Deprecated functions in inlabru

These functions still attempt to do their job, but will be removed in a future version.

Usage

ipoints(
  samplers = NULL,
  domain = NULL,
  name = NULL,
  group = NULL,
  int.args = NULL,
  project = deprecated()
)

cprod(..., na.rm = NULL, .blockwise = FALSE)

gmap(...)

gm(...)

integration_weight_aggregation(mesh, integ)

mesh_triangle_integration(mesh, tri_subset = NULL, nsub = NULL)

bru_int_polygon(...)

# Default S3 method
bru_mapper(...)

bru_mapper_offset(...)

is.inside(mesh, loc, mesh.coords = NULL)

vertices.inla.mesh(...)

pixels(mesh, nx = 150, ny = 150, mask = TRUE)

row_kron(M1, M2, repl = NULL, n.repl = NULL, weights = NULL)

Arguments

samplers

Description of the integration region boundary. In 1D, a length 2 vector or two-column matrix where each row describes an interval, or NULL In 2D either a SpatialPolygon or a SpatialLinesDataFrame with a weight column defining the width of the a transect line, and optionally further columns used by the group argument, or NULL. When domain is NULL, samplers may also be an inla.mesh.1d or inla.mesh object, that is then treated as a domain argument instead.

domain

Either

when samplers is a 1D interval(s) definition only, domain can be a single integer for the number of integration points to place in each 1D interval, overriding int.args[["nsub1"]], and otherwise
when samplers is NULL, domain can be a numeric vector of points, each given integration weight 1 (and no additional points are added in between),
an inla.mesh.1d object for continuous 1D integration, or
an inla.mesh.2d object for continuous 2D integration.

name

Character array stating the name of the domains dimension(s). If NULL, the names are taken from coordinate names from samplers for Spatial* objects, otherwise "x", "y", "z" for 2D regions and "x" for 1D regions

group

Column names of the samplers object (if applicable) for which the integration points are calculated independently and not merged when aggregating to mesh nodes.

int.args

List of arguments passed to bru_int_polygon.

method: "stable" (to aggregate integration weights onto mesh nodes) or "direct" (to construct a within triangle/segment integration scheme without aggregating onto mesh nodes)
nsub1, nsub2: integers controlling the number of internal integration points before aggregation. Points per triangle: (nsub2+1)^2. Points per knot segment: nsub1
poly_method: if set to "legacy", selects an old polygon integration method that doesn't handle holes. No longer supported, and will generate an error.

project

Deprecated in favour of int.args(method=...). If TRUE, aggregate the integration points to mesh vertices. Default: project = (identical(int.args$method, "stable"))

...

Usually passed on to other methods

na.rm

logical; if TRUE, the rows with weight NA from the non-overlapping full_join will be removed; if FALSE, set the undefined weights to NA. If NULL (default), act as TRUE, but warn if any elements needed removing.

.blockwise

logical; if FALSE, computes full tensor product integration. If TRUE, computes within-block tensor product integration (used internally by fmesher::fm_int()). Default FALSE

mesh

An inla.mesh object

integ

list of loc, integration points, and weight, integration weights, or a SpatialPointsDataFrame. Only the coordinates and weight column are handled.

tri_subset

Optional triangle index vector for integration on a subset of the mesh triangles (Default NULL)

nsub

number of subdivision points along each triangle edge, giving (nsub + 1)^2 proto-integration points used to compute the vertex weights (default NULL=9, giving 100 integration points for each triangle)

loc

Points in space stored either as data.frame, a two-column matrix of x and y coordinates or a SpatialPoints object.

mesh.coords

Coordinate names of the mesh. Use only if loc is a data.frame with respective column names.

nx

Number of pixels in x direction

ny

Number of pixels in y direction

mask

If logical and TRUE, remove pixels that are outside the mesh. If mask is a Spatial object, only return pixels covered by this object.

M1

A matrix that can be transformed into a sparse Matrix.

M2

A matrix that can be transformed into a sparse Matrix.

repl

An optional index vector. For each entry, specifies which replicate the row belongs to, in the sense used in INLA::inla.spde.make.A

n.repl

The maximum replicate index, in the sense used in INLA::inla.spde.make.A().

weights

Optional scaling weights to be applied row-wise to the resulting matrix.

Value

ipoints(): A data.frame, tibble, sf, or SpatialPointsDataFrame of 1D and 2D integration points, including a weight column and .block column.

A data.frame, sf, or SpatialPointsDataFrame of multidimensional integration points and their weights

mesh_triangle_integration returns a list with elements loc and weight with integration points for the mesh

is.inside(): Single column matrix of Boolean values indicating if a point is inside the mesh.

SpatialPixelsDataFrame covering the mesh

Functions

ipoints(): in favour of fmesher::fm_int()
cprod(): (Blockwise) cross product of integration points.

Calculates the groupwise cross product of integration points in different dimensions and multiplies their weights accordingly. If the object defining points in a particular dimension has no weights attached to it all weights are assumed to be 1.

Legacy wrapper for fmesher::fm_cprod()
gmap(): Plot a map using extent of a spatial object

This function is deprecated as ggmap isn't supported.

Used ggmap::get_map() to query map services like Google Maps for a region centered around the spatial object provided. Then calls ggmap() to plot the map.

This function required the ggmap package.
gm(): This function is deprecated as ggmap isn't supported.

ggplot geom for spatial data

gm is a wrapper for the gg method. It will take the first argument and transform its coordinate system to latitude and longitude. Thereafter, gg is called using the transformed data and the arguments provided via .... gm is intended to replace gg whenever the data is supposed to be plotted over a spatial map generated by gmap, which only works if the coordinate system is latitude/longitude.
integration_weight_aggregation(): Aggregate integration weights onto mesh nodes

Use fmesher::fm_vertex_projection() instead.
mesh_triangle_integration(): Integration scheme for mesh triangle interiors

Use fmesher::fm_int_mesh_2d_core() instead.
bru_int_polygon(): Integration points for polygons inside an inla.mesh

Use fmesher::fm_int() instead.
bru_mapper(default): Calls bru_mapper_define, passing all arguments along. Mapper implementations should call bru_mapper_define() instead, and supply at least a new_class class name. Use of the bru_mapper.default method was deprecated from version 2.7.0, and removed in version 2.11.0
bru_mapper_offset(): Creates a bru_mapper_const() mapper.
is.inside(): Find out which points are inside a mesh. in favour of fmesher::fm_is_within(). Replace is.inside(mesh, loc) with fm_is_within(loc, mesh).
vertices.inla.mesh(): Extract vertex locations from an inla.mesh. Converts the vertices of an inla.mesh object into a SpatialPointsDataFrame. Deprecated in favour of fmesher::fm_vertices() and no longer exported.
pixels(): Generate SpatialPixels covering an inla.mesh. in favour of fmesher::fm_pixels()
row_kron(): Row-wise Kronecker products in favour of fmesher::fm_row_kron().

Takes two Matrices and computes the row-wise Kronecker product. Optionally applies row-wise weights and/or applies an additional 0/1 row-wise Kronecker matrix product.

Returns a Matrix::sparseMatrix object.

Author

Finn Lindgren finn.lindgren@gmail.com

Usage

Arguments

Value

Functions

See also

Author