Harmonise link methods (#308)

DESCRIPTION

@@ -90,6 +90,7 @@ Collate:
     'LongitudinalQuantities.R'
     'LongitudinalRandomSlope.R'
     'LongitudinalSteinFojo.R'
+    'Promise.R'
     'SimGroup.R'
     'SimJointData.R'
     'SimLongitudinal.R'
@@ -104,6 +105,7 @@ Collate:
     'defaults.R'
     'external-exports.R'
     'jmpost-package.R'
+    'link_generics.R'
     'settings.R'
     'zzz.R'
 VignetteBuilder: knitr

NAMESPACE

@@ -17,6 +17,7 @@ S3method(as.StanModule,LinkComponent)
 S3method(as.StanModule,Parameter)
 S3method(as.StanModule,ParameterList)
 S3method(as.StanModule,Prior)
+S3method(as.StanModule,PromiseLinkComponent)
 S3method(as.character,JointModel)
 S3method(as.character,Parameter)
 S3method(as.character,Prior)
@@ -89,18 +90,25 @@ S3method(initialValues,StanModel)
 S3method(length,Link)
 S3method(length,QuantityCollapser)
 S3method(linkDSLD,LongitudinalGSF)
-S3method(linkDSLD,LongitudinalModel)
 S3method(linkDSLD,LongitudinalRandomSlope)
 S3method(linkDSLD,LongitudinalSteinFojo)
+S3method(linkDSLD,PromiseLongitudinalModel)
+S3method(linkDSLD,default)
 S3method(linkIdentity,LongitudinalGSF)
-S3method(linkIdentity,LongitudinalModel)
 S3method(linkIdentity,LongitudinalRandomSlope)
 S3method(linkIdentity,LongitudinalSteinFojo)
+S3method(linkIdentity,PromiseLongitudinalModel)
+S3method(linkIdentity,default)
 S3method(linkTTG,LongitudinalGSF)
-S3method(linkTTG,LongitudinalModel)
 S3method(linkTTG,LongitudinalSteinFojo)
+S3method(linkTTG,PromiseLongitudinalModel)
+S3method(linkTTG,default)
+S3method(names,LinkComponent)
 S3method(names,Parameter)
 S3method(names,ParameterList)
+S3method(resolvePromise,Link)
+S3method(resolvePromise,PromiseLinkComponent)
+S3method(resolvePromise,default)
 S3method(sampleObservations,SimLongitudinalGSF)
 S3method(sampleObservations,SimLongitudinalRandomSlope)
 S3method(sampleObservations,SimLongitudinalSteinFojo)
@@ -138,6 +146,8 @@ export(LongitudinalSteinFojo)
 export(Parameter)
 export(ParameterList)
 export(Prior)
+export(PromiseLinkComponent)
+export(PromiseLongitudinalModel)
 export(STAN_BLOCKS)
 export(SimGroup)
 export(SimJointData)
@@ -169,11 +179,8 @@ export(generateQuantities)
 export(initialValues)
 export(linkDSLD)
 export(linkIdentity)
+export(linkNone)
 export(linkTTG)
-export(link_dsld)
-export(link_identity)
-export(link_none)
-export(link_ttg)
 export(merge)
 export(prior_beta)
 export(prior_cauchy)
@@ -186,6 +193,7 @@ export(prior_normal)
 export(prior_std_normal)
 export(prior_student_t)
 export(prior_uniform)
+export(resolvePromise)
 export(sampleObservations)
 export(sampleStanModel)
 export(sampleSubjects)
@@ -205,6 +213,9 @@ exportClasses(LongitudinalSteinFojo)
 exportClasses(Parameter)
 exportClasses(ParameterList)
 exportClasses(Prior)
+exportClasses(Promise)
+exportClasses(PromiseLinkComponent)
+exportClasses(PromiseLongitudinalModel)
 exportClasses(SimGroup)
 exportClasses(SimJointData)
 exportClasses(SimLongitudinal)

R/JointModel.R

@@ -56,11 +56,10 @@ setClassUnion("SurvivalModel_OR_NULL", c("SurvivalModel", "NULL"))
 JointModel <- function(
     longitudinal = NULL,
     survival = NULL,
-    link = link_none()
+    link = Link()
 ) {
 
-    # Ensure that it is a link object (e.g. wrap link components in a Link object)
-    link <- Link(link)
+    link <- resolvePromise(Link(link), longitudinal)
 
     if (length(link) > 0) {
         longitudinal <- enableLink(longitudinal)
@@ -81,7 +80,7 @@ JointModel <- function(
         .x = base_model,
         longitudinal = add_missing_stan_blocks(as.list(longitudinal)),
         survival = add_missing_stan_blocks(as.list(survival)),
-        link = add_missing_stan_blocks(as.list(link, model = longitudinal)),
+        link = add_missing_stan_blocks(as.list(link)),
         priors = add_missing_stan_blocks(as.list(parameters))
     )
     # Unresolved Jinja code within the longitudinal / Survival / Link

