From e960d1e68069e7a0e370d0e612c78097d9fb53e5 Mon Sep 17 00:00:00 2001
From: Sean Anderson <sean@seananderson.ca>
Date: Tue, 10 Oct 2023 18:39:02 -0700
Subject: [PATCH] Revert to inla.spde2.matern

---
 R/mesh.R         | 10 +++++-----
 man/make_mesh.Rd |  3 ++-
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/R/mesh.R b/R/mesh.R
index e2ad794c0..11929d2c3 100644
--- a/R/mesh.R
+++ b/R/mesh.R
@@ -25,8 +25,7 @@
 #'
 #' @export
 #'
-#' @examples
-#'
+#' @examplesIf inla_installed()
 #' \donttest{
 #' mesh <- make_mesh(pcod, c("X", "Y"), cutoff = 5, type = "cutoff")
 #' plot(mesh)
@@ -38,6 +37,7 @@
 #' plot(mesh)
 #'
 #'}
+#'
 # # Defining a mesh directly with fmesher (formerly in INLA):
 # bnd <- fmesher::fm_nonconvex_hull(cbind(pcod$X, pcod$Y), convex = -0.05)
 # inla_mesh <- fmesher::fm_mesh_2d_inla(
@@ -128,11 +128,11 @@ make_mesh <- function(data, xy_cols,
     loc_centers <- NA
   }
   # TODO:
-  # spde <- INLA::inla.spde2.matern(mesh)
-  # mesh_inla <- INLA::inla.mesh.create(loc_xy, refine = TRUE, cutoff = cutoff)
+  spde <- INLA::inla.spde2.matern(mesh)
+  mesh_inla <- INLA::inla.mesh.create(loc_xy, refine = TRUE, cutoff = cutoff)
   # names(spde_inla$param.inla)
 
-  spde <- fmesher::fm_matern_precision(mesh, alpha = 2)
+  # spde <- fmesher::fm_matern_precision(mesh, alpha = 2, rho = )
   # A_inla <- INLA::inla.spde.make.A(mesh, loc = loc_xy)
   A <- fmesher::fm_basis(mesh, loc = loc_xy)
 
diff --git a/man/make_mesh.Rd b/man/make_mesh.Rd
index 6d2709f4b..5ed2505b8 100644
--- a/man/make_mesh.Rd
+++ b/man/make_mesh.Rd
@@ -60,7 +60,7 @@ pass \code{your_mesh$mesh} to  \code{\link[inlabru:gg]{inlabru::gg()}}.
 Construct an SPDE mesh for use with sdmTMB.
 }
 \examples{
-
+\dontshow{if (inla_installed()) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 \donttest{
 mesh <- make_mesh(pcod, c("X", "Y"), cutoff = 5, type = "cutoff")
 plot(mesh)
@@ -72,4 +72,5 @@ mesh <- make_mesh(pcod, c("X", "Y"), n_knots = 50, type = "kmeans")
 plot(mesh)
 
 }
+\dontshow{\}) # examplesIf}
 }