NEWS.md

In inlabru-org/inlabru: Bayesian Latent Gaussian Modelling using INLA and Extensions

inlabru (development version)

Feature updates

• Add support for the scale parameter to like().
• Fix regression bug in "bym" model support, where the latent state size wasn't correctly handled by the mapper system (version 2.10.1.9002)
• New toypoints example data set, for basic modelling examples (version 2.10.1.9003)
• Updated convergence plots, reducing random effect aspects to summary statistics, improving speed and visual coherence (version 2.10.1.9004)
• Add options to bru_convergence_plot() to control the number of iterations shown, and optionally show the initial values that are stored from this version (version 2.10.1.9005)

inlabru 2.10.1

Feature updates

• Add new web article on ZIP/ZAP models (zero inflated Poisson models) where the non-zero probability is modelled with a separate predictor from the predictor for the Poisson model parameter: https://inlabru-org.github.io/inlabru/articles/zip_zap_models.html. (Thanks to Dmytro Perepolkin)

Bug fixes and dependency simplification

• Remove dependence on the ggpolypath package, and the ggplot2::fortify.SpatialPolygons/DataFrame() methods that were deprecated in ggplot2 version 3.4.4. Code using gg.SpatialPolygons() together with coord_fixed()/coord_equal() for coordinate axis control needs to use coord_sf() instead.
• Detect the need for vectorised parameters in bru_forward_transformation to allow bru_mapper_marginal to be applied with e.g. spatially varying parameters. (version 2.10.0.9001)
• Detect terra version >= 1.7-66 that removes the need for detecting special cases (nrow(where) == 1 and terra::nlyr(data) == 1). Workaround code used for versions < 1.7-66. (version 2.10.0.9002) (Thanks to Robert J. Hijmans)

inlabru 2.10.0

Feature updates

• Add new ibm_simplify() generic to handle mapper simplification more generally; needed to properly support non-linear component mappers. (version 2.9.0.9004)
• Add new bru_mapper_marginal() mapper class that can be used as part of component mapper pipelines. (version 2.9.0.9004)
• Add new ibm_eval2() generic that computes both evaluation and Jacobian, avoiding double-computing of the Jacobian, when practical. (version 2.9.0.9005)
• Add new bru_timings_plot() function that plots the time used for each nonlinear iteration (version 2.9.0.9007)
• Speed up bru_fill_missing() (by orders of magnitude) by changing method for finding the nearest available data point. (version 2.9.0.9011)
• Add new bru_mapper_shift() mapper class that works like bru_mapper_scale() but for additive shifts instead of multiplicative scaling. (version 2.9.0.9012)
• Added more checks for invalid component or predictor evaluations, to help catch user errors sooner, and with more informative messages. (version 2.9.0.9013)
• Expand bru_mapper_matrix, previously used only for component model = "fixed", to allow integer indexing in addition to the previous factor/character-only indexing. (version 2.9.0.9014)

Bug fixes

• The is_linear flag wasn't correctly set for bru_mapper_logsumexp mappers. Since previous versions did not accept non-linear component mappers, this is unlikely to have affected any user code. (Fixed in version 2.9.0.9001)
• Improved error messages for missing or incomplete LGCP domain specification. (version 2.9.0.9002 and 2.9.0.9006)
• Allow NULL in automatic component usage detection. (version 2.9.0.9003)
• Corrected the crs information for gorillas$plotsample$counts and gorillas_sf$plotsample$counts from +units=m to +units=km. (version 2.9.0.9010) The geometry information in counts is unlikely to have been used in examples or analysis code, as the problem would have been immediately obvious; plotting or other geometric operations that use the crs information would heve been completely wrong, and is only detected now that more code uses the crs information at all. Thanks to Dmytro Perepolkin for reporting in issue #205
• Fix problem in bru_fill_missing() for cases where the input data object also has missing values. (version 2.9.0.9011)
• Make eval_spatial() transform the where coordinates to the same crs as the input data, for SpatRaster and sf inputs, to allow different crs specifications. (version 2.9.0.9012)

inlabru 2.9.0

Feature updates

• Conversion of code to use fmesher for mesh and geometry handling; the interface supports existing objects and methods. See https://inlabru-org.github.io/fmesher/articles/inla_conversion.html for more information.
• General speed improvements, see below for details.
• Added gg.sf() method.
• Add experimental support for stars via eval_spatial(). (version 2.8.0.9007)
• Move the sp package from 'Depends' to 'Imports'. This means that user code should either use sp:: or library("sp") to access sp methods. The bru_safe_sp() helper function can be used to check for a safe sp package configuration during the transition from rgdal to sf, and is only needed if you may run on systems with sp installations older than "2.0-0" or with sp::get_evolution_status() < 2. (version 2.8.2011)
• Now preserves the previous log output when using bru_rerun(), and bru_log() is now a set of S3 methods, supporting extracting the full inlabru log as well bru-object specific logs (version 2.8.0.9008).

