documentation

R/class_mrgmod.R

@@ -406,7 +406,7 @@ setMethod("project", "packmod", function(x,...) {
 })
 
 #' @rdname cmtn
-#' @param tag compartment name
+#' @param tag compartment name.
 #' @export
 setMethod("cmtn", "mrgmod", function(x,tag,...) {
   return(which(cmt(x)==tag))
@@ -434,9 +434,9 @@ CAPTUREI <- function(x) c(length(x@capture),x@Icap-1L)
 #' This is also the directory where the model is built, which could be the 
 #' value of [tempdir()].
 #'
-#' @param x model object
-#' @param short logical; if `TRUE`, `soloc`s will
-#'  be rendered  with a short path name
+#' @param x model object.
+#' @param short logical; if `TRUE`, `soloc`s will be rendered  with a short 
+#' path name.
 #' 
 #' @examples
 #' mod <- mrgsolve::house()
@@ -493,7 +493,7 @@ setMethod("names", "mrgmod", function(x) {
 #' 
 #' @param x a model object.
 #' @param deep if `TRUE`, extra information is returned in the output list
-#' (see details). 
+#' (see **Details**). 
 #' @param ... not used.
 #' 
 #' @details 

R/class_mrgsims.R

@@ -1,4 +1,4 @@
-# Copyright (C) 2013 - 2019  Metrum Research Group
+# Copyright (C) 2013 - 2024  Metrum Research Group
 #
 # This file is part of mrgsolve.
 #
@@ -44,21 +44,23 @@ setClass("batch_mrgsims",contains="mrgsims",
 )
 
 
-##' Check if an object is mrgsim output
-##' 
-##' @param x any object
-##' 
-##' @return \code{TRUE} if \code{x} inherits \code{mrgsims}.
-##' 
-##' @export
+#' Check if an object is mrgsims output
+#' 
+#' @param x any object.
+#' 
+#' @return `TRUE` if `x` inherits `mrgsims`.
+#' 
+#' @md
+#' @export
 is.mrgsims <- function(x) inherits(x,"mrgsims")
 
 
-##' Coerce an mrgsims object to list
-##' 
-##' @param x an mrgsims object
-##' @param ... not used
-##' @export
+#' Coerce an mrgsims object to list
+#' 
+#' @param x an mrgsims object.
+#' @param ... not used.
+#' @md
+#' @export
 setMethod("as.list", "mrgsims", function(x, ...) {
   to_get <- slotNames("mrgsims") 
   out <- vector("list",length(to_get))

R/env.R

@@ -1,4 +1,4 @@
-# Copyright (C) 2013 - 2019  Metrum Research Group
+# Copyright (C) 2013 - 2024  Metrum Research Group
 #
 # This file is part of mrgsolve.
 #
@@ -16,33 +16,34 @@
 # along with mrgsolve.  If not, see <http://www.gnu.org/licenses/>.
 
 
-##' Re-evaluate the code in the ENV block
-##' 
-##' The \code{$ENV} block is a block of R code that can 
-##' realize any sort of R object that might be used in running 
-##' a model.
-##' 
-##' @seealso \code{\link{env_get}}, \code{\link{env_ls}}
-##' 
-##' @param x model object
-##' @param seed passed to \code{\link{set.seed}} if a numeric value is supplied
-##' 
-##' @export
+#' Re-evaluate the code in the ENV block
+#' 
+#' The `$ENV` block is a block of R code that can realize any sort of R object 
+#' that might be used in running a model.
+#' 
+#' @seealso [env_get()], [env_ls()]
+#' 
+#' @param x a model object.
+#' @param seed passed to [set.seed()] if a numeric value is supplied.
+#' 
+#' @md
+#' @export
 env_eval <- function(x,seed=NULL) {
   if(is.numeric(seed)) set.seed(seed)
   eval_ENV_block(x=x@envir$.code,where=project(x),envir=x@envir)
   return(invisible(x))
 }
 
