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Changelog

Source: NEWS.md

MetricGraph (development version)

  • fetch_osm() and metric_graph_from_osm() retry transient Overpass failures (HTTP 429/5xx and connection errors) with exponential backoff, controlled by the new retries argument, and endpoint may now be a vector of mirrors tried in order. A failed download no longer leaves the error page behind at cache_path.
  • posterior_crossvalidation() is now the S3 generic from rSPDE, re-exported by MetricGraph, which provides the graph_lme method. Loading rSPDE after MetricGraph therefore no longer masks MetricGraph’s version, and a list of models may mix graph_lme and rspde_lme fits. Requires rSPDE >= 2.6.0.9001.
  • Graph construction no longer materializes dense point-by-edge matrices. metric_graph$new() used to densify the st_is_within_distance() result into an nEdges x nVertices logical matrix before snapping vertices to nearby edges, and snapPointsToLines() (used by add_observations() with data_coords = "spatial", coordinates() and which_component()) built a full nPoints x nEdges distance matrix. Both are now replaced by sparse candidate sets and C++ kernels (snap_points_to_edges_cpp() and a grid-indexed nearest_edge_cpp()), which return the same graphs and the same snapped locations.
  • The edge-edge intersection search (tolerance$edge_edge > 0) also keeps its neighbour list sparse instead of building an nEdges x nEdges logical matrix.
  • Edge weights are no longer copied once per edge split. add_vertices() now records which weight row each new edge inherits and materializes the weight table once, instead of rbind-ing the whole table inside every split_edge() call. set_edge_weights() builds the per-edge weight rows without a [.data.frame call per edge. The values are unchanged but row names of weight rows duplicated by a split are now e.g. "990509915.1" rather than "9905099151".
  • prune_vertices() no longer pays a [.data.frame call per edge when rebuilding the edge attributes, and the serial fallback for closed-loop chains compacts the weight table once instead of once per removed vertex.
  • Added metric_graph$get_largest(), which returns only the largest connected component. It is equivalent to get_components()[[1]] but constructs just that component.
  • Added a mirrored closed-form directional OU covariance fast path for out-trees, including direction-reversed K1 continuity graphs. Reversed river networks now share the K1/K2 C++ pairwise kernel, using a cached Euler/RMQ LCA index and source-normalized transfers instead of allocating R objects or walking parent chains for every covariance pair.
  • Added C++-backed directional alpha-1 edge precision and closed-form directional OU covariance calculations. The C++ paths are now the default, with pure-R reference implementations retained for validation and fallback.
  • Added a packaged-data Mid-Columbia speed example covering K1, K2, reversed-continuity and covariance likelihood evaluation.
  • Fixed a sign-convention inconsistency in the exact α = 2 codes. The observation-/bridge-side covariance blocks treated the endpoint-derivative states as −u′, while the prior precision (Q00 / Qalpha2) and the vertex constraints used +u′. Because both enter the same quadratic forms, α = 2 covariances, likelihoods, posteriors and exact samples were biased on graphs containing cycles.
  • Fixed the same α = 2 sign-convention bug in the profiled-likelihood (v2) code path (profile_lik_core_alpha2 in R/graph_likelihoods_v2.R), which had reimplemented the affected S-matrix construction independently and was not covered by the fix above.
  • Added simulate.metric_graph() S3 method and simulate_parallel() for unconditional prior simulation of Whittle-Matérn fields: Method A (method = "direct", O(m³) per edge), Method B (method = "kriging", O(m) per edge), and the extended method (method = "extended", single sparse Cholesky on the graph with simulation locations promoted to vertices). Both α = 1 and α = 2 are supported.
  • C++ (Rcpp/Eigen) implementations of the per-edge bridge draws, draw_edge_direct_cpp and draw_edge_kriging_cpp, are now the default (impl = "cpp"); the pure-R reference implementations remain available via impl = "R".
  • Updated examples/fast_simulation/run_study.R with warm-up iterations, n_rep = 5 medians, extended n_pts sweep {8,…,2048}, and all three simulation methods.
  • Added examples/fast_simulation/benchmark.R for per-edge R vs C++ speedup and whole-field method comparison.

