Title: Graph/Network Visualization
Description: Build graph/network structures using functions for stepwise
addition and deletion of nodes and edges. Work with data available in
tables for bulk addition of nodes, edges, and associated metadata. Use
graph selections and traversals to apply changes to specific nodes or
edges. A wide selection of graph algorithms allow for the analysis of
graphs. Visualize the graphs and take advantage of any aesthetic
properties assigned to nodes and edges.
Author: Richard Iannone [aut, cre] ,
Olivier Roy [aut]
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 1.0.10 dated 2023-05-18 and 1.0.11 dated 2024-02-02
DiagrammeR-1.0.10/DiagrammeR/R/pipe.R |only DiagrammeR-1.0.11/DiagrammeR/DESCRIPTION | 53 DiagrammeR-1.0.11/DiagrammeR/MD5 | 743 +++++----- DiagrammeR-1.0.11/DiagrammeR/NEWS.md | 81 - DiagrammeR-1.0.11/DiagrammeR/R/DiagrammeR-package.R |only DiagrammeR-1.0.11/DiagrammeR/R/DiagrammeR.R | 29 DiagrammeR-1.0.11/DiagrammeR/R/add_balanced_tree.R | 74 DiagrammeR-1.0.11/DiagrammeR/R/add_cycle.R | 65 DiagrammeR-1.0.11/DiagrammeR/R/add_edge.R | 93 - DiagrammeR-1.0.11/DiagrammeR/R/add_edge_clone.R | 52 DiagrammeR-1.0.11/DiagrammeR/R/add_edge_df.R | 27 DiagrammeR-1.0.11/DiagrammeR/R/add_edges_from_table.R | 99 - DiagrammeR-1.0.11/DiagrammeR/R/add_edges_w_string.R | 32 DiagrammeR-1.0.11/DiagrammeR/R/add_forward_edges_ws.R | 44 DiagrammeR-1.0.11/DiagrammeR/R/add_full_graph.R | 114 - DiagrammeR-1.0.11/DiagrammeR/R/add_global_graph_attrs.R | 36 DiagrammeR-1.0.11/DiagrammeR/R/add_gnm_graph.R | 66 DiagrammeR-1.0.11/DiagrammeR/R/add_gnp_graph.R | 65 DiagrammeR-1.0.11/DiagrammeR/R/add_graph_action.R | 37 DiagrammeR-1.0.11/DiagrammeR/R/add_graph_to_graph_series.R | 18 DiagrammeR-1.0.11/DiagrammeR/R/add_grid_2d.R | 78 - DiagrammeR-1.0.11/DiagrammeR/R/add_grid_3d.R | 93 - DiagrammeR-1.0.11/DiagrammeR/R/add_growing_graph.R | 65 DiagrammeR-1.0.11/DiagrammeR/R/add_islands_graph.R | 58 DiagrammeR-1.0.11/DiagrammeR/R/add_n_node_clones.R | 66 DiagrammeR-1.0.11/DiagrammeR/R/add_n_nodes.R | 46 DiagrammeR-1.0.11/DiagrammeR/R/add_n_nodes_ws.R | 124 - DiagrammeR-1.0.11/DiagrammeR/R/add_node.R | 353 ++-- DiagrammeR-1.0.11/DiagrammeR/R/add_node_clones_ws.R | 59 DiagrammeR-1.0.11/DiagrammeR/R/add_node_df.R | 22 DiagrammeR-1.0.11/DiagrammeR/R/add_nodes_from_df_cols.R | 42 DiagrammeR-1.0.11/DiagrammeR/R/add_nodes_from_table.R | 36 DiagrammeR-1.0.11/DiagrammeR/R/add_pa_graph.R | 72 DiagrammeR-1.0.11/DiagrammeR/R/add_path.R | 67 DiagrammeR-1.0.11/DiagrammeR/R/add_prism.R | 85 - DiagrammeR-1.0.11/DiagrammeR/R/add_reverse_edges_ws.R | 60 DiagrammeR-1.0.11/DiagrammeR/R/add_smallworld_graph.R | 58 DiagrammeR-1.0.11/DiagrammeR/R/add_star.R | 65 DiagrammeR-1.0.11/DiagrammeR/R/base64.R | 7 DiagrammeR-1.0.11/DiagrammeR/R/clear_selection.R | 18 DiagrammeR-1.0.11/DiagrammeR/R/colorize_edge_attrs.R | 42 DiagrammeR-1.0.11/DiagrammeR/R/colorize_node_attrs.R | 42 DiagrammeR-1.0.11/DiagrammeR/R/combine_edfs.R | 8 DiagrammeR-1.0.11/DiagrammeR/R/combine_graphs.R | 63 DiagrammeR-1.0.11/DiagrammeR/R/combine_ndfs.R | 6 DiagrammeR-1.0.11/DiagrammeR/R/copy_edge_attrs.R | 33 DiagrammeR-1.0.11/DiagrammeR/R/copy_node_attrs.R | 33 DiagrammeR-1.0.11/DiagrammeR/R/count_asymmetric_node_pairs.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/count_automorphisms.R | 20 DiagrammeR-1.0.11/DiagrammeR/R/count_edges.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/count_graphs_in_graph_series.R | 2 DiagrammeR-1.0.11/DiagrammeR/R/count_loop_edges.R | 19 DiagrammeR-1.0.11/DiagrammeR/R/count_mutual_node_pairs.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/count_nodes.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/count_s_connected_cmpts.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/count_unconnected_node_pairs.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/count_unconnected_nodes.R | 28 DiagrammeR-1.0.11/DiagrammeR/R/count_w_connected_cmpts.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/create_edge_df.R | 26 DiagrammeR-1.0.11/DiagrammeR/R/create_graph.R | 148 + DiagrammeR-1.0.11/DiagrammeR/R/create_graph_series.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/create_node_df.R | 95 - DiagrammeR-1.0.11/DiagrammeR/R/delete_cache.R | 35 DiagrammeR-1.0.11/DiagrammeR/R/delete_edge.R | 120 - DiagrammeR-1.0.11/DiagrammeR/R/delete_edges_ws.R | 42 DiagrammeR-1.0.11/DiagrammeR/R/delete_global_graph_attrs.R | 38 DiagrammeR-1.0.11/DiagrammeR/R/delete_graph_actions.R | 31 DiagrammeR-1.0.11/DiagrammeR/R/delete_loop_edges_ws.R | 34 DiagrammeR-1.0.11/DiagrammeR/R/delete_node.R | 42 DiagrammeR-1.0.11/DiagrammeR/R/delete_nodes_ws.R | 36 DiagrammeR-1.0.11/DiagrammeR/R/deselect_edges.R | 17 DiagrammeR-1.0.11/DiagrammeR/R/deselect_nodes.R | 17 DiagrammeR-1.0.11/DiagrammeR/R/display_metagraph.R | 39 DiagrammeR-1.0.11/DiagrammeR/R/do_bfs.R | 30 DiagrammeR-1.0.11/DiagrammeR/R/do_dfs.R | 29 DiagrammeR-1.0.11/DiagrammeR/R/docs_node_edge_aes_data.R | 2 DiagrammeR-1.0.11/DiagrammeR/R/drop_edge_attrs.R | 30 DiagrammeR-1.0.11/DiagrammeR/R/drop_node_attrs.R | 33 DiagrammeR-1.0.11/DiagrammeR/R/edge_aes.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/edge_data.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/export_csv.R | 16 DiagrammeR-1.0.11/DiagrammeR/R/export_graph.R | 115 - DiagrammeR-1.0.11/DiagrammeR/R/filter_graph_series.R | 17 DiagrammeR-1.0.11/DiagrammeR/R/from_adj_matrix.R | 20 DiagrammeR-1.0.11/DiagrammeR/R/from_igraph.R | 9 DiagrammeR-1.0.11/DiagrammeR/R/fully_connect_nodes_ws.R | 36 DiagrammeR-1.0.11/DiagrammeR/R/fully_disconnect_nodes_ws.R | 38 DiagrammeR-1.0.11/DiagrammeR/R/generate_dot.R | 136 - DiagrammeR-1.0.11/DiagrammeR/R/get_adhesion.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_agg_degree_in.R | 33 DiagrammeR-1.0.11/DiagrammeR/R/get_agg_degree_out.R | 34 DiagrammeR-1.0.11/DiagrammeR/R/get_agg_degree_total.R | 34 DiagrammeR-1.0.11/DiagrammeR/R/get_all_connected_nodes.R | 15 DiagrammeR-1.0.11/DiagrammeR/R/get_alpha_centrality.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/get_articulation_points.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/get_authority_centrality.R | 40 DiagrammeR-1.0.11/DiagrammeR/R/get_betweenness.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/get_cache.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/get_closeness.R | 17 DiagrammeR-1.0.11/DiagrammeR/R/get_closeness_vitality.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_cmty_edge_btwns.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/get_cmty_fast_greedy.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/get_cmty_l_eigenvec.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/get_cmty_louvain.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/get_cmty_walktrap.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/get_common_nbrs.R | 16 DiagrammeR-1.0.11/DiagrammeR/R/get_coreness.R | 17 DiagrammeR-1.0.11/DiagrammeR/R/get_degree_distribution.R | 23 DiagrammeR-1.0.11/DiagrammeR/R/get_degree_histogram.R | 25 DiagrammeR-1.0.11/DiagrammeR/R/get_degree_in.R | 14 DiagrammeR-1.0.11/DiagrammeR/R/get_degree_out.R | 14 DiagrammeR-1.0.11/DiagrammeR/R/get_degree_total.R | 14 DiagrammeR-1.0.11/DiagrammeR/R/get_dice_similarity.R | 15 DiagrammeR-1.0.11/DiagrammeR/R/get_eccentricity.R | 17 DiagrammeR-1.0.11/DiagrammeR/R/get_edge_attrs.R | 33 DiagrammeR-1.0.11/DiagrammeR/R/get_edge_attrs_ws.R | 23 DiagrammeR-1.0.11/DiagrammeR/R/get_edge_count_w_multiedge.R | 23 DiagrammeR-1.0.11/DiagrammeR/R/get_edge_df.R | 13 DiagrammeR-1.0.11/DiagrammeR/R/get_edge_df_ws.R | 17 DiagrammeR-1.0.11/DiagrammeR/R/get_edge_ids.R | 14 DiagrammeR-1.0.11/DiagrammeR/R/get_edge_info.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/get_edges.R | 19 DiagrammeR-1.0.11/DiagrammeR/R/get_eigen_centrality.R | 45 DiagrammeR-1.0.11/DiagrammeR/R/get_girth.