RxODE v0.9.0-8

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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
add.sampling Add sampling to eventTable
.rxRmIni Remove INIs
coef.RxODE Return the RxODE coefficients
.clearPipe Clear/Set pipeline
cvPost Sample a covariance Matrix from the Posteior Inverse Wishart distribution.
as.tbl.rxEt Convert to tbl
.rxFindPow Find power THETAs for appropriate scaling
RxODE Create an ODE-based model specification
as.et Coerce object to data.frame
add.dosing Add dosing to eventTable
eventTable Create an event table object
findLhs Find the assignments in R expression
.rxRmPrint Remove print statements
+.rxSolve Update Solved object with '+'
is.rxSolve Check to see if this is an rxSolve object.
.rxRmJac Remove Jacobian
etRep Repeat an RxODE event table
rxChain rxChain Chain or add item to solved system of equations
etRbind Combining event tables
rxChain2 Second command in chaining commands
.rxRmSens Remove sensitivity equations
.rxWinRtoolsPath Setup Rtools path
rxAddReturn Add a return statment to a function.
print.rxCoefSolve Print the rxCoefSolve object
et Event Table Function
.rxSymPyJacobian Calculate the full Jacobian for a model
print.RxODE Print information about the RxODE object.
rxDfdy Jacobian and parameter derivatives
rxDelete Delete the DLL for the model
print.rxCoef Print the rxCoef object
rxC14 Setup C++14 support in windows (required for nlmixr)
rxCat Use cat when RxODE.verbose is TRUE
rxCondition Current Condition for RxODE object
rxIsCurrent Checks if the RxODE object was built with the current build
rxIsLoaded Determine if the DLL associated with the RxODE object is loaded
rxAssignPtr Assign pointer based on model variables
genShinyApp.template Generate an example (template) of a dosing regimen shiny app
etTrans Event translation for RxODE
etSeq Sequence of event tables
is.rxEt Check to see if this is an rxEt object.
rinvchisq Scaled Inverse Chi Squared distribution
rxDynUnload Unload RxODE object
reexports Objects exported from other packages
print.rxDll Print rxDll object
rxModelVars All model variables for a RxODE object
rxReload Reload RxODE DLL
rxMd5 Return the md5 of an RxODE object or file
rxProgress RxODE progress bar functions
rxCores Get the number of cores in a system
rxIs Check the type of an object using Rcpp
rxInv Invert matrix using Rcpp Armadilo.
rxFoExpandEta First Order Expansion of ETA
rxExpandIfElse Expand if/else clauses into mutiple different types of lines.
rxClean Cleanup anonymous DLLs
rxLhs Left handed Variables
rxBlockZeros Creates a logical matrix for block matrixes.
rxC Return the C file associated with the RxODE object
rxOptExpr Optimize RxODE for computer evaluation
rxCompile Compile a model if needed
rxForget Clear memoise cache for RxODE
rxParams Parameters specified by the model
rxReq Require namespace, otherwise throw error.
rxOptions Options for RxODE
rxSetProd Choose the type of product to use in RxODE. These are used in the RxODE prod blocks
rxParseErr Prepare Error function for inclusion in RxODE
rxSetSum Choose the type of sums to use for RxODE.
rxSetupIni Setup the initial conditions.
rxLinCmtTrans This translates the parameters specified by the model in the correct type of solving.
rxPermissive Permissive or Strict RxODE sytax options
rxDynLoad Load RxODE object
rxDll Return the DLL associated with the RxODE object
rxGetModel Get model properties without compiling it.
rxHtml Format rxSolve and related objects as html.
rxInits Initial Values and State values for a RxODE object
rxPhysicalDrives Returns a list of physical drives that have been or currently are mounted to the computer.
rxSyPyAddVars Add undefined variables to SymPy
rxSimThetaOmega Simulate Parameters from a Theta/Omega specification
rxControl Solving \& Simulation of a ODE/solved system (and solving options) equation
rxSymInvChol Get Omega^-1 and derivatives
rxSumProdModel Recast model in terms of sum/prod
rxSymInvCholN Return the dimension of the built-in derivatives/inverses
rxState State variables
rxSymInvCholCreate Creates an object for calculating Omega/Omega^-1 and derivatives
rxSetupScale Setup the initial conditions.
rxShiny Use Shiny to help develop an RxODE model
rxSymPyReserved Return a list of reserved functions and variables from sympy
rxVersion Version and repository for this dparser package.
rxSymPySensitivity Calculate the sensitivity equations for a model
rxWinPythonSetup Setup Python and SymPy for windows
rxSymPyStart Start SymPy
rxSymPySetupPred Setup Pred function based on RxODE object.
rxGetRxODE Get RxODE model from object
rxModels_ Get the rxModels information
rxSymPyClear Delete variable if exists.
rxParsePk Parse PK function for inclusion in RxODE
rxParsePred Prepare Pred function for inclusion in RxODE
rxSymPyDfDy Calculate df/dy derivatives
rxSymPySetup Setup a SymPy environment that sets up the specified RxODE model.
rxNorm Get the normalized model
rxSplitPlusQ This function splits a function based on + or - terms
rxStack Stack a solved object for things like ggplot
rxSplitLines Split line into multiple lines at + or - breaks
rxSymPyClean Remove variables created by RxODE from the SymPy environment.
rxSolveFree Free the C solving information.
rxSymPy Execute sympy statement.
rxSymPyFix Fix SymPy expressions to be R parsable expressions
rxUse Use model object in your package
rxSymPyExpand Return the expanded expression (via SymPy)
rxSymPyExec Execute Python statement without getting the return value.
rxSymPyVars Setup SymPy variables
rxSymPySetupIf Setup SymPy environment if needed
rxSymPyVersion Return the version of SymPy that is running
rxSymPyFunctions Setup SymPy functions
rxValidate Validate RxODE
rxSymPyLincmtDvdx This creates the dv/dx RxODE model for a linear solved system
rxSymPyExists Does the varaible exist in the SymPy Python environment?
rxSyncOptions Sync options with RxODE varaibles
rxTempDir Get the RxODE temporary directory
summary.rxDll Summary of rxDll object
tibble type_sum function for units
rxToSymPy Converts model specification to/from a SymPy language
rxTrans Translate the model to C code if needed
rxWinSetup Setup Windows components for RxODE
summary.RxODE Print expanded information about the RxODE object.
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Vignettes of RxODE

Name
Model_schematic_w500.png
RxODE-cmt.Rmd
RxODE-covariates.Rmd
RxODE-data-frame.Rmd
RxODE-events.Rmd
RxODE-intro.Rmd
RxODE-model-types.Rmd
RxODE-rxUse.Rmd
RxODE-shiny.Rmd
RxODE-stiff.Rmd
RxODE-syntax.Rmd
RxODE-transit-compartments.Rmd
alpha-lincmt.csv
cl-lincmt.csv
kel-lincmt.csv
logo.png
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