From ab2b589d4ae933c6f13b408bb31ffefcdff8d690 Mon Sep 17 00:00:00 2001
From: gowerc <craig.gower-page@roche.com>
Date: Tue, 25 Jun 2024 16:23:29 +0100
Subject: [PATCH 1/8] Initital attempt

---
 NAMESPACE                                     |  1 +
 R/JointModel.R                                |  7 ++--
 R/JointModelSamples.R                         | 34 ++++++++++++++-----
 R/generics.R                                  |  5 +--
 R/utilities.R                                 |  5 +++
 inst/stan/lm-stein-fojo/quantities.stan       |  6 ++--
 man/as.StanModule.JointModelSamples.Rd        | 24 +++++++++++++
 man/write_stan.Rd                             |  8 +++--
 tests/testthat/test-LongitudinalGSF.R         | 23 +++++++++++++
 tests/testthat/test-LongitudinalRandomSlope.R | 23 +++++++++++++
 tests/testthat/test-LongitudinalSteinFojo.R   | 25 +++++++++++++-
 vignettes/model_fitting.Rmd                   |  3 +-
 12 files changed, 143 insertions(+), 21 deletions(-)
 create mode 100644 man/as.StanModule.JointModelSamples.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 0f2bebee..856533ea 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -18,6 +18,7 @@ S3method(as.QuantityGenerator,GridObserved)
 S3method(as.QuantityGenerator,GridPopulation)
 S3method(as.QuantityGenerator,GridPrediction)
 S3method(as.StanModule,JointModel)
+S3method(as.StanModule,JointModelSamples)
 S3method(as.StanModule,Link)
 S3method(as.StanModule,LinkComponent)
 S3method(as.StanModule,Parameter)
diff --git a/R/JointModel.R b/R/JointModel.R
index 183f130b..aa91d0ff 100755
--- a/R/JointModel.R
+++ b/R/JointModel.R
@@ -142,8 +142,11 @@ as.character.JointModel <- function(x, ...) {
 
 #' @rdname write_stan
 #' @export
-write_stan.JointModel <- function(object, file_path) {
-    fi <- file(file_path, open = "w")
+write_stan.JointModel <- function(object, destination) {
+    if (is_connection(destination)) {
+        return(writeLines(as.character(object), fi))
+    }
+    fi <- file(destination, open = "w")
     writeLines(as.character(object), fi)
     close(fi)
 }
diff --git a/R/JointModelSamples.R b/R/JointModelSamples.R
index 76a1f5b4..c0df8311 100644
--- a/R/JointModelSamples.R
+++ b/R/JointModelSamples.R
@@ -38,7 +38,30 @@ generateQuantities.JointModelSamples <- function(object, generator, type, ...) {
         append(as_stan_list(object@model@parameters)) |>
         append(as_stan_list(generator, data = object@data, model = object@model))
 
+    stanobj <- as.StanModule(object, generator = generator, type = type)
+    model <- compileStanModel(stanobj)
+
+    devnull <- utils::capture.output(
+        results <- model$generate_quantities(
+            data = data,
+            fitted_params = object@results
+        )
+    )
+    return(results)
+}
+
+
+#' `JointModelSamples` -> `StanModule`
+#'
+#' Converts a `JointModelSamples` object into a `StanModule` object ensuring
+#' that the resulting `StanModule` object is able to generate post sampling
+#' quantities.
+#'
+#' @inheritParams generateQuantities
+#' @export
+as.StanModule.JointModelSamples <- function(object, generator, type, ...) {
     assert_that(
+        is(generator, "QuantityGenerator"),
         length(type) == 1,
         type %in% c("survival", "longitudinal")
     )
@@ -60,17 +83,10 @@ generateQuantities.JointModelSamples <- function(object, generator, type, ...) {
             quant_stanobj
         )
     )
+    stanobj
+}
 
-    model <- compileStanModel(stanobj)
 
-    devnull <- utils::capture.output(
-        results <- model$generate_quantities(
-            data = data,
-            fitted_params = object@results
-        )
-    )
-    return(results)
-}
 