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_global_graph_attr_info.R | 17 DiagrammeR-1.0.11/DiagrammeR/R/get_graph_actions.R | 16 DiagrammeR-1.0.11/DiagrammeR/R/get_graph_from_graph_series.R | 14 DiagrammeR-1.0.11/DiagrammeR/R/get_graph_info.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_graph_log.R | 16 DiagrammeR-1.0.11/DiagrammeR/R/get_graph_name.R | 13 DiagrammeR-1.0.11/DiagrammeR/R/get_graph_series_info.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_graph_time.R | 13 DiagrammeR-1.0.11/DiagrammeR/R/get_jaccard_similarity.R | 76 - DiagrammeR-1.0.11/DiagrammeR/R/get_last_edges_created.R | 56 DiagrammeR-1.0.11/DiagrammeR/R/get_last_nodes_created.R | 50 DiagrammeR-1.0.11/DiagrammeR/R/get_leverage_centrality.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_max_eccentricity.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_mean_distance.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_min_cut_between.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_min_eccentricity.R | 19 DiagrammeR-1.0.11/DiagrammeR/R/get_multiedge_count.R | 20 DiagrammeR-1.0.11/DiagrammeR/R/get_nbrs.R | 14 DiagrammeR-1.0.11/DiagrammeR/R/get_node_attrs.R | 16 DiagrammeR-1.0.11/DiagrammeR/R/get_node_attrs_ws.R | 23 DiagrammeR-1.0.11/DiagrammeR/R/get_node_df.R | 13 DiagrammeR-1.0.11/DiagrammeR/R/get_node_df_ws.R | 17 DiagrammeR-1.0.11/DiagrammeR/R/get_node_ids.R | 20 DiagrammeR-1.0.11/DiagrammeR/R/get_node_info.R | 24 DiagrammeR-1.0.11/DiagrammeR/R/get_non_nbrs.R | 14 DiagrammeR-1.0.11/DiagrammeR/R/get_pagerank.R | 16 DiagrammeR-1.0.11/DiagrammeR/R/get_paths.R | 82 - DiagrammeR-1.0.11/DiagrammeR/R/get_periphery.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_predecessors.R | 18 DiagrammeR-1.0.11/DiagrammeR/R/get_radiality.R | 30 DiagrammeR-1.0.11/DiagrammeR/R/get_reciprocity.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/get_s_connected_cmpts.R | 14 DiagrammeR-1.0.11/DiagrammeR/R/get_selection.R | 18 DiagrammeR-1.0.11/DiagrammeR/R/get_similar_nbrs.R | 28 DiagrammeR-1.0.11/DiagrammeR/R/get_successors.R | 18 DiagrammeR-1.0.11/DiagrammeR/R/get_w_connected_cmpts.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/grViz.R | 9 DiagrammeR-1.0.11/DiagrammeR/R/graph-type-check.R |only DiagrammeR-1.0.11/DiagrammeR/R/import-standalone-obj-type.R |only DiagrammeR-1.0.11/DiagrammeR/R/import-standalone-types-check.R |only DiagrammeR-1.0.11/DiagrammeR/R/import_graph.R | 120 - DiagrammeR-1.0.11/DiagrammeR/R/invert_selection.R | 28 DiagrammeR-1.0.11/DiagrammeR/R/is_edge_loop.R | 45 DiagrammeR-1.0.11/DiagrammeR/R/is_edge_multiple.R | 55 DiagrammeR-1.0.11/DiagrammeR/R/is_edge_mutual.R | 54 DiagrammeR-1.0.11/DiagrammeR/R/is_edge_present.R | 94 - DiagrammeR-1.0.11/DiagrammeR/R/is_graph_connected.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/is_graph_dag.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/is_graph_directed.R | 13 DiagrammeR-1.0.11/DiagrammeR/R/is_graph_empty.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/is_graph_simple.R | 10 DiagrammeR-1.0.11/DiagrammeR/R/is_graph_undirected.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/is_graph_weighted.R | 24 DiagrammeR-1.0.11/DiagrammeR/R/is_node_present.R | 30 DiagrammeR-1.0.11/DiagrammeR/R/is_property_graph.R | 27 DiagrammeR-1.0.11/DiagrammeR/R/join_edge_attrs.R | 38 DiagrammeR-1.0.11/DiagrammeR/R/join_node_attrs.R | 38 DiagrammeR-1.0.11/DiagrammeR/R/layout_nodes_w_string.R | 46 DiagrammeR-1.0.11/DiagrammeR/R/mermaid.R | 5 DiagrammeR-1.0.11/DiagrammeR/R/mutate_edge_attrs.R | 36 DiagrammeR-1.0.11/DiagrammeR/R/mutate_edge_attrs_ws.R | 47 DiagrammeR-1.0.11/DiagrammeR/R/mutate_node_attrs.R | 32 DiagrammeR-1.0.11/DiagrammeR/R/mutate_node_attrs_ws.R | 43 DiagrammeR-1.0.11/DiagrammeR/R/node_aes.R | 6 DiagrammeR-1.0.11/DiagrammeR/R/node_data.R | 12 DiagrammeR-1.0.11/DiagrammeR/R/nudge_node_positions_ws.R | 44 DiagrammeR-1.0.11/DiagrammeR/R/open_graph.R | 25 DiagrammeR-1.0.11/DiagrammeR/R/print.R | 94 - DiagrammeR-1.0.11/DiagrammeR/R/recode_edge_attrs.R | 39 DiagrammeR-1.0.11/DiagrammeR/R/recode_node_attrs.R | 39 DiagrammeR-1.0.11/DiagrammeR/R/remove_graph_from_graph_series.R | 2 DiagrammeR-1.0.11/DiagrammeR/R/rename_edge_attrs.R | 49 DiagrammeR-1.0.11/DiagrammeR/R/rename_node_attrs.R | 45 DiagrammeR-1.0.11/DiagrammeR/R/render_graph.R | 696 ++++----- DiagrammeR-1.0.11/DiagrammeR/R/render_graph_from_graph_series.R | 13 DiagrammeR-1.0.11/DiagrammeR/R/reorder_graph_actions.R | 30 DiagrammeR-1.0.11/DiagrammeR/R/rescale_edge_attrs.R | 56 DiagrammeR-1.0.11/DiagrammeR/R/rescale_node_attrs.R | 52 DiagrammeR-1.0.11/DiagrammeR/R/rev_edge_dir.R | 30 DiagrammeR-1.0.11/DiagrammeR/R/rev_edge_dir_ws.R | 44 DiagrammeR-1.0.11/DiagrammeR/R/save_graph.R | 31 DiagrammeR-1.0.11/DiagrammeR/R/select_edges.R | 72 DiagrammeR-1.0.11/DiagrammeR/R/select_edges_by_edge_id.R | 29 DiagrammeR-1.0.11/DiagrammeR/R/select_edges_by_node_id.R | 36 DiagrammeR-1.0.11/DiagrammeR/R/select_last_edges_created.R | 54 DiagrammeR-1.0.11/DiagrammeR/R/select_last_nodes_created.R | 58 DiagrammeR-1.0.11/DiagrammeR/R/select_nodes.R | 51 DiagrammeR-1.0.11/DiagrammeR/R/select_nodes_by_degree.R | 30 DiagrammeR-1.0.11/DiagrammeR/R/select_nodes_by_id.R | 33 DiagrammeR-1.0.11/DiagrammeR/R/select_nodes_in_neighborhood.R | 30 DiagrammeR-1.0.11/DiagrammeR/R/set_cache.R | 27 DiagrammeR-1.0.11/DiagrammeR/R/set_edge_attr_to_display.R | 72 DiagrammeR-1.0.11/DiagrammeR/R/set_edge_attrs.R | 46 DiagrammeR-1.0.11/DiagrammeR/R/set_edge_attrs_ws.R | 32 DiagrammeR-1.0.11/DiagrammeR/R/set_graph_directed.R | 15 DiagrammeR-1.0.11/DiagrammeR/R/set_graph_name.R | 15 DiagrammeR-1.0.11/DiagrammeR/R/set_graph_time.R | 31 DiagrammeR-1.0.11/DiagrammeR/R/set_graph_undirected.R | 15 DiagrammeR-1.0.11/DiagrammeR/R/set_node_attr_to_display.R | 77 - 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DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-add_nodes_edges_from_table.R | 461 +++--- DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-cache_attrs.R | 47 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-colorize_nodes_edges.R | 59 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-combine_graphs.R | 59 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-copy_drop_mutate_recode_attrs.R | 34 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-count_entities.R | 17 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-create_combine_edges.R | 16 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-create_combine_nodes.R | 62 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-create_graph.R | 187 +- DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-create_subgraph.R | 33 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-degree_total_in_out.R | 14 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-delete_node_edge.R | 21 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-dfs_bfs.R | 65 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-generate_dot.R | 6 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-get_aggregate_degree.R | 2 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-get_cmty.R | 45 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-get_graph_metrics.R | 79 - 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DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-traversals_copying_attr_vals.R | 2 DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-write_graph_backup.R | 131 - DiagrammeR-1.0.11/DiagrammeR/tests/testthat/test-x11_hex.R | 18 370 files changed, 6306 insertions(+), 9749 deletions(-)
Title: Collection of Helper Functions
Description: Provides a collection of lightweight helper functions (imps) both
for interactive use and for inclusion within other packages. These include
functions for visualising colour palettes, quoting user input, searching rows
of a data frame and capturing string tokens.
