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] }, { "page": "dot-nlmixr0preProcessNpMuExpand", "title": "Preprocessing hook: mu-expand non-mu structural fixed-effect thetas for the nonparametric engines, before the rest of the pipeline builds on the ui. Doing it here (rather than mutating the ui mid-setup) keeps the injected pseudo-etas consistent through covariate/mu processing and model compilation. Off when control$muExpand is FALSE.", "topics": [ ".nlmixr0preProcessNpMuExpand" ] }, { "page": "dot-nlmixrPreprocessLiteralFix", "title": "This literally fixes parameters in the model", "topics": [ ".nlmixrPreprocessLiteralFix" ] }, { "page": "dot-preProcessDataUi", "title": "Preprocess the zero omegas", "topics": [ ".preProcessDataUi" ] }, { "page": "dot-preProcessLinCmtOde", "title": "Translate a mixed `linCmt()`/ODE model to all-ODEs", "topics": [ ".preProcessLinCmtOde" ] }, { "page": "dot-preProcessVaeNonMuTheta", "title": "VAE preprocessing hook: inject etas for non-mu-referenced thetas per vaeControl(nonMuTheta=).", "topics": [ ".preProcessVaeNonMuTheta" ] }, { "page": "dot-preProcessZeroOmega", "title": "Preprocess the zero omegas", "topics": [ ".preProcessZeroOmega" ] }, { "page": "dot-preProcessZeroTheta", "title": "Nudge exactly-zero theta initial estimates off zero (FOCEi family)", "topics": [ ".preProcessZeroTheta" ] }, { "page": "aaaCranNlmixrThreads", "title": "This function is to set the number of threads to 2", "topics": [ "aaaCranNlmixrThreads" ] }, { "page": "addCwres", "title": "Add CWRES", "topics": [ "addCwres" ] }, { "page": "addNpde", "title": "NPDE calculation for nlmixr2", "topics": [ "addNpde" ] }, { "page": "addTable", "title": "Add table information to nlmixr2 fit object without tables", "topics": [ "addTable" ] }, { "page": "agqControl", "title": "Control options for the agq estimation method", "topics": [ "agqControl" ] }, { "page": "assertNlmixrFit", "title": "Assert that this is a nlmixr2 fit object", "topics": [ "assertNlmixrFit" ] }, { "page": "assertNlmixrFitData", "title": "Assert that this is a nlmixr2 fit data object", "topics": [ "assertNlmixrFitData" ] }, { "page": "bobyqaControl", "title": "Control for bobyqa estimation method in nlmixr2", "topics": [ "bobyqaControl" ] }, { "page": "boxCox", "title": "Cox Box, Yeo Johnson and inverse transformation", "topics": [ "boxCox", "iBoxCox", "iYeoJohnson", "yeoJohnson" ] }, { "page": "cholSE", "title": "Generalized Cholesky Matrix Decomposition", "topics": [ "cholSE" ] }, { "page": "emviControl", "title": "Control for the variational inference methods emvi and fbvi in nlmixr2", "topics": [ "emviControl" ] }, { "page": "fbviControl", "title": "Control for the fbvi (full-Bayes variational inference) method", "topics": [ "fbviControl" ] }, { "page": "foceControl", "title": "Control options for the foce estimation method", "topics": [ "foceControl" ] }, { "page": "foceiControl", "title": "Control Options for FOCEi", "concept": [ "Estimation control" ], "topics": [ "foceiControl" ] }, { "page": "foceiLikIterPrintStart", "title": "Iteration printing / parameter history over a loaded likelihood", "topics": [ "foceiLikIterPrintEnd", "foceiLikIterPrintStart" ] }, { "page": "foceiLikLoad", "title": "Load a general FOCE-family likelihood into memory", "topics": [ "foceiLikLoad" ] }, { "page": "foceiLikRun", "title": "Evaluate a loaded general