "topics": [ "ConstantInternalFluxRateList_by_PoolName,list-method" ] }, { "page": "ConstantOutFluxRate_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "ConstantOutFluxRate_by_PoolIndex" ] }, { "page": "ConstantOutFluxRate_by_PoolIndex-class", "title": "S4 Class to represent a single constant out-flux rate with the source pool specified by an index", "topics": [ "ConstantOutFluxRate_by_PoolIndex-class" ] }, { "page": "ConstantOutFluxRate_by_PoolIndex-numeric-numeric-method", "title": "automatic title", "topics": [ "ConstantOutFluxRate_by_PoolIndex,numeric,numeric-method" ] }, { "page": "ConstantOutFluxRate_by_PoolName-class", "title": "S4 Class to represent a single constant out-flux rate with the source pool specified by name", "topics": [ "ConstantOutFluxRate_by_PoolName-class" ] }, { "page": "ConstantOutFluxRateList_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "ConstantOutFluxRateList_by_PoolIndex" ] }, { "page": "ConstantOutFluxRateList_by_PoolIndex-class", "title": "Describes a list of flux rates.", "topics": [ "ConstantOutFluxRateList_by_PoolIndex-class" ] }, { "page": "ConstantOutFluxRateList_by_PoolIndex-list-method", "title": "constructor from a normal list", "topics": [ "ConstantOutFluxRateList_by_PoolIndex,list-method" ] }, { "page": "ConstantOutFluxRateList_by_PoolIndex-numeric-method", "title": "automatic title", "topics": [ "ConstantOutFluxRateList_by_PoolIndex,numeric-method" ] }, { "page": "ConstantOutFluxRateList_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "ConstantOutFluxRateList_by_PoolName" ] }, { "page": "ConstantOutFluxRateList_by_PoolName-class", "title": "Describes a list of flux rates.", "topics": [ "ConstantOutFluxRateList_by_PoolName-class" ] }, { "page": "ConstantOutFluxRateList_by_PoolName-list-method", "title": "constructor from a normal list", "topics": [ "ConstantOutFluxRateList_by_PoolName,list-method" ] }, { "page": "ConstantOutFluxRateList_by_PoolName-numeric-method", "title": "automatic title", "topics": [ "ConstantOutFluxRateList_by_PoolName,numeric-method" ] }, { "page": "ConstFc", "title": "creates an object containing the initial values for the 14C fraction needed to create models in SoilR", "topics": [ "ConstFc" ] }, { "page": "ConstFc-class", "title": "S4 class representing a constant 14C fraction", "topics": [ "ConstFc-class" ] }, { "page": "ConstInFluxes", "title": "Constant input fluxes", "topics": [ "ConstInFluxes" ] }, { "page": "ConstInFluxes-class", "title": "S4 class for a constant influx vector", "topics": [ "ConstInFluxes-class" ] }, { "page": "ConstInFluxes-ConstantInFluxList_by_PoolIndex-numeric-method", "title": "automatic title", "topics": [ "ConstInFluxes,ConstantInFluxList_by_PoolIndex,numeric-method" ] }, { "page": "ConstInFluxes-numeric-ANY-method", "title": "automatic title", "topics": [ "ConstInFluxes,numeric,ANY-method" ] }, { "page": "ConstLinDecompOp", "title": "Generic constructor for the class with the same name", "topics": [ "ConstLinDecompOp" ] }, { "page": "ConstLinDecompOp_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "ConstLinDecompOp_by_PoolName" ] }, { "page": "ConstLinDecompOp-class", "title": "A class to represent a constant (=nonautonomous,linear) compartmental matrix or equivalently a combination of ordered constant internal flux rates and constant out flux rates.", "topics": [ "ConstLinDecompOp-class" ] }, { "page": "ConstLinDecompOp-matrix-missing-missing-missing-missing-method", "title": "Constructor of object of ConstLinDecompOp class", "topics": [ "ConstLinDecompOp,matrix,missing,missing,missing,missing-method" ] }, { "page": "ConstLinDecompOpWithLinearScalarFactor", "title": "Generic constructor for the class with the same name", "topics": [ "ConstLinDecompOpWithLinearScalarFactor" ] }, { "page": "ConstLinDecompOpWithLinearScalarFactor-class", "title": "A class to represent a constant (=nonautonomous,linear) compartmental matrix with a time dependent (linear) scalar pre factor This is a special case of a linear compartmental operator/matrix", "topics": [ "ConstLinDecompOpWithLinearScalarFactor-class" ] }, { "page": "cycling", "title": "Cycling analysis of compartmental matrices", "topics": [ "cycling" ] }, { "page": "DecompOp-class", "title": "S4-class to represent compartmental operators", "topics": [ "DecompOp-class" ] }, { "page": "DecompositionOperator-class", "title": "automatic title", "topics": [ "DecompositionOperator-class" ] }, { "page": "Delta14C", "title": "Conversion of radiocarbon values", "topics": [ "Delta14C" ] }, { "page": "Delta14C_from_AbsoluteFractionModern", "title": "Conversion of radiocarbon values", "topics": [ "Delta14C_from_AbsoluteFractionModern" ] }, { "page": "Delta14C_from_AbsoluteFractionModern-matrix-method", "title": "Conversion of radiocarbon values", "topics": [ "Delta14C_from_AbsoluteFractionModern,matrix-method" ] }, { "page": "Delta14C_from_AbsoluteFractionModern-numeric-method", "title": "Conversion of radiocarbon values", "topics": [ "Delta14C_from_AbsoluteFractionModern,numeric-method" ] }, { "page": "Delta14C-BoundFc-method", "title": "automatic title", "topics": [ "Delta14C,BoundFc-method" ] }, { "page": "Delta14C-ConstFc-method", "title": "automatic title", "topics": [ "Delta14C,ConstFc-method" ] }, { "page": "deSolve.lsoda.wrapper", "title": "deSolve.lsoda.wrapper", "topics": [ "deSolve.lsoda.wrapper" ] }, { "page": "eCO2", "title": "Soil CO2 efflux from an incubation experiment", "topics": [ "eCO2" ] }, { "page": "entropyRatePerJump", "title": "Entropy rate per jump", "topics": [ "entropyRatePerJump" ] }, { "page": "entropyRatePerTime", "title": "Entropy rate per time", "topics": [ "entropyRatePerTime" ] }, { "page": "euler", "title": "euler", "topics": [ "euler" ] }, { "page": "example.2DBoundInFluxesFromFunction", "title": "example.2DBoundInFluxesFromFunction", "topics": [ "example.2DBoundInFluxesFromFunction" ] }, { "page": "example.2DBoundLinDecompOpFromFunction", "title": "example.2DBoundLinDecompOpFromFunction", "topics": [ "example.2DBoundLinDecompOpFromFunction" ] }, { "page": "example.2DConstFc.Args", "title": "example.2DConstFc.Args", "topics": [ "example.2DConstFc.Args" ] }, { "page": "example.2DConstInFluxesFromVector", "title": "2D example for constant Influx", "topics": [ "example.2DConstInFluxesFromVector" ] }, { "page": "example.2DGeneralDecompOpArgs", "title": "example.2DGeneralDecompOpArgs", "topics": [ "example.2DGeneralDecompOpArgs" ] }, { "page": "example.2DInFluxes.Args", "title": "example.2DInFluxes.Args", "topics": [ "example.2DInFluxes.Args" ] }, { "page": "example.2DUnBoundLinDecompOpFromFunction", "title": "example.2DUnBoundLinDecompOpFromFunction", "topics": [ "example.2DUnBoundLinDecompOpFromFunction" ] }, { "page": "example.ConstlinDecompOpFromMatrix", "title": "example.ConstlinDecompOpFromMatrix", "topics": [ "example.ConstlinDecompOpFromMatrix" ] }, { "page": "example.nestedTime2DMatrixList", "title": "create an example nested list that can be", "topics": [ "example.nestedTime2DMatrixList" ] }, { "page": "example.Time2DArrayList", "title": "create an example TimeMap from 2D array", "topics": [ "example.Time2DArrayList" ] }, { "page": "example.Time3DArrayList", "title": "create an example TimeFrame from 3D array", "topics": [ "example.Time3DArrayList" ] }, { "page": "example.TimeMapFromArray", "title": "create an example TimeFrame from 3D array", "topics": [ "example.TimeMapFromArray" ] }, { "page": "Fc-class", "title": "automatic title", "topics": [ "Fc-class" ] }, { "page": "FcAtm.from.Dataframe", "title": "FcAtm.from.Dataframe", "topics": [ "FcAtm.from.Dataframe" ] }, { "page": "fT.Arrhenius", "title": "Effects of temperature on decomposition rates according the Arrhenius equation", "topics": [ "fT.Arrhenius" ] }, { "page": "fT.Century1", "title": "Effects of temperature on decomposition rates according the the CENTURY model", "topics": [ "fT.Century1" ] }, { "page": "fT.Century2", "title": "Effects of temperature on decomposition rates according the the CENTURY model", "topics": [ "fT.Century2" ] }, { "page": "fT.Daycent1", "title": "Effects of temperature on decomposition rates according to the DAYCENT model", "topics": [ "fT.Daycent1" ] }, { "page": "fT.Daycent2", "title": "Effects of temperature on decomposition rates according to the DAYCENT model", "topics": [ "fT.Daycent2" ] }, { "page": "fT.Demeter", "title": "Effects of temperature on decomposition rates according to the DEMETER model", "topics": [ "fT.Demeter" ] }, { "page": "fT.KB", "title": "Effects of temperature on decomposition rates according to a model proposed by M. Kirschbaum (1995)", "topics": [ "fT.KB" ] }, { "page": "fT.LandT", "title": "Effects of temperature on decomposition rates according to a function proposed by Lloyd and Taylor (1994)", "topics": [ "fT.LandT" ] }, { "page": "fT.linear", "title": "Effects of temperature on decomposition rates according to a linear model", "topics": [ "fT.linear" ] }, { "page": "fT.Q10", "title": "Effects of temperature on decomposition rates according to a Q10 function", "topics": [ "fT.Q10" ] }, { "page": "fT.RothC", "title": "Effects of temperature on decomposition rates according to the functions included in the RothC model", "topics": [ "fT.RothC" ] }, { "page": "fT.Standcarb", "title": "Effects of temperature on decomposition rates according to the StandCarb model", "topics": [ "fT.Standcarb" ] }, { "page": "fW.Candy", "title": "Effects of moisture on decomposition rates according to the Candy model", "topics": [ "fW.Candy" ] }, { "page": "fW.Century", "title": "Effects of moisture on decomposition rates according to the CENTURY model", "topics": [ "fW.Century" ] }, { "page": "fW.Daycent1", "title": "Effects of moisture on decomposition rates according to the DAYCENT model", "topics": [ "fW.Daycent1" ] }, { "page": "fW.Daycent2", "title": "Effects of moisture on decomposition rates according to the DAYCENT model", "topics": [ "fW.Daycent2" ] }, { "page": "fW.Demeter", "title": "Effects of moisture on decomposition rates according to the DEMETER model", "topics": [ "fW.Demeter" ] }, { "page": "fW.Gompertz", "title": "Effects of moisture on decomposition rates according to the Gompertz function", "topics": [ "fW.Gompertz" ] }, { "page": "fW.Moyano", "title": "Effects of moisture on decomposition rates according to the function proposed by Moyano et al. (2013)", "topics": [ "fW.Moyano" ] }, { "page": "fW.RothC", "title": "Effects of moisture on decomposition rates according to the RothC model", "topics": [ "fW.RothC" ] }, { "page": "fW.Skopp", "title": "Effects of moisture on decomposition rates according to the function proposed by Skopp et al. 1990", "topics": [ "fW.Skopp" ] }, { "page": "fW.Standcarb", "title": "Effects of moisture on decomposition rates according to the StandCarb model", "topics": [ "fW.Standcarb" ] }, { "page": "GaudinskiModel14", "title": "Implementation of a the six-pool C14 model proposed by Gaudinski et al. 2000", "topics": [ "GaudinskiModel14" ] }, { "page": "GeneralDecompOp", "title": "A generic factory for subclasses of GeneralDecompOp", "topics": [ "GeneralDecompOp" ] }, { "page": "GeneralDecompOp-DecompOp-method", "title": "Pass through factory for objects of subclasses of DecompOp", "topics": [ "GeneralDecompOp,DecompOp-method" ] }, { "page": "GeneralDecompOp-function-method", "title": "automatic title", "topics": [ "GeneralDecompOp,function-method" ] }, { "page": "GeneralDecompOp-list-method", "title": "automatic title", "topics": [ "GeneralDecompOp,list-method" ] }, { "page": "GeneralDecompOp-matrix-method", "title": "automatic title", "topics": [ "GeneralDecompOp,matrix-method" ] }, { "page": "GeneralDecompOp-TimeMap-method", "title": "automatic title", "topics": [ "GeneralDecompOp,TimeMap-method" ] }, { "page": "GeneralModel", "title": "additional function to create Models", "topics": [ "GeneralModel" ] }, { "page": "GeneralModel_14", "title": "create objects of class Model_14", "topics": [ "GeneralModel_14" ] }, { "page": "GeneralNlModel", "title": "Use this function to create objects of class NlModel.", "topics": [ "GeneralNlModel" ] }, { "page": "GeneralPoolId", "title": "General pool Id", "topics": [ "GeneralPoolId" ] }, { "page": "GeneralPoolId-character-method", "title": "automatic title", "topics": [ "GeneralPoolId,character-method" ] }, { "page": "GeneralPoolId-numeric-method", "title": "generic factory for this virtual class", "topics": [ "GeneralPoolId,numeric-method" ] }, { "page": "getAccumulatedRelease", "title": "Accumulated release flux out of the pools", "topics": [ "getAccumulatedRelease" ] }, { "page": "getAccumulatedRelease-Model-method", "title": "Compute the time integral of the relaese fluxes over time", "topics": [ "getAccumulatedRelease,Model-method" ] }, { "page": "getC", "title": "Calculates the content of the pools", "topics": [ "getC" ] }, { "page": "getC-Model_by_PoolNames-method", "title": "Pool Contents for all times", "topics": [ "getC,Model_by_PoolNames-method" ] }, { "page": "getC-Model-method", "title": "Pool Contents for all times", "topics": [ "getC,Model-method" ] }, { "page": "getC-NlModel-method", "title": "Pool Contents for all times", "topics": [ "getC,NlModel-method" ] }, { "page": "getC14", "title": "Generic that yields the 14C content for all pools and all times", "topics": [ "getC14" ] }, { "page": "getC14-Model_14-method", "title": "automatic title", "topics": [ "getC14,Model_14-method" ] }, { "page": "getCompartmentalMatrixFunc", "title": "Compartmental matrix function", "topics": [ "getCompartmentalMatrixFunc" ] }, { "page": "getCompartmentalMatrixFunc-BoundLinDecompOp-method", "title": "automatic title", "topics": [ "getCompartmentalMatrixFunc,BoundLinDecompOp-method" ] }, { "page": "getCompartmentalMatrixFunc-ConstLinDecompOp-method", "title": "Compartmental matrix function", "topics": [ "getCompartmentalMatrixFunc,ConstLinDecompOp-method" ] }, { "page": "getCompartmentalMatrixFunc-TransportDecompositionOperator-method", "title": "automatic title", "topics": [ "getCompartmentalMatrixFunc,TransportDecompositionOperator-method" ] }, { "page": "getCompartmentalMatrixFunc-UnBoundNonLinDecompOp-method", "title": "Extract the matrix valued function of time and state vector for the compartmental matrix", "topics": [ "getCompartmentalMatrixFunc,UnBoundNonLinDecompOp-method" ] }, { "page": "getConstantCompartmentalMatrix", "title": "Constant compartmental matrix", "topics": [ "getConstantCompartmentalMatrix" ] }, { "page": "getConstantCompartmentalMatrix-ConstLinDecompOp-method", "title": "Constant compartmental matrix", "topics": [ "getConstantCompartmentalMatrix,ConstLinDecompOp-method" ] }, { "page": "getConstantCompartmentalMatrix-ConstLinDecompOpWithLinearScalarFactor-method", "title": "automatic title", "topics": [ "getConstantCompartmentalMatrix,ConstLinDecompOpWithLinearScalarFactor-method" ] }, { "page": "getConstantInFluxVector", "title": "Input flux vector", "topics": [ "getConstantInFluxVector" ] }, { "page": "getConstantInFluxVector-ConstInFluxes-method", "title": "automatic title", "topics": [ "getConstantInFluxVector,ConstInFluxes-method" ] }, { "page": "getConstantInternalFluxRateList_by_PoolIndex", "title": "Constant internal flux rate list by pool index", "topics": [ "getConstantInternalFluxRateList_by_PoolIndex" ] }, { "page": "getConstantInternalFluxRateList_by_PoolIndex-ConstLinDecompOp-method", "title": "Constant internal flux rate list by pool index", "topics": [ "getConstantInternalFluxRateList_by_PoolIndex,ConstLinDecompOp-method" ] }, { "page": "getConstantOutFluxRateList_by_PoolIndex", "title": "Constant out flux rate list by pool index", "topics": [ "getConstantOutFluxRateList_by_PoolIndex" ] }, { "page": "getConstantOutFluxRateList_by_PoolIndex-ConstLinDecompOp-method", "title": "Constant out flux rate list by pool index", "topics": [ "getConstantOutFluxRateList_by_PoolIndex,ConstLinDecompOp-method" ] }, { "page": "getConstLinDecompOp", "title": "Constant linear decomposition operator", "topics": [ "getConstLinDecompOp" ] }, { "page": "getConstLinDecompOp-ConstLinDecompOpWithLinearScalarFactor-method", "title": "automatic title", "topics": [ "getConstLinDecompOp,ConstLinDecompOpWithLinearScalarFactor-method" ] }, { "page": "getCumulativeC", "title": "Cummulative pool contents", "topics": [ "getCumulativeC" ] }, { "page": "getCumulativeC-NlModel-method", "title": "automatic title", "topics": [ "getCumulativeC,NlModel-method" ] }, { "page": "getDecompOp", "title": "Decomposition operator of a model", "topics": [ "getDecompOp" ] }, { "page": "getDecompOp-Model-method", "title": "Extract the Compartmental Operator", "topics": [ "getDecompOp,Model-method" ] }, { "page": "getDecompOp-NlModel-method", "title": "Extract the Compartmental Operator", "topics": [ "getDecompOp,NlModel-method" ] }, { "page": "getDotOut", "title": "Dot out", "topics": [ "getDotOut" ] }, { "page": "getDotOut-TransportDecompositionOperator-method", "title": "automatic title", "topics": [ "getDotOut,TransportDecompositionOperator-method" ] }, { "page": "getF14", "title": "Generic that yields the 14C fraction for the content all pools and all times", "topics": [ "getF14" ] }, { "page": "getF14-Model_14-method", "title": "automatic title", "topics": [ "getF14,Model_14-method" ] }, { "page": "getF14C", "title": "Generic that yields the 14C fraction for the cumulative content of all pools and all times", "topics": [ "getF14C" ] }, { "page": "getF14C-Model_14-method", "title": "automatic title", "topics": [ "getF14C,Model_14-method" ] }, { "page": "getF14R", "title": "Generic that yields the 14C fraction for the release flux of all pools and all times", "topics": [ "getF14R" ] }, { "page": "getF14R-Model_14-method", "title": "automatic title", "topics": [ "getF14R,Model_14-method" ] }, { "page": "getFormat", "title": "Get format of SoilR object", "topics": [ "getFormat" ] }, { "page": "getFormat-Fc-method", "title": "automatic title", "topics": [ "getFormat,Fc-method" ] }, { "page": "getFunctionDefinition", "title": "Function definition of SoilR model", "topics": [ "getFunctionDefinition" ] }, { "page": "getFunctionDefinition-ConstInFluxes-method", "title": "automatic title", "topics": [ "getFunctionDefinition,ConstInFluxes-method" ] }, { "page": "getFunctionDefinition-ConstLinDecompOp-method", "title": "Function describing an object of class ConstLinDecompOp", "topics": [ "getFunctionDefinition,ConstLinDecompOp-method" ] }, { "page": "getFunctionDefinition-ConstLinDecompOpWithLinearScalarFactor-method", "title": "convert names of vectors or lists to class ConstantOutFluxRate convert names of vectors or lists to class ConstantInternalFluxRate helper function", "topics": [ "getFunctionDefinition,ConstLinDecompOpWithLinearScalarFactor-method" ] }, { "page": "getFunctionDefinition-DecompositionOperator-method", "title": "automatic title", "topics": [ "getFunctionDefinition,DecompositionOperator-method" ] }, { "page": "getFunctionDefinition-InFluxList_by_PoolIndex-method", "title": "automatic title", "topics": [ "getFunctionDefinition,InFluxList_by_PoolIndex-method" ] }, { "page": "getFunctionDefinition-InFluxList_by_PoolName-method", "title": "automatic title", "topics": [ "getFunctionDefinition,InFluxList_by_PoolName-method" ] }, { "page": "getFunctionDefinition-StateDependentInFluxVector-method", "title": "automatic title", "topics": [ "getFunctionDefinition,StateDependentInFluxVector-method" ] }, { "page": "getFunctionDefinition-TimeMap-method", "title": "automatic title", "topics": [ "getFunctionDefinition,TimeMap-method" ] }, { "page": "getFunctionDefinition-TransportDecompositionOperator-method", "title": "automatic title", "topics": [ "getFunctionDefinition,TransportDecompositionOperator-method" ] }, { "page": "getFunctionDefinition-UnBoundInFluxes-method", "title": "automatic title", "topics": [ "getFunctionDefinition,UnBoundInFluxes-method" ] }, { "page": "getFunctionDefinition-UnBoundLinDecompOp-method", "title": "Extracts the time dependent matrix valued function (compartmental matrix)", "concept": [ "UnBoundLinDecompOp_constructor" ], "topics": [ "getFunctionDefinition,UnBoundLinDecompOp-method" ] }, { "page": "getInFluxes", "title": "Extract the influxes", "topics": [ "getInFluxes" ] }, { "page": "getInFluxes-Model-method", "title": "Extract the InFluxes as provided during creation of the model", "topics": [ "getInFluxes,Model-method" ] }, { "page": "getInFluxes-NlModel-method", "title": "automatic title", "topics": [ "getInFluxes,NlModel-method" ] }, { "page": "getInitialValues", "title": "Initial values of SoilR object", "topics": [ "getInitialValues" ] }, { "page": "getInitialValues-NlModel-method", "title": "automatic title", "topics": [ "getInitialValues,NlModel-method" ] }, { "page": "getLinearScaleFactor", "title": "Linear scale factor", "topics": [ "getLinearScaleFactor" ] }, { "page": "getLinearScaleFactor-ConstLinDecompOpWithLinearScalarFactor-method", "title": "automatic title", "topics": [ "getLinearScaleFactor,ConstLinDecompOpWithLinearScalarFactor-method" ] }, { "page": "getMeanTransitTime", "title": "Mean transit time for SoilR objects", "topics": [ "getMeanTransitTime" ] }, { "page": "getMeanTransitTime-ConstLinDecompOp-method", "title": "Mean transit time obtained through a numerical simulation. It produces an estimate with numerical errors. We recommend to use the function transitTime instead.", "topics": [ "getMeanTransitTime,ConstLinDecompOp-method" ] }, { "page": "getNumberOfPools", "title": "Number of pools in a model", "topics": [ "getNumberOfPools" ] }, { "page": "getNumberOfPools-MCSim-method", "title": "automatic title", "topics": [ "getNumberOfPools,MCSim-method" ] }, { "page": "getNumberOfPools-NlModel-method", "title": "automatic title", "topics": [ "getNumberOfPools,NlModel-method" ] }, { "page": "getNumberOfPools-TransportDecompositionOperator-method", "title": "automatic title", "topics": [ "getNumberOfPools,TransportDecompositionOperator-method" ] }, { "page": "getOutputFluxes", "title": "Generic Function to obtain the fluxes out of of the pools", "topics": [ "getOutputFluxes" ] }, { "page": "getOutputFluxes-NlModel-method", "title": "automatic title", "topics": [ "getOutputFluxes,NlModel-method" ] }, { "page": "getOutputReceivers", "title": "Pools receiving outputs from other pools", "topics": [ "getOutputReceivers" ] }, { "page": "getOutputReceivers-TransportDecompositionOperator-numeric-method", "title": "automatic title", "topics": [ "getOutputReceivers,TransportDecompositionOperator,numeric-method" ] }, { "page": "getParticleMonteCarloSimulator", "title": "automatic title", "topics": [ "getParticleMonteCarloSimulator" ] }, { "page": "getParticleMonteCarloSimulator-NlModel-method", "title": "automatic title", "topics": [ "getParticleMonteCarloSimulator,NlModel-method" ] }, { "page": "getReleaseFlux", "title": "Generic Function to obtain the vector of release fluxes out of the pools for all times.", "topics": [ "getReleaseFlux" ] }, { "page": "getReleaseFlux-Model_by_PoolNames-method", "title": "automatic title", "topics": [ "getReleaseFlux,Model_by_PoolNames-method" ] }, { "page": "getReleaseFlux-Model-method", "title": "The release fluxes [content]/[time] for all pools.", "topics": [ "getReleaseFlux,Model-method" ] }, { "page": "getReleaseFlux-NlModel-method", "title": "automatic title", "topics": [ "getReleaseFlux,NlModel-method" ] }, { "page": "getReleaseFlux14", "title": "Generic that yields the 14C fraction in the release flux", "topics": [ "getReleaseFlux14" ] }, { "page": "getReleaseFlux14-Model_14-method", "title": "automatic title", "topics": [ "getReleaseFlux14,Model_14-method" ] }, { "page": "getRightHandSideOfODE", "title": "Right hand side of ODE of a SoilR model", "topics": [ "getRightHandSideOfODE" ] }, { "page": "getRightHandSideOfODE-Model_by_PoolNames-method", "title": "Provide the (vector valued) derivative of the stocks with respect to time", "topics": [ "getRightHandSideOfODE,Model_by_PoolNames-method" ] }, { "page": "getRightHandSideOfODE-Model-method", "title": "Derivative of the state variables as function", "topics": [ "getRightHandSideOfODE,Model-method" ] }, { "page": "getSolution", "title": "Calculates all stocks all fluxes to ,in and out of the compartment system and also their integrals over time", "topics": [ "getSolution" ] }, { "page": "getSolution-Model_by_PoolNames-method", "title": "All Fluxes and stocks for all times", "topics": [ "getSolution,Model_by_PoolNames-method" ] }, { "page": "getTimeRange", "title": "Time range of a model simulation", "topics": [ "getTimeRange" ] }, { "page": "getTimeRange-ConstInFluxes-method", "title": "automatic title", "topics": [ "getTimeRange,ConstInFluxes-method" ] }, { "page": "getTimeRange-ConstLinDecompOp-method", "title": "Time range of a simulation described in an object of class ConstLinDecompOp", "topics": [ "getTimeRange,ConstLinDecompOp-method" ] }, { "page": "getTimeRange-ConstLinDecompOpWithLinearScalarFactor-method", "title": "automatic title", "topics": [ "getTimeRange,ConstLinDecompOpWithLinearScalarFactor-method" ] }, { "page": "getTimeRange-DecompositionOperator-method", "title": "automatic title", "topics": [ "getTimeRange,DecompositionOperator-method" ] }, { "page": "getTimeRange-TimeMap-method", "title": "The time interval where the function is defined", "topics": [ "getTimeRange,TimeMap-method" ] }, { "page": "getTimeRange-UnBoundInFluxes-method", "title": "automatic title", "topics": [ "getTimeRange,UnBoundInFluxes-method" ] }, { "page": "getTimeRange-UnBoundLinDecompOp-method", "title": "Extracts the time interval for which the function is valid.", "topics": [ "getTimeRange,UnBoundLinDecompOp-method" ] }, { "page": "getTimes", "title": "Time vector of SoilR object", "topics": [ "getTimes" ] }, { "page": "getTimes-Model_by_PoolNames-method", "title": "Extract the times vector", "topics": [ "getTimes,Model_by_PoolNames-method" ] }, { "page": "getTimes-Model-method", "title": "Extract the times vector", "topics": [ "getTimes,Model-method" ] }, { "page": "getTimes-NlModel-method", "title": "automatic title", "topics": [ "getTimes,NlModel-method" ] }, { "page": "getTransferCoefficients", "title": "Transfer coefficients", "topics": [ "getTransferCoefficients" ] }, { "page": "getTransferCoefficients-NlModel-method", "title": "automatic title", "topics": [ "getTransferCoefficients,NlModel-method" ] }, { "page": "getTransferCoefficients-TransportDecompositionOperator-method", "title": "automatic title", "topics": [ "getTransferCoefficients,TransportDecompositionOperator-method" ] }, { "page": "getTransferMatrix", "title": "deprecated, use getTransferMatrixFunc instead", "topics": [ "getTransferMatrix" ] }, { "page": "getTransferMatrixFunc", "title": "Transfer matrix function", "topics": [ "getTransferMatrixFunc" ] }, { "page": "getTransferMatrixFunc-TransportDecompositionOperator-method", "title": "automatic title", "topics": [ "getTransferMatrixFunc,TransportDecompositionOperator-method" ] }, { "page": "getTransitTimeDistributionDensity", "title": "Transit time distribution for SoilR objects", "topics": [ "getTransitTimeDistributionDensity" ] }, { "page": "getTransitTimeDistributionDensity-ConstLinDecompOp-method", "title": "Transit time distribution obtained through a numerical simulation. It introduces numerical errors. We recommend to use the function transitTime instead", "topics": [ "getTransitTimeDistributionDensity,ConstLinDecompOp-method" ] }, { "page": "getValues", "title": "Get values of SoilR object", "topics": [ "getValues" ] }, { "page": "getValues-ConstFc-method", "title": "automatic title", "topics": [ "getValues,ConstFc-method" ] }, { "page": "Graven2017", "title": "Compiled records of radicarbon in atmospheric CO2 for historical simulations in CMIP6", "topics": [ "Graven2017" ] }, { "page": "HarvardForest14CO2", "title": "Delta14C in soil CO2 efflux from Harvard Forest", "topics": [ "HarvardForest14CO2" ] }, { "page": "Hua2013", "title": "Atmospheric radiocarbon for the period 1950-2010 from Hua et al. (2013)", "topics": [ "Hua2013" ] }, { "page": "Hua2021", "title": "Atmospheric radiocarbon for the period 1950-2019 from Hua et al. (2021)", "topics": [ "Hua2021" ] }, { "page": "ICBM_N", "title": "Implementation of the ICBM/N model", "topics": [ "ICBM_N" ] }, { "page": "ICBMModel", "title": "Implementation of the Introductory Carbon Balance Model (ICBM)", "topics": [ "ICBMModel" ] }, { "page": "incubation_experiment", "title": "Soil CO2 efflux from an incubation experiment, along