 #' `JointModelSamples` -> Printable `Character`
 #'
diff --git a/R/generics.R b/R/generics.R
index ec0e45ee..90d305ee 100755
--- a/R/generics.R
+++ b/R/generics.R
@@ -44,10 +44,11 @@ NULL
 #' Write the Stan code for a Stan module.
 #'
 #' @param object the module.
-#' @param file_path (`string`)\cr output file.
+#' @param destination (`character` or  `connection`)\cr Where to write stan code to.
+#' @param ... Additional arguements
 #'
 #' @export
-write_stan <- function(object, file_path) {
+write_stan <- function(object, destination, ...) {
     UseMethod("write_stan")
 }
 
diff --git a/R/utilities.R b/R/utilities.R
index 03958256..87b9de8a 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -329,3 +329,8 @@ decompose_subjects <- function(subjects, all_subjects) {
 is_cmdstanr_available <- function() {
     requireNamespace("cmdstanr", quietly = TRUE)
 }
+
+
+is_connection <- function(obj) {
+    inherits(obj, "connection")
+}
diff --git a/inst/stan/lm-stein-fojo/quantities.stan b/inst/stan/lm-stein-fojo/quantities.stan
index 92c07fdb..7352540c 100644
--- a/inst/stan/lm-stein-fojo/quantities.stan
+++ b/inst/stan/lm-stein-fojo/quantities.stan
@@ -15,9 +15,9 @@ generated quantities {
     // Source - lm-stein-fojo/quantities.stan
     //
     matrix[n_subjects, 3] long_gq_parameters;
-    long_gq_parameters[, 1] = lm_gsf_psi_bsld;
-    long_gq_parameters[, 2] = lm_gsf_psi_ks;
-    long_gq_parameters[, 3] = lm_gsf_psi_kg;
+    long_gq_parameters[, 1] = lm_sf_psi_bsld;
+    long_gq_parameters[, 2] = lm_sf_psi_ks;
+    long_gq_parameters[, 3] = lm_sf_psi_kg;
 
     matrix[gq_n_quant, 3] long_gq_pop_parameters;
     long_gq_pop_parameters[, 1] = exp(lm_sf_mu_bsld[gq_long_pop_study_index]);
diff --git a/man/as.StanModule.JointModelSamples.Rd b/man/as.StanModule.JointModelSamples.Rd
new file mode 100644
index 00000000..fe70d01b
--- /dev/null
+++ b/man/as.StanModule.JointModelSamples.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/JointModelSamples.R
+\name{as.StanModule.JointModelSamples}
+\alias{as.StanModule.JointModelSamples}
+\title{\code{JointModelSamples} -> \code{StanModule}}
+\usage{
+\method{as.StanModule}{JointModelSamples}(object, generator, type, ...)
+}
+\arguments{
+\item{object}{object to obtain generated quantities from}
+
+\item{generator}{(\code{QuantityGenerator})\cr object that specifies which subjects and time points
+to calculate the quantities at}
+
+\item{type}{(\code{character})\cr type of quantities to be generated, must be either "survival" or
+"longitudinal".}
+
+\item{...}{additional options.}
+}
+\description{
+Converts a \code{JointModelSamples} object into a \code{StanModule} object ensuring
+that the resulting \code{StanModule} object is able to generate post sampling
+quantities.
+}
diff --git a/man/write_stan.Rd b/man/write_stan.Rd
index 5b64623b..7cc055e8 100644
--- a/man/write_stan.Rd
+++ b/man/write_stan.Rd
@@ -5,14 +5,16 @@
 \alias{write_stan.JointModel}
 \title{\code{write_stan}}
 \usage{
-write_stan(object, file_path)
+write_stan(object, destination, ...)
 
-\method{write_stan}{JointModel}(object, file_path)
+\method{write_stan}{JointModel}(object, destination)
 }
 \arguments{
 \item{object}{the module.}
 
