Converting legacy INLA mesh code to fmesher
In fmesher: Triangle Meshes and Related Geometry Tools

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

suppressPackageStartupMessages(library(fmesher))
suppressPackageStartupMessages(library(tibble))

convert_fun_links <- function(df) {
  webref <- list(
    fmesher = "../reference/",
    inlabru = "https://inlabru-org.github.io/inlabru/reference/"
  )
  for (k in seq_len(nrow(df))) {
    df$INLA[[k]] <- paste0("`", df$INLA[[k]], "`")
    df$fmesher[[k]] <-
      vapply(
        df$fmesher[[k]],
        function(x) {
          pkg_name <- sub(
            pattern = "^(([^:]*)::)?([^(]+)(\\(.*\\))(<-)?$",
            replacement = "\\2",
            x = x
          )
          if (identical(pkg_name, "")) {
            pkg_name <- "fmesher"
          }
          nm <- sub(
            pattern = "^(([^:]*)::)?([^(]+)(\\(.*\\))(<-)?$",
            replacement = "\\3",
            x = x
          )
          args <- sub(
            pattern = "^(([^:]*)::)?([^(]+)(\\(.*\\))(<-)?$",
            replacement = "\\4\\5",
            x = x
          )
          help_name <- basename(utils::help((nm), package = (pkg_name)))
          paste0(
            '<a href="', webref[[pkg_name]], help_name, '.html">`',
            if (!identical(pkg_name, "fmesher")) {
              paste0(pkg_name, "::")
            } else {
              ""
            },
            nm,
            args,
            "`</a>"
          )
        },
        ""
      )
  }
  df
}

Deprecation warnings

Three INLA::inla.getOption()/INLA::inla.setOption() options control the transition behaviour of the INLA package use of fmesher.

fmesher.evolution, integer:
1L uses the intermediate fm_* methods in fmesher that were already available via inlabru from 2.8.0, but calls the INLA built-in fmesher standalone programme for mesh construction and related operations. (From INLA version 23.06.29)
2L uses the full range of fmesher package methods, and does not use the standalone fmesher programme. (From INLA around version 23.08.20)
fmesher.evolution.warn, logical: When TRUE, INLA will show deprecation methods for all the methods in INLA that are being replaced by fmesher package methods. When FALSE, no warnings will be shown. Set this option to TRUE if you want to update your own code, but keep it at FALSE when you need to run existing code without changing it.
fmesher.evolution.verbosity, character: Either "soft", "warn", or "stop", indicating the minimum warning level when fmesher.evolution.warn is TRUE. Set this to "warn" or "stop" to get more immediate feedback when testing conversion of old code, e.g. in package testing.

Compatibility

Great effort has been taken to preserve backwards compatibility as far as practical, with in particular the old inla.mesh, inla.mesh.1d, and inla.mesh.segment object classes given fallback methods that carry out methods for the new fm_mesh_2d, fm_mesh_1d, and fm_segm classes.

An important change is that the handling of mesh crs information is now more flexible, but stricter in the sense that user code should make no assumption about how the information is stored in the mesh, and should therefore avoid the direct mesh$crs access, and instead use the fm_crs() and fm_CRS() access methods, depending on what type of CRS object is needed. The ideal way to specify crs information is in the initial mesh creation call. If the crs needs to be explicitly assigned a new value, use the fm_crs(mesh) <- crs assignment method.

For mesh and curve creation, the fm_rcdt_2d_inla(), fm_mesh_2d_inla(), and fm_nonconvex_hull_inla() methods will keep the interface syntax used by inla.mesh.create(), inla.mesh.2d(), and inla.nonconvex.hull() functions, respectively, whereas the fm_rcdt_2d(), fm_mesh_2d(), and fm_nonconvex_hull() interfaces may change in the future.

