From f3557d004d5f031f38c3067bed273f613ac48717 Mon Sep 17 00:00:00 2001
From: gowerc <craig.gower-page@roche.com>
Date: Thu, 29 Feb 2024 14:18:33 +0000
Subject: [PATCH] Fix cicd; fix review comments

---
 R/settings.R                  | 20 +++++++-------------
 man/jmpost-settings.Rd        | 18 ++++++------------
 tests/testthat/test-options.R | 14 ++++----------
 3 files changed, 17 insertions(+), 35 deletions(-)

diff --git a/R/settings.R b/R/settings.R
index d801625d..3e1662ff 100644
--- a/R/settings.R
+++ b/R/settings.R
@@ -37,18 +37,13 @@
 #' Default = 15
 #'
 #' In most cases the survival function of the joint model does not have a closed form
-#' and as such is calculated by integrating the hazard function. `jmpost` estimates this
-#' via Gaussian Quadrature, in particular it uses [`statmod::gauss.quad`] to create the
-#' nodes and weights.
+#' and as such it is calculated by integrating the hazard function. `jmpost` estimates this
+#' via Gaussian Quadrature, in particular it uses [`statmod::gauss.quad`] with
+#' `kind = "legendre"` to create the nodes and weights.
 #'
-#' This option specifies the `n` arguement in the call to [`statmod::gauss.quad`].
-#'
-#' ## `jmpost.gauss_quad_kind`
-#'
-#' Default = `"legendre"`
-#'
-#' This option specifies the `kind` arguement in the call to [`statmod::gauss.quad`].
-#' See the `jmpost.gauss_quad_n` option description for more details.
+#' This option specifies the `n` arguement in the call to [`statmod::gauss.quad`]. In general
+#' higher values of `n` lead to better accuracy of the approximation but at the cost of
+#' increased computational time.
 #'
 #' @examples
 #' \dontrun{
@@ -67,8 +62,7 @@ set_options <- function() {
     jmpost_opts <- list(
         jmpost.cache_dir = cache_dir,
         jmpost.prior_shrinkage = 0.5,
-        jmpost.gauss_quad_n = 15,
-        jmpost.gauss_quad_kind = "legendre"
+        jmpost.gauss_quad_n = 15
     )
     for (opt in names(jmpost_opts)) {
         if (!opt %in% current_opts) {
diff --git a/man/jmpost-settings.Rd b/man/jmpost-settings.Rd
index 88457758..f3eeb610 100644
--- a/man/jmpost-settings.Rd
+++ b/man/jmpost-settings.Rd
@@ -41,19 +41,13 @@ the given R session. Can also be set via the environment variable \code{JMPOST_C
 Default = 15
 
 In most cases the survival function of the joint model does not have a closed form
-and as such is calculated by integrating the hazard function. \code{jmpost} estimates this
-via Gaussian Quadrature, in particular it uses \code{\link[statmod:gauss.quad]{statmod::gauss.quad}} to create the
-nodes and weights.
+and as such it is calculated by integrating the hazard function. \code{jmpost} estimates this
+via Gaussian Quadrature, in particular it uses \code{\link[statmod:gauss.quad]{statmod::gauss.quad}} with
+\code{kind = "legendre"} to create the nodes and weights.
 
-This option specifies the \code{n} arguement in the call to \code{\link[statmod:gauss.quad]{statmod::gauss.quad}}.
-}
-
-\subsection{\code{jmpost.gauss_quad_kind}}{
-
-Default = \code{"legendre"}
-
-This option specifies the \code{kind} arguement in the call to \code{\link[statmod:gauss.quad]{statmod::gauss.quad}}.
-See the \code{jmpost.gauss_quad_n} option description for more details.
+This option specifies the \code{n} arguement in the call to \code{\link[statmod:gauss.quad]{statmod::gauss.quad}}. In general
+higher values of \code{n} lead to better accuracy of the approximation but at the cost of
+increased computational time.
 }
 }
 \examples{
diff --git a/tests/testthat/test-options.R b/tests/testthat/test-options.R
index ccb14720..0e8d2540 100644
--- a/tests/testthat/test-options.R
+++ b/tests/testthat/test-options.R
@@ -2,7 +2,7 @@
 
 
 
-test_that("Can alter Gaussian Quadrature arguements", {
+test_that("Can alter Gaussian Quadrature arguments", {
     x <- data.frame(
         vpt = c("b", "a", "c", "d", "e"),
         vtime = c(10, 20, 30, 25, 15),
@@ -25,10 +25,7 @@ test_that("Can alter Gaussian Quadrature arguements", {
 
 
     ## Test modified values
-    options(
-        "jmpost.gauss_quad_n" = 20,
-        "jmpost.gauss_quad_kind" = "chebyshev2"
-    )
+    options( "jmpost.gauss_quad_n" = 20)
     df <- DataSurvival(
         data = x,
         formula = Surv(vtime, vevent) ~ vcov1 * vcov2
@@ -37,13 +34,10 @@ test_that("Can alter Gaussian Quadrature arguements", {
     expect_equal(li$n_nodes, 20)
     expect_equal(
         li[c("nodes", "weights")],
-        statmod::gauss.quad(20, "chebyshev2")
+        statmod::gauss.quad(20, "legendre")
     )
 
 
     ## Reset back to default to not impact additional tests
-    options(
-        "jmpost.gauss_quad_n" = 15,
-        "jmpost.gauss_quad_kind" = "legendre"
-    )
+    options( "jmpost.gauss_quad_n" = 15)
 })