R/Link.R

@@ -2,6 +2,7 @@
 #' @include LongitudinalModel.R
 #' @include ParameterList.R
 #' @include LinkComponent.R
+#' @include Prior.R
 NULL
 
 
@@ -19,21 +20,22 @@ NULL
 
 
 
-
 #' `Link`
 #'
-#' @slot components (`list`)\cr a list of [`LinkComponent`] objects.
+#' @slot components (`list`)\cr a list of [`LinkComponent`] or [`PromiseLinkComponent`] objects.
+#' @slot resolved (`logical`)\cr indicates if all the `components` have been resolved.
 #'
-#' @param ... ([`LinkComponent`])\cr an arbitrary number of link components.
+#' @param ... ([`LinkComponent`] or [`PromiseLinkComponent`])\cr
+#' an arbitrary number of link components.
 #'
 #' @description
 #' Simple container class to enable the use of multiple link components in a joint model.
 #' Note that the constructor of this object is idempotent e.g. `Link(Link(x)) == Link(x)`
 #'
 #' @examples
 #' Link(
-#'     link_dsld(),
-#'     link_ttg()
+#'     linkDSLD(),
+#'     linkTTG()
 #' )
 #'
 #' @family Link
@@ -42,7 +44,8 @@ NULL
 .Link <- setClass(
     Class = "Link",
     slots = list(
-        components = "list"
+        components = "list",
+        resolved = "logical"
     )
 )
 
@@ -51,26 +54,65 @@ NULL
 Link <- function(...) {
     components <- list(...)
 
-    # Enable copy constructor e.g. if passed a Link just return the Link
+    # If the input is already a Link object, return it (e.g. implement
+    # a constructor that is idempotent)
     if (length(components) == 1 && is(components[[1]], "Link")) {
         return(components[[1]])
     }
-    .Link(components = components)
+
+    .Link(
+        components = components,
+        resolved = !any(vapply(components, \(x) is(x, "PromiseLinkComponent"), logical(1)))
+    )
 }
 
 
+#' Resolve any promises
+#'
+#' Loops over all components and ensures that any [`PromiseLinkComponent`] objects
+#' are resolved to [`LinkComponent`] objects.
+#'
+#' @param object ([`Link`])\cr a link object.
+#' @param model ([`LongitudinalModel`])\cr the model object.
+#' @param ... Not Used.
+#'
+#' @export
+resolvePromise.Link <- function(object, model, ...) {
+    if (length(object) == 0) {
+        return(object)
+    }
+    assert_that(
+        is(model, "LongitudinalModel"),
+        msg = "model must be of class `LongitudinalModel`"
+    )
+    do.call(Link, lapply(object@components, resolvePromise, model = model))
+}
+
 
 setValidity(
     Class = "Link",
     method = function(object) {
-        if (length(object@components) == 0) {
-            return(TRUE)
-        }
-        for (component in object@components) {
-            if (!is(component, "LinkComponent")) {
-                return("Link components must be of class `LinkComponent`.")
+
+        for (i in object@components) {
+            if (!(is(i, "LinkComponent") || is(i, "PromiseLinkComponent"))) {
+                return("All components must be of class `LinkComponent` or `PromiseLinkComponent`")
             }
         }
+
+        contains_promise <- any(
+            vapply(
+                object@components,
+                \(x) is(x, "PromiseLinkComponent"),
+                logical(1)
+            )
+        )
+        if (contains_promise & object@resolved) {
+            return("Object cannot be resolved if it contains promises")
+        }
+
+        if (length(object@resolved) > 1) {
+            return("The `resolved` slot must be a logical scalar")
+        }
         return(TRUE)
     }
 )
@@ -108,8 +150,7 @@ as.StanModule.Link <- function(object, ...) {
 
     stan_list <- lapply(
         object@components,
-        as.StanModule,
-        ...
+        as.StanModule
     )
 
     stan <- Reduce(
@@ -182,13 +223,13 @@ as_print_string.Link <- function(object, ...) {
     if (length(object) == 0) {
         return("\nNo Link")
     }
+
+    strings <- vapply(object@components, as_print_string, character(1))
+
     paste(
         c(
             "\nLink with the following components/parameters:",
-            paste0(
-                "    ",
-                vapply(object@components, as_print_string, character(1))
-            )
+            paste0("    ", strings)
         ),
         collapse = "\n"
     )