Implement growth link function (#330)

NAMESPACE

@@ -110,6 +110,11 @@ S3method(linkDSLD,LongitudinalRandomSlope)
 S3method(linkDSLD,LongitudinalSteinFojo)
 S3method(linkDSLD,PromiseLongitudinalModel)
 S3method(linkDSLD,default)
+S3method(linkGrowth,LongitudinalGSF)
+S3method(linkGrowth,LongitudinalRandomSlope)
+S3method(linkGrowth,LongitudinalSteinFojo)
+S3method(linkGrowth,PromiseLongitudinalModel)
+S3method(linkGrowth,default)
 S3method(linkIdentity,LongitudinalGSF)
 S3method(linkIdentity,LongitudinalRandomSlope)
 S3method(linkIdentity,LongitudinalSteinFojo)
@@ -198,6 +203,7 @@ export(generateQuantities)
 export(getPredictionNames)
 export(initialValues)
 export(linkDSLD)
+export(linkGrowth)
 export(linkIdentity)
 export(linkNone)
 export(linkTTG)

R/LongitudinalGSF.R

@@ -162,6 +162,15 @@ linkIdentity.LongitudinalGSF <- function(prior = prior_normal(0, 2), model, ...)
     )
 }
 
+#' @export
+linkGrowth.LongitudinalGSF <- function(prior = prior_normal(0, 2), model, ...) {
+    LinkComponent(
+        key = "link_growth",
+        stan = StanModule("lm-gsf/link_growth.stan"),
+        prior = prior
+    )
+}
+
 
 #' @rdname getPredictionNames
 #' @export

R/LongitudinalRandomSlope.R

@@ -88,6 +88,14 @@ linkIdentity.LongitudinalRandomSlope <- function(prior = prior_normal(0, 2), mod
     )
 }
 
+#' @export
+linkGrowth.LongitudinalRandomSlope <- function(prior = prior_normal(0, 2), model, ...) {
+    LinkComponent(
+        key = "link_growth",
+        stan = StanModule("lm-random-slope/link_growth.stan"),
+        prior = prior
+    )
+}
 
 #' @rdname getPredictionNames
 #' @export

R/LongitudinalSteinFojo.R

@@ -147,6 +147,15 @@ linkIdentity.LongitudinalSteinFojo <- function(prior = prior_normal(0, 2), model
     )
 }
 
+#' @export
+linkGrowth.LongitudinalSteinFojo <- function(prior = prior_normal(0, 2), model, ...) {
+    LinkComponent(
+        key = "link_growth",
+        stan = StanModule("lm-stein-fojo/link_growth.stan"),
+        prior = prior
+    )
+}
+
 #' @rdname getPredictionNames
 #' @export
 getPredictionNames.LongitudinalSteinFojo <- function(object, ...) {

R/SimLongitudinalGSF.R

@@ -19,6 +19,7 @@ NULL
 #' @param link_dsld (`number`)\cr the link coefficient for the derivative contribution.
 #' @param link_ttg (`number`)\cr the link coefficient for the time-to-growth contribution.
 #' @param link_identity (`number`)\cr the link coefficient for the SLD Identity contribution.
+#' @param link_growth (`number`)\cr the link coefficient for the growth parameter contribution.
 #'
 #' @slot sigma (`numeric`)\cr See arguments.
 #' @slot mu_s (`numeric`)\cr See arguments.
@@ -32,6 +33,7 @@ NULL
 #' @slot link_dsld (`numeric`)\cr See arguments.
 #' @slot link_ttg (`numeric`)\cr See arguments.
 #' @slot link_identity (`numeric`)\cr See arguments.
+#' @slot link_growth (`numeric`)\cr See arguments.
 #' @family SimLongitudinal
 #' @name SimLongitudinalGSF-class
 #' @exportClass SimLongitudinalGSF
@@ -50,7 +52,8 @@ NULL
         omega_g = "numeric",
         link_dsld = "numeric",
         link_ttg = "numeric",
-        link_identity = "numeric"
+        link_identity = "numeric",
+        link_growth = "numeric"
     )
 )
 
