From 28daf1f7c21db3a333d9752661e1771ca4d259bb Mon Sep 17 00:00:00 2001
From: Paul Regular <Paul.Regular@dfo-mpo.gc.ca>
Date: Mon, 18 Sep 2023 11:00:38 -0230
Subject: [PATCH] Add conditional use of INLA to examples

---
 CRAN-SUBMISSION           |  4 ++--
 R/sim_dist_spde.R         | 41 +++++++++++++++++++++++++--------------
 man/make_mesh.Rd          |  6 ++++--
 man/sim_ays_covar_spde.Rd | 33 +++++++++++++++++--------------
 4 files changed, 50 insertions(+), 34 deletions(-)

diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
index 1ca92b5..1aa32a0 100644
--- a/CRAN-SUBMISSION
+++ b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
 Version: 0.1.6
-Date: 2023-09-15 16:02:07 UTC
-SHA: 8a489a48ddcde0fd7b4554e983c3c3b9ffd77acf
+Date: 2023-09-15 18:15:02 UTC
+SHA: 03782485a4ec155145da49da0476c498a1b019e2
diff --git a/R/sim_dist_spde.R b/R/sim_dist_spde.R
index e561534..5efdae8 100644
--- a/R/sim_dist_spde.R
+++ b/R/sim_dist_spde.R
@@ -73,22 +73,25 @@
 #'
 #' \donttest{
 #'
-#' ## Make a grid
-#' my_grid <- make_grid(res = c(10,10))
+#' if (requireNamespace("INLA")) {
 #'
-#' ## Make a mesh based off it
+#'   ## Make a grid
+#'   my_grid <- make_grid(res = c(10,10))
 #'
-#' my_mesh <- make_mesh(my_grid)
-#' sim <- sim_abundance(ages = 1:10, years = 1:10) %>%
-#'          sim_distribution(grid = my_grid,
-#'                           ays_covar = sim_ays_covar_spde(phi_age = 0.8,
-#'                                                          phi_year = 0.1,
-#'                                                          model = "spde",
-#'                                                          mesh = my_mesh),
-#'                           depth_par = sim_parabola(mu = 200,
-#'                                                    sigma = 50))
-#' plot_distribution(sim, ages = 1:5, years = 1:5, type = "heatmap")
+#'   ## Make a mesh based off it
 #'
+#'   my_mesh <- make_mesh(my_grid)
+#'   sim <- sim_abundance(ages = 1:10, years = 1:10) %>%
+#'           sim_distribution(grid = my_grid,
+#'                            ays_covar = sim_ays_covar_spde(phi_age = 0.8,
+#'                                                           phi_year = 0.1,
+#'                                                           model = "spde",
+#'                                                           mesh = my_mesh),
+#'                            depth_par = sim_parabola(mu = 200,
+#'                                                     sigma = 50))
+#'   plot_distribution(sim, ages = 1:5, years = 1:5, type = "heatmap")
+#'
+#' }
 #'
 #' }
 #'
@@ -107,6 +110,12 @@ sim_ays_covar_spde <- function(sd = 2.8,
 
   function(x = NULL, ages = NULL, years = NULL, cells = NULL){
 
+    for (pkg in c("INLA")) {
+      if (!requireNamespace(pkg, quietly = TRUE)) {
+        stop(paste(pkg, "is needed for make_mesh to work. Please install it."), call. = FALSE)
+      }
+    }
+
     na <- length(ages)
     ny <- length(years)
     nc <- length(cells)
@@ -222,8 +231,10 @@ sim_ays_covar_spde <- function(sd = 2.8,
 #'
 #' \donttest{
 #'
-#' basic_mesh <- make_mesh()
-#' plot(basic_mesh)
+#' if (requireNamespace("INLA")) {
+#'   basic_mesh <- make_mesh()
+#'   plot(basic_mesh)
+#' }
 #'
 #' }
 #'
diff --git a/man/make_mesh.Rd b/man/make_mesh.Rd
index 6787c3f..2c3bc6a 100644
--- a/man/make_mesh.Rd
+++ b/man/make_mesh.Rd
@@ -36,8 +36,10 @@ are designed for the default grid. Just a basic interface between the grid and i
 
 \donttest{
 
-basic_mesh <- make_mesh()
-plot(basic_mesh)
+if (requireNamespace("INLA")) {
+  basic_mesh <- make_mesh()
+  plot(basic_mesh)
+}
 
 }
 
diff --git a/man/sim_ays_covar_spde.Rd b/man/sim_ays_covar_spde.Rd
index 8010804..b27f47c 100644
--- a/man/sim_ays_covar_spde.Rd
+++ b/man/sim_ays_covar_spde.Rd
@@ -51,22 +51,25 @@ generate the error term.
 
 \donttest{
 
-## Make a grid
-my_grid <- make_grid(res = c(10,10))
-
-## Make a mesh based off it
-
-my_mesh <- make_mesh(my_grid)
-sim <- sim_abundance(ages = 1:10, years = 1:10) \%>\%
-         sim_distribution(grid = my_grid,
-                          ays_covar = sim_ays_covar_spde(phi_age = 0.8,
-                                                         phi_year = 0.1,
-                                                         model = "spde",
-                                                         mesh = my_mesh),
-                          depth_par = sim_parabola(mu = 200,
-                                                   sigma = 50))
-plot_distribution(sim, ages = 1:5, years = 1:5, type = "heatmap")
+if (requireNamespace("INLA")) {
 
+  ## Make a grid
+  my_grid <- make_grid(res = c(10,10))
+
+  ## Make a mesh based off it
+
+  my_mesh <- make_mesh(my_grid)
+  sim <- sim_abundance(ages = 1:10, years = 1:10) \%>\%
+          sim_distribution(grid = my_grid,
+                           ays_covar = sim_ays_covar_spde(phi_age = 0.8,
+                                                          phi_year = 0.1,
+                                                          model = "spde",
+                                                          mesh = my_mesh),
+                           depth_par = sim_parabola(mu = 200,
+                                                    sigma = 50))
+  plot_distribution(sim, ages = 1:5, years = 1:5, type = "heatmap")
+
+}
 
 }