Address review comments

Genentech · Mar 25, 2024 · a7e91f3 · a7e91f3
1 parent bfd86f2
commit a7e91f3
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Showing 8 changed files with 9 additions and 12 deletions.
diff --git a/R/JointModel.R b/R/JointModel.R
@@ -75,7 +75,7 @@ JointModel <- function(
         )
     )
 
-    base_model <- paste0(read_stan("base/base.stan"), collapse = "\n")
+    base_model <- read_stan("base/base.stan")
 
     stan_full <- decorated_render(
         .x = base_model,

diff --git a/R/Link.R b/R/Link.R
@@ -101,7 +101,7 @@ as.StanModule.Link <- function(object, ...) {
 
     base_stan <- StanModule(
         decorated_render(
-            .x = paste(read_stan("base/link.stan"), collapse = "\n"),
+            .x = read_stan("base/link.stan"),
             items = as.list(keys)
         )
     )

diff --git a/R/LongitudinalGSF.R b/R/LongitudinalGSF.R
@@ -58,7 +58,7 @@ LongitudinalGSF <- function(
 ) {
 
     gsf_model <- StanModule(decorated_render(
-        .x = paste0(read_stan("lm-gsf/model.stan"), collapse = "\n"),
+        .x = read_stan("lm-gsf/model.stan"),
         centred = centred
     ))
 

diff --git a/R/LongitudinalModel.R b/R/LongitudinalModel.R
@@ -28,10 +28,7 @@ LongitudinalModel <- function(
     ...
 ) {
 
-    base_stan <- paste0(
-        read_stan("base/longitudinal.stan"),
-        collapse = "\n"
-    )
+    base_stan <- read_stan("base/longitudinal.stan")
 
     stan_full <- decorated_render(
         .x = base_stan,

diff --git a/R/LongitudinalSteinFojo.R b/R/LongitudinalSteinFojo.R
@@ -50,7 +50,7 @@ LongitudinalSteinFojo <- function(
 ) {
 
     sf_model <- StanModule(decorated_render(
-        .x = paste0(read_stan("lm-stein-fojo/model.stan"), collapse = "\n"),
+        .x = read_stan("lm-stein-fojo/model.stan"),
         centred = centred
     ))
 

diff --git a/R/StanModule.R b/R/StanModule.R
@@ -237,8 +237,7 @@ as.list.StanModule <- function(x, stan_blocks = STAN_BLOCKS, ...) {
 #' @param filename (`string`)\cr file name.
 #'
 #' @keywords internal
-is_file <- function(filename = NULL) {
-    if (is.null(filename)) {
+is_file <- function(filename = NULL) { if (is.null(filename)) {
         return(FALSE)
     }
     assert_that(
@@ -262,6 +261,7 @@ is_file <- function(filename = NULL) {
 #' @param string Character, either the absolute path of a stan file, or the name of the stan
 #' file in the package directory or the stan code as a string.
 read_stan <- function(string) {
+    string <- paste0(string, collapse = "\n")
     local_inst_file <- file.path("inst", "stan", string)
     system_file <- system.file(file.path("stan", string), package = "jmpost")
     local_file <- string

diff --git a/R/SurvivalModel.R b/R/SurvivalModel.R
@@ -27,7 +27,7 @@ SurvivalModel <- function(
     name = "<Unnamed>",
     ...
 ) {
-    base_stan <- paste0(read_stan("base/survival.stan"), collapse = "\n")
+    base_stan <- read_stan("base/survival.stan")
     stan_full <- decorated_render(
         .x = base_stan,
         stan = add_missing_stan_blocks(as.list(stan))

diff --git a/tests/testthat/test-LongitudinalQuantiles.R b/tests/testthat/test-LongitudinalQuantiles.R
@@ -126,7 +126,7 @@ test_that("LongitudinalQuantities can recover known results", {
 })
 
 
-test_that("LongitudinalQuantities correctly subsets patients and rebuilds correct value for each smaple", {
+test_that("LongitudinalQuantities correctly subsets patients and rebuilds correct value for each sample", {
     set.seed(101)
     ensure_test_data_1()
     times <- c(-100, 0, 1, 100, 200)