-\item{file_path}{(\code{string})\cr output file.}
+\item{destination}{(\code{character} or  \code{connection})\cr Where to write stan code to.}
+
+\item{...}{Additional arguements}
 }
 \description{
 Write the Stan code for a Stan module.
diff --git a/tests/testthat/test-LongitudinalGSF.R b/tests/testthat/test-LongitudinalGSF.R
index 571f8a48..fb6c56bf 100644
--- a/tests/testthat/test-LongitudinalGSF.R
+++ b/tests/testthat/test-LongitudinalGSF.R
@@ -197,3 +197,26 @@ test_that("Can recover known distributional parameters from a full GSF joint mod
     expect_true(all(dat$q99 >= true_values))
     expect_true(all(dat$ess_bulk > 100))
 })
+
+
+
+test_that("Quantity models pass the parser", {
+    mock_samples <- .JointModelSamples(
+        model = JointModel(longitudinal = LongitudinalGSF(centred = FALSE)),
+        data = structure(1, class = "DataJoint"),
+        results = structure(1, class = "CmdStanMCMC")
+    )
+    stanmod <- as.StanModule(
+        mock_samples,
+        generator = QuantityGeneratorPopulation(1, "A", "B"),
+        type = "longitudinal"
+    )
+    expect_stan_syntax(stanmod)
+
+    stanmod <- as.StanModule(
+        mock_samples,
+        generator = QuantityGeneratorSubject(1, "A"),
+        type = "longitudinal"
+    )
+    expect_stan_syntax(stanmod)
+})
diff --git a/tests/testthat/test-LongitudinalRandomSlope.R b/tests/testthat/test-LongitudinalRandomSlope.R
index ff60e437..ca151791 100644
--- a/tests/testthat/test-LongitudinalRandomSlope.R
+++ b/tests/testthat/test-LongitudinalRandomSlope.R
@@ -295,3 +295,26 @@ test_that("Random Slope Model left-censoring works as expected", {
     )
     expect_gt(lmer_cor, 0.99)
 })
+
+
+test_that("Quantity models pass the parser", {
+    mock_samples <- .JointModelSamples(
+        model = JointModel(longitudinal = LongitudinalRandomSlope()),
+        data = structure(1, class = "DataJoint"),
+        results = structure(1, class = "CmdStanMCMC")
+    )
+    stanmod <- as.StanModule(
+        mock_samples,
+        generator = QuantityGeneratorPopulation(1, "A", "B"),
+        type = "longitudinal"
+    )
+    expect_stan_syntax(stanmod)
+
+    stanmod <- as.StanModule(
+        mock_samples,
+        generator = QuantityGeneratorSubject(1, "A"),
+        type = "longitudinal"
+    )
+    expect_stan_syntax(stanmod)
+})
+
diff --git a/tests/testthat/test-LongitudinalSteinFojo.R b/tests/testthat/test-LongitudinalSteinFojo.R
index 9af17236..03d42b09 100644
--- a/tests/testthat/test-LongitudinalSteinFojo.R
+++ b/tests/testthat/test-LongitudinalSteinFojo.R
@@ -1,5 +1,4 @@
 
-
 test_that("LongitudinalSteinFojo works as expected with default arguments", {
     result <- expect_silent(LongitudinalSteinFojo())
     expect_s4_class(result, "LongitudinalSteinFojo")
@@ -90,6 +89,7 @@ test_that("Non-Centralised parameterisation compiles without issues", {
 
 
 
+
 test_that("Can recover known distributional parameters from a SF joint model", {
 
     skip_if_not(is_full_test())
@@ -388,3 +388,26 @@ test_that("Can recover known distributional parameters from a SF joint model wit
     expect_true(all(dat$q99 >= true_values))
     expect_true(all(dat$ess_bulk > 100))
 })
+
+
+
+test_that("Quantity models pass the parser", {
+    mock_samples <- .JointModelSamples(
+        model = JointModel(longitudinal = LongitudinalSteinFojo(centred = TRUE)),
+        data = structure(1, class = "DataJoint"),
+        results = structure(1, class = "CmdStanMCMC")
+    )
+    stanmod <- as.StanModule(
+        mock_samples,
+        generator = QuantityGeneratorPopulation(1, "A", "B"),
+        type = "longitudinal"
+    )
+    expect_stan_syntax(stanmod)
+
+    stanmod <- as.StanModule(
+        mock_samples,
+        generator = QuantityGeneratorSubject(1, "A"),
+        type = "longitudinal"
+    )
+    expect_stan_syntax(stanmod)
+})
diff --git a/vignettes/model_fitting.Rmd b/vignettes/model_fitting.Rmd
index 9c12088e..de50f7dd 100644
--- a/vignettes/model_fitting.Rmd
+++ b/vignettes/model_fitting.Rmd
@@ -237,9 +237,10 @@ It is always possible to read out the Stan code that is contained in the
 
 ```{r debug_stan}
 tmp <- tempfile()
-write_stan(simple_model, file_path = tmp)
+write_stan(simple_model, destination = tmp)
 first_part <- head(readLines(tmp), 10)
 cat(paste(first_part, collapse = "\n"))
+close(tmp)
 ```
 
 ## Sampling Parameters

From 0ca508eeb51f4476f151eec50727b9c8912e128b Mon Sep 17 00:00:00 2001
From: gowerc <craig.gower-page@roche.com>
Date: Tue, 25 Jun 2024 16:34:23 +0100
Subject: [PATCH 2/8] fix cicd failures