FOCE-family likelihood at supplied etas", "topics": [ "foceiLikRun" ] }, { "page": "foceiLikUnload", "title": "Unload the general FOCE-family likelihood from memory", "topics": [ "foceiLikUnload" ] }, { "page": "focepControl", "title": "Control options for the focep (FOCE+) estimation method", "topics": [ "focepControl" ] }, { "page": "foControl", "title": "Control options for the FO estimation method", "topics": [ "foControl" ] }, { "page": "foiControl", "title": "Control options foir the FOI estimation method", "topics": [ "foiControl" ] }, { "page": "formatMinWidth", "title": "Format numeric values to minimize the printing width", "topics": [ "formatMinWidth" ] }, { "page": "getValidNlmixrControl", "title": "Get valid nlmixr control object", "topics": [ "getValidNlmixrControl", "getValidNlmixrCtl", "getValidNlmixrCtl.agq", "getValidNlmixrCtl.agqf", "getValidNlmixrCtl.bfgs", "getValidNlmixrCtl.bobyqa", "getValidNlmixrCtl.brent", "getValidNlmixrCtl.cg", "getValidNlmixrCtl.default", "getValidNlmixrCtl.emvi", "getValidNlmixrCtl.fagq", "getValidNlmixrCtl.fbvi", "getValidNlmixrCtl.flaplace", "getValidNlmixrCtl.fo", "getValidNlmixrCtl.foce", "getValidNlmixrCtl.focef", "getValidNlmixrCtl.focei", "getValidNlmixrCtl.foceif", "getValidNlmixrCtl.focep", "getValidNlmixrCtl.focepf", "getValidNlmixrCtl.foi", "getValidNlmixrCtl.iagq", "getValidNlmixrCtl.iagqf", "getValidNlmixrCtl.ifagq", "getValidNlmixrCtl.iflaplace", "getValidNlmixrCtl.ifoce", "getValidNlmixrCtl.ifocef", "getValidNlmixrCtl.ifocei", "getValidNlmixrCtl.ifoceif", "getValidNlmixrCtl.ifocep", "getValidNlmixrCtl.ifocepf", "getValidNlmixrCtl.ilaplace", "getValidNlmixrCtl.imp", "getValidNlmixrCtl.impmap", "getValidNlmixrCtl.inpag", "getValidNlmixrCtl.inpb", "getValidNlmixrCtl.laplace", "getValidNlmixrCtl.lbfgsb", "getValidNlmixrCtl.lbfgsb3c", "getValidNlmixrCtl.magq", "getValidNlmixrCtl.magqf", "getValidNlmixrCtl.mfagq", "getValidNlmixrCtl.mflaplace", "getValidNlmixrCtl.mfoce", "getValidNlmixrCtl.mfocef", "getValidNlmixrCtl.mfocei", "getValidNlmixrCtl.mfoceif", "getValidNlmixrCtl.mfocep", "getValidNlmixrCtl.mfocepf", "getValidNlmixrCtl.mlaplace", "getValidNlmixrCtl.mnpag", "getValidNlmixrCtl.mnpb", "getValidNlmixrCtl.n1qn1", "getValidNlmixrCtl.neldermead", "getValidNlmixrCtl.newuoa", "getValidNlmixrCtl.nlm", "getValidNlmixrCtl.nlme", "getValidNlmixrCtl.nlminb", "getValidNlmixrCtl.nls", "getValidNlmixrCtl.npag", "getValidNlmixrCtl.npb", "getValidNlmixrCtl.optim", "getValidNlmixrCtl.posthoc", "getValidNlmixrCtl.predict", "getValidNlmixrCtl.qrpem", "getValidNlmixrCtl.rxSolve", "getValidNlmixrCtl.saem", "getValidNlmixrCtl.sann", "getValidNlmixrCtl.simulate", "getValidNlmixrCtl.simulation", "getValidNlmixrCtl.tableControl", "getValidNlmixrCtl.trust", "getValidNlmixrCtl.uobyqa", "getValidNlmixrCtl.vae" ] }, { "page": "iagqControl", "title": "Control options for the iagq estimation method", "topics": [ "iagqControl" ] }, { "page": "ifoceControl", "title": "Control options for the ifoce estimation method", "topics": [ "ifoceControl" ] }, { "page": "ifoceiControl", "title": "Control options for the ifocei estimation method", "topics": [ "ifoceiControl" ] }, { "page": "ifocepControl", "title": "Control options for the ifocep (IRLS FOCE+) estimation method", "topics": [ "ifocepControl" ] }, { "page": "ilaplaceControl", "title": "Control options for the ilaplace estimation method", "topics": [ "ilaplaceControl" ] }, { "page": "impControl", "title": "Control for the imp (importance-sampling EM without MAP search) method", "topics": [ "impControl" ] }, { "page": "impCovControl", "title": "Options for the importance-sampling covariance in setCov()", "topics": [ "impCovControl" ] }, { "page": "impmapControl", "title": "Control options for the impmap (importance-sampling EM) estimation method", "topics": [ "impmapControl" ] }, { "page": "iterPrintControl", "title": "Control iteration-time print formatting", "topics": [ "iterPrintControl" ] }, { "page": "laplaceControl", "title": "Control options for the Laplace estimation method", "topics": [ "laplaceControl" ] }, { "page": "lbfgsb3cControl", "title": "Control for lbfgsb3c estimation method in nlmixr2", "topics": [ "lbfgsb3cControl" ] }, { "page": "magqControl", "title": "Control options for the magq estimation method", "topics": [ "magqControl" ] }, { "page": "mfoceControl", "title": "Control options for the mfoce estimation method", "topics": [ "mfoceControl" ] }, { "page": "mfoceiControl", "title": "Control options for the mfocei estimation method", "topics": [ "mfoceiControl" ] }, { "page": "mfocepControl", "title": "Control options for the mfocep (mu-referenced FOCE+) estimation method", "topics": [ "mfocepControl" ] }, { "page": "mlaplaceControl", "title": "Control options for the mlaplace estimation method", "topics": [ "mlaplaceControl" ] }, { "page": "n1qn1Control", "title": "Control for n1qn1 estimation method in nlmixr2", "topics": [ "n1qn1Control" ] }, { "page": "newuoaControl", "title": "Control for newuoa estimation method in nlmixr2", "topics": [ "newuoaControl" ] }, { "page": "nlmControl", "title": "nlmixr2 defaults controls for nlm", "topics": [ "nlmControl" ] }, { "page": "nlminbControl", "title": "nlmixr2 nlminb defaults", "topics": [ "nlminbControl" ] }, { "page": "nlmixr2", "title": "nlmixr2 fits population PK and PKPD non-linear mixed effects models.", "topics": [ "nlmixr", "nlmixr2", "nlmixr2.function", "nlmixr2.nlmixr2FitCore", "nlmixr2.nlmixr2FitCoreSilent", "nlmixr2.nlmixr2FitData", "nlmixr2.rxUi" ] }, { "page": "nlmixr2AllEst", "title": "Show all the current estimation methods", "topics": [ "nlmixr2AllEst" ] }, { "page": "nlmixr2AllEstType", "title": "Tagged list of the available nlmixr2 estimation methods", "topics": [ "nlmixr2AllEstType" ] }, { "page": "nlmixr2AugPredSolve", "title": "Augmented Prediction for nlmixr2 fit", "topics": [ "augPred.nlmixr2FitData", "nlmixr2AugPredSolve" ] }, { "page": "nlmixr2CreateOutputFromUi", "title": "Create nlmixr output from the UI", "topics": [ "nlmixr2CreateOutputFromUi" ] }, { "page": "nlmixr2Est", "title": "Generic for nlmixr2 estimation methods", "topics": [ "nlmixr2Est", "nlmixr2Est.agq", "nlmixr2Est.agqf", "nlmixr2Est.bfgs", "nlmixr2Est.bobyqa", "nlmixr2Est.brent", "nlmixr2Est.cg", "nlmixr2Est.default", "nlmixr2Est.emvi", "nlmixr2Est.fagq", "nlmixr2Est.fbvi", "nlmixr2Est.flaplace", "nlmixr2Est.fo", "nlmixr2Est.foce", "nlmixr2Est.focef", "nlmixr2Est.focei", "nlmixr2Est.foceif", "nlmixr2Est.focep", "nlmixr2Est.focepf", "nlmixr2Est.foi", "nlmixr2Est.iagq", "nlmixr2Est.iagqf", "nlmixr2Est.ifagq", "nlmixr2Est.iflaplace", "nlmixr2Est.ifoce", "nlmixr2Est.ifocef", "nlmixr2Est.ifocei", "nlmixr2Est.ifoceif", "nlmixr2Est.ifocep", "nlmixr2Est.ifocepf", "nlmixr2Est.ilaplace", "nlmixr2Est.imp", "nlmixr