Author: Tim Taylor [aut, cre, cph] ,
R Core Team [cph] ,
Toby Hocking [cph]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ympes versions 0.5.0 dated 2023-11-03 and 1.0.0 dated 2024-02-02
ympes-0.5.0/ympes/R/defunct.R |only ympes-0.5.0/ympes/man/assertions.Rd |only ympes-0.5.0/ympes/man/ympes-defunct.Rd |only ympes-1.0.0/ympes/DESCRIPTION | 43 ++-- ympes-1.0.0/ympes/MD5 | 26 +- ympes-1.0.0/ympes/NAMESPACE | 42 --- ympes-1.0.0/ympes/NEWS.md | 11 + ympes-1.0.0/ympes/R/assert.R | 197 +++++------------- ympes-1.0.0/ympes/R/fstrcapture.R |only ympes-1.0.0/ympes/R/greprows.R | 10 ympes-1.0.0/ympes/README.md | 14 - ympes-1.0.0/ympes/inst/tinytest/test_assertions.R | 222 ++++++++++----------- ympes-1.0.0/ympes/inst/tinytest/test_fstrcapture.R |only ympes-1.0.0/ympes/man/fstrcapture.Rd |only ympes-1.0.0/ympes/man/greprows.Rd | 2 ympes-1.0.0/ympes/man/ympes-package.Rd | 12 - ympes-1.0.0/ympes/tests/tinytest.R | 1 17 files changed, 242 insertions(+), 338 deletions(-)
Title: Quantile Composite Path Modeling
Description: Implements the Quantile Composite-based Path Modeling approach
(Davino and Vinzi, 2016 <doi:10.1007/s11634-015-0231-9>;
Dolce et al., 2021 <doi:10.1007/s11634-021-00469-0>). The method complements the traditional PLS Path Modeling approach, analyzing the entire distribution of outcome variables and, therefore, overcoming the classical exploration of only average effects. It exploits quantile regression to investigate changes in the relationships among constructs and between constructs and observed variables.
Author: Giuseppe Lamberti [aut, cre],
Cristina Davino [ctb],
Pasquale Dolce [ctb],
Domenico Vistocco [ctb]
Maintainer: Giuseppe Lamberti <giuseppelamb@hotmail.com>
Diff between qcpm versions 0.2 dated 2022-04-06 and 0.3 dated 2024-02-02
qcpm-0.2/qcpm/R/07_thresholds.R |only qcpm-0.2/qcpm/man/thresholds.Rd |only qcpm-0.3/qcpm/DESCRIPTION | 6 ++-- qcpm-0.3/qcpm/MD5 | 24 +++++++--------- qcpm-0.3/qcpm/NAMESPACE | 1 qcpm-0.3/qcpm/R/01_province_data.R | 52 +++++++++++++++++------------------ qcpm-0.3/qcpm/R/02_qcpm.R | 44 +++++++++++++++++++----------- qcpm-0.3/qcpm/R/04_assessment.R | 8 ++++- qcpm-0.3/qcpm/R/05_boot.R | 18 +++++++++--- qcpm-0.3/qcpm/R/06_reliability.R | 2 - qcpm-0.3/qcpm/R/get_element.R | 2 - qcpm-0.3/qcpm/R/get_paths.R | 7 ++-- qcpm-0.3/qcpm/man/get_names_MV.Rd | 2 - qcpm-0.3/qcpm/man/province.Rd | 54 ++++++++++++++++++------------------- 14 files changed, 123 insertions(+), 97 deletions(-)
Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file forma [...truncated...]
Author: Tim Schaefer [aut, cre]
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between freesurferformats versions 0.1.17 dated 2022-02-11 and 0.1.18 dated 2024-02-02
DESCRIPTION | 14 LICENSE | 4 MD5 | 84 NAMESPACE | 1 R/helpers.R | 224 +- R/read_fs_annot.R | 1338 +++++++------- R/read_fs_curv.R | 568 +++--- R/read_fs_surface.R | 2960 ++++++++++++++++----------------- R/read_fs_transform.R | 549 +++--- R/write_fs_annot.R | 444 ++-- R/write_fs_curv.R | 624 +++--- R/write_fs_label.R | 252 +- R/write_fs_mgh.R | 514 ++--- R/write_fs_surface.R | 1660 +++++++++--------- build/vignette.rds |binary inst/doc/freesurferformats.R | 252 +- inst/doc/freesurferformats.html | 1139 ++++++++---- inst/doc/freesurferformats_header.R | 44 inst/doc/freesurferformats_header.html | 656 ++++--- inst/doc/freesurferformats_write.R | 100 - inst/doc/freesurferformats_write.html | 783 +++++--- man/assert.surface.Rd | 6 man/check.dtype.for.data.Rd | 6 man/fread3.Rd | 4 man/fwrite3.Rd | 4 man/has_pandoc.Rd | 30 man/polygon.soup.to.indexed.mesh.Rd | 4 man/read.fs.annot.Rd | 94 - man/read.fs.annot.gii.Rd | 76 man/write.fs.annot.Rd | 114 - man/write.fs.annot.gii.Rd | 96 - man/write.fs.label.Rd | 106 - man/write.fs.surface.Rd | 134 - man/write.fs.surface.asc.Rd | 114 - man/write.fs.surface.byu.Rd | 118 - man/write.fs.surface.gii.Rd | 124 - man/write.fs.surface.mz3.Rd | 122 - man/write.fs.surface.obj.Rd | 94 - man/write.fs.surface.off.Rd | 90 - man/write.fs.surface.off.ply2.Rd | 96 - man/write.fs.surface.ply.Rd | 104 - man/write.fs.surface.ply2.Rd | 84 man/write.fs.surface.vtk.Rd | 112 - 43 files changed, 7389 insertions(+), 6553 deletions(-)
More information about freesurferformats at CRAN
Permanent link
Title: Access and Analyze Data from 'DeFiLlama'
Description: Provides an interface to access and analyze data from
'DeFiLlama'<https://defillama.com>. This package simplifies the
process of fetching and manipulating 'DeFiLlama' data for further
analysis and visualization.
Author: Alexey Ivanov [aut, cre, cph]
Maintainer: Alexey Ivanov <twor.2r@gmail.com>
Diff between rllama versions 0.4.3 dated 2023-11-28 and 0.4.4 dated 2024-02-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/get_defillama_protocol_tvl.R | 2 +- R/get_defillama_stablecoin_data.R | 3 ++- man/get_defillama_stablecoin_data.Rd | 2 +- 6 files changed, 16 insertions(+), 11 deletions(-)
Title: Download and Manage Optional Package Data
Description: Manage optional data for your package. The data can be hosted anywhere, and you have to give a Uniform Resource Locator (URL) for each file. File integrity checks are supported. This is useful for package authors who need to ship more than the 5 Megabyte of data currently allowed by the the Comprehensive R Archive Network (CRAN).