---
 R/generics.R      | 2 +-
 _pkgdown.yml      | 1 +
 man/write_stan.Rd | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/generics.R b/R/generics.R
index 90d305ee..cb5082ed 100755
--- a/R/generics.R
+++ b/R/generics.R
@@ -45,7 +45,7 @@ NULL
 #'
 #' @param object the module.
 #' @param destination (`character` or  `connection`)\cr Where to write stan code to.
-#' @param ... Additional arguements
+#' @param ... Additional arguments
 #'
 #' @export
 write_stan <- function(object, destination, ...) {
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 868e3a63..9af2868b 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -141,6 +141,7 @@ reference:
       - as.StanModule.JointModel
       - as.StanModule.Link
       - as.StanModule.LinkComponent
+      - as.StanModule.JointModelSamples
       - as.character.Parameter
       - as.character.Prior
       - show-object
diff --git a/man/write_stan.Rd b/man/write_stan.Rd
index 7cc055e8..4080f495 100644
--- a/man/write_stan.Rd
+++ b/man/write_stan.Rd
@@ -14,7 +14,7 @@ write_stan(object, destination, ...)
 
 \item{destination}{(\code{character} or  \code{connection})\cr Where to write stan code to.}
 
-\item{...}{Additional arguements}
+\item{...}{Additional arguments}
 }
 \description{
 Write the Stan code for a Stan module.

From d4509d7163c7cbe4978c48f7dbbeda3088de8841 Mon Sep 17 00:00:00 2001
From: gowerc <craig.gower-page@roche.com>
Date: Tue, 25 Jun 2024 16:35:06 +0100
Subject: [PATCH 3/8] pedantic lintr

---
 tests/testthat/test-LongitudinalRandomSlope.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-LongitudinalRandomSlope.R b/tests/testthat/test-LongitudinalRandomSlope.R
index ca151791..4afbb6ff 100644
--- a/tests/testthat/test-LongitudinalRandomSlope.R
+++ b/tests/testthat/test-LongitudinalRandomSlope.R
@@ -317,4 +317,3 @@ test_that("Quantity models pass the parser", {
     )
     expect_stan_syntax(stanmod)
 })
-

From 851987ad6728570ae2b2b97f760adfa9004f43d4 Mon Sep 17 00:00:00 2001
From: gowerc <craig.gower-page@roche.com>
Date: Wed, 26 Jun 2024 10:42:05 +0100
Subject: [PATCH 4/8] Fix broken close command

---
 vignettes/model_fitting.Rmd | 1 -
 1 file changed, 1 deletion(-)