2Est.impmap", "nlmixr2Est.inpag", "nlmixr2Est.inpb", "nlmixr2Est.laplace", "nlmixr2Est.lbfgsb", "nlmixr2Est.lbfgsb3c", "nlmixr2Est.magq", "nlmixr2Est.magqf", "nlmixr2Est.mfagq", "nlmixr2Est.mflaplace", "nlmixr2Est.mfoce", "nlmixr2Est.mfocef", "nlmixr2Est.mfocei", "nlmixr2Est.mfoceif", "nlmixr2Est.mfocep", "nlmixr2Est.mfocepf", "nlmixr2Est.mlaplace", "nlmixr2Est.mnpag", "nlmixr2Est.mnpb", "nlmixr2Est.n1qn1", "nlmixr2Est.neldermead", "nlmixr2Est.newuoa", "nlmixr2Est.nlm", "nlmixr2Est.nlme", "nlmixr2Est.nlminb", "nlmixr2Est.nls", "nlmixr2Est.npag", "nlmixr2Est.npb", "nlmixr2Est.optim", "nlmixr2Est.output", "nlmixr2Est.posthoc", "nlmixr2Est.predict", "nlmixr2Est.qrpem", "nlmixr2Est.rxSolve", "nlmixr2Est.saem", "nlmixr2Est.sann", "nlmixr2Est.simulate", "nlmixr2Est.simulation", "nlmixr2Est.trust", "nlmixr2Est.uobyqa", "nlmixr2Est.vae" ] }, { "page": "nlmixr2fix", "title": "Try to fix a nlmixr2 fit", "topics": [ "nlmixr2fix" ] }, { "page": "nlmixr2Gill83", "title": "Get the optimal forward difference interval by Gill83 method", "topics": [ "nlmixr2Gill83" ] }, { "page": "nlmixr2Hess", "title": "Calculate Hessian", "topics": [ "nlmixr2Hess" ] }, { "page": "nlmixr2Keywords", "title": "A list and description of the fields in the nlmxir2 object", "topics": [ "nlmixr2Keywords" ] }, { "page": "nlmixr2Logo", "title": "Messages the nlmixr2 logo...", "topics": [ "nlmixr2Logo" ] }, { "page": "nlmixr2NlmeControl", "title": "Control Values for nlme Fit with extra options for nlmixr", "concept": [ "Estimation control" ], "topics": [ "nlmeControl", "nlmixr2NlmeControl" ] }, { "page": "nlmixr2Validate", "title": "Validate nlmixr2", "topics": [ "nlmixr2Validate", "nmTest" ] }, { "page": "nlmixr2Version", "title": "Display nlmixr2's version", "topics": [ "nlmixr2Version" ] }, { "page": "nlmixrAddObjectiveFunctionDataFrame", "title": "Add objective function data frame to the current objective function", "topics": [ "nlmixrAddObjectiveFunctionDataFrame" ] }, { "page": "nlmixrAddTiming", "title": "Manually add time to a nlmixr2 object", "topics": [ "nlmixrAddTiming" ] }, { "page": "nlmixrCbind", "title": "nlmixrCbind", "topics": [ "nlmixrCbind" ] }, { "page": "nlmixrClone", "title": "Clone nlmixr environment", "topics": [ "nlmixrClone" ] }, { "page": "nlmixrWithTiming", "title": "Time a part of a nlmixr operation and add to nlmixr object", "topics": [ "nlmixrWithTiming" ] }, { "page": "nlsControl", "title": "nlmixr2 defaults controls for nls", "topics": [ "nlsControl" ] }, { "page": "nmNearPD", "title": "C++ implementation of Matrix's nearPD", "topics": [ "nmNearPD" ] }, { "page": "nmObjGetControl", "title": "Get control object from fit", "topics": [ "nmObjGetControl", "nmObjGetControl.agq", "nmObjGetControl.bobyqa", "nmObjGetControl.default", "nmObjGetControl.emvi", "nmObjGetControl.fbvi", "nmObjGetControl.fo", "nmObjGetControl.foce", "nmObjGetControl.focei", "nmObjGetControl.focep", "nmObjGetControl.foi", "nmObjGetControl.iagq", "nmObjGetControl.ifoce", "nmObjGetControl.ifocei", "nmObjGetControl.ifocep", "nmObjGetControl.ilaplace", "nmObjGetControl.imp", "nmObjGetControl.impmap", "nmObjGetControl.inpag", "nmObjGetControl.inpb", "nmObjGetControl.laplace", "nmObjGetControl.lbfgsb3c", "nmObjGetControl.magq", "nmObjGetControl.mfoce", "nmObjGetControl.mfocei", "nmObjGetControl.mfocep", "nmObjGetControl.mlaplace", "nmObjGetControl.mnpag", "nmObjGetControl.mnpb", "nmObjGetControl.n1qn1", "nmObjGetControl.newuoa", "nmObjGetControl.nlm", "nmObjGetControl.nlme", "nmObjGetControl.nlminb", "nmObjGetControl.nls", "nmObjGetControl.npag", "nmObjGetControl.npb", "nmObjGetControl.optim", "nmObjGetControl.posthoc", "nmObjGetControl.qrpem", "nmObjGetControl.saem", "nmObjGetControl.trust", "nmObjGetControl.uobyqa", "nmObjGetControl.vae" ] }, { "page": "nmObjGetEstimationModel", "title": "Get