Author: Tim Schaefer [aut, cre]
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between pkgfilecache versions 0.1.4 dated 2021-05-17 and 0.1.5 dated 2024-02-02
DESCRIPTION | 10 LICENSE | 4 MD5 | 60 - NAMESPACE | 22 R/filecache.R | 920 ++++++++++---------- build/vignette.rds |binary inst/doc/pkgfilecache.R | 178 +-- inst/doc/pkgfilecache.Rmd | 416 ++++----- inst/doc/pkgfilecache.html | 910 ++++++++++++------- inst/extdata/file1.txt | 2 inst/extdata/file2.txt | 2 man/are_files_available.Rd | 52 - man/download_files_with_md5_mismatch.Rd | 52 - man/ensure_files_available.Rd | 98 +- man/erase_file_cache.Rd | 34 man/files_exist_md5.Rd | 40 man/flatten_filepath.Rd | 36 man/get_abs_filenames.Rd | 40 man/get_absolute_path_for_files.Rd | 50 - man/get_cache_dir.Rd | 46 - man/get_filepath.Rd | 52 - man/get_pkg_info.Rd | 54 - man/get_relative_file_subdir.Rd | 40 man/list_available.Rd | 44 man/make_pgk_cache_subdir_for_all_relative_files.Rd | 34 man/make_pgk_cache_subdir_for_relative_file.Rd | 34 man/remove_cached_files.Rd | 48 - tests/testthat.R | 8 tests/testthat/teardown-cran.R | 14 tests/testthat/test-filecache.R | 700 +++++++-------- vignettes/pkgfilecache.Rmd | 416 ++++----- 31 files changed, 2346 insertions(+), 2070 deletions(-)
Title: Generalized Autoregressive Score Models
Description: Estimation, forecasting, and simulation of generalized
autoregressive score (GAS) models of Creal, Koopman, and Lucas (2013)
<doi:10.1002/jae.1279> and Harvey (2013) <doi:10.1017/cbo9781139540933>.
Model specification allows for various data types and distributions,
different parametrizations, exogenous variables, joint and separate modeling
of exogenous variables and dynamics, higher score and autoregressive orders,
custom and unconditional initial values of time-varying parameters, fixed
and bounded values of coefficients, and missing values. Model estimation is
performed by the maximum likelihood method.
Author: Vladimir Holy [aut, cre]
Maintainer: Vladimir Holy <vladimir.holy@vse.cz>
Diff between gasmodel versions 0.5.1 dated 2023-08-29 and 0.6.0 dated 2024-02-02
gasmodel-0.5.1/gasmodel/data/bookshop_sales.rda |only gasmodel-0.5.1/gasmodel/data/german_car_market_cap.rda |only gasmodel-0.5.1/gasmodel/data/sp500_daily.rda |only gasmodel-0.5.1/gasmodel/man/bookshop_sales.Rd |only gasmodel-0.5.1/gasmodel/man/german_car_market_cap.Rd |only gasmodel-0.5.1/gasmodel/man/sp500_daily.Rd |only gasmodel-0.6.0/gasmodel/DESCRIPTION | 14 gasmodel-0.6.0/gasmodel/MD5 | 150 +- gasmodel-0.6.0/gasmodel/NEWS.md | 14 gasmodel-0.6.0/gasmodel/R/data.R | 70 gasmodel-0.6.0/gasmodel/R/distr_bisa_scale.R | 1 gasmodel-0.6.0/gasmodel/R/distr_burr_scale.R |only gasmodel-0.6.0/gasmodel/R/distr_explog_rate.R |only gasmodel-0.6.0/gasmodel/R/distr_fisk_scale.R |only gasmodel-0.6.0/gasmodel/R/distr_kuma_conc.R |only gasmodel-0.6.0/gasmodel/R/distr_logistic_meanscale.R |only gasmodel-0.6.0/gasmodel/R/distr_logitnorm_logitmeanvar.R |only gasmodel-0.6.0/gasmodel/R/distr_lognorm_logmeanvar.R |only gasmodel-0.6.0/gasmodel/R/distr_lomax_scale.R |only gasmodel-0.6.0/gasmodel/R/distr_rayleigh_scale.R |only gasmodel-0.6.0/gasmodel/R/distr_zigeom_mean.R | 3 gasmodel-0.6.0/gasmodel/R/helper_likelihood.R | 43 gasmodel-0.6.0/gasmodel/R/helper_matrix.R | 42 gasmodel-0.6.0/gasmodel/R/helper_reparam.R | 54 gasmodel-0.6.0/gasmodel/R/helper_setup.R | 233 ++- gasmodel-0.6.0/gasmodel/R/helper_starting.R | 18 gasmodel-0.6.0/gasmodel/R/main_bootstrap.R | 23 gasmodel-0.6.0/gasmodel/R/main_distr.R | 36 gasmodel-0.6.0/gasmodel/R/main_estimate.R | 62 gasmodel-0.6.0/gasmodel/R/main_filter.R | 37 gasmodel-0.6.0/gasmodel/R/main_forecast.R | 40 gasmodel-0.6.0/gasmodel/R/main_simulate.R | 27 gasmodel-0.6.0/gasmodel/R/package.R | 2 gasmodel-0.6.0/gasmodel/R/sysdata.rda |binary gasmodel-0.6.0/gasmodel/README.md | 166 +- gasmodel-0.6.0/gasmodel/build/partial.rdb |binary gasmodel-0.6.0/gasmodel/build/vignette.rds |binary gasmodel-0.6.0/gasmodel/data/bookshop_orders.rda |only gasmodel-0.6.0/gasmodel/data/toilet_paper_sales.rda |only gasmodel-0.6.0/gasmodel/inst/doc/case_durations.Rmd | 202 +- gasmodel-0.6.0/gasmodel/inst/doc/case_durations.html | 427 ++--- gasmodel-0.6.0/gasmodel/inst/doc/case_rankings.Rmd | 124 - gasmodel-0.6.0/gasmodel/inst/doc/case_rankings.html | 145 - gasmodel-0.6.0/gasmodel/inst/doc/compare_gas.Rmd |only gasmodel-0.6.0/gasmodel/inst/doc/compare_gas.html |only gasmodel-0.6.0/gasmodel/inst/doc/distributions.Rmd | 404 +++++ gasmodel-0.6.0/gasmodel/inst/doc/distributions.html | 731 ++++++++-- gasmodel-0.6.0/gasmodel/man/bookshop_orders.Rd |only gasmodel-0.6.0/gasmodel/man/distr.Rd | 4 gasmodel-0.6.0/gasmodel/man/distr_density.Rd | 6 gasmodel-0.6.0/gasmodel/man/distr_fisher.Rd | 5 gasmodel-0.6.0/gasmodel/man/distr_mean.Rd | 5 gasmodel-0.6.0/gasmodel/man/distr_random.Rd | 5 gasmodel-0.6.0/gasmodel/man/distr_score.Rd | 6 gasmodel-0.6.0/gasmodel/man/distr_var.Rd | 5 gasmodel-0.6.0/gasmodel/man/figures/README-example-1.png |binary gasmodel-0.6.0/gasmodel/man/gas.Rd | 35 gasmodel-0.6.0/gasmodel/man/gas_bootstrap.Rd | 21 gasmodel-0.6.0/gasmodel/man/gas_filter.Rd | 21 gasmodel-0.6.0/gasmodel/man/gas_forecast.Rd | 23 gasmodel-0.6.0/gasmodel/man/gas_simulate.Rd | 10 gasmodel-0.6.0/gasmodel/man/gasmodel-package.Rd | 2 gasmodel-0.6.0/gasmodel/man/toilet_paper_sales.Rd |only gasmodel-0.6.0/gasmodel/tests/manual/test_case_bookshop.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_case_ecoli.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_case_hockey.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_case_oil.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_case_robbery.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_case_sp500.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_case_transaction.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_distr_burr_scale.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_distr_explog_rate.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_distr_fisk_scale.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_distr_kuma_conc.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_distr_logistic_meanscale.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_distr_logitnorm_logitmeanvar.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_distr_lognorm_logmeanvar.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_distr_lomax_scale.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_distr_rayleigh_scale.r |only gasmodel-0.6.0/gasmodel/tests/manual/test_score_fast.r |only gasmodel-0.6.0/gasmodel/tests/testthat/test_case_lake.R | 4 gasmodel-0.6.0/gasmodel/vignettes/case_durations.Rmd | 202 +- gasmodel-0.6.0/gasmodel/vignettes/case_durations.Rmd.orig | 39 gasmodel-0.6.0/gasmodel/vignettes/case_rankings.Rmd | 124 - gasmodel-0.6.0/gasmodel/vignettes/case_rankings.Rmd.orig | 36 gasmodel-0.6.0/gasmodel/vignettes/compare_gas.Rmd |only gasmodel-0.6.0/gasmodel/vignettes/compare_gas.Rmd.orig |only gasmodel-0.6.0/gasmodel/vignettes/distributions.Rmd | 404 +++++ gasmodel-0.6.0/gasmodel/vignettes/durations_boot_plot-1.png |binary gasmodel-0.6.0/gasmodel/vignettes/durations_sim_plot-1.png |binary gasmodel-0.6.0/gasmodel/vignettes/durations_trend_tv_plot-1.png |binary gasmodel-0.6.0/gasmodel/vignettes/durations_tv_plot-1.png |binary gasmodel-0.6.0/gasmodel/vignettes/rankings_tv_plot-1.png |binary gasmodel-0.6.0/gasmodel/vignettes/rankings_tv_plot-2.png |binary gasmodel-0.6.0/gasmodel/vignettes/rankings_tv_plot-3.png |binary gasmodel-0.6.0/gasmodel/vignettes/table_distr.csv |only gasmodel-0.6.0/gasmodel/vignettes/table_fun.csv |only 97 files changed, 2740 insertions(+), 1285 deletions(-)
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 4.4-1 dated 2023-06-29 and 4.4-2 dated 2024-02-02
DESCRIPTION | 8 +- MD5 | 6 - NEWS | 8 ++ src/devEMF.cpp | 220 ++++++++++++++++++++++++++++----------------------------- 4 files changed, 124 insertions(+), 118 deletions(-)
More information about xegaSelectGene at CRAN
Permanent link
More information about goweragreement at CRAN
Permanent link
Title: Adaptive Weights Smoothing
Description: We provide a collection of R-functions implementing
adaptive smoothing procedures in 1D, 2D and 3D. This includes the
Propagation-Separation Approach to adaptive smoothing,
the Intersecting Confidence Intervals (ICI), variational approaches and a non-local means filter.