Note: From version 2.9.0, use bru_log() to access the global log, and bru_log(fit) to access a stored estimation log.

Up to version 2.8.0, bru_log() was a deprecated alias for bru_log_message(). When running on 2.8.0 or earlier, use bru_log_get() to access the global log, and cat(fit$bru_iinla$log, sep = "\n") to print a stored estimation object log.

Bug fixes and speed improvements

• Covariate object component inputs of type SpatialPolygonsDataFrame were not automatically passed on to eval_spatial(). The logic has now changed so that any object with a eval_spatial() method will trigger a call to eval_spatial(). See ?input_eval for further information. (version 2.8.0.9001)
• fm_crs_is_null(), fm_transform() now supports oblique fm_crs CRS objects, and is.na() methods for the fm_crs and inla.CRS classes have been added. (version 2.8.0.9003)
• Significant speed up predict() by using quantile(..., names = FALSE). (version 2.8.0.9004)
• Improved row_kron() code, causing speedups of a factor 2-30 in randomised test cases. (version 2.8.0.9005)
• Removed incorrect code for sf method for eval_spatial(), causing failure when extracting from multiple layers in a single call. (version 2.8.0.9007)
• Improved handling of posterior sample variable extraction in generate() and predict(). Now much faster for large models. (version 2.8.0.9009)
• Fixed linearisation issue when using only the *_latent form of a component. (version 2.8.0.9015)
• Workaround for equivalent but textually different CRS/WKT information in bru_fill_missing(). (version 2.8.0.9016, fixes #200)

Deprecation of old functions

• eval_SpatialDF removed, deprecated since 2.8.0. See eval_spatial instead.
• stransform, ibm_amatrix, ibm_valid_input removed, deprecated since 2.7.0. See fm_transform and ibm_jacobian instead.
• bru_mapper_offset, deprecated since 2.6.0 now returns a pure bru_mapper_const object, and all bru_mapper_offset ibm_* methods have been removed.
• init.tutorial removed, deprecated since 2.5.0
• generate.inla and predict.inla removed, deprecated since 2.1.0

inlabru 2.8.0

Feature updates

• The iterative inla method has been given both sharper internal inla() optimisation criteria for the iterations (thanks to Haavard Rue), and a more relaxed nonlinear iteration stopping criterion; the default bru_method$rel_tol values has been changed from 1 to 10 percent change. The iterations are terminated when all latent and hyper-parameter mode changes fullfil |change|/SD < rel_tol, and the non-linear line search is inactive. This seems to strike a useful balance between the different optimisation criteria, allowing the iterations to converge faster and also detect that convergence sooner.
• The logic for which components are needed for a predictor expression (in like() or generate()/predict()) has been updated to when possible extract the list of components from the expression itself. The user can override this default if necessary, using the include/exclude arguments.

The bru_used() methods are used to guess the needed component names, applied to the right-hand side of the formula arguments. The allow_latent argument to like() has been deprecated in favour of include_latent (by default auto-detected for use of _latent and _eval).

The internal information storage is handled by the new bru_used() methods, that can also be used directly by the user and supplied via the used argument to like()/generate()/predict(). Add fm_int() integration methods, replacing the old ipmaker() and ipoints() methods. Supports both sf and sp sampler objects. Add fm_pixels() methods for gridded points. The old pixels() method now calls fm_pixels(..., format = "sp") eval_spatial support for sf objects (for point-in-polygon data lookups) Allow precomputed spatial covariates in the data for point process observations Add edge|int|ext.linewidth arguments to gg.inla.mesh #188 Rename the predict() and generate() data arguments to newdata, for better compatibility with other predict() methods. The old argument name will still be accepted, but give a warning. Code that does not name the data argument is not affected. * Note: Coordinate names for Spatial* objects have been inconsistently available in the predictor expression evaluation. However, due to how internal conversions might inadvertently change these names, they can not be relied on, and they are no longer being made available to the predictor expression. As a side effect, this change also speeds up some bru() runs by around a factor 2, since it avoids converting the Spatial* to a regular data.frame in time-sensitive core evaluation code.

If you need access to the raw coordinate values, use explicit calls to sp::coordinates(.data.) (e.g. for custom spatial covariate evaluation.). When possible, use the built-in covariate evaluation method, eval_spatial(), either implicitly with comp(covariate, ...) or explicitly, comp(eval_spatial(covariate, where = .data.), ...), that handles crs information correctly. Also consider transitioning from sp to sf data storage, using geometry instead of raw coordinates.