MetricGraph 1.6.0

CRAN release: 2026-05-06

  • metric_graph now fully supports disconnected graphs, and graph_components has therefore been deprecated.
  • The internal data storage system has been improved to reduce memory requirements.
  • Several improvements to internal methods to speed up the construction and data handling for of very large graphs.
  • Various stability improvements and bug fixes.
  • Added a cross_validation() function for inlabru fits on metric graphs, mirroring rSPDE::cross_validation().
  • Bumped minimum rSPDE version to 2.5.0 and added rlang to Imports.
  • Added various unit tests covering input validation, smoke tests, multi-model comparison, all CV types, inla and inlabru models.

MetricGraph 1.5.1

  • Added precompute_lgcp_graph() to precompute expensive quantities for LGCP models.
  • Added update_graph() method to update graph objects to newer versions of the package.
  • Added lower and upper bounds for hyperparameters in SPDE and LGCP exact models.
  • Improved speed and robustness of the observations_to_vertex method.
  • Converted fem_basis computation to C for improved performance.
  • Updated SPDE result object for exact models.
  • Fixed a prediction bug in graph_lme.
  • Fixed handling of units in edge weights.
  • Fixed documentation macros in graph_lgcp_sim() and lgcp_graph() man pages.

MetricGraph 1.5.0

CRAN release: 2025-05-19

  • Several optimization improvements for the models in graph_lme.
  • Added a parallel option to posterior_crossvalidation.
  • Created an INLA interface for LGCP processes on metric graphs.

MetricGraph 1.4.1

CRAN release: 2025-03-02

  • Adding selected inverse function, for computing the inverse matrix elements only on nonzero entries of the original sparse matrix.
  • Adjusts on add_observations() and plot_function() methods.
  • Adding helper functions to use stlnpp objects.

MetricGraph 1.4.0

CRAN release: 2024-12-13

  • Added an INLA implementation for alpha=2.
  • Added a vignette for handling multiple likelihoods in R-INLA and inlabru, and updated the graph_spde_data() function for such cases.
  • Added an INLA implementation for directional models.
  • Added support for directional edge weights.
  • Added support for creating metric graphs from SSN, osmdata_sp and osmdata_sf objects. In such cases, if available, edge weights and data will be automatically added to the graph.
  • Now if one creates the metric graph from SpatialLinesDataFrame, LINESTRING, MULTILINESTRING, etc., if the object contain edge data, they will be automatically added as edge weights.
  • Added an option to not perform merges (which is now the default), that makes the graph creation faster and using less memory.
  • Added vignettes with a river example and with an example of directional models.
  • Updated the vignettes to account for the additions.
  • prune_vertices now has an option to avoid creating circles when pruning.
  • Several updates and quality of life improvements for building very large graphs faster.
  • Added the export() method, that allows one to export a MetricGraph object as an sf, sp or SSN2 object.
  • Added wrappers for leaflet and mapview as methods.
  • Added get_edges() and get_vertices() methods were created, that return the edges and vertices, respectively, in either ‘sf’, ‘sp’ or the internal formats.
  • Added an option format to the get_data() method that allows one to also return the data in sf or sp formats.
  • The plot method now has an argument type, that now also allows one to set type to mapview, thus it can return ggplot2, plotly and mapview objects.
  • Adding methods to do data manipulation on weights, mutate_weight, select_weights, filter_weights, summarise_weights and drop_na_weights. They have a format argument that allows one to also return sf or sp objects.
  • Updated the methods, mutate, filter, select, drop_na and summarise to have a format argument to also return sf or sp objects.
  • Massive improvement on the observation_to_vertex method.
  • Massive improvement on the metric graph creation speed.
  • Deprecated improve_plot option, as now all plots from plot_function() method are improved.
  • Added merge_strategy option for add_observations() method, for handling observations that are very close.
  • Update the metric graph data vignette for illustrating how to use the new tools for data manipulation.
  • Massive improvement for building constraint matrices for alpha=2, and for building directional constraints.
  • Updated starting values to use bounding boxes to be more efficient.

