diff --git a/R/rxode2.R b/R/rxode2.R index d35b8ada4..ab880b93a 100644 --- a/R/rxode2.R +++ b/R/rxode2.R @@ -1244,13 +1244,13 @@ rxDllLoaded <- rxIsLoaded #' #' @return An rxDll object that has the following components #' -#' * `dll`{DLL path} -#' * `model`{model specification} -#' * `.c`{A function to call C code in the correct context from the DLL -#' using the [.C()] function.} -#' * `.call`{A function to call C code in the correct context from the DLL -#' using the [.Call()] function.} -#' * `args`{A list of the arguments used to create the rxDll object.} +#' * `dll` DLL path +#' * `model` model specification +#' * `.c` A function to call C code in the correct context from the DLL +#' using the [.C()] function. +#' * `.call` A function to call C code in the correct context from the DLL +#' using the [.Call()] function. +#' * `args` A list of the arguments used to create the rxDll object. #' @inheritParams rxode2 #' @seealso [rxode2()] #' @author Matthew L.Fidler @@ -1776,17 +1776,17 @@ rxModels_ <- # nolint #' #' @return A list of rxode2 model properties including: #' -#' * `params`{ a character vector of names of the model parameters} -#' * `lhs`{ a character vector of the names of the model calculated parameters} -#' * `state`{ a character vector of the compartments in rxode2 object} -#' * `trans`{ a named vector of translated model properties +#' * `params` a character vector of names of the model parameters +#' * `lhs` a character vector of the names of the model calculated parameters +#' * `state` a character vector of the compartments in rxode2 object +#' * `trans` a named vector of translated model properties #' including what type of jacobian is specified, the `C` function prefixes, -#' as well as the `C` functions names to be called through the compiled model.} -#' * `md5`{a named vector that gives the digest of the model (`file_md5`) and the parsed model -#' (`parsed_md5`)} -#' * `model`{ a named vector giving the input model (`model`), +#' as well as the `C` functions names to be called through the compiled model. +#' * `md5` a named vector that gives the digest of the model (`file_md5`) and the parsed model +#' (`parsed_md5`) +#' * `model` a named vector giving the input model (`model`), #' normalized model (no comments and standard syntax for parsing, `normModel`), -#' and interim code that is used to generate the final C file `parseModel`} +#' and interim code that is used to generate the final C file `parseModel` #' #' @keywords internal #' @family Query model information diff --git a/man/reexports.Rd b/man/reexports.Rd index 365c14ab7..f1310e9e9 100644 --- a/man/reexports.Rd +++ b/man/reexports.Rd @@ -82,4 +82,3 @@ below to see their documentation. \item{rxode2random}{\code{\link[rxode2random:dot-cbindOme]{.cbindOme}}, \code{\link[rxode2random:dot-expandPars]{.expandPars}}, \code{\link[rxode2random:dot-vecDf]{.vecDf}}, \code{\link[rxode2random]{cvPost}}, \code{\link[rxode2random]{invWR1d}}, \code{\link[rxode2random]{phi}}, \code{\link[rxode2random]{rinvchisq}}, \code{\link[rxode2random]{rLKJ1}}, \code{\link[rxode2random]{rxGetSeed}}, \code{\link[rxode2random]{rxGetSeed}}, \code{\link[rxode2random]{rxRmvn}}, \code{\link[rxode2random]{rxSeedEng}}, \code{\link[rxode2random]{rxSetSeed}}, \code{\link[rxode2random]{rxSetSeed}}, \code{\link[rxode2random]{rxSetSeed}}, \code{\link[rxode2random:rxWithSeed]{rxWithPreserveSeed}}, \code{\link[rxode2random]{rxWithSeed}}, \code{\link[rxode2random]{rxWithSeed}}} }} -\value{ Inherited from parent routine } diff --git a/man/rxCompile.Rd b/man/rxCompile.Rd index 25685936e..f9cf56615 100644 --- a/man/rxCompile.Rd +++ b/man/rxCompile.Rd @@ -92,13 +92,13 @@ function.} \value{ An rxDll object that has the following components \itemize{ -\item \code{dll}{DLL path} -\item \code{model}{model specification} -\item \code{.c}{A function to call C code in the correct context from the DLL -using the \code{\link[=.C]{.C()}} function.