Bug and dependency updates

• Remove rgdal and maptools dependencies #178
• Add bru_safe_sp() to check if sp can be used safely (checks rgdal availability and sp evolution status, optionally forcing use of sf) #178
• Remove PROJ4 support #178
• Change rgl.* functions to *3d. Thanks to Duncan Murdoch #181
• Speed up ibm_jacobian.bru_mapper_harmonics for large models
• Add workarounds for inconsistent polygon orientation resulting from sf::st_* calls that don't account for the geos canonical representation being CW, whereas the canonical Simple Features representation being CCW. See https://github.com/r-spatial/sf/issues/2096

inlabru 2.7.0

Feature overview

• Added support for sf and terra inputs to most methods
• Expanded geometry and mesh handling methods
• Expanded bru_mapper() system
• Added convergence diagnostics plot with bru_convergence_plot()

Feature details

• Allow NA input for default 1D mappers to generate effect zero, like in inla().
• New and expanded methods fm_crs(), fm_CRS(), fm_transform(), fm_ellipsoid_radius(), and fm_length_unit() to further support sf objects. The fm_crs() extraction method also supports terra objects.
• bru_fill_missing() now supports terra SpatRaster data and and sf locations.
• New experimental methods fm_evaluator() and fm_evaluate(), replacing the INLA inla.mesh.projector and inla.mesh.project methods.
• Experimental integration support for sphere and globe meshes.
• Allow sf input to family="cp" models.

• Further bru_mapper() method updates;

• Deprecated ibm_amatrix() and names() methods, replaced by ibm_jacobian() and ibm_names().

• Introduced bru_mapper_pipe(), used to link mappers in sequence.
• Introduced bru_mapper_aggregate() and bru_mapper_logsumexp(), used for blockwise weighted sums and log-sum-exp mappings, output[k] = sum(weights[block==k]*state[block==k]))) and output[k] = log(sum(weights[block==k]*exp(state[block==k]))), with optional weight normalisation within each block. Allows providing the weights as log-weights, and uses block-wise shifts to avoid potential overflow.
• summary methods for bru_mapper objects (summary.bru_mapper())
• Removed methods argument from bru_mapper_define(). Implementations should register S3 methods instead.

Bug fixes

• Remove unused spatstat.core dependency. Fixes #165
• Fixed issue with plain mapper evaluation in the ibm_eval.default() and ibm_eval.bru_mapper_collect() methods, where they would return zeros instead of the intended values. The main component evaluation and estimation code was not directly affected as that is based on the bru_mapper_multi() class methods that rely on the Jacobians instead. The bug would therefore mainly have impacted the future, not yet supported nonlinear mapper extensions.
• Fix for eval_spatial.SpatRaster; Work around inconsistent logic in terra::extract(..., layer) when length(layer)==1 or nrow(where)==1. Fixes #169
• Add indexed logical option to bru_mapper_factor(), to allow factor inputs to be mapped to index values, as needed for group and replicate. Fixes #174

inlabru 2.6.0

Features

• Add bru_get_mapper generic, and associated methods for inla.spde and inla.rgeneric objects. This allows inlabru to automatically extract the appropriate bru_mapper object for each model component, and can be used as a hook by external packages implementing new INLA object classes.
• Add a weights argument for like(), for likelihood-specific log-likelihood weights, passed on to the INLA::inla() weights argument. Evaluated in the data context.
• The <component>_eval() methods available in predictor expressions now handle optional scaling weights, like in ordinary component effect evaluation.
• Add terra support for covariate inputs
• The component *_layer arguments are now evaluated in the data context, to allow dynamic layer selection for spatial raster covariates. A new generic eval_spatial() provides support for grid/pixel based Spatial*DataFrame evaluation, and SpatRaster. Expanded support is in progress.
• New vignettes on the bru_mapper system, component definitions, and prediction_scores

• General overhaul of the bru_mapper and linearised predictor system, to prepare for new features.

• Add ibm_eval generic for evaluating mappers for given states.

• Add bru_mapper_taylor, used as an internal mapper for linearised mappers. This and ibm_eval is aimed at future support for nonlinear mappers. Associated new generic methods: ibm_{is_linear,jacobian,linear}.
• New mapper implementations should use ibm_jacobian instead of ibm_amatrix. This allows defining a linearised mapper via ibm_eval(input, state0) + ibm_jacobian(input, state0) %*% (state - state0).
• New mapper class bru_mapper_const, which replaces bru_mapper_offset. bru_mapper_offset is now deprecated and will produce warnings.

