Move add_barrier_mesh() to sdmTMBextra

.github/workflows/R-CMD-check.yaml

@@ -73,7 +73,6 @@ jobs:
           remotes::install_cran("sf")
           remotes::install_cran("rcmdcheck")
           remotes::install_cran("textshaping")
-          remotes::install_cran("rgdal")
         shell: Rscript {0}
 
       - name: Install dependencies Ubuntu

.github/workflows/pkgdown.yaml

@@ -31,7 +31,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::pkgdown, local::., any::rgdal, any::textshaping, any::remotes
+          extra-packages: any::pkgdown, local::., any::textshaping, any::remotes
           needs: website
 
       - name: Install extra packages for web-only vignettes

DESCRIPTION

@@ -92,13 +92,8 @@ Suggests:
     glmmTMB,
     ggplot2,
     inlabru,
-    INLAspacetime,
-    INLA,
     knitr,
-    rgdal,
     rmarkdown,
-    rnaturalearth,
-    rnaturalearthdata,
     sf,
     splancs,
     testthat,

R/deprecated.R

@@ -3,7 +3,7 @@
 #' Moved to the \href{https://github.com/pbs-assess/sdmTMBextra}{sdmTMBextra}
 #' package
 #'
-#' @param object **Deprecated** See the \href{https://github.com/pbs-assess/sdmTMBextra}{sdmTMBextra} package.
+#' @param object **Deprecated** See the \href{https://github.com/pbs-assess/sdmTMBextra}{sdmTMBextra} package. Make sure to load \pkg{sdmTMBextra} *after* \pkg{sdmTMB}.
 #'
 #' @return
 #' Deprecated. See the
@@ -22,7 +22,7 @@ extract_mcmc <- function(object = deprecated()) {
 #' DHARMa residuals
 #'
 #' Moved to the \href{https://github.com/pbs-assess/sdmTMBextra}{sdmTMBextra}
-#' package
+#' package. Make sure to load \pkg{sdmTMBextra} *after* \pkg{sdmTMB}.
 #'
 #' @param simulated_response **Deprecated** See the \pkg{sdmTMBextra} package.
 #' @param object **Deprecated** See the \pkg{sdmTMBextra} package.
@@ -42,3 +42,34 @@ extract_mcmc <- function(object = deprecated()) {
 dharma_residuals <- function(simulated_response = deprecated(), object, plot = TRUE, ...) {
   deprecate_stop("0.2.2", "dharma_residuals()", details = "Load the sdmTMBextra package to use this function: https://github.com/pbs-assess/sdmTMBextra")
 }
+
+#' Transform a mesh object into a mesh with correlation barriers
+#'
+#' Moved to the \href{https://github.com/pbs-assess/sdmTMBextra}{sdmTMBextra}
+#' package. Make sure to load \pkg{sdmTMBextra} *after* \pkg{sdmTMB}.
+#'
+#' @param spde_obj Output from [make_mesh()].
+#' @param barrier_sf An sf object with polygons defining the barriers. For
+#'   example, a coastline dataset for ocean data. **Note that this object must
+#'   have the same projection as the data used to generate the x and y columns
+#'   in `spde_obj`.**
+#' @param range_fraction The fraction of the spatial range that barrier
+#'   triangles have.
+#' @param proj_scaling If `spde_obj` was created with scaling of the coordinates
+#'   after the projection (e.g., dividing UTMs by 1000 so the spatial range is
+#'   on a reasonable scale) the x and y values in `spde_obj` are multiplied by
+#'   this scaling factor before applying the projection from `barrier_sf`.
+#' @param plot Logical.
+#' @export
+#' @keywords internal
+#' @return
+#' Deprecated. See the
+#' \href{https://github.com/pbs-assess/sdmTMBextra}{sdmTMBextra} package.
+#' @examples
+#' \dontrun{
+#' add_barrier_mesh()
+#' }
+add_barrier_mesh <- function(spde_obj = deprecated(), barrier_sf = deprecated(), range_fraction = 0.2,
+  proj_scaling = 1, plot = FALSE) {
+  deprecate_stop("0.3.0", "add_barrier_mesh()", details = "Load the sdmTMBextra package to use this function: https://github.com/pbs-assess/sdmTMBextra \n We may move this back to the main package once the functionality joins fmesher. For now, this function requires INLA.")
+}

R/fit.R

@@ -389,18 +389,19 @@ NULL
 #' # Perform several 'sanity' checks:
 #' sanity(fit)
 #'
-#' # Visualize depth effect: (see ?visreg_delta)
-#' visreg::visreg(fit, xvar = "depth") # link space; randomized quantile residuals
-#' visreg::visreg(fit, xvar = "depth", scale = "response")
-#' visreg::visreg(fit, xvar = "depth", scale = "response", gg = TRUE, rug = FALSE)
-#'
 #' # Predict on the fitted data; see ?predict.sdmTMB
 #' p <- predict(fit)
 #'
 #' # Predict on new data:
 #' p <- predict(fit, newdata = qcs_grid)
 #' head(p)
 #'
+#' \donttest{
+#' # Visualize depth effect: (see ?visreg_delta)
+#' visreg::visreg(fit, xvar = "depth") # link space; randomized quantile residuals
+#' visreg::visreg(fit, xvar = "depth", scale = "response")
+#' visreg::visreg(fit, xvar = "depth", scale = "response", gg = TRUE, rug = FALSE)
+#'
 #' # Add spatiotemporal random fields:
 #' fit <- sdmTMB(
 #'   density ~ 0 + as.factor(year),
@@ -410,7 +411,6 @@ NULL
 #' )
 #' fit
 #'
-#' \donttest{
 #' # Make the fields AR1:
 #' fit <- sdmTMB(
 #'   density ~ s(depth),

R/get-index-sims.R

@@ -54,13 +54,14 @@
 #'
 #' @export
 #' @examples
-#' m <- sdmTMB(density ~ 0 + as.factor(year) + depth_scaled + depth_scaled2,
+#' m <- sdmTMB(density ~ 0 + as.factor(year),
 #'   data = pcod_2011, mesh = pcod_mesh_2011, family = tweedie(link = "log"),
 #'   time = "year"
 #' )
 #' qcs_grid_2011 <- replicate_df(qcs_grid, "year", unique(pcod_2011$year))
 #' p <- predict(m, newdata = qcs_grid_2011, nsim = 100)
 #' x <- get_index_sims(p)
+#' \donttest{
 #' x_sims <- get_index_sims(p, return_sims = TRUE)
 #'
 #' if (require("ggplot2", quietly = TRUE)) {
@@ -77,6 +78,7 @@
 #'   agg_function = function(x) sum(x),
 #'   area_function = function(x, area) x * area
 #' )
+#' }
 get_index_sims <- function(obj,
                            level = 0.95,
                            return_sims = FALSE,