documentation

R/chain.R

@@ -16,34 +16,35 @@
 # along with mrgsolve.  If not, see <http://www.gnu.org/licenses/>.
 
 
-##' Request simulated output
-##' 
-##' Use this function to select, by name, either compartments or derived 
-##' variables that have been captured (see \code{\link{CAPTURE}}) into
-##' the simulated output.
-##'
-##' @param x model object
-##' @param ... unquoted names of compartments or tabled items
-##' 
-##' @details
-##' There is also a \code{Req} argument to \code{\link{mrgsim}} that can 
-##' be set to accomplish the same thing as a call to \code{Req} in 
-##' the pipeline.
-##' 
-##' Note the difference between \code{req} and \code{Req}: the former only 
-##' selects compartments to appear in output while the latter selects both 
-##' compartments and captured items.  Also, when there are items are explicitly
-##' listed in \code{Req}, all other compartments or captured items not listed
-##' there are ignored.  But when compartments are selected with \code{req}
-##' all of the captured items are returned.  Remember that \code{req} is 
-##' strictly for compartments.
-##' 
-##' @examples
-##' mod <- mrgsolve::house()
-##'
-##' mod %>% Req(CP,RESP) %>% ev(amt=1000) %>%  mrgsim
-##'
-##' @export
+#' Request simulated output
+#' 
+#' Use this function to select, by name, either compartments or derived 
+#' variables that have been captured (see [CAPTURE]) into
+#' the simulated output.
+#'
+#' @param x model object.
+#' @param ... unquoted names of compartments or tabled items.
+#' 
+#' @details
+#' There is also a `Req` argument to [mrgsim()] that can 
+#' be set to accomplish the same thing as a call to `Req` in 
+#' the pipeline.
+#' 
+#' Note the difference between `req` and `Req`: the former only 
+#' selects compartments to appear in output while the latter selects both 
+#' compartments and captured items.  Also, when there are items are explicitly
+#' listed in `Req`, all other compartments or captured items not listed
+#' there are ignored.  But when compartments are selected with `req`
+#' all of the captured items are returned.  Remember that `req` is 
+#' strictly for compartments.
+#' 
+#' @examples
+#' mod <- mrgsolve::house()
+#'
+#' mod %>% Req(CP,RESP) %>% ev(amt=1000) %>%  mrgsim()
+#'
+#' @md
+#' @export
 Req <- function(x,...) UseMethod("Req")
 
 #' @export
@@ -52,12 +53,12 @@ Req.mrgmod <- function(x,...) {
   x  
 }
 
-##' @rdname Req
-##' @export
+#' @rdname Req
+#' @export
 req <- function(x,...) UseMethod("req")
 
-##' @export
-##' @rdname Req
+#' @export
+#' @rdname Req
 req.mrgmod <- function(x,...) {
   x <- update_request(x,as.character(match.call()[-1]))
   x
@@ -104,25 +105,26 @@ carry.out <- function(x,...) {
   x
 }
 
-##' Re-scale time in the simulated output
-##'
-##' @param x model object
-##' @param value value by which time will be scaled
-##' @param ... passed along
-##' 
-##' @details
-##' There is also a \code{tscale} argument to \code{\link{mrgsim}} that can 
-##' be set to accomplish the same thing as a call to \code{tscale} in 
-##' the pipeline.
-##' 
-##' @examples
-##' # The model is in hours:
-##' mod <- mrgsolve::house()
-##' 
-##' # The output is in days:
-##' mod %>% tscale(1/24) %>% mrgsim
-##' 
-##' @export
+#' Re-scale time in the simulated output
+#'
+#' @param x model object.
+#' @param value value by which time will be scaled.
+#' @param ... not used.
+#' 
+#' @details
+#' There is also a `tscale` argument to [mrgsim()] that can 
+#' be set to accomplish the same thing as a call to `tscale` in 
+#' the pipeline.
+#' 
+#' @examples
+#' # The model is in hours:
+#' mod <- mrgsolve::house()
+#' 
+#' # The output is in days:
+#' mod %>% tscale(1/24) %>% mrgsim()
+#' 
+#' @md
+#' @export
 tscale <- function(x,value=1,...) {
   x@args[["tscale"]] <- value
   x
@@ -131,7 +133,7 @@ tscale <- function(x,value=1,...) {
 #' Collect only observation records in the simulated output
 #'
 #' @param x model object.
-#' @param value the value for `obsonly`.
+#' @param value use `TRUE` to collect and return observation records only.
 #' @param ... not used.
 #' 
 #' @details

R/class_mrgmod.R

@@ -1,4 +1,4 @@
-# Copyright (C) 2013 - 2022 Metrum Research Group
+# Copyright (C) 2013 - 2024 Metrum Research Group
 #
 # This file is part of mrgsolve.
 #