with the soil mass and carbon concentration measurements.", "topics": [ "incubation_experiment" ] }, { "page": "InFlux", "title": "Generic constructor for the class with the same name", "topics": [ "InFlux" ] }, { "page": "InFlux_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "InFlux_by_PoolIndex" ] }, { "page": "InFlux_by_PoolIndex-class", "title": "S4 class for the influx to a single pool identified by the index", "topics": [ "InFlux_by_PoolIndex-class" ] }, { "page": "InFlux_by_PoolIndex-function-numeric-method", "title": "Constructor from an ordered pair of PoolIndex (integer like) objects", "topics": [ "InFlux_by_PoolIndex,function,numeric-method" ] }, { "page": "InFlux_by_PoolName", "title": "Generic constructor for an influx to a single pool from an ordered pair of PoolName (string like) and function objects", "topics": [ "InFlux_by_PoolName" ] }, { "page": "InFlux_by_PoolName-class", "title": "S4 class for the influx to a single pool identified by the name", "topics": [ "InFlux_by_PoolName-class" ] }, { "page": "InFlux_by_PoolName-function-character-method", "title": "Constructor from an ordered pair of PoolName (string like) and function objects", "topics": [ "InFlux_by_PoolName,function,character-method" ] }, { "page": "InFluxes", "title": "A generic factory for subclasses of InFluxes", "topics": [ "InFluxes" ] }, { "page": "InFluxes-class", "title": "A virtual S4-class representing (different subclasses) of in-fluxes to the system", "topics": [ "InFluxes-class" ] }, { "page": "InFluxes-ConstantInFluxList_by_PoolIndex-method", "title": "automatic title", "topics": [ "InFluxes,ConstantInFluxList_by_PoolIndex-method" ] }, { "page": "InFluxes-function-method", "title": "automatic title", "topics": [ "InFluxes,function-method" ] }, { "page": "InFluxes-InFluxes-method", "title": "automatic title", "topics": [ "InFluxes,InFluxes-method" ] }, { "page": "InFluxes-list-method", "title": "automatic title", "topics": [ "InFluxes,list-method" ] }, { "page": "InFluxes-numeric-method", "title": "automatic title", "topics": [ "InFluxes,numeric-method" ] }, { "page": "InFluxes-StateIndependentInFluxList_by_PoolIndex-method", "title": "automatic title", "topics": [ "InFluxes,StateIndependentInFluxList_by_PoolIndex-method" ] }, { "page": "InFluxes-TimeMap-method", "title": "automatic title", "topics": [ "InFluxes,TimeMap-method" ] }, { "page": "InFluxList_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "InFluxList_by_PoolIndex" ] }, { "page": "InFluxList_by_PoolIndex-class", "title": "Describes a list of flux rates.", "topics": [ "InFluxList_by_PoolIndex-class" ] }, { "page": "InFluxList_by_PoolIndex-list-method", "title": "constructor from a normal list after checking the elements", "topics": [ "InFluxList_by_PoolIndex,list-method" ] }, { "page": "InFluxList_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "InFluxList_by_PoolName" ] }, { "page": "InFluxList_by_PoolName-class", "title": "Class for a list of influxes indexed by the names of the target pools", "topics": [ "InFluxList_by_PoolName-class" ] }, { "page": "InFluxList_by_PoolName-list-method", "title": "constructor from a normal list", "topics": [ "InFluxList_by_PoolName,list-method" ] }, { "page": "initialize-ConstLinDecompOp-method", "title": "automatic title", "topics": [ "initialize,ConstLinDecompOp-method" ] }, { "page": "initialize-DecompositionOperator-method", "title": "automatic title", "topics": [ "initialize,DecompositionOperator-method" ] }, { "page": "initialize-MCSim-method", "title": "automatic title", "topics": [ "initialize,MCSim-method" ] }, { "page": "initialize-Model_14-method", "title": "Internal method to supervise creation of objects of this class", "topics": [ "initialize,Model_14-method" ] }, { "page": "initialize-Model_by_PoolNames-method", "title": "automatic title", "topics": [ "initialize,Model_by_PoolNames-method" ] }, { "page": "initialize-Model-method", "title": "Internal method to supervise creation of objects of this class", "topics": [ "initialize,Model-method" ] }, { "page": "initialize-NlModel-method", "title": "automatic title", "topics": [ "initialize,NlModel-method" ] }, { "page": "initialize-TimeMap-method", "title": "automatic title", "topics": [ "initialize,TimeMap-method" ] }, { "page": "initialize-TransportDecompositionOperator-method", "title": "automatic title", "topics": [ "initialize,TransportDecompositionOperator-method" ] }, { "page": "initialize-UnBoundInFluxes-method", "title": "automatic title", "topics": [ "initialize,UnBoundInFluxes-method" ] }, { "page": "initialize-UnBoundLinDecompOp-method", "title": "automatic title", "topics": [ "initialize,UnBoundLinDecompOp-method" ] }, { "page": "IntCal09", "title": "Northern Hemisphere atmospheric radiocarbon for the pre-bomb period", "topics": [ "IntCal09" ] }, { "page": "IntCal13", "title": "Atmospheric radiocarbon for the 0-50,000 yr BP period", "topics": [ "IntCal13" ] }, { "page": "IntCal20", "title": "The IntCal20 northern hemisphere radiocarbon curve for the 0-55,000 yr BP period", "topics": [ "IntCal20" ] }, { "page": "InternalFlux_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "InternalFlux_by_PoolIndex" ] }, { "page": "InternalFlux_by_PoolIndex-class", "title": "S4-class for a single internal flux with source and destination pools specified by indices", "topics": [ "InternalFlux_by_PoolIndex-class" ] }, { "page": "InternalFlux_by_PoolIndex-function-numeric-numeric-missing-method", "title": "constructor from an ordered pair of PoolIndex (integer like) objects and a function with vector argument", "topics": [ "InternalFlux_by_PoolIndex,function,numeric,numeric,missing-method" ] }, { "page": "InternalFlux_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "InternalFlux_by_PoolName" ] }, { "page": "InternalFlux_by_PoolName-class", "title": "S4-class for a single internal flux with source and destination pools specified by name", "topics": [ "InternalFlux_by_PoolName-class" ] }, { "page": "InternalFlux_by_PoolName-function-character-character-missing-method", "title": "constructor from an ordered pair of PoolName (string like) objects and a function with the set of formal argument names forming a subset of the state_variable_names", "topics": [ "InternalFlux_by_PoolName,function,character,character,missing-method" ] }, { "page": "InternalFlux_by_PoolName-function-missing-missing-character-method", "title": "automatic title", "topics": [ "InternalFlux_by_PoolName,function,missing,missing,character-method" ] }, { "page": "InternalFluxList_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "InternalFluxList_by_PoolIndex" ] }, { "page": "InternalFluxList_by_PoolIndex-class", "title": "S4-class for a list of internal fluxes with source and destination pool inidices", "topics": [ "InternalFluxList_by_PoolIndex-class" ] }, { "page": "InternalFluxList_by_PoolIndex-list-method", "title": "Constructor from a normal list after checking the elements", "topics": [ "InternalFluxList_by_PoolIndex,list-method" ] }, { "page": "InternalFluxList_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "InternalFluxList_by_PoolName" ] }, { "page": "InternalFluxList_by_PoolName-class", "title": "S4-class