diff --git a/vignettes/model_fitting.Rmd b/vignettes/model_fitting.Rmd
index de50f7dd..c1d8f5df 100644
--- a/vignettes/model_fitting.Rmd
+++ b/vignettes/model_fitting.Rmd
@@ -240,7 +240,6 @@ tmp <- tempfile()
 write_stan(simple_model, destination = tmp)
 first_part <- head(readLines(tmp), 10)
 cat(paste(first_part, collapse = "\n"))
-close(tmp)
 ```
 
 ## Sampling Parameters

From cc1d765d269df7285b1c88e6a820f1b25fffb51d Mon Sep 17 00:00:00 2001
From: Craig Gower-Page <craig.gower-page@roche.com>
Date: Wed, 26 Jun 2024 10:44:04 +0100
Subject: [PATCH 5/8] Update R/JointModel.R

Co-authored-by: Isaac Gravestock <83659704+gravesti@users.noreply.github.com>
---
 R/JointModel.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/JointModel.R b/R/JointModel.R
index aa91d0ff..3d2b5e01 100755
--- a/R/JointModel.R
+++ b/R/JointModel.R
@@ -144,7 +144,7 @@ as.character.JointModel <- function(x, ...) {
 #' @export
 write_stan.JointModel <- function(object, destination) {
     if (is_connection(destination)) {
-        return(writeLines(as.character(object), fi))
+        return(writeLines(as.character(object), con = destination))
     }
     fi <- file(destination, open = "w")
     writeLines(as.character(object), fi)

From 53c6dbae7cc2906f2cac3dd50c2f2d0d133fdad4 Mon Sep 17 00:00:00 2001
From: gowerc <craig.gower-page@roche.com>
Date: Wed, 26 Jun 2024 10:44:44 +0100
Subject: [PATCH 6/8] use explicit arguments

---
 R/JointModel.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/JointModel.R b/R/JointModel.R
index 3d2b5e01..c553b25c 100755
--- a/R/JointModel.R
+++ b/R/JointModel.R
@@ -147,7 +147,7 @@ write_stan.JointModel <- function(object, destination) {
         return(writeLines(as.character(object), con = destination))
     }
     fi <- file(destination, open = "w")
-    writeLines(as.character(object), fi)
+    writeLines(as.character(object), con = fi)
     close(fi)
 }
 

From e95396efd3c967c3dde6c1ea693ebda5fb849a94 Mon Sep 17 00:00:00 2001
From: gowerc <craig.gower-page@roche.com>
Date: Wed, 26 Jun 2024 10:46:33 +0100
Subject: [PATCH 7/8] add test for claretBruno

---
 tests/testthat/test-LongitudinalClaretBruno.R | 22 +++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/tests/testthat/test-LongitudinalClaretBruno.R b/tests/testthat/test-LongitudinalClaretBruno.R
index 4e059c8b..de2b35b8 100644
--- a/tests/testthat/test-LongitudinalClaretBruno.R
+++ b/tests/testthat/test-LongitudinalClaretBruno.R
@@ -273,3 +273,25 @@ test_that("Can recover known distributional parameters from a SF joint model", {
     expect_true(all(dat$q99 >= true_values))
     expect_true(all(dat$ess_bulk > 100))
 })
+
+
+test_that("Quantity models pass the parser", {
+    mock_samples <- .JointModelSamples(
+        model = JointModel(longitudinal = LongitudinalClaretBruno()),
+        data = structure(1, class = "DataJoint"),
+        results = structure(1, class = "CmdStanMCMC")
+    )
+    stanmod <- as.StanModule(
+        mock_samples,
+        generator = QuantityGeneratorPopulation(1, "A", "B"),
+        type = "longitudinal"
+    )
+    expect_stan_syntax(stanmod)
+
+    stanmod <- as.StanModule(
+        mock_samples,
+        generator = QuantityGeneratorSubject(1, "A"),
+        type = "longitudinal"
+    )
+    expect_stan_syntax(stanmod)
+})

From 627b514ec361f2a09bbc43009946ac8da7b0c1fb Mon Sep 17 00:00:00 2001
From: gowerc <craig.gower-page@roche.com>
Date: Wed, 26 Jun 2024 11:14:58 +0100
Subject: [PATCH 8/8] Fix R CMD check warnings

---
 R/JointModel.R                 | 2 +-
 R/SimLongitudinalClaretBruno.R | 2 +-
 man/clbr_sld.Rd                | 4 ++--
 man/write_stan.Rd              | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/JointModel.R b/R/JointModel.R
index c553b25c..19aa1115 100755
--- a/R/JointModel.R
+++ b/R/JointModel.R
@@ -142,7 +142,7 @@ as.character.JointModel <- function(x, ...) {
 
 #' @rdname write_stan
 #' @export
-write_stan.JointModel <- function(object, destination) {
+write_stan.JointModel <- function(object, destination, ...) {
     if (is_connection(destination)) {
         return(writeLines(as.character(object), con = destination))
     }
diff --git a/R/SimLongitudinalClaretBruno.R b/R/SimLongitudinalClaretBruno.R
index 5ca97a1d..7c949c34 100644
--- a/R/SimLongitudinalClaretBruno.R
+++ b/R/SimLongitudinalClaretBruno.R
@@ -175,7 +175,7 @@ sampleSubjects.SimLongitudinalClaretBruno <- function(object, subjects_df) {
 
 #' Claret-Bruno Functionals
 #'
-#' @param time (`numeric`)\cr time grid.
+#' @param t (`numeric`)\cr time grid.
 #' @param b (`number`)\cr baseline sld.
 #' @param g (`number`)\cr growth rate.
 #' @param c (`number`)\cr resistance rate.
diff --git a/man/clbr_sld.Rd b/man/clbr_sld.Rd
index e194cf30..fea332cd 100644
--- a/man/clbr_sld.Rd
+++ b/man/clbr_sld.Rd
@@ -13,6 +13,8 @@ clbr_ttg(t, b, g, c, p)
 clbr_dsld(t, b, g, c, p)
 }
 \arguments{
+\item{t}{(\code{numeric})\cr time grid.}
+
 \item{b}{(\code{number})\cr baseline sld.}
 
 \item{g}{(\code{number})\cr growth rate.}
@@ -20,8 +22,6 @@ clbr_dsld(t, b, g, c, p)
 \item{c}{(\code{number})\cr resistance rate.}
 
 \item{p}{(\code{number})\cr growth inhibition.}
-
-\item{time}{(\code{numeric})\cr time grid.}
 }
 \value{
 The function results.
diff --git a/man/write_stan.Rd b/man/write_stan.Rd
index 4080f495..86d2933d 100644
--- a/man/write_stan.Rd
+++ b/man/write_stan.Rd
@@ -7,7 +7,7 @@
 \usage{
 write_stan(object, destination, ...)
 
-\method{write_stan}{JointModel}(object, destination)
+\method{write_stan}{JointModel}(object, destination, ...)
 }
 \arguments{
 \item{object}{the module.}