R/env.R

@@ -39,7 +39,7 @@ env_eval <- function(x,seed=NULL) {
 #' 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 x a model object.
 #' @param ... passed to [ls()].
 #' 
 #' @md

R/events.R

@@ -554,14 +554,13 @@ ev_repeat <- function(x, n, wait = 0, as.ev = FALSE) {
 #' Use this function when you want to schedule two or more event objects in time
 #' according the dosing interval (`ii`) and additional doses (`addl`).
 #' 
-#' @param ... Event objects or numeric arguments named `wait` or `ii` to 
-#' implement a period of no-dosing activity in the sequence (see details).
-#' @param ID Numeric vector of subject IDs.
-#' @param .dots A list of event objects that replaces `...`.
-#' @param id Deprecated; use `ID`.
+#' @param ... event objects or numeric arguments named `wait` or `ii` to 
+#' implement a period of no-dosing activity in the sequence (see **Details**).
+#' @param ID numeric vector of subject IDs.
+#' @param .dots a list of event objects that replaces `...`.
+#' @param id deprecated; use `ID`.
 #' 
 #' @details
-#' 
 #' Use the generic [seq()] when the first argument is an event object.  If a 
 #' waiting period (`wait` or `ii`) is the first event, you will need to use 
 #' [ev_seq()].  When an event object has multiple rows, the end time for that 
@@ -570,7 +569,7 @@ ev_repeat <- function(x, n, wait = 0, as.ev = FALSE) {
 #' 
 #' The doses for the next event line start after all of the doses from the 
 #' previous event line plus one dosing interval from the previous event line 
-#' (see examples).  
+#' (see **Examples**).  
 #' 
 #' When numerics named `wait` or `ii` are mixed in with the event objects, 
 #' a period with no dosing activity is incorporated into the sequence,
@@ -595,10 +594,9 @@ ev_repeat <- function(x, n, wait = 0, as.ev = FALSE) {
 #' warning if you use `.ii`. Please use `ii` instead.
 #' 
 #' Values for `time` in any event object act like a prefix time spacer wherever 
-#' that event occurs in the event sequence (see examples).
+#' that event occurs in the event sequence (see **Examples**).
 #' 
 #' @examples
-#' 
 #' e1 <- ev(amt = 100, ii = 12, addl = 1)
 #' 
 #' e2 <- ev(amt = 200)

R/mrgsim_q.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.
 #

R/nmxml.R

@@ -1,4 +1,4 @@
-# Copyright (C) 2013 - 2023  Metrum Research Group
+# Copyright (C) 2013 - 2024  Metrum Research Group
 #
 # This file is part of mrgsolve.
 #

R/utils.R

@@ -330,28 +330,28 @@ cvec.character <- as.cvec
 ##' @keywords internal
 s_ <- function(...) as.character(match.call(expand.dots=TRUE))[-1] #nocov
 
-##' Access or clear arguments for calls to mrgsim
-##' 
-##' As a model object navigates a pipeline prior to simulation, arguments are
-##' collected to eventually be passed to [mrgsim()]. `simargs` lets you 
-##' intercept and possibly clear those arguments.
-##'
-##' @param x model object
-##' @param clear logical indicating whether or not to clear `args` from 
-##' the model object
-##' @param which character with length 1 naming a single arg to get
-##' @param ... passed along
-##' 
-##' @return If `clear` is `TRUE`, the argument list is 
-##' cleared and the model object is returned.  Otherwise, the argument 
-##' list is returned.
-##' 
-##' @examples
-##' mod <- mrgsolve::house()
-##' mod %>% Req(CP, RESP) %>% carry_out(evid, WT, FLAG) %>% simargs()
-##' 
-##' @md
-##' @export
+#' Access or clear arguments for calls to mrgsim()
+#' 
+#' As a model object navigates a pipeline prior to simulation, arguments are
+#' collected to eventually be passed to [mrgsim()]. `simargs()` lets you 
+#' intercept and possibly clear those arguments.
+#'
+#' @param x model object.
+#' @param clear logical indicating whether or not to clear `args` from 
+#' the model object.
+#' @param which character with length 1 naming a single arg to get.
+#' @param ... not used. 
+#' 
+#' @return If `clear` is `TRUE`, the argument list is 
+#' cleared and the model object is returned.  Otherwise, the argument 
+#' list is returned.
+#' 
+#' @examples
+#' mod <- mrgsolve::house()
+#' mod %>% Req(CP, RESP) %>% carry_out(evid, WT, FLAG) %>% simargs()
+#' 
+#' @md
+#' @export
 simargs <- function(x, which = NULL, clear = FALSE,...) {
 
   if(clear) {