for a list of internal fluxes with indexed by (source and destination pool) names", "topics": [ "InternalFluxList_by_PoolName-class" ] }, { "page": "InternalFluxList_by_PoolName-list-method", "title": "constructor from a normal list", "topics": [ "InternalFluxList_by_PoolName,list-method" ] }, { "page": "linearScalarModel", "title": "Implementation of a general model for linear non-autonomous systems with scalar modifiers", "topics": [ "linearScalarModel" ] }, { "page": "linesCPool", "title": "Add lines with the output of 'getC14', 'getC', or 'getReleaseFlux' to an existing plot", "topics": [ "linesCPool" ] }, { "page": "listProduct", "title": "tensor product of lists", "topics": [ "listProduct" ] }, { "page": "MCSim-class", "title": "Experimental Class for a Monte Carlo Simulation of particles leaving the pool", "topics": [ "MCSim-class" ] }, { "page": "Model", "title": "Constructor for class Model", "topics": [ "Model" ] }, { "page": "Model_14", "title": "general constructor for class Model_14", "topics": [ "Model_14" ] }, { "page": "Model_14-class", "title": "S4-class to represent a 14C model run", "topics": [ "Model_14-class" ] }, { "page": "Model_by_PoolNames", "title": "Constructor for 'Model_by_PoolNames'", "topics": [ "Model_by_PoolNames" ] }, { "page": "Model_by_PoolNames-class", "title": "A model run based on flux functions", "topics": [ "Model_by_PoolNames-class" ] }, { "page": "Model-class", "title": "S4 class representing a model run", "topics": [ "Model-class" ] }, { "page": "NlModel-class", "title": "deprecated class for a non-linear model run.", "topics": [ "NlModel-class" ] }, { "page": "OnepModel", "title": "Implementation of a one pool model", "topics": [ "OnepModel" ] }, { "page": "OnepModel14", "title": "Implementation of a one-pool C14 model", "topics": [ "OnepModel14" ] }, { "page": "OutFlux", "title": "Generic constructor for the class with the same name", "topics": [ "OutFlux" ] }, { "page": "OutFlux_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "OutFlux_by_PoolIndex" ] }, { "page": "OutFlux_by_PoolIndex-class", "title": "S4 class for a single out-flux with source pool index", "topics": [ "OutFlux_by_PoolIndex-class" ] }, { "page": "OutFlux_by_PoolIndex-function-numeric-method", "title": "constructor from a PoolIndex (integer like) objects and a function with vector argument", "topics": [ "OutFlux_by_PoolIndex,function,numeric-method" ] }, { "page": "OutFlux_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "OutFlux_by_PoolName" ] }, { "page": "OutFlux_by_PoolName-class", "title": "S4 class for a single out-flux with source pool name", "topics": [ "OutFlux_by_PoolName-class" ] }, { "page": "OutFlux_by_PoolName-function-character-method", "title": "constructor from a PoolName (integer like) object and a function", "topics": [ "OutFlux_by_PoolName,function,character-method" ] }, { "page": "OutFluxList_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "OutFluxList_by_PoolIndex" ] }, { "page": "OutFluxList_by_PoolIndex-class", "title": "A list of outfluxes", "topics": [ "OutFluxList_by_PoolIndex-class" ] }, { "page": "OutFluxList_by_PoolIndex-list-method", "title": "constructor from a normal list", "topics": [ "OutFluxList_by_PoolIndex,list-method" ] }, { "page": "OutFluxList_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "OutFluxList_by_PoolName" ] }, { "page": "OutFluxList_by_PoolName-class", "title": "S4 class for a list of out-fluxes indexed by source pool name", "topics": [ "OutFluxList_by_PoolName-class" ] }, { "page": "OutFluxList_by_PoolName-list-method", "title": "constructor from a normal list", "topics": [ "OutFluxList_by_PoolName,list-method" ] }, { "page": "ParallelModel", "title": "models for unconnected pools", "topics": [ "ParallelModel" ] }, { "page": "pathEntropy", "title": "Path Entropy", "topics": [ "pathEntropy" ] }, { "page": "plot-MCSim-method", "title": "automatic title", "topics": [ "plot,MCSim-method" ] }, { "page": "plot-Model_by_PoolNames-method", "title": "Plot the graph of pool connections", "topics": [ "plot,Model_by_PoolNames-method" ] }, { "page": "plot-Model-method", "title": "Create an overview plot", "topics": [ "plot,Model-method" ] }, { "page": "plot-NlModel-method", "title": "automatic title", "topics": [ "plot,NlModel-method" ] }, { "page": "plot-TimeMap-method", "title": "automatic title", "topics": [ "plot,TimeMap-method" ] }, { "page": "plotC14Pool", "title": "Plots the output of 'getF14' for each pool over time", "topics": [ "plotC14Pool" ] }, { "page": "plotCPool", "title": "Plots the output of 'getC' or 'getReleaseFlux' for each pool over time", "topics": [ "plotCPool" ] }, { "page": "plotPoolGraph", "title": "Generic plotter", "topics": [ "plotPoolGraph" ] }, { "page": "plotPoolGraph-SymbolicModel_by_PoolNames-method", "title": "Plot the graph of pool connections", "topics": [ "plotPoolGraph,SymbolicModel_by_PoolNames-method" ] }, { "page": "plotPoolGraphFromTupleLists", "title": "Helper function to draw connectivity graphs", "topics": [ "plotPoolGraphFromTupleLists" ] }, { "page": "PoolConnection_by_PoolIndex", "title": "Pool connection by pool index", "topics": [ "PoolConnection_by_PoolIndex" ] }, { "page": "PoolConnection_by_PoolIndex-class", "title": "Objects that have a source and a destination described by integer like objects ( of class PoolIndex)", "topics": [ "PoolConnection_by_PoolIndex-class" ] }, { "page": "PoolConnection_by_PoolIndex-ANY-ANY-missing-method", "title": "constructor from an ordered pair of PoolId objects", "topics": [ "PoolConnection_by_PoolIndex,ANY,ANY,missing-method" ] }, { "page": "PoolConnection_by_PoolIndex-missing-missing-character-method", "title": "constructor from strings of the form '1_to_2'", "topics": [ "PoolConnection_by_PoolIndex,missing,missing,character-method" ] }, { "page": "PoolConnection_by_PoolName", "title": "Pool connection by pool name", "topics": [ "PoolConnection_by_PoolName" ] }, { "page": "PoolConnection_by_PoolName-class", "title": "Objects that have a source and a destination determined by a string like object of class PoolName", "topics": [ "PoolConnection_by_PoolName-class" ] }, { "page": "PoolConnection_by_PoolName-ANY-ANY-missing-method", "title": "constructor from an ordered pair of PoolName objects", "topics": [ "PoolConnection_by_PoolName,ANY,ANY,missing-method" ] }, { "page": "PoolId-class", "title": "common class for pool ids", "topics": [ "PoolId-class" ] }, { "page": "PoolIndex", "title": "Pool index", "topics": [ "PoolIndex" ] }, { "page": "PoolIndex-class", "title": "S4 class for pool indices", "topics": [ "PoolIndex-class" ] }, { "page": "PoolIndex-character-method", "title": "construct from number string like '1' or '3'", "topics": [ "PoolIndex,character-method" ] }, { "page": "PoolIndex-numeric-method", "title": "construct from number", "topics": [ "PoolIndex,numeric-method" ] }, { "page": "PoolIndex-PoolIndex-method", "title": "pass through constructor fron an object of the same class", "topics": [ "PoolIndex,PoolIndex-method" ] }, { "page": "PoolIndex-PoolName-method", "title": "convert to