The package is described in detail in Polzehl J, Papafitsoros K, Tabelow K (2020).
Patch-Wise Adaptive Weights Smoothing in R. Journal of Statistical Software, 95(6), 1-27.
<doi:10.18637/jss.v095.i06>,
Usage of the package in MR imaging is illustrated in Polzehl and Tabelow (2019),
Magnetic Resonance Brain Imaging, Appendix A, Springer, Use R! Series.
<doi:10.1007/978-3-030-29184-6_6>.
Author: Joerg Polzehl [aut, cre],
Felix Anker [ctb]
Maintainer: Joerg Polzehl <joerg.polzehl@wias-berlin.de>
Diff between aws versions 2.5-3 dated 2023-06-21 and 2.5-4 dated 2024-02-02
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/ICIsmooth.r | 2 +- build/partial.rdb |binary inst/doc/aws-Example.pdf |binary src/awslp.f | 5 +++-- src/caws.f | 10 ++++++---- src/estimateComplexSigma.f | 5 +++-- src/pcaws.f | 15 +++++++++------ src/smooth3d.f | 10 ++++++---- src/smse3.f | 15 +++++++++------ src/varest.f | 20 ++++++++++++-------- 12 files changed, 64 insertions(+), 48 deletions(-)
Title: Read and Write 'wal' Bitmap Image Files and Other 'Quake' Assets
Description: Read 'Quake' assets including bitmap images and textures in 'wal' file format. This package also provides support for extracting these assets from 'WAD' and 'PAK' file archives. It can also read models in 'MDL' and 'MD2' formats.
Author: Tim Schaefer [aut, cre]
Maintainer: Tim Schaefer <ts+code@rcmd.org>
Diff between wal versions 0.1.0 dated 2021-01-17 and 0.1.1 dated 2024-02-02
DESCRIPTION | 9 MD5 | 14 R/read_wal.R | 664 +++++++++++++++++++++--------------------- build/vignette.rds |binary inst/doc/wal.R | 80 ++--- inst/doc/wal.html | 615 ++++++++++++++++++++++++++++---------- man/get.wal.mipmap.heights.Rd | 4 man/get.wal.mipmap.widths.Rd | 2 8 files changed, 832 insertions(+), 556 deletions(-)
More information about REffectivePred at CRAN
Permanent link
Title: Computation and Decomposition of the Mutual Information Index
Description: The Mutual Information Index (M) introduced to social science literature by
Theil and Finizza (1971) <doi:10.1080/0022250X.1971.9989795> is a multigroup
segregation measure that is highly decomposable and that according to Frankel
and Volij (2011) <doi:10.1016/j.jet.2010.10.008> and Mora and Ruiz-Castillo
(2011) <doi:10.1111/j.1467-9531.2011.01237.x> satisfies the Strong Unit
Decomposability and Strong Group Decomposability properties. This package allows
computing and decomposing the total index value into its "between" and
"within" terms. These last terms can also be decomposed into their
contributions, either by group or unit characteristics. The factors that produce
each "within" term can also be displayed at the user's request. The results can
be computed considering a variable or sets of variables that define separate
clusters.
Author: Rafael Fuentealba-Chaura [aut, cre],
Ricardo Mora [aut],
Julio Rojas-Mora [aut],
FONDECYT/ANID Project 11170583 [fnd],
MCIN/AEI/10.13039/501100011033 [fnd],
UCT VIP Project FEQUIP2019-INRN-03 [fnd]
Maintainer: Rafael Fuentealba-Chaura <rafael.fuentealba97@gmail.com>
Diff between mutualinf versions 1.1.3 dated 2023-03-27 and 1.2.2 dated 2024-02-02
DESCRIPTION | 16 +++++++-------- MD5 | 15 +++++++------- R/M.R | 45 +++++++++++++++++++++++++++++-------------- R/M_within.R | 31 ++++++++++++++--------------- R/get_contribution.R | 41 ++++++++++++++++++++++++++------------- R/get_general_contribution.R | 40 ++++++++++++++++++++++++++++---------- R/mutual.R | 17 +++++++++++++--- R/mutual_inv.R |only build/partial.rdb |binary 9 files changed, 134 insertions(+), 71 deletions(-)
Title: Fast Functional Mixed Models using Fast Univariate Inference
Description: Implementation of the fast univariate inference approach (Cui et al. (2022) <doi:10.1080/10618600.2021.1950006>, Loewinger et al. (2023) <doi:10.1101/2023.11.06.565896>) for fitting functional mixed models.
Author: Erjia Cui [aut, cre],
Gabriel Loewinger [aut]
Maintainer: Erjia Cui <ecui@umn.edu>
Diff between fastFMM versions 0.1.0 dated 2023-11-14 and 0.2.0 dated 2024-02-02
DESCRIPTION | 10 ++++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/fui.R | 20 ++++++++++++++++---- README.md | 16 ++++++++++++++-- inst/doc/fastFMM-vignette.pdf |binary 6 files changed, 45 insertions(+), 15 deletions(-)
Title: Expectile and Quantile Regression
Description: Expectile and quantile regression of models with nonlinear effects
e.g. spatial, random, ridge using least asymmetric weighed squares / absolutes
as well as boosting; also supplies expectiles for common distributions.
Author: Fabian Otto-Sobotka [cre],
Elmar Spiegel [aut],
Sabine Schnabel [aut],
Linda Schulze Waltrup [aut],
Paul Eilers [ctb],
Thomas Kneib [ths],
Goeran Kauermann [ctb]
Maintainer: Fabian Otto-Sobotka <fabian.otto-sobotka@uni-oldenburg.de>
Diff between expectreg versions 0.52 dated 2022-03-15 and 0.53 dated 2024-02-02
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/plot.expectreg.R | 4 ++-- R/predict.regbase.R | 10 +++++----- R/rb.R | 6 +++--- build/vignette.rds |binary inst/CITATION | 8 ++++---- inst/doc/expectreg.pdf |binary man/expectreg-package.Rd | 9 --------- man/india.Rd | 2 +- man/india.bnd.Rd | 2 +- man/plot.expectreg.Rd | 2 +- man/update.expectreg.Rd | 2 +- 14 files changed, 38 insertions(+), 44 deletions(-)
Title: Bayesian Modeling and Causal Inference for Multivariate
Longitudinal Data
Description: Easy-to-use and efficient interface for
Bayesian inference of complex panel (time series) data using dynamic
multivariate panel models by Helske and Tikka (2022)
<doi:10.31235/osf.io/mdwu5>. The package supports joint modeling of multiple
measurements per individual, time-varying and time-invariant effects, and a
wide range of discrete and continuous distributions. Estimation of these
dynamic multivariate panel models is carried out via 'Stan'. For an
in-depth tutorial of the package, see (Tikka and Helske, 2023)
<arxiv:2302.01607>.
