RxODE v0.8.0-9

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Facilities for Simulating from ODE-Based Models

Facilities for running simulations from ordinary differential equation (ODE) models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The VODE and LSODA are in the public domain. The information is available in the inst/COPYRIGHTS.

Functions in RxODE

Name Description
coef.RxODE Return the RxODE coefficients
cvPost Sample a covariance Matrix from the Posteior Inverse Wishart distribution.
is.rxSolve Check to see if this is an rxSolve object.
.rxRmPrint Remove print statements
.rxRtoolsBaseWin Return Rtools base
+.rxSolve Update Solved object with '+'
.rxRmIni Remove INIs
rxBlockZeros Creates a logical matrix for block matrixes.
print.RxODE Print information about the RxODE object.
.rxSymPyJacobian Calculate the full Jacobian for a model
.rxWinRtoolsPath Setup Rtools path
rxC Return the C file associated with the RxODE object
print.rxCoef Print the rxCoef object
rxCores Get the number of cores in a system
reexports Objects exported from other packages
rinvchisq Scaled Inverse Chi Squared distribution
rxChain2 Second command in chaining commands
rxClean Cleanup anonymous DLLs
rxCompile Compile a model if needed
rxCondition Current Condition for RxODE object
rxDelete Delete the DLL for the model
rxForget Clear memoise cache for RxODE
rxExpandIfElse Expand if/else clauses into mutiple different types of lines.
rxFoExpandEta First Order Expansion of ETA
add.sampling Add sampling to eventTable
cholSE Generalized Cholesky Matrix Decomposition
rxInits Initial Values and State values for a RxODE object
rxIs Check the type of an object using Rcpp
RxODE Create an ODE-based model specification
rxGetModel Get model properties without compiling it.
eventTable Create an event table object
rxPermissive Permissive or Strict RxODE sytax options
rxIsCurrent Checks if the RxODE object was built with the current build
rxLhs Left handed Variables
rxParsePred Prepare Pred function for inclusion in RxODE
rxIsLoaded Determine if the DLL associated with the RxODE object is loaded
rxPhysicalDrives Returns a list of physical drives that have been or currently are mounted to the computer.
findLhs Find the assignments in R expression
add.dosing Add dosing to eventTable
print.rxCoefSolve Print the rxCoefSolve object
rxInv Invert matrix using Rcpp Armadilo.
rxPrint Print x using the message facility
rxProgress RxODE progress bar functions
foceiFitCpp_ Fit/Evaulate FOCEi
genShinyApp.template Generate an example (template) of a dosing regimen shiny app
rxMd5 Return the md5 of an RxODE object or file
rxLinCmtTrans This translates the parameters specified by the model in the correct type of solving.
rxAddReturn Add a return statment to a function.
rxAssignPtr Assign pointer based on model variables
print.rxDll Print rxDll object
rxSolveFree Free the C solving information.
rxDfdy Jacobian and parameter derivatives
rxReload Reload RxODE DLL
rxSetSum Choose the type of sums to use for RxODE.
rxCat Use cat when RxODE.verbose is TRUE
rxChain rxChain Chain or add item to solved system of equations
rxSymInvChol Get Omega^-1 and derivatives
rxSetupIni Setup the initial conditions.
rxSymInvCholCreate Creates an object for calculating Omega/Omega^-1 and derivatives
rxReq Require namespace, otherwise throw error.
rxGetRxODE Get RxODE model from object
rxSymPyReserved Return a list of reserved functions and variables from sympy
rxSplitLines Split line into multiple lines at + or - breaks
rxDll Return the DLL associated with the RxODE object
rxSymPySensitivity Calculate the sensitivity equations for a model
rxHtml Format rxSolve and related objects as html.
rxSymPyClear Delete variable if exists.
rxSymPyClean Remove variables created by RxODE from the SymPy environment.
rxDynLoad Load RxODE object
rxSymPyExists Does the varaible exist in the SymPy Python environment?
rxValidate Validate RxODE
rxSetProd Choose the type of product to use in RxODE. These are used in the RxODE prod blocks
rxSymPyExpand Return the expanded expression (via SymPy)
rxNorm Get the normalized model
rxDynUnload Unload RxODE object
rxSumProdModel Recast model in terms of sum/prod
rxVersion Version and repository for this dparser package.
rxSyPyAddVars Add undefined variables to SymPy
rxModelVars All model variables for a RxODE object
rxModels_ Get the rxModels information
rxParseErr Prepare Error function for inclusion in RxODE
rxOptExpr Optimize RxODE for computer evaluation
rxSymPySetup Setup a SymPy environment that sets up the specified RxODE model.
rxSyncOptions Sync options with RxODE varaibles
rxParsePk Parse PK function for inclusion in RxODE
rxOptions Options for RxODE
summary.rxDll Summary of rxDll object
yeoJohnson Yeo-Johnson Transformation
rxSymPySetupIf Setup SymPy environment if needed
rxParams Parameters specified by the model
rxSymPySetupPred Setup Pred function based on RxODE object.
rxSimThetaOmega Simulate Parameters from a Theta/Omega specification
rxSymPyStart Start SymPy
rxSetupScale Setup the initial conditions.
rxThetaEta Format theta and eta for parameter estimate values in RxODE
rxSolve Solves a ODE equation
rxSplitPlusQ This function splits a function based on + or - terms
rxShiny Use Shiny to help develop an RxODE model
rxSymPyFix Fix SymPy expressions to be R parsable expressions
rxState State variables
sqrtm Return the square root of general square matrix A
rxSymPyFunctions Setup SymPy functions
rxSymInvCholN Return the dimension of the built-in derivatives/inverses
summary.RxODE Print expanded information about the RxODE object.
rxSymPy Execute sympy statement.
rxSymPyDfDy Calculate df/dy derivatives
rxSymPyExec Execute Python statement without getting the return value.
rxSymPyVersion Return the version of SymPy that is running
rxSymPyVars Setup SymPy variables
rxTrans Translate the model to C code if needed
rxToSymPy Converts model specification to/from a SymPy language
rxWinPythonSetup Setup Python and SymPy for windows
rxWinSetup Setup Windows components for RxODE
.rxRmJac Remove Jacobian
coxBox Cox Box transformation
.rxRmSens Remove sensitivity equations
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Vignettes of RxODE

Name
Model_schematic_w500.png
RxODE-covariates.Rmd
RxODE-data-frame.Rmd
RxODE-events.Rmd
RxODE-intro.Rmd
RxODE-mix-lin-ode.Rmd
RxODE-shiny.Rmd
RxODE-sim-var.Rmd
RxODE-stiff.Rmd
RxODE-syntax.Rmd
RxODE-transit-compartments.Rmd
logo.png
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