RxODE v0.9.0-8

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by Wenping Wang View Source

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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Last month downloads

Details

BugReports	https://github.com/nlmixrdevelopment/RxODE/issues
NeedsCompilation	yes
VignetteBuilder	knitr
License	GPL (>= 2)
URL	https://nlmixrdevelopment.github.io/RxODE/
RoxygenNote	6.1.1
Biarch	true
LinkingTo	dparser(>= 0.1.8), Rcpp (>= 0.12.3), RcppArmadillo(>= 0.9.300.2.0), PreciseSums (>= 0.3)
Encoding	UTF-8
LazyData	true
Packaged	2019-06-20 14:46:11 UTC; annie
Repository	CRAN
Date/Publication	2019-06-21 08:20:35 UTC

imports	assertthat , brew , cli , crayon , digest , dparser (>= 0.1.8) , ggforce , ggplot2 , inline , lotri , magrittr , Matrix , memoise , methods , mvnfast , n1qn1 (>= 6.0.1-2) , pillar , PreciseSums (>= 0.3) , Rcpp (>= 0.12.3) , remotes , rex , sys , units (>= 0.6-0) , utils
suggests	covr , curl , devtools , dplyr (>= 0.8.0) , DT , gridExtra , htmltools , installr , knitr , microbenchmark , nlme , reticulate , rlang , rmarkdown , scales , shiny , SnakeCharmR , stringi , tcltk , testthat , tibble , tidyr , usethis
depends	R (>= 3.4.0)
linkingto	RcppArmadillo (>= 0.9.300.2.0)
Contributors	odepack authors, Melissa Hallow, Hadley Wickham, R Core team, Robert Gentleman, Heng Li, Ross Ihaka, G Grothendieck, Simon Frost, Matthew Fidler, Justin Wilkins, Zufar Mulyukov, Yu Feng, Alan Hindmarsh, Linda Petzold, Ernst Hairer, Gerhard Wanner, J Colinge