Added 'internal.opt' to options

In this way, the default value for 'internal.opt' is set in options
hrue · Nov 27, 2023 · ea95f97 · ea95f97
1 parent 29e4524
commit ea95f97
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Showing 7 changed files with 18 additions and 7 deletions.
diff --git a/r-inla.org/doc/hyper/likelihood/ggaussian.tex b/r-inla.org/doc/hyper/likelihood/ggaussian.tex
@@ -14,7 +14,7 @@
 	 	 	\item[initial] \verb!4!
 	 	 	\item[fixed] \verb!FALSE!
 	 	 	\item[prior] \verb!normal!
-	 	 	\item[param] \verb!0 10!
+	 	 	\item[param] \verb!9.33 0.61!
 	 	 	\item[to.theta] \verb!function(x) x!
 	 	 	\item[from.theta] \verb!function(x) x!
 	 	 \end{description}

diff --git a/r-inla.org/doc/likelihood/ggaussian.pdf b/r-inla.org/doc/likelihood/ggaussian.pdf
diff --git a/rinla/R/options.R b/rinla/R/options.R
@@ -36,6 +36,8 @@
 #' 
 #' \item{save.memory}{Save memory at the cost of (minor) accuracy and computing time?}
 #' 
+#' \item{internal.opt}{Do internal online optimisations or not}
+#' 
 #' \item{working.directory}{The name of the working directory.}
 #' 
 #' \item{silent}{Run the inla-program in a silent mode?}
@@ -121,6 +123,7 @@ NULL
             keep = FALSE,
             verbose = FALSE,
             save.memory = FALSE,
+            internal.opt = TRUE,
             working.directory = NULL,
             silent = TRUE,
             debug = FALSE,
@@ -152,6 +155,7 @@ NULL
                                  "keep",
                                  "verbose",
                                  "save.memory",
+                                 "internal.opt",
                                  "working.directory",
                                  "silent",
                                  "debug",
@@ -244,6 +248,7 @@ NULL
                                           "keep",
                                           "verbose",
                                           "save.memory",
+                                          "internal.opt",
                                           "working.directory",
                                           "silent",
                                           "debug",

diff --git a/rinla/R/sections.R b/rinla/R/sections.R
@@ -1265,10 +1265,14 @@
     inla.write.boolean.field("mlik", mlik, file)
     inla.write.boolean.field("q", q, file)
     inla.write.boolean.field("graph", graph, file)
+
+    if (is.null(internal.opt)) {
+        internal.opt <- inla.getOption("internal.opt")
+    }
     inla.write.boolean.field("internal.opt", internal.opt, file)
 
     if (is.null(save.memory))
-        save.memory <- inla.getOption('save.memory')
+        save.memory <- inla.getOption("save.memory")
     inla.write.boolean.field("save.memory", save.memory, file)
 
     config.lite <- FALSE

diff --git a/rinla/R/set.default.arguments.R b/rinla/R/set.default.arguments.R
@@ -376,8 +376,8 @@ control.gcpo <-
             graph = FALSE,
 
             #' @param internal.opt A boolean variable, if to do internal online
-            #' optimisations or not. (Default TRUE.)
-            internal.opt = TRUE,
+            #' optimisations or not. (Default `inla.getOption("internal.opt")`)
+            internal.opt = NULL, 
 
             #' @param save.memory A boolean variable, make choices which
             #' saves memory over accuracy. (Default 'inla.getOption("save.memory")')

diff --git a/rinla/man/control.compute.Rd b/rinla/man/control.compute.Rd
diff --git a/rinla/man/options.Rd b/rinla/man/options.Rd