MetricGraph 1.3.0

CRAN release: 2024-02-27

  • Handlers were added in add_observations() for situations where observations are projected at the same location, specifically for the duplicated_strategy argument.
  • A simulate method was added for graph_lme objects.
  • The possibility of fixing parameters during estimation was added.
  • The Spoints argument in add_observations() has been deprecated. Now, SpatialPointsDataFrame can be added directly in the data argument.
  • sf objects containing data can also be directly added using the add_observations() method in the data argument.
  • The option of using a graph_lme object to provide starting values when fitting a model using graph_lme() was added.
  • The option of fitting a directional Whittle-Matérn model with alpha=1 when using graph_lme() was added.
  • The kirchhoff_weights argument was added to obtain weights for Kirchhoff vertex conditions from edge_weights.
  • Handling of edge weights was improved. For example, if pruning changes any edge weight, a warning will be given.
  • The edgeweight_to_data() method was added to turn edge weights into data in the internal metric graph format.
  • edge_weight and edge_width_weight were added to the plot() method so that plots on metric graphs can be produced with the weights providing colors to the edges, and also with (possibly different) weights providing the thickness of the edges.
  • edge_weights were added to graph_components so that the connected components will have the correct corresponding edge weights.
  • edge_weight and edge_width_weight were added to the plot_function() method, where they work in a similar manner to their counterparts for the plot() method. The difference is that the weights are plotted as piecewise constant functions.
  • The prune_vertices now has an option to not prune vertices whose edges have incompatible edge weights.
  • The plot method has an interactive argument that returns the 2D plot as a plotly object, which is interactive when using ggplotly.
  • The dependency on the viridis package has been removed.

MetricGraph 1.2.0

CRAN release: 2023-11-07

  • Changed argument data to newdata in predict methods. The argument data was deprecated.
  • Bugfixes on sample_spde and when adding observations based on Euclidean positions.
  • Added options vertex_unit and length_unit on graph creations. Units are given in edge lengths with the get_edge_lengths() method.
  • Added a method to check if the graph is a tree.
  • The graph construction was thoroughly refactored. The resulting construction is faster and cleaner.
  • The graph constructions now accepts list of coordinates (where the coordinates are given as either matrices or data frames), SpatialLines, SpatialLinesDataFrames or MULTILINESTRING.
  • Adding two options (sf package or sp package) for handling longlat by using the which_longlat option.
  • Adding crs (if using sf) and proj4string (if using sp) for handling general coordinate reference systems.
  • Moving data to the private environment.
  • Several data manipulation helper tools and methods were introduced, together with a vignette with a brief tutorial on these tools.
  • The method mesh_A() has been deprecated, use fem_basis() instead.
  • Several quality of life improvements.
  • Improved the plot() method with the option plotly=TRUE.
  • Improved the plot_function() method to accept data and newdata.
  • Included a process_data() method for metric graphs
  • Renamed the data internal structure from “__group”, “__edge_number”, “__distance_on_edge”, “__coord_x”, “__coord_y” to “.group”, “.edge_number”, “.distance_on_edge”, “.coord_x” and “.coord_y”.
  • Added an “advanced grouping” option, in which the group variable can be a combination of several columns.
  • Improved graph_lme() behavior to avoid having NaN as std.errors.
  • Added check for distance consistency and, more generally, check to see if the graph has euclidean edges.
  • Added method get_groups() to get the unique groups, and also to retrieve the columns that were used to create the group variable.
  • Added the get_data() method to get the data in a user-friendly manner.
  • Added glance() and augment() methods for graph_lme() objects.
  • Added get_vertices_incomp_dir() method to return vertices with incompatible directions.
  • Added print(), summary(), compute_characteristics(), check_euclidean(), check_distance_consistency() methods.
  • Added support for edge weights.
  • Created vertices element in the metric graph object, containing information such as degrees, indegrees, outdegrees.
  • Created print methods for edges, vertices, and for their entries.
  • Added the improve_plot option on plot_function.
  • Added support for discontinuous meshes (at the vertices).
  • Added support for discontinuous functions (at the vertices) for plot_function().

MetricGraph 1.1.2

CRAN release: 2023-07-04

  • Adjusts to ensure compatibility with future releases of the Matrix package.

MetricGraph 1.1.1

CRAN release: 2023-06-01

  • Adjusts on documentation for CRAN.

MetricGraph 1.1.0

  • Improved the documentation.
  • Reorganized some functions.

MetricGraph 1.0.0

  • First version of the package.