Author: Santtu Tikka [aut, cre] ,
Jouni Helske [aut] ,
Nicholas Clark [rev],
Lucy D’Agostino McGowan [rev]
Maintainer: Santtu Tikka <santtuth@gmail.com>
Diff between dynamite versions 1.4.5 dated 2023-08-23 and 1.4.9 dated 2024-02-02
dynamite-1.4.5/dynamite/tests/testthat/Rplots.pdf |only dynamite-1.4.9/dynamite/DESCRIPTION | 6 dynamite-1.4.9/dynamite/MD5 | 122 dynamite-1.4.9/dynamite/NEWS.md | 22 dynamite-1.4.9/dynamite/R/as_data_frame.R | 248 - dynamite-1.4.9/dynamite/R/as_data_table.R | 1310 +++--- dynamite-1.4.9/dynamite/R/as_draws.R | 170 dynamite-1.4.9/dynamite/R/ci.R | 104 dynamite-1.4.9/dynamite/R/coef.R | 160 dynamite-1.4.9/dynamite/R/dynamite-package.R | 538 +- dynamite-1.4.9/dynamite/R/dynamite.R | 2375 +++++------ dynamite-1.4.9/dynamite/R/dynamiteformula.R | 1422 +++--- dynamite-1.4.9/dynamite/R/fitted.R | 176 dynamite-1.4.9/dynamite/R/getters.R | 732 +-- dynamite-1.4.9/dynamite/R/lags.R | 1124 ++--- dynamite-1.4.9/dynamite/R/latent_factor.R | 158 dynamite-1.4.9/dynamite/R/lfo.R | 666 +-- dynamite-1.4.9/dynamite/R/loo.R | 176 dynamite-1.4.9/dynamite/R/mcmc_diagnostics.R | 224 - dynamite-1.4.9/dynamite/R/ndraws.R | 60 dynamite-1.4.9/dynamite/R/nobs.R | 72 dynamite-1.4.9/dynamite/R/plot.R | 1036 ++-- dynamite-1.4.9/dynamite/R/predict.R | 11 dynamite-1.4.9/dynamite/R/predict_helpers.R | 2924 +++++++------- dynamite-1.4.9/dynamite/R/prepare_stan_input.R | 2467 +++++------ dynamite-1.4.9/dynamite/R/print.R | 180 dynamite-1.4.9/dynamite/R/random.R | 92 dynamite-1.4.9/dynamite/R/specials.R | 636 +-- dynamite-1.4.9/dynamite/R/splines.R | 196 dynamite-1.4.9/dynamite/R/stanblocks.R | 30 dynamite-1.4.9/dynamite/R/summary.R | 44 dynamite-1.4.9/dynamite/R/sysdata.rda |binary dynamite-1.4.9/dynamite/R/update.R | 265 - dynamite-1.4.9/dynamite/data/categorical_example_fit.rda |binary dynamite-1.4.9/dynamite/data/gaussian_example_fit.rda |binary dynamite-1.4.9/dynamite/data/gaussian_simulation_fit.rda |binary dynamite-1.4.9/dynamite/data/multichannel_example_fit.rda |binary dynamite-1.4.9/dynamite/inst/doc/dynamite.R | 6 dynamite-1.4.9/dynamite/inst/doc/dynamite.Rmd | 1154 ++--- dynamite-1.4.9/dynamite/inst/doc/dynamite.html | 52 dynamite-1.4.9/dynamite/inst/doc/dynamite_priors.R | 4 dynamite-1.4.9/dynamite/inst/doc/dynamite_priors.Rmd | 202 dynamite-1.4.9/dynamite/inst/doc/dynamite_priors.html | 2 dynamite-1.4.9/dynamite/inst/doc/dynamite_simulation.Rmd | 382 - dynamite-1.4.9/dynamite/man/dynamite.Rd | 25 dynamite-1.4.9/dynamite/tests/testthat/test-cmdstanr.R | 402 - dynamite-1.4.9/dynamite/tests/testthat/test-edgecases.R | 6 dynamite-1.4.9/dynamite/tests/testthat/test-errors.R | 2770 ++++++------- dynamite-1.4.9/dynamite/tests/testthat/test-extended.R | 532 +- dynamite-1.4.9/dynamite/tests/testthat/test-grunfeld.R | 166 dynamite-1.4.9/dynamite/tests/testthat/test-internals.R | 382 - dynamite-1.4.9/dynamite/tests/testthat/test-lfactor.R | 414 - dynamite-1.4.9/dynamite/tests/testthat/test-output.R | 642 +-- dynamite-1.4.9/dynamite/tests/testthat/test-predict.R | 850 ++-- dynamite-1.4.9/dynamite/tests/testthat/test-priors.R | 266 - dynamite-1.4.9/dynamite/tests/testthat/test-random.R | 574 +- dynamite-1.4.9/dynamite/tests/testthat/test-recovery.R | 1002 ++-- dynamite-1.4.9/dynamite/tests/testthat/test-scaling.R | 348 - dynamite-1.4.9/dynamite/tests/testthat/test-warnings.R | 586 +- dynamite-1.4.9/dynamite/vignettes/custom_code.stan |only dynamite-1.4.9/dynamite/vignettes/dynamite.Rmd | 1154 ++--- dynamite-1.4.9/dynamite/vignettes/dynamite_priors.Rmd | 202 dynamite-1.4.9/dynamite/vignettes/dynamite_simulation.Rmd | 382 - 63 files changed, 15193 insertions(+), 15058 deletions(-)
Title: Bayesian Mortality Modelling
Description: Fit Bayesian graduation mortality using the Heligman-Pollard model, as seen in Heligman, L., & Pollard, J. H. (1980) <doi:10.1017/S0020268100040257> and Dellaportas, Petros, et al. (2001) <doi:10.1111/1467-985X.00202>, and dynamic linear model (Campagnoli, P., Petris, G., and Petrone, S. (2009) <doi:10.1007/b135794_2>). While Heligman-Pollard has parameters with a straightforward interpretation yielding some rich analysis, the dynamic linear model provides a very flexible adjustment of the mortality curves by controlling the discount factor value. Closing methods for both Heligman-Pollard and dynamic linear model were also implemented according to Dodd, Erengul, et al. (2018) <https://www.jstor.org/stable/48547511>. The Bayesian Lee-Carter model is also implemented to fit historical mortality tables time series to predict the mortality in the following years and to do improvement analysis, as seen in Lee, R. D., & Carter, L. R. (1992) <doi:10.1080/016 [...truncated...]
Author: Laboratorio de Matematica Aplicada
Maintainer: Luiz Fernando Figueiredo <labmapackage@gmail.com>
Diff between BayesMortalityPlus versions 0.1.1 dated 2023-09-06 and 0.2.2 dated 2024-02-02
DESCRIPTION | 11 MD5 | 112 ++++---- NAMESPACE | 135 +++++----- R/Heatmap_default.R | 36 +- R/PT.R | 36 +- R/blc.R | 15 - R/dlm.R | 97 ++++--- R/dlm_close.R | 42 ++- R/expectancy_blc.R | 288 ++++++++++----------- R/expectancy_default.R | 60 ++-- R/expectancy_dlm.R | 38 +- R/expectancy_hp.R | 32 +- R/ffbs.R | 151 ++++------- R/fitted_dlm.R | 18 - R/fitted_hp.R | 15 - R/fun_aux.R | 174 ++++++------- R/globals.R | 17 - R/heatmap_blc.R | 226 ++++++++--------- R/heatmap_dlm.R | 14 - R/heatmap_hp.R | 12 R/heatmap_list.R | 6 R/hp.R | 40 ++- R/hp_binomial.R | 11 R/hp_binomial_reduced.R | 15 - R/hp_close.R | 36 ++ R/hp_lognormal.R | 11 R/hp_lognormal_reduced.R | 14 - R/hp_poisson.R | 11 R/hp_poisson_reduced.R | 15 - R/plot_blc.R | 2 R/plot_blc_pred.R | 262 +++++++++---------- R/plot_chain.R | 620 +++++++++++++++++++++++------------------------ R/plot_dlm.R | 43 +-- R/plot_hp.R | 514 +++++++++++++++++++------------------- R/plot_list.R | 534 ++++++++++++++++++++-------------------- R/predict_dlm.R | 60 ++-- R/print_blc.R | 2 R/print_dlm.R | 122 ++++----- R/print_hp.R | 96 +++---- R/sir_gompertz.R | 126 ++++----- R/summary_dlm.R | 128 ++++----- R/summary_hp.R | 86 +++--- data/USA.rda |binary man/Heatmap.DLM.Rd | 2 man/blc.Rd | 8 man/dlm.Rd | 45 +-- man/dlm_close.Rd | 30 ++ man/expectancy.DLM.Rd | 2 man/fitted.DLM.Rd | 2 man/hp.Rd | 8 man/hp_close.Rd | 33 ++ man/plot.DLM.Rd | 5 man/plot.list.Rd | 6 man/plot_chain.Rd | 2 man/predict.DLM.Rd | 6 man/print.DLM.Rd | 2 man/summary.DLM.Rd | 2 57 files changed, 2298 insertions(+), 2138 deletions(-)
More information about BayesMortalityPlus at CRAN
Permanent link
Title: Vaccine Induced Cellular Immunogenicity with Bivariate Modeling
Description: A shiny app for accurate estimation of vaccine induced immunogenicity
with bivariate linear modeling. Method is detailed in: Lhomme, Hejblum, Lacabaratz,
Wiedemann, Lelievre, Levy, Thiebaut & Richert (2020). Journal of Immunological Methods,
477:112711. <doi:10.1016/j.jim.2019.112711>.
