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.
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. Starting in November 2024
however, some of this direct fallback support is being phased out, so
that old stored objects may need to be explicitly converted to
fmesher objects using for example fm_as_fm().
New code, in particular in packages that use fmesher
objects, should use the new interface methods, and replace references to
inla.mesh, inla.mesh.1d, and
inla.mesh.segment with fm_mesh_2d,
fm_mesh_1d, and fm_segm, respectively, as the
old class names will eventually be dropped from the mesh classes. This
in particular applies to S3 method naming and class checking, where
inherits(mesh, "inla.mesh") must be replaced with
inherits(mesh, "fm_mesh_2d") in order to work in the
future.
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.
| INLA | fmesher |
|---|---|
inla.mesh.create() |
fm_rcdt_2d()
,
fm_rcdt_2d_inla() |
inla.mesh.2d() |
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() |
fm_nonconvex_hull(),
fm_extensions()
,
fm_simplify() |
inla.nonconvex.hull() ,
inla.contour.segment(),
inla.simplify.curve() |
fm_nonconvex_hull_inla(),
fm_simplify_helper()
,
fm_segm_contour_helper() |
| INLA | fmesher | inlabru |
|---|---|---|
inla.mesh.projector() |
fm_evaluator() |
|
inla.mesh.project() |
fm_evaluate() |
|
inla.spde.make.A() |
fm_basis()
,
fm_row_kron(),
fm_block()
,
fm_block_eval() |
inlabru::bru_mapper_multi()
,
inlabru::ibm_jacobian()
,
inlabru::bru_mapper_aggregate() |
inla.mesh.deriv() |
fm_basis() |
| INLA | fmesher | Comments |
|---|---|---|
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 computing 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() |
| INLA | fmesher | Comments |
|---|---|---|
summary.inla.mesh() |
print.fm_mesh_2d(),
print.fm_segm()
,
print.fm_mesh_1d() |
Use print(mesh) etc. |
| INLA | fmesher | Comments |
|---|---|---|
inla.spTransform() |
fm_transform() |
|
mesh$crs |
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. |
| INLA | fmesher | inlabru | Comments |
|---|---|---|---|
No ggplot support |
geom_fm(data = mesh),
geom_fm(data = segm) |
inlabru::gg(mesh) |
Use ggplot() + geom_fm(data = mesh) and
inlabru::gg() methods |
plot.inla.mesh(rgl = FALSE) |
plot.fm_mesh_2d()
,
lines.fm_mesh_2d() |
Use plot() or lines() |
|
lines.inla.mesh.segment(rgl = FALSE) |
plot.fm_segm()
,
lines.fm_segm() |
Use plot() or lines() |
|
plot.inla.mesh(rgl = TRUE) |
plot_rgl()
,
lines_rgl() |
||
lines.inla.mesh.segment(rgl = TRUE) |
plot_rgl()
,
lines_rgl() |