Implemented prior_init_only

NAMESPACE

@@ -115,7 +115,6 @@ export(prior_invgamma)
 export(prior_logistic)
 export(prior_loglogistic)
 export(prior_lognormal)
-export(prior_none)
 export(prior_normal)
 export(prior_std_normal)
 export(prior_student_t)

R/LongitudinalGSF.R

@@ -73,17 +73,33 @@ LongitudinalGSF <- function(
 
         Parameter(name = "lm_gsf_a_phi", prior = a_phi, size = "n_arms"),
         Parameter(name = "lm_gsf_b_phi", prior = b_phi, size = "n_arms"),
-        Parameter(name = "lm_gsf_psi_phi", prior = prior_none(), size = "Nind"),
+        Parameter(
+            name = "lm_gsf_psi_phi",
+            prior = prior_init_only(prior_beta(a_phi@init, b_phi@init)),
+            size = "Nind"
+        ),
 
         Parameter(name = "lm_gsf_sigma", prior = sigma, size = 1)
     )
 
     assert_flag(centered)
     parameters_extra <- if (centered) {
         list(
-            Parameter(name = "lm_gsf_psi_bsld", prior = prior_none(), size = "Nind"),
-            Parameter(name = "lm_gsf_psi_ks", prior = prior_none(), size = "Nind"),
-            Parameter(name = "lm_gsf_psi_kg", prior = prior_none(), size = "Nind")
+            Parameter(
+                name = "lm_gsf_psi_bsld",
+                prior = prior_init_only(prior_lognormal(mu_bsld@init, omega_bsld@init)),
+                size = "Nind"
+            ),
+            Parameter(
+                name = "lm_gsf_psi_ks",
+                prior = prior_init_only(prior_lognormal(mu_ks@init, omega_ks@init)),
+                size = "Nind"
+            ),
+            Parameter(
+                name = "lm_gsf_psi_kg",
+                prior = prior_init_only(prior_lognormal(mu_kg@init, omega_kg@init)),
+                size = "Nind"
+            )
         )
     } else {
         list(

R/LongitudinalRandomSlope.R

@@ -46,7 +46,11 @@ LongitudinalRandomSlope <- function(
                 Parameter(name = "lm_rs_slope_mu", prior = slope_mu, size = "n_arms"),
                 Parameter(name = "lm_rs_slope_sigma", prior = slope_sigma, size = 1),
                 Parameter(name = "lm_rs_sigma", prior = sigma, size = 1),
-                Parameter(name = "lm_rs_ind_rnd_slope", prior = prior_none(), size = "Nind")
+                Parameter(
+                    name = "lm_rs_ind_rnd_slope",
+                    prior = prior_init_only(prior_normal(slope_mu@init, slope_sigma@init)),
+                    size = "Nind"
+                )
             )
         )
     )

R/Prior.R

@@ -339,17 +339,23 @@ prior_beta <- function(a, b) {
 
 #' Only Initial Values Specification
 #'
+#' @param dist (`Prior`)\cr a prior Distribution
 #' @family Prior
+#' @description
+#' This function is used to specify only the initial values for a parameter.
+#' This is primarily used for heiracrhical parameters whose distributions
+#' are fixed within the model and cannot be altered by the user.
 #'
-#' @export
-prior_none <- function() {
+prior_init_only <- function(dist) {
     Prior(
         parameters = list(),
         display = "<None>",
         repr_model = "",
         repr_data = "",
-        sample = \(n) local_runif(n, -4, 4),
-        init = 0,
+        sample = \(n) {
+            dist@sample(n)
+        },
+        init = dist@init,
         validation = list()
     )
 }

_pkgdown.yml

@@ -55,11 +55,11 @@ reference:
       - prior_logistic
       - prior_loglogistic
       - prior_lognormal
-      - prior_none
       - prior_normal
       - prior_uniform
       - prior_std_normal
       - prior_student_t
+      - prior_init_only
 
   - title: Longitudinal Model Specification
     contents:

tests/testthat/_snaps/Prior.md

@@ -51,7 +51,7 @@
 ---
 
     Code
-      print(prior_none())
+      print(prior_init_only(prior_normal(1, 4)))
     Output
       
       Prior Object:

tests/testthat/test-Parameter.R

@@ -19,6 +19,6 @@ test_that("show() works for Paramneter objects", {
     x <- Parameter(prior_beta(0.5, 0.2), "var1", "size1")
     expect_snapshot(print(x))
 
-    x <- Parameter(prior_none(), "x", "size1")
+    x <- Parameter(prior_init_only(prior_normal(0, 1)), "x", "size1")
     expect_snapshot(print(x))
 })

tests/testthat/test-ParameterList.R

@@ -47,7 +47,7 @@ test_that("show() works for ParameterList objects", {
         Parameter(name = "bob", prior = prior_normal(1, 4)),
         Parameter(name = "sam", prior = prior_beta(3, 1)),
         Parameter(name = "dave", prior = prior_lognormal(3, 2), size = 4),
-        Parameter(name = "steve", prior = prior_none())
+        Parameter(name = "steve", prior = prior_init_only(prior_normal(4, 2)))
     )
 
     expect_snapshot(print(x))

tests/testthat/test-Prior.R

@@ -137,7 +137,7 @@ test_that("Invalid prior parameters are rejected", {
 
 
     # Ensure that validation doesn't wrongly reject priors with no user specified parameters
-    expect_s4_class(prior_none(), "Prior")
+    expect_s4_class(prior_init_only(prior_normal(3, 1)), "Prior")
     expect_s4_class(prior_std_normal(), "Prior")
 })
 
@@ -149,7 +149,7 @@ test_that("show() works for Prior objects", {
     expect_snapshot(print(prior_std_normal()))
     expect_snapshot(print(prior_beta(5, 1)))
     expect_snapshot(print(prior_gamma(2.56, 12)))
-    expect_snapshot(print(prior_none()))
+    expect_snapshot(print(prior_init_only(prior_normal(1, 4))))
     expect_snapshot(print(prior_uniform(8, 10)))
     expect_snapshot(print(prior_student_t(3, 10, 4)))
     expect_snapshot(print(prior_logistic(sigma = 2, 10)))

tests/testthat/test-initialValues.R

@@ -81,3 +81,18 @@ test_that("ensure_initial_values() works as expected", {
     expect_equal(res[[1]]$p2, array(c(2, 3), dim = c(2)))
     expect_equal(res[[1]]$p3, array(c(4, 5, 6), dim = c(3)))
 })
+
+
+test_that("intial values for fixed distributions gives valid values", {
+
+    set.seed(3150)
+    gsfmodel <- LongitudinalGSF(centered = TRUE)
+    ivs <- initialValues(gsfmodel, n_chains = 100)
+
+    for (values in ivs) {
+        expect_true(values$lm_gsf_psi_phi > 0 & values$lm_gsf_psi_phi < 1)
+        expect_true(values$lm_gsf_psi_bsld > 0)
+        expect_true(values$lm_gsf_psi_ks > 0)
+        expect_true(values$lm_gsf_psi_kg > 0)
+    }
+})