-##' List objects in the model environment
-##' 
-##' Each model keeps an internal environment that allows the user 
-##' to carry any \code{R} object along.  Objects are coded in \code{$ENV}.
-##' 
-##' @param x model object
-##' @param ... passed to \code{\link{ls}}
-##' 
-##' @export
+#' List objects in the model environment
+#' 
+#' Each model keeps an internal environment that allows the user 
+#' to carry any `R` object along.  Objects are coded in `$ENV`.
+#' 
+#' @param x amodel object.
+#' @param ... passed to [ls()].
+#' 
+#' @md
+#' @export
 env_ls <- function(x,...) {
   objects <- ls(x@envir,...)
   cl <- sapply(objects,function(o) {
@@ -53,12 +54,13 @@ env_ls <- function(x,...) {
   arrange__(ans, .dots=c("class"))
 }
 
-##' Return model environment
-##' 
-##' @param x model object
-##' @param tolist should the environment be coerced to \code{list}?
-##' 
-##' @export
+#' Return model environment
+#' 
+#' @param x a model object.
+#' @param tolist should the environment be coerced to `list`?
+#' 
+#' @md
+#' @export
 env_get <- function(x,tolist=TRUE) {
   if(tolist) {
     return(as.list(x@envir))  
@@ -67,36 +69,38 @@ env_get <- function(x,tolist=TRUE) {
   }
 }
 
-##' @rdname env_get
-##' @export
+#' @rdname env_get
+#' @export
 env_get_env <- function(x) {
   x@envir 
 }
 
-##' Update objects in model environment
-##' 
-##' @param .x model object
-##' @param .dots list of objects to updated
-##' @param ... objects to update
-##' 
-##' @export
+#' Update objects in model environment
+#' 
+#' @param .x a model object.
+#' @param .dots list of objects to updated.
+#' @param ... objects to update.
+#' 
+#' @md
+#' @export
 env_update <- function(.x,...,.dots=list()) {
   right <- c(list(...),.dots)
   left <- as.list(.x@envir)
   .x@envir <- as.environment(merge.list(left,right))
   return(invisible(.x))
 }
 
-##' Run the model cama function
-##' 
-##' @param mod model object
-##' @param fn function name
-##' @param ... passed to update
-##' 
-##' @details \code{sah-mah}
-##' 
-##' @keywords internal
-##' @export
+#' Run the model cama function
+#' 
+#' @param mod a model object.
+#' @param fn function name.
+#' @param ... passed to update.
+#' 
+#' @details `sah-mah`
+#' 
+#' @keywords internal
+#' @md
+#' @export
 cama <- function(mod,fn="cama",...) {
   stop("this function is deprecated.")
   # object_exists(fn, mod@envir, "function", inherits=FALSE)

R/generics.R

@@ -1,4 +1,4 @@
-# Copyright (C) 2013 - 2020  Metrum Research Group
+# Copyright (C) 2013 - 2024  Metrum Research Group
 #
 # This file is part of mrgsolve.
 #
@@ -15,15 +15,17 @@
 # You should have received a copy of the GNU General Public License
 # along with mrgsolve.  If not, see <http://www.gnu.org/licenses/>.
 
-##' Get the compartment number from a compartment name
-##'
-##' @param x model object
-##' @param ... passed along
-##'
-##' @examples
-##' mod <- mrgsolve::house()
-##' mod %>% cmtn("CENT")
-##' @export
+#' Get the compartment number from a compartment name
+#'
+#' @param x model object.
+#' @param ... not used.
+#'
+#' @examples
+#' mod <- mrgsolve::house()
+#' cmtn(mod, "CENT")
+#' 
+#' @md
+#' @export
 setGeneric("cmtn", function(x,...) standardGeneric("cmtn"))
 
 #' Print model code to the console
@@ -37,6 +39,7 @@ setGeneric("cmtn", function(x,...) standardGeneric("cmtn"))
 #' @param ... not used.
 #' @return `NULL` is returned invisibly when `raw` is `FALSE`; when `raw` is 
 #' set to `TRUE`, the model code is returned as a character vector.
+#' @md
 #' @export
 setGeneric("see", function(x,...) standardGeneric("see"))
 

R/init.R

@@ -1,4 +1,4 @@
-# Copyright (C) 2013 - 2020  Metrum Research Group
+# Copyright (C) 2013 - 2024  Metrum Research Group
 #
 # This file is part of mrgsolve.
 #
@@ -16,50 +16,55 @@
 # along with mrgsolve.  If not, see <http://www.gnu.org/licenses/>.
 
