R CMD check fixes [skip ci]

DESCRIPTION

@@ -91,7 +91,6 @@ Suggests:
     ggforce,
     glmmTMB,
     ggplot2,
-    inlabru,
     knitr,
     rmarkdown,
     sf,

R/mesh.R

@@ -234,27 +234,27 @@ binary_search_knots <- function(loc_xy,
 #' @rdname make_mesh
 #' @export
 plot.sdmTMBmesh <- function(x, ...) {
-  r1 <- requireNamespace("inlabru", quietly = TRUE)
-  r2 <- requireNamespace("ggplot2", quietly = TRUE)
-  if (r1 && r2) {
-    dat <- data.frame(
-      x = x$loc_xy[,1,drop=TRUE],
-      y = x$loc_xy[,2,drop=TRUE]
-    )
-    ggplot2::ggplot() +
-      inlabru::gg(x$mesh, ext.color = "grey20", ext.linewidth = 0.5, edge.color = "grey50") +
-      # ggplot2::coord_sf() +
-      # fmesher::geom_fm(data = x$mesh) +
-      ggplot2::geom_point(
-        data = dat,
-        mapping = ggplot2::aes(x = .data$x, y = .data$y), alpha = 0.4, pch = 20, colour = "#3182BD") +
-      ggplot2::coord_fixed() +
-      ggplot2::labs(x = x$xy_cols[[1]], y = x$xy_cols[[2]])
-  } else {
+  # r1 <- requireNamespace("inlabru", quietly = TRUE)
+  # r2 <- requireNamespace("ggplot2", quietly = TRUE)
+  # if (r1 && r2) {
+  #   dat <- data.frame(
+  #     x = x$loc_xy[,1,drop=TRUE],
+  #     y = x$loc_xy[,2,drop=TRUE]
+  #   )
+  #   ggplot2::ggplot() +
+  #     # inlabru::gg(x$mesh, ext.color = "grey20", ext.linewidth = 0.5, edge.color = "grey50") +
+  #     ggplot2::coord_sf() +
+  #     fmesher::geom_fm(data = x$mesh) +
+  #     ggplot2::geom_point(
+  #       data = dat,
+  #       mapping = ggplot2::aes(x = .data$x, y = .data$y), alpha = 0.4, pch = 20, colour = "#3182BD") +
+  #     # ggplot2::coord_fixed() +
+  #     ggplot2::labs(x = x$xy_cols[[1]], y = x$xy_cols[[2]])
+  # } else {
     plot(x$mesh, main = NA, edge.color = "grey60", asp = 1, ...)
-    points(x$loc_xy, pch = ".", col = "#00000070")
+    points(x$loc_xy, pch = 21, cex = 0.3, col = "#00000080")
     points(x$loc_centers, pch = 20, col = "red")
-  }
+  # }
 }
 
 # from TMB examples repository:

R/plot.R

@@ -17,7 +17,7 @@
 #' spatiotemporal range (distance at which correlation is effectively
 #' independent) in any direction from zero. Uses \pkg{ggplot2}. If anisotropy
 #' was turned off when fitting the model, `NULL` is returned instead of a
-#' {ggplot2} object.
+#' \pkg{ggplot2} object.
 #'
 #' `plot_anisotropy2()`: A plot of eigenvectors illustrating the estimated
 #' anisotropy. A list of the plotted data is invisibly returned. Uses base

R/priors.R

@@ -151,6 +151,7 @@ mvnormal <- function(location = 0, scale = diag(length(location))) {
 #' pc_matern(range_gt = 5, sigma_lt = 1)
 #' plot_pc_matern(range_gt = 5, sigma_lt = 1)
 #'
+#' \donttest{
 #' d <- subset(pcod, year > 2011)
 #' pcod_spde <- make_mesh(d, c("X", "Y"), cutoff = 30)
 #'
@@ -194,6 +195,7 @@ mvnormal <- function(location = 0, scale = diag(length(location))) {
 #'     matern_s = pc_matern(range_gt = 5, sigma_lt = 1),
 #'     matern_st = pc_matern(range_gt = 5, sigma_lt = 1))
 #' )
+#' }
 pc_matern <- function(range_gt, sigma_lt, range_prob = 0.05, sigma_prob = 0.05) {
   assert_that(range_prob > 0 && range_prob < 1)
   assert_that(sigma_prob > 0 && sigma_prob < 1)

R/stacking.R

@@ -31,6 +31,7 @@
 #'
 #'
 #' @examples
+#' \donttest{
 #' # Set parallel processing if desired. See 'Details' in ?sdmTMB_cv
 #'
 #' # Depth as quadratic:
@@ -59,6 +60,7 @@
 #' models <- list(m_cv_1, m_cv_2, m_cv_3)
 #' weights <- sdmTMB_stacking(models)
 #' weights
+#' }
 sdmTMB_stacking <- function(model_list, include_folds = NULL) {
   n_models <- length(model_list)
   if (is.null(include_folds)) {