@@ -69,7 +72,8 @@ SimLongitudinalGSF <- function(
     omega_g = 0.2,
     link_dsld = 0,
     link_ttg = 0,
-    link_identity = 0
+    link_identity = 0,
+    link_growth = 0
 ) {
     .SimLongitudinalGSF(
         times = times,
@@ -84,7 +88,8 @@ SimLongitudinalGSF <- function(
         omega_g = omega_g,
         link_dsld = link_dsld,
         link_ttg = link_ttg,
-        link_identity = link_identity
+        link_identity = link_identity,
+        link_growth = link_growth
     )
 }
 
@@ -102,7 +107,12 @@ setValidity(
             return("The parameters `mu_s`, `mu_g`, `a_phi`, and `b_phi` must have the same length.")
         }
 
-        for (par in c("sigma", "omega_b", "omega_s", "omega_g", "link_dsld", "link_ttg", "link_identity")) {
+        len_1_pars <- c(
+            "sigma", "omega_b", "omega_s", "omega_g",
+            "link_dsld", "link_ttg", "link_identity",
+            "link_growth"
+        )
+        for (par in len_1_pars) {
             if (length(slot(object, par)) != 1) {
                 return(sprintf("The `%s` parameter must be a length 1 numeric.", par))
             }
@@ -129,7 +139,8 @@ sampleObservations.SimLongitudinalGSF <- function(object, times_df) {
             log_haz_link =
                 (object@link_dsld * .data$dsld) +
                 (object@link_ttg * .data$ttg) +
-                (object@link_identity * .data$mu_sld)
+                (object@link_identity * .data$mu_sld) +
+                (object@link_growth * .data$psi_g)
         )
 }
 

R/SimLongitudinalSteinFojo.R

@@ -16,6 +16,7 @@ NULL
 #' @param link_dsld (`number`)\cr the link coefficient for the derivative contribution.
 #' @param link_ttg (`number`)\cr the link coefficient for the time-to-growth contribution.
 #' @param link_identity (`number`)\cr the link coefficient for the SLD Identity contribution.
+#' @param link_growth (`number`)\cr the link coefficient for the growth parameter contribution.
 #'
 #' @slot sigma (`numeric`)\cr See arguments.
 #' @slot mu_s (`numeric`)\cr See arguments.
@@ -27,6 +28,7 @@ NULL
 #' @slot link_dsld (`numeric`)\cr See arguments.
 #' @slot link_ttg (`numeric`)\cr See arguments.
 #' @slot link_identity (`numeric`)\cr See arguments.
+#' @slot link_growth (`numeric`)\cr See arguments.
 #'
 #' @family SimLongitudinal
 #' @name SimLongitudinalSteinFojo-class
@@ -44,7 +46,8 @@ NULL
         omega_g = "numeric",
         link_dsld = "numeric",
         link_ttg = "numeric",
-        link_identity = "numeric"
+        link_identity = "numeric",
+        link_growth = "numeric"
     )
 )
 
@@ -61,7 +64,8 @@ SimLongitudinalSteinFojo <- function(
     omega_g = 0.2,
     link_dsld = 0,
     link_ttg = 0,
-    link_identity = 0
+    link_identity = 0,
+    link_growth = 0
 ) {
     .SimLongitudinalSteinFojo(
         times = times,
@@ -74,7 +78,8 @@ SimLongitudinalSteinFojo <- function(
         omega_g = omega_g,
         link_dsld = link_dsld,
         link_ttg = link_ttg,
-        link_identity = link_identity
+        link_identity = link_identity,
+        link_growth = link_growth
     )
 }
 