number like object", "topics": [ "PoolIndex,PoolName-method" ] }, { "page": "PoolName", "title": "Pool name", "topics": [ "PoolName" ] }, { "page": "PoolName-class", "title": "class for pool-name-strings", "topics": [ "PoolName-class" ] }, { "page": "PoolName-character-method", "title": "construct from string with checks", "topics": [ "PoolName,character-method" ] }, { "page": "PoolName-PoolIndex-method", "title": "convert to string like object", "topics": [ "PoolName,PoolIndex-method" ] }, { "page": "PoolName-PoolName-method", "title": "pass through constructor fron an object of the same class", "topics": [ "PoolName,PoolName-method" ] }, { "page": "predefinedModels", "title": "PREDEFINED MODELS", "topics": [ "predefinedModels" ] }, { "page": "print-NlModel-method", "title": "automatic title", "topics": [ "print,NlModel-method" ] }, { "page": "RespirationCoefficients", "title": "helper function to compute respiration coefficients", "topics": [ "RespirationCoefficients" ] }, { "page": "RothCModel", "title": "Implementation of the RothCModel", "topics": [ "RothCModel" ] }, { "page": "ScalarTimeMap", "title": "Constructor for 'ScalarTimeMap-class'", "topics": [ "ScalarTimeMap" ] }, { "page": "ScalarTimeMap-class", "title": "S4 class for a scalar time dependent function on a finite time interval", "topics": [ "ScalarTimeMap-class" ] }, { "page": "ScalarTimeMap-data.frame-missing-missing-missing-missing-method", "title": "constructor for data given as 2 column data.frame", "topics": [ "ScalarTimeMap,data.frame,missing,missing,missing,missing-method" ] }, { "page": "ScalarTimeMap-function-missing-missing-missing-missing-method", "title": "manual constructor for just a function", "topics": [ "ScalarTimeMap,function,missing,missing,missing,missing-method" ] }, { "page": "ScalarTimeMap-function-numeric-numeric-missing-missing-method", "title": "manual constructor for a function and an interval", "topics": [ "ScalarTimeMap,function,numeric,numeric,missing,missing-method" ] }, { "page": "ScalarTimeMap-missing-missing-missing-missing-numeric-method", "title": "special case for a time map from a constant", "topics": [ "ScalarTimeMap,missing,missing,missing,missing,numeric-method" ] }, { "page": "ScalarTimeMap-missing-missing-missing-numeric-numeric-method", "title": "constructor for data and times given as vectors", "topics": [ "ScalarTimeMap,missing,missing,missing,numeric,numeric-method" ] }, { "page": "SeriesLinearModel", "title": "General m-pool linear model with series structure", "topics": [ "SeriesLinearModel" ] }, { "page": "SeriesLinearModel14", "title": "General m-pool linear C14 model with series structure", "topics": [ "SeriesLinearModel14" ] }, { "page": "SHCal20", "title": "The SHCal20 southern hemisphere radiocarbon curve for the 0-55,000 yr BP period", "topics": [ "SHCal20" ] }, { "page": "show-NlModel-method", "title": "automatic title", "topics": [ "show,NlModel-method" ] }, { "page": "SoilR.F0.new", "title": "deprecated function that used to create an object of class SoilR.F0", "topics": [ "SoilR.F0.new" ] }, { "page": "state_variable_names", "title": "determine the minimum set of statevariables", "topics": [ "state_variable_names" ] }, { "page": "StateDependentInFluxVector-class", "title": "Input vector that is a function of the pool contenst and time", "topics": [ "StateDependentInFluxVector", "StateDependentInFluxVector-class" ] }, { "page": "StateIndependentInFlux_by_PoolIndex-class", "title": "Constructor for the class with the same name", "topics": [ "StateIndependentInFlux_by_PoolIndex", "StateIndependentInFlux_by_PoolIndex-class" ] }, { "page": "StateIndependentInFluxList_by_PoolIndex", "title": "Generic constructor for the class with the same name", "topics": [ "StateIndependentInFluxList_by_PoolIndex" ] }, { "page": "StateIndependentInFluxList_by_PoolIndex-class", "title": "Subclass of list that is guaranteed to contain only elements of type StateIndependentInFlux_by_PoolIndex", "topics": [ "StateIndependentInFluxList_by_PoolIndex-class" ] }, { "page": "StateIndependentInFluxList_by_PoolIndex-list-method", "title": "constructor from a normal list", "topics": [ "StateIndependentInFluxList_by_PoolIndex,list-method" ] }, { "page": "StateIndependentInFluxList_by_PoolName", "title": "Generic constructor for the class with the same name", "topics": [ "StateIndependentInFluxList_by_PoolName" ] }, { "page": "SymbolicModel_by_PoolNames-class", "title": "A symbolic model description based on flux functions", "topics": [ "SymbolicModel_by_PoolNames", "SymbolicModel_by_PoolNames-class" ] }, { "page": "systemAge", "title": "System and pool age for constant compartment models", "topics": [ "systemAge" ] }, { "page": "ThreepairMMmodel", "title": "Implementation of a 6-pool Michaelis-Menten model", "topics": [ "ThreepairMMmodel" ] }, { "page": "ThreepFeedbackModel", "title": "Implementation of a three pool model with feedback structure", "topics": [ "ThreepFeedbackModel" ] }, { "page": "ThreepFeedbackModel14", "title": "Implementation of a three-pool C14 model with feedback structure", "topics": [ "ThreepFeedbackModel14" ] }, { "page": "ThreepParallelModel", "title": "Implementation of a three pool model with parallel structure", "topics": [ "ThreepParallelModel" ] }, { "page": "ThreepParallelModel14", "title": "Implementation of a three-pool C14 model with parallel structure", "topics": [ "ThreepParallelModel14" ] }, { "page": "ThreepSeriesModel", "title": "Implementation of a three pool model with series structure", "topics": [ "ThreepSeriesModel" ] }, { "page": "ThreepSeriesModel14", "title": "Implementation of a three-pool C14 model with series structure", "topics": [ "ThreepSeriesModel14" ] }, { "page": "TimeMap", "title": "Constructor for 'TimeMap-class'", "topics": [ "TimeMap" ] }, { "page": "TimeMap-class", "title": "S4 class for a time dependent function", "topics": [ "TimeMap-class" ] }, { "page": "TimeMap-data.frame-missing-missing-missing-missing-method", "title": "automatic title", "topics": [ "TimeMap,data.frame,missing,missing,missing,missing-method" ] }, { "page": "TimeMap-function-missing-missing-missing-missing-method", "title": "manual constructor for just a function", "topics": [ "TimeMap,function,missing,missing,missing,missing-method" ] }, { "page": "TimeMap-function-numeric-numeric-missing-missing-method", "title": "manual constructor for a function and an interval", "topics": [ "TimeMap,function,numeric,numeric,missing,missing-method" ] }, { "page": "TimeMap-list-missing-missing-missing-missing-method", "title": "automatic title", "topics": [ "TimeMap,list,missing,missing,missing,missing-method" ] }, { "page": "TimeMap-missing-missing-missing-numeric-array-method", "title": "automatic title", "topics": [ "TimeMap,missing,missing,missing,numeric,array-method" ] }, { "page": "TimeMap-missing-missing-missing-numeric-list-method", "title": "automatic title", "topics": [ "TimeMap,missing,missing,missing,numeric,list-method" ] }, { "page": "TimeMap-missing-missing-missing-numeric-matrix-method", "title": "automatic title", "topics": [ "TimeMap,missing,missing,missing,numeric,matrix-method" ] }, { "page": "TimeMap-missing-missing-missing-numeric-numeric-method", "title": "automatic title", "topics": [ "TimeMap,missing,missing,missing,numeric,numeric-method" ] }, { "page": "TimeMap-TimeMap-ANY-ANY-ANY-ANY-method", "title": "automatic title", "topics": [ "TimeMap,TimeMap,ANY,ANY,ANY,ANY-method" ] }, { "page": "TimeMap.from.Dataframe", "title": "TimeMap.from.Dataframe", "topics": [ "TimeMap.from.Dataframe" ] }, { "page": "TimeMap.new", "title": "deprecated constructor of the class TimeMap.", "topics": [ "TimeMap.new" ] }, { "page": "TimeRangeIntersection", "title": "The time interval where both functions are defined", "topics": [ "TimeRangeIntersection" ] }, { "page": "transitTime", "title": "Transit times for compartment models", "topics": [ "transitTime" ] }, { "page": "TransportDecompositionOperator-class", "title": "automatic title", "topics": [ "TransportDecompositionOperator-class" ] }, { "page": "turnoverFit", "title": "Estimation of the turnover time from a radiocarbon sample.", "topics": [ "turnoverFit" ] }, { "page": "TwopFeedbackModel", "title": "Implementation of a two pool model with feedback structure", "topics": [ "TwopFeedbackModel" ] }, { "page": "TwopFeedbackModel14", "title": "Implementation of a two-pool C14 model with feedback structure", "topics": [ "TwopFeedbackModel14" ] }, { "page": "TwopMMmodel", "title": "Implementation of a two-pool Michaelis-Menten model", "topics": [ "TwopMMmodel" ] }, { "page": "TwopParallelModel", "title": "Implementation of a linear two pool model with parallel structure", "topics": [ "TwopParallelModel" ] }, { "page": "TwopParallelModel14", "title": "Implementation of a two-pool C14 model with parallel structure", "topics": [ "TwopParallelModel14" ] }, { "page": "TwopSeriesModel", "title": "Implementation of a two pool model with series structure", "topics": [ "TwopSeriesModel" ] }, { "page": "TwopSeriesModel14", "title": "Implementation of a two-pool C14 model with series structure", "topics": [ "TwopSeriesModel14" ] }, { "page": "UnBoundInFluxes", "title": "Unbound input fluxes", "topics": [ "UnBoundInFluxes" ] }, { "page": "UnBoundInFluxes-class", "title": "automatic title", "topics": [ "UnBoundInFluxes-class" ] }, { "page": "UnBoundInFluxes-function-method", "title": "automatic title", "topics": [ "UnBoundInFluxes,function-method" ] }, { "page": "UnBoundLinDecompOp", "title": "Generic constructor for the class with the same name", "topics": [ "UnBoundLinDecompOp" ] }, { "page": "UnBoundLinDecompOp-class", "title": "An S4 class to represent a linear nonautonomous compartmental matrix", "topics": [ "UnBoundLinDecompOp-class" ] }, { "page": "UnBoundLinDecompOp-function-method", "title": "Generic constructor for the class with the same name", "concept": [ "UnBoundLinDecompOp_constructor" ], "topics": [ "UnBoundLinDecompOp,function-method" ] }, { "page": "UnBoundNonLinDecompOp", "title": "Generic constructor for the class with the same name", "topics": [ "UnBoundNonLinDecompOp" ] }, { "page": "UnBoundNonLinDecompOp_by_PoolNames", "title": "Generic constructor for the class with the same name", "topics": [ "UnBoundNonLinDecompOp_by_PoolNames" ] }, { "page": "UnBoundNonLinDecompOp_by_PoolNames-class", "title": "An S4 class to represent the of nonlinear nonautonomous compartmental system independently of the order of state variables", "topics": [ "UnBoundNonLinDecompOp_by_PoolNames-class" ] }, { "page": "UnBoundNonLinDecompOp-class", "title": "An S4 class to represent a nonlinear nonautonomous compartmental matrix", "topics": [ "UnBoundNonLinDecompOp-class" ] }, { "page": "UnBoundNonLinDecompOp-function-missing-missing-missing-method", "title": "Constructor for the class with the same name", "concept": [ "UnBoundNonLinDecompOp_constructor" ], "topics": [ "UnBoundNonLinDecompOp,function,missing,missing,missing-method" ] }, { "page": "UnBoundNonLinDecompOp-missing-vector-vector-numeric-method", "title": "Constructor for the class with the same name", "concept": [ "UnBoundNonLinDecompOp_constructor" ], "topics": [ "UnBoundNonLinDecompOp,missing,vector,vector,numeric-method" ] }, { "page": "Yasso07Model", "title": "Implementation of the Yasso07 model", "topics": [ "Yasso07Model" ] }, { "page": "YassoModel", "title": "Implementation of the Yasso model.", "topics": [ "YassoModel" ] } ], "_rundeps": [ "assertthat", "cli", "cpp11", "deSolve", "expm", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "pkgconfig", "purrr", "rlang", "sets", "vctrs" ], "_score": 3.0523090996473234, "_indexed": true, "_nocasepkg": "soilr", "_universes": [ "crlsierra" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.107", "date": "2026-05-28T08:16:13.000Z", "distro": "noble", "commit": "6d63c04336e3ce208a804462828bab40cebf5c99", "fileid": "4f4827eee3c2f5ab1bad34e8240aecc7a526e9b00d993d6d9e41eac9147b56df", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/crlsierra/actions/runs/26562866143" }, { "r": "4.6.0", "os": "linux", "version": "1.2.107", "date": "2026-05-28T08:16:26.000Z", "distro": "noble", "commit": "6d63c04336e3ce208a804462828bab40cebf5c99", "fileid": "fa55260866f39fa8d245e623610883a59a0203c729aff443a214593e139d20a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/crlsierra/actions/runs/26562866143" }, { "r": "4.5.3", "os": "mac", "version": "1.2.107", "date": "2026-05-28T08:16:31.000Z", "commit": "6d63c04336e3ce208a804462828bab40cebf5c99", "fileid": "f53fadd0d9d5319e233d22a1cb3375c132465447b582a7c72a32e211f95b5228", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/crlsierra/actions/runs/26562866143" }, { "r": "4.6.0", "os": "mac", "version": "1.2.107", "date": "2026-05-28T08:16:22.000Z", "commit": "6d63c04336e3ce208a804462828bab40cebf5c99", "fileid": "1f01dd2e0a676d188cb4c04587330964c6e7b4b311475b1d8845e64efc784a74", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/crlsierra/actions/runs/26562866143" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.107", "date": "2026-05-28T08:16:17.000Z", "commit": "6d63c04336e3ce208a804462828bab40cebf5c99", "fileid": "43bf2d1a043488d601b0181d02a8881d5b8a8b97507c7cf39297bcda7a755721", "status": "success", "buildurl": "https://github.com/r-universe/crlsierra/actions/runs/26562866143" }, { "r": "4.7.0", "os": "win", "version": "1.2.107", "date": "2026-05-28T08:15:41.000Z", "commit": "6d63c04336e3ce208a804462828bab40cebf5c99", "fileid": "5c35da3197b2bcc89c6d5f0f0067c9cda6c4a9960e06cb10796cc77f5cab0234", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/crlsierra/actions/runs/26562866143" }, { "r": "4.5.3", "os": "win", "version": "1.2.107", "date": "2026-05-28T08:15:34.000Z", "commit": "6d63c04336e3ce208a804462828bab40cebf5c99", "fileid": "e44b7981575d621af21998cfef322c15f70b8d8dc9efbb09e4e0cd59fa8e51dc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/crlsierra/actions/runs/26562866143" }, { "r": "4.6.0", "os": "win", "version": "1.2.107", "date": "2026-05-28T08:15:52.000Z", "commit": "6d63c04336e3ce208a804462828bab40cebf5c99", "fileid": "94aea9fba3134d5d0a47dfb98f65596f29635d57a7037f45518e9ba3b25eb703", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/crlsierra/actions/runs/26562866143" } ] }