Mesh construction

df <- tribble(
  ~INLA, ~fmesher,
  "inla.mesh.create()", c("fm_rcdt_2d()", "fm_rcdt_2d_inla()"),
  "inla.mesh.2d()", c("fm_mesh_2d()", "fm_mesh_2d_inla()"),
  "inla.delaunay()", "fm_delaunay_2d()",
  "inla.mesh.1d()", "fm_mesh_1d()",
  "inla.mesh.lattice()", "fm_lattice_2d()",
  "inla.mesh.segment()", "fm_segm()",
  "inla.nonconvex.hull()", c("fm_nonconvex_hull()", "fm_extensions()", "fm_simplify()"),
  c(
    "inla.nonconvex.hull()",
    "inla.contour.segment()",
    "inla.simplify.curve()"
  ),
  c(
    "fm_nonconvex_hull_inla()",
    "fm_simplify_helper()",
    "fm_segm_contour_helper()"
  )
)
df <- convert_fun_links(df)

knitr::kable(df)

Basis and function evaluation

df <- tribble(
  ~INLA, ~fmesher,
  "inla.mesh.projector()", "fm_evaluator()",
  "inla.mesh.project()", "fm_evaluate()",
  "inla.spde.make.A()", c(
    "fm_basis()",
    "fm_row_kron()",
    "inlabru::bru_mapper_multi()",
    "inlabru::ibm_jacobian()",
    "fm_block()",
    "fm_block_eval()",
    "inlabru::bru_mapper_aggregate()"
  ),
  "inla.mesh.deriv()", "fm_basis()"
)
df <- convert_fun_links(df)

knitr::kable(df)

Finite element methods

df <- tribble(
  ~INLA, ~fmesher, ~Comment,
  c("inla.mesh.fem()", "inla.mesh.1d.fem()"), "fm_fem()", " ",
  " ", "fm_matern_precision()", " ",
  " ", "fm_matern_sample()", "Convenience function that combines `fm_matern_precision()` and `fm_sample()`.",
  " ", "fm_covariance()", "Basic helper function for compution covariances between different locations. Can produce sparse inverses like `inla.qinv()`, but currently (version 0.1.1) only by a 'brute force' method.",
  " ", "fm_sample()", "Basic sampling method, like `inla.qsample()`"
)
df <- convert_fun_links(df)

knitr::kable(df)

Printing

df <- tribble(
  ~INLA,
  ~fmesher,
  ~Comments,
  "summary.inla.mesh()",
  c(
    "print.fm_mesh_2d()",
    "print.fm_segm()",
    "print.fm_mesh_1d()"
  ),
  "Use `print(mesh)` etc."
)
df <- convert_fun_links(df)

knitr::kable(df)

CRS information and coordinate transformations

df <- convert_fun_links(
  tibble::tribble(
    ~INLA, ~fmesher, ~Comments,
    "inla.spTransform()", "fm_transform()", "",
    "mesh$crs", c("fm_crs(mesh)", "fm_CRS(mesh)"), "The crs may now be stored in different formats; use `fm_crs()` for `sf` format, and `fm_CRS()` for `sp` format. `fmesher` will attempt to convert when needed.",
    "mesh$crs<-", "fm_crs(mesh)<-", "Direct assignment of crs information should be avoided, but is allowed as long as its compatible with the actual mesh coordinates."
  )
)

knitr::kable(df)

Plotting

df <- tribble(
  ~INLA, ~fmesher, ~Comment,
  "No ggplot support", c("geom_fm(data = mesh)", "geom_fm(data = segm)"), "Use `ggplot() + geom_fm(data = mesh)` and `inlabru::gg()` methods",
  "plot.inla.mesh(rgl = FALSE)", c("plot.fm_mesh_2d()", "lines.fm_mesh_2d()"), "Use `plot()` or `lines()`",
  "lines.inla.mesh.segment(rgl = FALSE)", c(
    "plot.fm_segm()",
    "lines.fm_segm()"
  ), "Use `plot()` or `lines()`",
  "plot.inla.mesh(rgl = TRUE)", c("plot_rgl()", "lines_rgl()"), "",
  "lines.inla.mesh.segment(rgl = TRUE)", c(
    "plot_rgl()",
    "lines_rgl()"
  ),
  ""
)
df <- convert_fun_links(df)