Code review

DESCRIPTION

@@ -9,6 +9,14 @@ Description:
   'nlmixr2targets' ensures minimal rework in model development with 'nlmixr2'
   and 'targets' by simplifying and standardizing models and datasets.
 License: GPL (>= 2)
+Depends: 
+    R (>= 4.1)
+Imports: 
+    checkmate,
+    digest,
+    nlmixr2est,
+    rxode2 (>= 2.0.14),
+    targets
 Suggests: 
     covr,
     knitr,
@@ -20,11 +28,5 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
-Imports: 
-    checkmate,
-    digest,
-    nlmixr2est,
-    rxode2 (>= 2.0.14),
-    targets
 URL: https://nlmixr2.github.io/nlmixr2targets/
 VignetteBuilder: knitr

R/simplify.R

@@ -11,7 +11,7 @@
 #' `cmt(initial)` will be converted to `cmt(0)` before passing to nlmixr2.
 #'
 #' @inheritParams nlmixr2est::nlmixr
-#' @return \code{object} converted to a nlmixrui object.  The model name is
+#' @returns \code{object} converted to a nlmixrui object.  The model name is
 #'   always "object".
 #' @family Simplifiers
 #' @export
@@ -65,7 +65,7 @@ nlmixr_object_simplify_zero_initial_helper <- function(object) {
 #' @inheritParams nlmixr2est::nlmixr
 #' @param object an nlmixr_ui object (e.g. the output of running
 #'   \code{nlmixr(object = model)}
-#' @return The data with the nlmixr2 column lower case and on the left and the
+#' @returns The data with the nlmixr2 column lower case and on the left and the
 #'   covariate columns on the right and alphabetically sorted.
 #' @family Simplifiers
 #' @export

R/tar_nlmixr.R

@@ -14,7 +14,7 @@
 #' @inheritParams targets::tar_target
 #' @param env The environment where the model is setup (not needed for typical
 #'   use)
-#' @return A list of targets for the model simplification, data simplification,
+#' @returns A list of targets for the model simplification, data simplification,
 #'   and model estimation.
 #' @examples
 #' \dontrun{
@@ -79,8 +79,6 @@ tar_nlmixr_raw <- function(name, object, data, est, control, table, object_simpl
   checkmate::assert_character(object_simple_name, len = 1, min.chars = 1, any.missing = FALSE)
   checkmate::assert_character(data_simple_name, len = 1, min.chars = 1, any.missing = FALSE)
 
-  # Make models with initial conditions set work within `targets` (see #15)
-  set_env_object_noinitial(object = object, env = env)
   list(
     object_simple =
       targets::tar_target_raw(
@@ -143,31 +141,6 @@ tar_nlmixr_raw <- function(name, object, data, est, control, table, object_simpl
   )
 }
 
-#' Ensure that an object is set in its initial environment so that it is
-#' protected from the `targets` domain-specific-language issue of
-#' `pd(0) <- initial`
-#'
-#' @inheritParams tar_nlmixr
-#' @return NULL (called for side effects)
-#' @noRd
-set_env_object_noinitial <- function(object, env) {
-  if (is.name(object)) {
-    object_env <- env[[as.character(object)]]
-    if (is.function(object_env)) {
-      object_result <- try(rxode2::assertRxUi(object_env), silent = TRUE)
-      if (inherits(object_result, "rxUi")) {
-        assign(x = as.character(object), value = object_result, envir = env)
-      }
-    }
-  } else if (is.call(object)) {
-    # Recursively iterate over all parts of the call
-    lapply(X = object, FUN = set_env_object_noinitial, env = env)
-  }
-  # If it's anything other than a name or a call, then we don't need to modify
-  # it or its sub-objects.
-  NULL
-}
-
 #' Replace the fit data with the original data, then return the modified fit
 #'
 #' This function is intended for use within `nlmixr2targets` target creation,

R/tar_nlmixr_multimodel.R

@@ -5,7 +5,7 @@
 #' @inheritParams nlmixr2est::nlmixr
 #' @inheritParams targets::tar_target
 #' @inheritParams tar_nlmixr
-#' @return A list of targets for the model simplification, data simplification,
+#' @returns A list of targets for the model simplification, data simplification,
 #'   and model estimation.
 #' @export
 tar_nlmixr_multimodel <- function(name, ..., data, est, control = list(), table = nlmixr2est::tableControl(), env = parent.frame()) {

cran-comments.md

@@ -0,0 +1,10 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* Even simple workflows for the `nlmixr2targets` library take significant
+  runtime, more than the few seconds allowed for examples.  And, typical
+  workflows also have a significant amount of code associated with them (tens to
+  hundreds of lines).  For these reasons, the individual functions do not have
+  running examples and user-focused examples are put into the vignette.
+* This is a new release.