the estimation model for a fit object depending on the object type", "topics": [ "nmObjGetEstimationModel" ] }, { "page": "nmObjGetFoceiControl", "title": "Method for getting focei compatible control object from nlmixr object", "topics": [ "nmObjGetFoceiControl", "nmObjGetFoceiControl.agq", "nmObjGetFoceiControl.default", "nmObjGetFoceiControl.emvi", "nmObjGetFoceiControl.fbvi", "nmObjGetFoceiControl.foce", "nmObjGetFoceiControl.focep", "nmObjGetFoceiControl.iagq", "nmObjGetFoceiControl.ifoce", "nmObjGetFoceiControl.ifocei", "nmObjGetFoceiControl.ifocep", "nmObjGetFoceiControl.ilaplace", "nmObjGetFoceiControl.imp", "nmObjGetFoceiControl.impmap", "nmObjGetFoceiControl.inpag", "nmObjGetFoceiControl.inpb", "nmObjGetFoceiControl.laplace", "nmObjGetFoceiControl.magq", "nmObjGetFoceiControl.mfoce", "nmObjGetFoceiControl.mfocei", "nmObjGetFoceiControl.mfocep", "nmObjGetFoceiControl.mlaplace", "nmObjGetFoceiControl.mnpag", "nmObjGetFoceiControl.mnpb", "nmObjGetFoceiControl.nlme", "nmObjGetFoceiControl.npag", "nmObjGetFoceiControl.npb", "nmObjGetFoceiControl.posthoc", "nmObjGetFoceiControl.qrpem", "nmObjGetFoceiControl.saem", "nmObjGetFoceiControl.vae" ] }, { "page": "nmObjGetIpredModel", "title": "Get the ipred model for a fit object depending on the object type", "topics": [ "nmObjGetEstimationModel.default", "nmObjGetEstimationModel.saem", "nmObjGetIpredModel", "nmObjGetIpredModel.default", "nmObjGetIpredModel.saem" ] }, { "page": "nmObjGetPredOnly", "title": "Get the pred-only model for a fit depending on the object type", "topics": [ "nmObjGetPredOnly", "nmObjGetPredOnly.default", "nmObjGetPredOnly.saem" ] }, { "page": "nmObjHandleControlObject", "title": "Handle the control object", "topics": [ "nmObjHandleControlObject", "nmObjHandleControlObject.agqControl", "nmObjHandleControlObject.bobyqaControl", "nmObjHandleControlObject.default", "nmObjHandleControlObject.emviControl", "nmObjHandleControlObject.foceControl", "nmObjHandleControlObject.foceiControl", "nmObjHandleControlObject.focepControl", "nmObjHandleControlObject.foControl", "nmObjHandleControlObject.foiControl", "nmObjHandleControlObject.iagqControl", "nmObjHandleControlObject.ifoceControl", "nmObjHandleControlObject.ifoceiControl", "nmObjHandleControlObject.ifocepControl", "nmObjHandleControlObject.ilaplaceControl", "nmObjHandleControlObject.impmapControl", "nmObjHandleControlObject.laplaceControl", "nmObjHandleControlObject.lbfgsb3cControl", "nmObjHandleControlObject.magqControl", "nmObjHandleControlObject.mfoceControl", "nmObjHandleControlObject.mfoceiControl", "nmObjHandleControlObject.mfocepControl", "nmObjHandleControlObject.mlaplaceControl", "nmObjHandleControlObject.n1qn1Control", "nmObjHandleControlObject.newuoaControl", "nmObjHandleControlObject.nlmControl", "nmObjHandleControlObject.nlmeControl", "nmObjHandleControlObject.nlminbControl", "nmObjHandleControlObject.nlsControl", "nmObjHandleControlObject.optimControl", "nmObjHandleControlObject.posthocControl", "nmObjHandleControlObject.saemControl", "nmObjHandleControlObject.trustControl", "nmObjHandleControlObject.uobyqaControl", "nmObjHandleControlObject.vaeControl" ] }, { "page": "nmObjHandleModelObject", "title": "Handle