Documentation and dependency updates for CRAN compatibility

See NEWS for version 2.3.0 for the major updates since version 2.1.13

The model component argument

`map`

has been deprecated. Use`main`

to specify the main component input,`~ elev(main = elevation, model = "rw2")`

. Unlike the old`map`

argument,`main`

is the first one, so the shorter version`~ elev(elevation, model = "rw2")`

also works.Intercept-like components should now have explicit inputs, e.g.

`~ Intercept(1)`

to avoid accidental confusion with other variables.The argument list for

`bru()`

has been simplified, so that all arguments except`components`

and`options`

must either be outputs from calls to`like()`

, or arguments that can be sent to a single`like()`

call.The option setting system has been replaced with a more coherent system; see

`?bru_options()`

for details.The

`samplers`

and`domain`

system for`lgcp`

models is now stricter, and requires explicit`domain`

definitions for all the point process dimensions. Alternatively, user-defined integration schemes can be supplied via the`ips`

argument.

The model component input arguments

`main`

,`group`

,`replicate`

, and`weights`

can now take general R expressions using the data inputs. Special cases are detected:`SpatialPixels/GridDataFrame`

objects are evaluated at spatial locations if the input data is a`SpatialPointsDataFrame`

object. Functions are evaluated on the data object, e.g.`field(coordinates, model = spde)`

The component arguments

`mapper`

,`group_mapper`

, and`replicate_mapper`

can be used for precise control of the mapping between inputs and latent variables. See`?bru_mapper`

for more details. Mapper information is automatically extracted from`INLA::inla.spde2.pcmatern()`

model objects.The R-INLA

`weights`

and`copy`

features are now supported.The predictor expressions can access the data object directly via

`.data.`

If data from several rows can affect the same output row, the

`allow_combine = TRUE`

argument must be supplied to`like()`

The

`include`

and`exclude`

arguments to`like()`

,`generate()`

, and`predict()`

can be used to specify which components are used for a given likelihood model or predictor expression. This can be used to prevent evaluation of components that are invalid for a likelihood or predictor.Predictor expressions can access the latent state of a model component directly, by adding the suffix

`_latent`

to the component name, e.g.`name_latent`

. For`like()`

, this requires`allow_latent = TRUE`

to activate the needed linearisation code for this.Predictor expressions can evaluate component effects for arbitrary inputs by adding the suffix

`_eval`

to access special evaluator functions, e.g.`name_eval(1:10)`

. This is useful for evaluating the 1D effect of spatial covariates. See the NEWS item for version 2.2.8 for further details.The internal system for predictor linearisation and iterated INLA inference has been rewritten to be faster and more robust

See the NEWS entries for versions 2.1.14 to 2.2.8 for further details on new features and bug fixes

Add

`_eval`

suffix feature for`generate.bru`

and`predict.bru`

, that provides a general evaluator function for each component, allowing evaluation of e.g. nonlinear effects of spatial covariates as a function of the covariate value instead of the by the spatial evaluator used in the component definition. For example, with`components = ~ covar(spatial_grid_df, model = "rw1")`

, the prediction expression can have`~ covar_eval(covariate)`

, where`covariate`

is a data column in the prediction data object.For components with

`group`

and`replicate`

features, these also need to be provided to the`_eval`

function, with`..._eval(..., group = ..., replicate = ...)`

This feature is built on top of the

`_latent`

suffix feature, that gives direct access to the latent state variables of a component, so in order to use`_eval`

in the model predictor itself, you must use`like(..., allow_latent = TRUE)`

in the model definition.

Add support for

`ngroup`

and`nrep`

in component definitionsUpdated

`mexdolphin`

and`mrsea`

data sets, with consistent km units and improved mesh designs

Add

`predict(..., include)`

discussion to distance sampling vignette, for handling non-spatial prediction in spatial models.Fix bugs in

`gg.SpatialLines`

Vignette corrections

Documentation improvements

Fix minor bug in

`Spatial*`

object handling and plotting

- Properly extract the joint latent conditional mode instead of the marginal latent conditional mode

Fixed issue with

`predict()`

logic for converting output to`Spatial*DataFrame`

Use

`control.mode=list(restart=FALSE)`

in the final inla run for nonlinear models, to avoid an unnecessary optimisation.Fix issues in

`pixels()`

and`bru_fill_missing()`

for`Spatial*DataFrame`

objects with`ncol=0`

data frame parts.

- Fixed code regression bug for function input of covariates

Support for the INLA “copy” feature,

`comp2(input, copy = "comp1")`

Allow component weights to be an unnamed parameter,

`comp(input, weights, ...)`

Direct access to the data objects in component inputs and predictor expressions, as

`.data.`

, allowing e.g.`covar(fun(.data.), ...)`

for a complex covariate extractor method`fun()`

Partial support for spherical manifold meshes

Uses INLA integration strategy “eb” for initial nonlinear iterations, and a specified integration strategy only for the final iteration, so that the computations are faster, and uses the conditional latent mode as linearisation point.

New options system

New faster linearisation method

New line search method to make the nonlinear inla iterations robust

Method for updating old stored estimation objects

System for supplying mappings between latent models and evaluated effects via

`bru_mapper`

objectsImproved factor support; Either as “contrast with the 1st level”, via the special

`"factor_contrast"`

model, or all levels with model`"factor_full"`

. Further options planned (e.g. a simpler options to fix the precision parameter). The estimated coefficients appear as random effects in the`inla()`

output.Interface restructuring to support new features while keeping most backwards compatibility. Change

`map=`

to`main=`

or unnamed first argument; Since`main`

is the first parameter, it doesn’t need to be a named argument.Keep components with zero derivative in the linearisation

PROJ6 support

Add random seed option for posterior sampling

Add package unit testing

New backend code to make extended feature support easier

New

`int.args`

option to control spatial integration resolution, thanks to Martin Jullum (`martinju`

)

- Fix CRAN complaint regarding documentation

- Workaround an integration points error for old (ca pre-2018) INLA versions

- Add CITATION file

- Fix internal sampling bug due to INLA changes

- Remove unused
`VignetteBuilder`

entry from`DESCRIPTION`

Update default options

Prevent

`int.polygon`

from integrating outside the mesh domain, and generally more robust integration scheme construction.Fix

`bru()`

to`like()`

parameter logic. (Thanks to Peter Vesk for bug example)

Added a

`NEWS.md`

file to track changes to the package.Added

`inla`

methods for`predict()`

and`generate()`

that convert`inla`

output into`bru`

objects before calling the`bru`

prediction and posterior sample generator.Added protection for examples requiring optional packages

Fix

`sample.lgcp`

output formatting, extended CRS support, and more efficient sampling algorithmAvoid dense matrices for effect mapping

`iinla()`

tracks convergence of both fixed and random effects

Added matrix geom

`gg.matrix()`

Fixed CRAN test issues