} -\item \code{.call}{A function to call C code in the correct context from the DLL -using the \code{\link[=.Call]{.Call()}} function.} -\item \code{args}{A list of the arguments used to create the rxDll object.} +\item \code{dll} DLL path +\item \code{model} model specification +\item \code{.c} A function to call C code in the correct context from the DLL +using the \code{\link[=.C]{.C()}} function. +\item \code{.call} A function to call C code in the correct context from the DLL +using the \code{\link[=.Call]{.Call()}} function. +\item \code{args} A list of the arguments used to create the rxDll object. } } \description{ diff --git a/man/rxModelVars.Rd b/man/rxModelVars.Rd index 8666a7baa..1b0f2b68f 100644 --- a/man/rxModelVars.Rd +++ b/man/rxModelVars.Rd @@ -21,17 +21,17 @@ rxModelVarsS3(obj) \value{ A list of rxode2 model properties including: \itemize{ -\item \code{params}{ a character vector of names of the model parameters} -\item \code{lhs}{ a character vector of the names of the model calculated parameters} -\item \code{state}{ a character vector of the compartments in rxode2 object} -\item \code{trans}{ a named vector of translated model properties +\item \code{params} a character vector of names of the model parameters +\item \code{lhs} a character vector of the names of the model calculated parameters +\item \code{state} a character vector of the compartments in rxode2 object +\item \code{trans} a named vector of translated model properties including what type of jacobian is specified, the \code{C} function prefixes, -as well as the \code{C} functions names to be called through the compiled model.} -\item \code{md5}{a named vector that gives the digest of the model (\code{file_md5}) and the parsed model -(\code{parsed_md5})} -\item \code{model}{ a named vector giving the input model (\code{model}), +as well as the \code{C} functions names to be called through the compiled model. +\item \code{md5} a named vector that gives the digest of the model (\code{file_md5}) and the parsed model +(\code{parsed_md5}) +\item \code{model} a named vector giving the input model (\code{model}), normalized model (no comments and standard syntax for parsing, \code{normModel}), -and interim code that is used to generate the final C file \code{parseModel}} +and interim code that is used to generate the final C file \code{parseModel} } } \description{ diff --git a/man/rxSetPipingAuto.Rd b/man/rxSetPipingAuto.Rd index 28225894b..c48a282e9 100644 --- a/man/rxSetPipingAuto.Rd +++ b/man/rxSetPipingAuto.Rd @@ -7,7 +7,7 @@ rxSetPipingAuto( thetamodelVars = rex::rex(or("tv", "t", "pop", "POP", "Pop", "TV", "T", "cov", "err", "eff")), - covariateExceptions = rex::rex(start, or("wt", "sex", "crcl"), end), + covariateExceptions = rex::rex(start, or("wt", "sex", "crcl", "kout"), end), etaParts = c("eta", "ETA", "Eta", "ppv", "PPV", "Ppv", "iiv", "Iiv", "bsv", "Bsv", "BSV", "bpv", "Bpv", "BPV", "psv", "PSV", "Psv") ) diff --git a/man/rxode2.Rd b/man/rxode2.Rd index 215a15ee6..d6a9d2d65 100644 --- a/man/rxode2.Rd +++ b/man/rxode2.Rd @@ -333,7 +333,7 @@ compilation model. \if{html}{\out{
}}\preformatted{## using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -## rxode2 2.0.14.9000 model named rx_f8a38012c74774242195a2bca079f175 model (ready). +## rxode2 2.0.14.9000 model named rx_8df102744d099fa953635863e30eb814 model (ready). ## x$state: depot, center ## x$stateExtra: cp ## x$params: tka, tcl, tv, add.sd, eta.ka, eta.cl, eta.v, rxerr.cp @@ -346,7 +346,7 @@ mod$simulationIniModel \if{html}{\out{
}}\preformatted{## using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ -## rxode2 2.0.14.9000 model named rx_8367e8f5e6c5a00454c7193fc896bf87 model (ready). +## rxode2 2.0.14.9000 model named rx_13bad113efb37636a1e6416e14daf8da model (ready). ## x$state: depot, center ## x$stateExtra: cp ## x$params: tka, tcl, tv, add.sd, eta.ka, eta.cl, eta.v, rxerr.cp