Bug fixes

• Enable both datum/ensemble container for ellipsoid information, to support epsg:4326. Fixes #154
• Make duplicated component names an error instead of a warning. Relates to #155
• Fix Tsparse assumptions in row_kron to prepare for Matrix 1.5-2. Fixes #162

inlabru 2.5.3

Features

• Add bru_mapper_harmonics mapper for cos and sin basis sets.
• Allow predict() input data to be be a list.
• Allow arbitrary quantile summaries in predict()
• Remove cv, var, smin, smax summaries from predict()
• Add mean.mc_std_err and sd.mc_std_err output to predict()
• Add robins_subset data set and associated variable coefficient web vignette

Bug fixes

• Propagate multi-likelihood A-matrix information instead of recomputing. Fixes iteration issue for bym2 and other bru_mapper_collect models.
• Turn on predictor summaries during iterations to allow inla.mode="classic" to use proper line search.
• Avoid deprecated Matrix (>=1.4-2) class coercion methods
• Work around for lack of full Matrix and ModelMatrix support for the unique method. Fixes #145

inlabru 2.5.2

• More robust package checks
• More robust namespace and INLA availability checks
• Add package vignette with links to the website examples

inlabru 2.5.1

• Revert to R language features compatible with R 4.0.5
• Use strategy="gaussian" during iterations.

inlabru 2.5.0

Features

• Add bru() timing information in $bru_timings and $bru_iinla$timings
• Add SpatialPolygonsDataFrame support to gg() methods
• Allow accessing E and Ntrials from response_data and data (further special arguments remain to be added)
• deltaIC improvements
• New transformation helper tools bru_{forward/inverse}_transformation()
• Experimental support for matrix and formula component inputs. E.g. with ~ name(~ -1 + a + b + a:b, model = "fixed"), covariate fixed effect interaction specifications can be made. For formula input, MatrixModels::model.Matrix() is called to construct matrix input that is then used as the A-matrix for fixed effects, one per column, added up to form the combined effect.
• Documentation and examples improvements

Bug fixes

• Fix A-matrix construction for evaluate_model() for cases where the inla_f argument matters
• More efficient and robust mesh integration code
• Cleanup of environment handling for component lists

inlabru 2.4.0

Features

• Allow predictors to have different size than the input data. The data argument is now allowed to be a list(), and the new argument response_data allows separate specification of component inputs and response variables.
• Add bru_mapper_collect class for handling sequential collections of mappers, including collections where all but the first mapper is hidden from the INLA::f() arguments n and values, as needed to support e.g. "bym2" models.
• Add control.family as a direct argument to like(). Gives a warning if a control.family argument is supplied to the the options argument of bru(), but at least one likelihood has control.family information. (Issue #109)

Bugfixes

• Fix support for SpatialPointsDataFrame and SpatialGridDataFrame input to bru_fill_missing()
• Force explicit model = "offset" components instead of special options, to avoid interfering with the linearisation system (Issue #123)
• Make the iterations more robust by resetting the internal INLA predictor states to initial value zero at each step

Miscellaneous

• Rename the option bru_method$stop_at_max_rel_deviation to bru_method$rel_tol. Automatic conversion to the new name, but a warning is given.
• Add option bru_method$max_step to control the largest allowed line search scaling factor. See ?bru_options
• New default option bru_compress_cp set to TRUE to compress the predictor expression for family="cp" to use a single element for the linear predictor sum.

inlabru 2.3.1

• Documentation and dependency updates for CRAN compatibility
• See NEWS for version 2.3.0 for the major updates since version 2.1.13

inlabru 2.3.0

Breaking changes 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.

New features since version 2.1.13

• 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

inlabru 2.2.8

• 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.

inlabru 2.2.7

• Add support for ngroup and nrep in component definitions
• Updated mexdolphin and mrsea data sets, with consistent km units and improved mesh designs

inlabru 2.2.6

• Add predict(..., include) discussion to distance sampling vignette, for handling non-spatial prediction in spatial models.
• Fix bugs in gg.SpatialLines

inlabru 2.2.5

• Vignette corrections
• Documentation improvements
• Fix minor bug in Spatial* object handling and plotting

inlabru 2.2.4

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

inlabru 2.2.2

• 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.

inlabru 2.2.1

• Fixed code regression bug for function input of covariates

inlabru 2.2.0

• 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.

inlabru 2.1.15

• 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 objects
• Improved 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)

inlabru 2.1.13

• Fix CRAN complaint regarding documentation

inlabru 2.1.12

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

inlabru 2.1.11

• Add CITATION file

inlabru 2.1.10

• Fix internal sampling bug due to INLA changes

inlabru 2.1.9

• Remove unused VignetteBuilder entry from DESCRIPTION

inlabru 2.1.8

• 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)

inlabru 2.1.7

• 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 algorithm
• Avoid dense matrices for effect mapping

inlabru 2.1.4

• iinla() tracks convergence of both fixed and random effects

inlabru 2.1.3

• Added matrix geom gg.matrix()
• Fixed CRAN test issues

inlabru-org/inlabru documentation built on May 5, 2024, 4:31 p.m.