Rann keep node assignment - #75
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- Introduced `contract_linear_nodes` function in C for efficient contraction of intermediate nodes in undirected graphs. - Added `drop_singletons_linear` helper function in R for linear-time singleton edge peeling. - Updated `consolidate_graph_core` to utilize the new functions, improving performance and functionality. - Enhanced tests to validate the new recursive modes for singleton edge handling and ensure correct behavior in various scenarios.
- Introduced multiple test cases to validate that the C and R implementations of the consolidate_graph function produce equivalent results. - Added a helper function to standardize data frames for comparison by stripping volatile attributes and sorting rows. - Tests cover various scenarios including simple chains, full recursion chains, parallel edge bundles, and weighted chains.
- Improved the merge_linear_nodes function to handle cases where C contraction does not progress, allowing for better error handling and reporting. - Added a condition to break the loop when no further contraction is possible, improving performance and preventing infinite loops. - Updated verbose output to reflect the number of candidates processed during contraction.
- Introduced `legacy_drop_singletons_recursive` function to replicate legacy behavior for dropping singletons. - Added `expect_singleton_peel_equiv` function to compare results of the new `drop_singletons_linear` with the legacy method. - Implemented multiple test cases to validate the equivalence of singleton peeling in various graph structures, including chains and random sparse graphs. - Enhanced test coverage for both recursive and non-recursive modes of singleton edge handling.
- Expanded test cases for `drop_singletons_linear` to include both recursive and non-recursive scenarios. - Introduced tests for varied graph topologies, including star graphs and disconnected components. - Enhanced coverage for random graph structures with multiple seed values to ensure robustness of singleton peeling behavior.
- Introduced `critical_link_analysis` function to compute edge-level detour costs and vulnerability ratios for graphs. - Updated documentation to include new function and its usage. - Added tests to validate the functionality and ensure correct behavior for various graph scenarios, including directed and undirected graphs. - Updated NAMESPACE and package documentation to reflect the new addition.
- Updated the aggregation logic to properly manage cases where no nodes are kept, returning a data frame of groups instead. - Added a new test case to validate the behavior of consolidate_graph with topology-only graphs, ensuring correct output structure and values.
- Added a note in the documentation to clarify that the spatial simplification method does not preserve intra-cluster topology. - Modified the `contract_edges` function to handle cases where the graph has no rows, ensuring proper attribute management and returning an empty graph when necessary. - Adjusted the centroid calculation to maintain consistency in handling dimensions.
Add node assignment helper function for clustering - Introduced `assign_nodes_to_keep` function to streamline the process of identifying nodes close to specified 'keep' nodes within a defined radius. - Updated `cluster_nodes` function to utilize the new helper for improved clarity and efficiency in clustering logic. - Enhanced verbose output for better tracking of processing steps when handling large datasets.
… for larger datasets.
- Introduced a new parameter `nodes.algo.rann` to enable the use of the RANN package for fast 3D Cartesian nearest-neighbor preselection when assigning nodes close to preserved nodes. - Updated the `compute_degrees`, `simplify_network`, and `cluster_nodes` functions to incorporate RANN-based logic. - Enhanced documentation to reflect the new functionality and its requirements. - Added tests to ensure the correctness of RANN-based node assignment against dense assignment methods.
- Updated the coordinate transformation to use the new `lonlat_to_xyz` function for improved accuracy. - Adjusted the epsilon parameter for the dbscan algorithm to utilize the `chord_radius_km` function, enhancing clustering precision. - Ensured that the dbscan function correctly identifies clusters without unassigned noise points.
…tering - Introduced `nearest_lonlat` function to enhance nearest neighbor search using RANN or haversine distance. - Updated `cluster_nodes` and `simplify_network` functions to utilize the new nearest neighbor logic for centroid calculations. - Enhanced verbose output in `simplify_network` to indicate completion of clustering steps and number of clusters identified.
- Introduced a new attribute `keep.edges` in the `contract_edges` function to track the indices of edges retained after clustering. - Updated documentation in `simplify_network` to include details about the `keep.edges` attribute, enhancing clarity on the output structure of the simplified graph.
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