@@ -89,14 +94,15 @@ setValidity(
         if (length(unique(par_lengths)) != 1) {
             return("The parameters `mu_s` and `mu_g` must have the same length.")
         }
-        if (length(object@sigma) != 1) {
-            return("The parameter `sigma` must have length 1.")
-        }
-        if (length(c(object@omega_b, object@omega_s, object@omega_g)) != 3) {
-            return("The parameters `omega_b`, `omega_s`, and `omega_g` must be length 1.")
-        }
-        if (length(c(object@link_dsld, object@link_ttg, object@link_identity)) != 3) {
-            return("The parameters `link_dsld`, `link_ttg`, and `link_identity` must be length 1.")
+        len_1_pars <- c(
+            "sigma", "omega_b", "omega_s", "omega_g",
+            "link_dsld", "link_ttg", "link_identity",
+            "link_growth"
+        )
+        for (par in len_1_pars) {
+            if (length(slot(object, par)) != 1) {
+                return(sprintf("The `%s` parameter must be a length 1 numeric.", par))
+            }
         }
         return(TRUE)
     }
@@ -119,7 +125,8 @@ sampleObservations.SimLongitudinalSteinFojo <- function(object, times_df) {
             log_haz_link =
                 (object@link_dsld * .data$dsld) +
                 (object@link_ttg * .data$ttg) +
-                (object@link_identity * .data$mu_sld)
+                (object@link_identity * .data$mu_sld) +
+                (object@link_growth * .data$psi_g)
         )
 }
 

R/link_generics.R

@@ -75,3 +75,18 @@ linkIdentity.PromiseLongitudinalModel <- function(prior = prior_normal(0, 2), mo
 linkIdentity.default <- function(prior, model, ...) {
     stop(sprintf("Method `linkIdentity` is not available for `%s`", class(model)[[1]]))
 }
+
+
+#' @describeIn standard-link-user Growth Parameter link
+#' @export
+linkGrowth <- function(prior, model = PromiseLongitudinalModel(), ...) {
+    UseMethod("linkGrowth", model)
+}
+#' @export
+linkGrowth.PromiseLongitudinalModel <- function(prior = prior_normal(0, 2), model, ...) {
+    PromiseLinkComponent(fun = linkGrowth, prior = prior, key = "link_growth")
+}
+#' @export
+linkGrowth.default <- function(prior, model, ...) {
+    stop(sprintf("Method `linkGrowth` is not available for `%s`", class(model)[[1]]))
+}

inst/stan/lm-gsf/link_growth.stan

@@ -0,0 +1,15 @@
+
+
+functions {
+    //
+    // Source - lm-gsf/link_growth.stan
+    //
+    matrix link_growth_contrib(
+        matrix time,
+        matrix link_function_inputs
+    ) {
+        int nrows = rows(link_function_inputs);
+        int ncols = cols(time);
+        return rep_matrix(link_function_inputs[,3], ncols);
+    }
+}

inst/stan/lm-random-slope/link_growth.stan

@@ -0,0 +1,18 @@
+
+functions {
+    //
+    // Source - lm-random-slope/link_dsld.stan
+    //
+    matrix link_growth_contrib(
+        matrix time,
+        matrix link_function_inputs
+    ) {
+        int nrows = rows(time);
+        int ncols = cols(time);
+        vector[nrows] lm_rs_ind_rnd_slope = link_function_inputs[,2];
+        matrix[nrows, ncols] rnd_slope_mat = rep_matrix(lm_rs_ind_rnd_slope, ncols);
+        return rnd_slope_mat;
+    }
+}
+
+

inst/stan/lm-stein-fojo/link_growth.stan

@@ -0,0 +1,15 @@
+
+
+functions {
+    //
+    // Source - lm-stein/link_growth.stan
+    //
+    matrix link_growth_contrib(
+        matrix time,
+        matrix link_function_inputs
+    ) {
+        int nrows = rows(link_function_inputs);
+        int ncols = cols(time);
+        return rep_matrix(link_function_inputs[,3], ncols);
+    }
+}

tests/testthat/test-LongitudinalGSF.R

@@ -28,7 +28,7 @@ test_that("Centralised parameterisation compiles without issues", {
     jm <- JointModel(
         longitudinal = LongitudinalGSF(centred = TRUE),
         survival = SurvivalWeibullPH(),
-        link = Link(linkTTG(), linkDSLD())
+        link = Link(linkTTG(), linkDSLD(), linkGrowth())
     )
     expect_false(any(
         c("lm_gsf_eta_tilde_kg", "lm_gsf_eta_tilde_bsld") %in% names(jm@parameters)