 
-##' Methods for working with the model compartment list
-##'
-##' Calling \code{init} with the model object as the first argument 
-##' will return the model initial conditions as a \code{numericlist} 
-##' object. See \code{\link{numericlist}} for methods to  deal with 
-##' \code{cmt_list} objects.
-##'
-##' @aliases init 
-##' @param .x the model object
-##' @param .y list to be merged into parameter list
-##' @param .pat a regular expression (character) to be applied as 
-##' a filter when printing compartments to the screen
-##' @param ... passed along
-##' @return an object of class \code{cmt_list} (see 
-##' \code{\link{numericlist}})
-##' @details
-##' Can be used to either get a compartment list object from a 
-##' \code{mrgmod} model object or to update the compartment initial 
-##' conditions in a model object.  For both uses, the return value 
-##' is a \code{cmt_list} object. For the former use, \code{init} 
-##' is usually called to print the compartment initial conditions 
-##' to the screen, but the \code{cmt_list} object can also be coerced 
-##' to a list or numeric R object.
-##'
-##' @examples
-##' ## example("init")
-##' mod <- mrgsolve::house()
-##'
-##' init(mod)
-##' init(mod, .pat="^C") ## may be useful for large models
-##'
-##' class(init(mod))
-##'
-##' init(mod)$CENT
-##'
-##' as.list(init(mod))
-##' as.data.frame(init(mod))
-
-##' @export
+#' Methods for working with the model compartment list
+#'
+#' Calling `init()` with the model object as the first argument 
+#' will return the model initial conditions as a [numericlist] 
+#' object. See [numericlist] for methods to  deal with 
+#' `cmt_list` objects.
+#'
+#' @aliases init 
+#' @param .x the model object.
+#' @param .y list to be merged into parameter list.
+#' @param .pat a regular expression (character) to be applied as 
+#' a filter when printing compartments to the screen.
+#' @param ... `name = value` assignments to update the initial conditions list.
+#' 
+#' @return An object of class `cmt_list` (see [numericlist]).
+#' 
+#' @details
+#' Can be used to either get a compartment list object from a 
+#' `mrgmod` model object or to update the compartment initial 
+#' conditions in a model object.  For both uses, the return value 
+#' is a `cmt_list` object. For the former use, `init()` 
+#' is usually called to print the compartment initial conditions 
+#' to the screen, but the `cmt_list` object can also be coerced 
+#' to a list or numeric R object.
+#'
+#' @examples
+#' ## example("init")
+#' mod <- mrgsolve::house()
+#'
+#' init(mod)
+#' 
+#' init(mod, .pat="^C") ## may be useful for large models
+#'
+#' class(init(mod))
+#'
+#' init(mod)$CENT
+#'
+#' as.list(init(mod))
+#' 
+#' as.data.frame(init(mod))
+#' 
+#' 
+#' @md
+#' @export
 setGeneric("init", function(.x,...) standardGeneric("init"))
 
 
-##' @export
-##' @rdname init
+#' @export
+#' @rdname init
 setMethod("init", "mrgmod", function(.x,.y=list(),..., .pat="*") {
 
   args <- c(as.list(.y),list(...))
@@ -80,26 +85,26 @@ setMethod("init", "mrgmod", function(.x,.y=list(),..., .pat="*") {
   return(.x@init)
 })
 
-##' @rdname init
-##' @export
+#' @rdname init
+#' @export
 setMethod("init", "mrgsims", function(.x,...) {
   init(mod(.x),...)
 }) 
 
-##' @rdname init
-##' @export
+#' @rdname init
+#' @export
 setMethod("init", "missing", function(...) {
   init(list(...))
 })
 
-##' @rdname init
-##' @export
+#' @rdname init
+#' @export
 setMethod("init", "list", function(.x,...) {
   create_numeric_list(.x,"cmt_list",...)
 })
 
-##' @rdname init
-##' @export
+#' @rdname init
+#' @export
 setMethod("init", "ANY", function(.x,...) {
   init(as.list(.x),...)
 })