Model Object", "topics": [ "nmObjHandleModelObject", "nmObjHandleModelObject.default", "nmObjHandleModelObject.foceiModelList", "nmObjHandleModelObject.saemModelList" ] }, { "page": "nmObjUiSetCompressed", "title": "Set if the nlmixr2 object will return a compressed ui", "topics": [ "nmObjUiSetCompressed" ] }, { "page": "nmsimplex", "title": "Nelder-Mead simplex search", "topics": [ "nmsimplex" ] }, { "page": "npagControl", "title": "Control for the npag (nonparametric adaptive grid) method", "topics": [ "npagControl" ] }, { "page": "npbControl", "title": "Control for the npb (nonparametric Bayes) method", "topics": [ "npbControl" ] }, { "page": "ofv", "title": "Return the objective function", "topics": [ "ofv" ] }, { "page": "optimControl", "title": "nlmixr2 optim defaults", "topics": [ "optimControl" ] }, { "page": "posthocControl", "title": "Control options for the posthoc estimation method", "topics": [ "posthocControl" ] }, { "page": "predict.nlmixr2FitCore", "title": "Predict method for nlmixr2 fit core objects", "topics": [ "predict.nlmixr2FitCore" ] }, { "page": "print.saemFit", "title": "Print an SAEM model fit summary", "topics": [ "print.saemFit" ] }, { "page": "qrpemControl", "title": "Control for the qrpem (quasi-random parametric EM) estimation method", "topics": [ "qrpemControl" ] }, { "page": "residuals.nlmixr2FitData", "title": "Extract residuals from the FOCEI fit", "topics": [ "residuals.nlmixr2FitData" ] }, { "page": "rmEta", "title": "Remove an eta from the model", "topics": [ "rmEta" ] }, { "page": "rsControl", "title": "Options for the finite-difference covariance in setCov()", "topics": [ "rsControl" ] }, { "page": "saControl", "title": "Options for the SAEM stochastic-approximation covariance in setCov()", "topics": [ "saControl" ] }, { "page": "saemControl", "title": "Control Options for SAEM", "concept": [ "Estimation control" ], "topics": [ "saemControl" ] }, { "page": "setCov", "title": "Set the covariance type based on prior calculated covariances", "topics": [ "setCov", "setCov.analytic", "setCov.default", "setCov.imp", "setCov.r", "setCov.r,s", "setCov.s", "setCov.sa" ] }, { "page": "setCov-set", "title": "Install an already-computed covariance result on a fit", "topics": [ "setCov<-" ] }, { "page": "setCovAllMethods", "title": "List the covariance methods setCov() can compute", "topics": [ "setCovAllMethods" ] }, { "page": "setCovOptions", "title": "The cache key of a covariance method's options", "topics": [ "setCovOptions", "setCovOptions.default", "setCovOptions.rsControl" ] }, { "page": "setCovValue", "title": "The covariance, method name and options a result installs", "topics": [ "setCovValue", "setCovValue.default", "setCovValue.matrix" ] }, { "page": "setOfv", "title": "Set/get Objective function type for a nlmixr2 object", "topics": [ "getOfvType", "setOfv" ] }, { "page": "sqrtm", "title": "Return the square root of general square matrix A", "topics": [ "sqrtm" ] }, { "page": "summary.saemFit", "title": "Print an SAEM model fit summary", "topics": [ "summary.saemFit" ] }, { "page": 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