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Changelog

Source: NEWS.md

MetricGraph (development version)

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.