Author: Boris Hejblum [cre, aut],
Melanie Huchon [aut],
Clement Nerestan [aut]
Maintainer: Boris Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between vici versions 0.7.0 dated 2023-04-26 and 0.7.3 dated 2024-02-02
vici-0.7.0/vici/inst/app/www/palette |only vici-0.7.3/vici/DESCRIPTION | 10 vici-0.7.3/vici/MD5 | 171 vici-0.7.3/vici/NAMESPACE | 120 vici-0.7.3/vici/NEWS.md | 70 vici-0.7.3/vici/R/BW_functions.R | 110 vici-0.7.3/vici/R/ICS_ex.R | 72 vici-0.7.3/vici/R/app_server.R | 310 - vici-0.7.3/vici/R/app_ui.R | 168 vici-0.7.3/vici/R/boxplot_VICI.R | 161 vici-0.7.3/vici/R/clean_output.R | 20 vici-0.7.3/vici/R/gls_ownfunctions.R | 316 - vici-0.7.3/vici/R/heatmap_VICI.R | 107 vici-0.7.3/vici/R/histogram_VICI.R |only vici-0.7.3/vici/R/interarm_fit.R | 146 vici-0.7.3/vici/R/interarm_postprocessres.R | 70 vici-0.7.3/vici/R/intraarm_fit.R | 119 vici-0.7.3/vici/R/intraarm_postprocessres.R | 72 vici-0.7.3/vici/R/make_nice_pvals.R | 72 vici-0.7.3/vici/R/mod_modelfit.R | 542 +-- vici-0.7.3/vici/R/mod_settings_pan.R | 1459 ++++---- vici-0.7.3/vici/R/myDownloadHandlerForPlots.R | 56 vici-0.7.3/vici/R/mygls.R | 346 +- vici-0.7.3/vici/R/onload.R | 16 vici-0.7.3/vici/R/run_app.R | 32 vici-0.7.3/vici/R/update_vars.R | 18 vici-0.7.3/vici/R/utils.R | 394 +- vici-0.7.3/vici/README.md | 108 vici-0.7.3/vici/data/ICS_ex.txt | 1082 +++--- vici-0.7.3/vici/inst/CITATION | 34 vici-0.7.3/vici/inst/app/server.R | 2 vici-0.7.3/vici/inst/app/tests/run_shinyTest.R | 18 vici-0.7.3/vici/inst/app/tests/shinytest.R | 6 vici-0.7.3/vici/inst/app/tests/shinytests/mytest-expected/001.json | 1444 ++++---- vici-0.7.3/vici/inst/app/tests/shinytests/mytest-expected/002.json | 1716 +++++----- vici-0.7.3/vici/inst/app/tests/shinytests/mytest.R | 18 vici-0.7.3/vici/inst/app/ui.R | 2 vici-0.7.3/vici/inst/app/www/favicon.ico |binary vici-0.7.3/vici/inst/app/www/logo.svg |only vici-0.7.3/vici/inst/app/www/palettes |only vici-0.7.3/vici/man/ICS_ex.Rd | 80 vici-0.7.3/vici/man/boxplot_VICI.Rd | 80 vici-0.7.3/vici/man/ddf_BW.Rd | 24 vici-0.7.3/vici/man/heatmap_vici.Rd | 48 vici-0.7.3/vici/man/histogram_VICI.Rd |only vici-0.7.3/vici/man/interarm_fit.Rd | 24 vici-0.7.3/vici/man/intraarm_fit.Rd | 24 vici-0.7.3/vici/man/mod_modelfit.Rd | 60 vici-0.7.3/vici/man/mod_settings_pan.Rd | 56 vici-0.7.3/vici/man/myDownloadHandlerForPlots.Rd | 46 vici-0.7.3/vici/man/run_app.Rd | 44 vici-0.7.3/vici/tests/testthat.R | 8 vici-0.7.3/vici/tests/testthat/test-golem-recommended.R | 80 vici-0.7.3/vici/tests/testthat/test-selenium.R | 356 +- vici-0.7.3/vici/tests/testthat/test-serv.R | 36 55 files changed, 5210 insertions(+), 5163 deletions(-)
Title: Construct Modeling Packages
Description: Building modeling packages is hard. A large amount of effort
generally goes into providing an implementation for a new method that
is efficient, fast, and correct, but often less emphasis is put on the
user interface. A good interface requires specialized knowledge about
S3 methods and formulas, which the average package developer might not
have. The goal of 'hardhat' is to reduce the burden around building
new modeling packages by providing functionality for preprocessing,
predicting, and validating input.
Author: Davis Vaughan [aut, cre],
Max Kuhn [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Davis Vaughan <davis@posit.co>
Diff between hardhat versions 1.3.0 dated 2023-03-30 and 1.3.1 dated 2024-02-02
hardhat-1.3.0/hardhat/build/hardhat.pdf |only hardhat-1.3.0/hardhat/man/modeling-package.Rd |only hardhat-1.3.1/hardhat/DESCRIPTION | 8 hardhat-1.3.1/hardhat/MD5 | 47 ++-- hardhat-1.3.1/hardhat/NEWS.md | 5 hardhat-1.3.1/hardhat/R/blueprint-recipe-default.R | 9 hardhat-1.3.1/hardhat/R/scream.R | 2 hardhat-1.3.1/hardhat/R/use.R | 6 hardhat-1.3.1/hardhat/build/vignette.rds |binary hardhat-1.3.1/hardhat/inst/doc/forge.R | 12 - hardhat-1.3.1/hardhat/inst/doc/forge.html | 24 +- hardhat-1.3.1/hardhat/inst/doc/mold.R | 6 hardhat-1.3.1/hardhat/inst/doc/mold.html | 57 ++--- hardhat-1.3.1/hardhat/inst/doc/package.R | 10 hardhat-1.3.1/hardhat/inst/doc/package.html | 12 - hardhat-1.3.1/hardhat/man/modeling-usethis.Rd |only hardhat-1.3.1/hardhat/man/scream.Rd | 2 hardhat-1.3.1/hardhat/tests/testthat/_snaps/forge-formula.md | 122 +++++++++++ hardhat-1.3.1/hardhat/tests/testthat/_snaps/forge-recipe.md | 49 ++++ hardhat-1.3.1/hardhat/tests/testthat/_snaps/forge-xy.md |only hardhat-1.3.1/hardhat/tests/testthat/_snaps/intercept.md | 8 hardhat-1.3.1/hardhat/tests/testthat/_snaps/scream.md |only hardhat-1.3.1/hardhat/tests/testthat/test-forge-formula.R | 100 ++------- hardhat-1.3.1/hardhat/tests/testthat/test-forge-recipe.R | 53 +--- hardhat-1.3.1/hardhat/tests/testthat/test-forge-xy.R | 29 +- hardhat-1.3.1/hardhat/tests/testthat/test-intercept.R | 7 hardhat-1.3.1/hardhat/tests/testthat/test-scream.R | 16 - 27 files changed, 356 insertions(+), 228 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oeyvind Langsrud [aut, cre],
Daniel Lupp [aut],
Hege Boevelstad [ctb],
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 0.7.0 dated 2023-06-07 and 0.8.0 dated 2024-02-02
GaussSuppression-0.7.0/GaussSuppression/R/DominanceRule.R |only GaussSuppression-0.7.0/GaussSuppression/man/DominanceRule.Rd |only GaussSuppression-0.8.0/GaussSuppression/DESCRIPTION | 12 - GaussSuppression-0.8.0/GaussSuppression/MD5 | 84 ++++---- GaussSuppression-0.8.0/GaussSuppression/NAMESPACE | 15 + GaussSuppression-0.8.0/GaussSuppression/NEWS.md | 34 +++ GaussSuppression-0.8.0/GaussSuppression/R/AdditionalSuppression.R | 18 + GaussSuppression-0.8.0/GaussSuppression/R/Candidates.R | 51 ++++- GaussSuppression-0.8.0/GaussSuppression/R/GaussSuppressionFromData.R | 65 +++++- GaussSuppression-0.8.0/GaussSuppression/R/GetDefault.R |only GaussSuppression-0.8.0/GaussSuppression/R/IncrementalTimeSuppression.R |only GaussSuppression-0.8.0/GaussSuppression/R/Intervals.R |only GaussSuppression-0.8.0/GaussSuppression/R/MagnitudeRule.R |only GaussSuppression-0.8.0/GaussSuppression/R/MaxContribution.R | 82 +++++++- GaussSuppression-0.8.0/GaussSuppression/R/NContributorsRule.R | 90 ++++++++ GaussSuppression-0.8.0/GaussSuppression/R/Ncontributors.R | 3 GaussSuppression-0.8.0/GaussSuppression/R/OutputFunction.R |only GaussSuppression-0.8.0/GaussSuppression/R/PackageSpecs.R | 6 GaussSuppression-0.8.0/GaussSuppression/R/PrimaryFromSuppressedData.R | 3 GaussSuppression-0.8.0/GaussSuppression/R/PrimaryRemoveWg.R |only GaussSuppression-0.8.0/GaussSuppression/R/Singleton.R | 74 ++++++- GaussSuppression-0.8.0/GaussSuppression/R/SuppressDominantCells.R | 71 ++++++ GaussSuppression-0.8.0/GaussSuppression/R/SuppressFewContributors.R | 20 + GaussSuppression-0.8.0/GaussSuppression/build/vignette.rds |binary GaussSuppression-0.8.0/GaussSuppression/inst/doc/Magnitude_table_suppression.R | 4 GaussSuppression-0.8.0/GaussSuppression/inst/doc/Magnitude_table_suppression.Rmd | 28 +- GaussSuppression-0.8.0/GaussSuppression/inst/doc/Magnitude_table_suppression.html | 66 ++++-- GaussSuppression-0.8.0/GaussSuppression/inst/doc/Small_count_frequency_table_suppression.R | 2 GaussSuppression-0.8.0/GaussSuppression/inst/doc/define_tables.R | 2 GaussSuppression-0.8.0/GaussSuppression/inst/doc/define_tables.Rmd | 2 GaussSuppression-0.8.0/GaussSuppression/man/AdditionalSuppression.Rd | 6 GaussSuppression-0.8.0/GaussSuppression/man/CandidatesDefault.Rd | 31 ++- GaussSuppression-0.8.0/GaussSuppression/man/ComputeIntervals.Rd |only GaussSuppression-0.8.0/GaussSuppression/man/FindDominantCells.Rd | 2 GaussSuppression-0.8.0/GaussSuppression/man/GaussSuppressionFromData.Rd | 17 + GaussSuppression-0.8.0/GaussSuppression/man/GetDefault.Rd |only GaussSuppression-0.8.0/GaussSuppression/man/IncrementalTimeSuppression.Rd |only GaussSuppression-0.8.0/GaussSuppression/man/MagnitudeRule.Rd |only GaussSuppression-0.8.0/GaussSuppression/man/MaxContribution.Rd | 39 +++ GaussSuppression-0.8.0/GaussSuppression/man/NContributorsRule.Rd | 19 + GaussSuppression-0.8.0/GaussSuppression/man/NcontributorsRule_identical.Rd | 13 - GaussSuppression-0.8.0/GaussSuppression/man/PackageSpecs.Rd | 2 GaussSuppression-0.8.0/GaussSuppression/man/PrimaryRemoveWg.Rd |only GaussSuppression-0.8.0/GaussSuppression/man/SingletonUniqueContributor.Rd | 22 ++ GaussSuppression-0.8.0/GaussSuppression/man/SuppressDominantCells.Rd | 23 +- GaussSuppression-0.8.0/GaussSuppression/man/SuppressFewContributors.Rd | 23 +- GaussSuppression-0.8.0/GaussSuppression/tests/testthat/test-GaussSuppressionFromData.R | 102 +++++++++- GaussSuppression-0.8.0/GaussSuppression/tests/testthat/test-Wrappers.R |only GaussSuppression-0.8.0/GaussSuppression/vignettes/Magnitude_table_suppression.Rmd | 28 +- GaussSuppression-0.8.0/GaussSuppression/vignettes/define_tables.Rmd | 2 50 files changed, 888 insertions(+), 173 deletions(-)
More information about GaussSuppression at CRAN
Permanent link
Title: Extreme Value Analysis
Description: General functions for performing extreme value analysis. In particular, allows for inclusion of covariates into the parameters of the extreme-value distributions, as well as estimation through MLE, L-moments, generalized (penalized) MLE (GMLE), as well as Bayes. Inference methods include parametric normal approximation, profile-likelihood, Bayes, and bootstrapping. Some bivariate functionality and dependence checking (e.g., auto-tail dependence function plot, extremal index estimation) is also included. For a tutorial, see Gilleland and Katz (2016) <doi: 10.18637/jss.v072.i08> and for bootstrapping, please see Gilleland (2020) <doi: 10.1175/JTECH-D-20-0070.1>.
Author: Eric Gilleland
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between extRemes versions 2.1-3 dated 2022-11-18 and 2.1-4 dated 2024-02-02
extRemes-2.1-3/extRemes/R/depmodels.R |only extRemes-2.1-3/extRemes/R/fbvpot.R |only extRemes-2.1-3/extRemes/man/bvpotbooter.Rd |only extRemes-2.1-3/extRemes/man/fbvpot.Rd |only extRemes-2.1-3/extRemes/man/logistic.Rd |only extRemes-2.1-3/extRemes/man/mixbeta.Rd |only extRemes-2.1-4/extRemes/DESCRIPTION | 8 ++--- extRemes-2.1-4/extRemes/MD5 | 36 +++++++++-------------- extRemes-2.1-4/extRemes/NAMESPACE | 3 - extRemes-2.1-4/extRemes/build/partial.rdb |binary extRemes-2.1-4/extRemes/man/Ozone4H.Rd | 2 - extRemes-2.1-4/extRemes/man/atdf.Rd | 6 +-- extRemes-2.1-4/extRemes/man/devd.Rd | 6 +-- extRemes-2.1-4/extRemes/man/extRemes-internal.Rd | 3 - extRemes-2.1-4/extRemes/man/fevd.Rd | 4 +- extRemes-2.1-4/extRemes/man/lr.test.Rd | 2 - extRemes-2.1-4/extRemes/man/pextRemes.Rd | 6 +-- extRemes-2.1-4/extRemes/man/profliker.Rd | 2 - extRemes-2.1-4/extRemes/man/return.level.Rd | 6 +-- extRemes-2.1-4/extRemes/man/rlevd.Rd | 6 +-- extRemes-2.1-4/extRemes/man/taildep.Rd | 2 - extRemes-2.1-4/extRemes/man/taildep.test.Rd | 2 - 22 files changed, 41 insertions(+), 53 deletions(-)
Title: Univariate Analysis of Cluster Trials with Multiple Outcomes
Description: Frequentist statistical inference for cluster randomised trials with
multiple outcomes that controls the family-wise error rate and provides nominal
coverage of confidence sets. A full description of the methods can be found in Watson et al. (2023) <doi:10.1002/sim.9831>.
Author: Sam Watson [aut, cre]
Maintainer: Sam Watson <s.i.watson@bham.ac.uk>
Diff between crctStepdown versions 0.5.1 dated 2023-09-14 and 0.5.2 dated 2024-02-02
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/simple_lm.cpp | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Gaussian Mixture Models (GMM)
Description: Multimodal distributions can be modelled as a mixture of components. The model is derived using the Pareto Density Estimation (PDE) for an estimation of the pdf. PDE has been designed in particular to identify groups/classes in a dataset. Precise limits for the classes can be calculated using the theorem of Bayes. Verification of the model is possible by QQ plot, Chi-squared test and Kolmogorov-Smirnov test. The package is based on the publication of Ultsch, A., Thrun, M.C., Hansen-Goos, O., Lotsch, J. (2015) <DOI:10.3390/ijms161025897>.
Author: Michael Thrun [aut, cre] ,
Onno Hansen-Goos [aut, rev],
Rabea Griese [ctr, ctb],
Catharina Lippmann [ctr],
Florian Lerch [ctb, rev],
Quirin Stier [ctb, rev],
Jorn Lotsch [dtc, rev, fnd, ctb],
Luca Brinkmann [ctb, rev],
Alfred Ultsch [aut, cph, ths]
Maintainer: Michael Thrun <m.thrun@gmx.net>
Diff between AdaptGauss versions 1.5.6 dated 2020-02-03 and 1.6 dated 2024-02-02
DESCRIPTION | 16 + MD5 | 56 +++--- NAMESPACE | 3 R/AdaptGauss.R | 2 R/Bayes4Mixtures.R | 12 - R/BayesDecisionBoundaries.R | 130 ++++++++------ R/BayesFor2GMM.R | 278 ++++++++++++++++--------------- R/Chi2testMixtures.R | 28 ++- R/GMMplot_ggplot2.R | 23 +- R/Intersect2Mixtures.R | 14 - R/KStestMixtures.R | 30 +-- R/LikelihoodRatio4Mixtures.R | 341 ++++++++++++++++++++------------------- R/PlotMixtures.R | 263 +++++++++++++++++------------- R/PlotMixturesAndBoundaries.R | 133 +++++++++------ R/QQplotGMM.R | 105 +++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/AdaptGauss.html | 284 ++++++++++++++++---------------- man/AdaptGauss-package.Rd | 5 man/AdaptGauss.Rd | 2 man/BayesFor2GMM.Rd | 106 ++++++------ man/Chi2testMixtures.Rd | 8 man/KStestMixtures.Rd | 5 man/LikelihoodRatio4Mixtures.Rd | 12 - man/PlotMixtures.Rd | 4 man/PlotMixturesAndBoundaries.Rd | 6 man/Symlognpdf.Rd | 2 man/qqplotGMM.Rd | 19 +- src/RcppExports.cpp | 5 29 files changed, 1026 insertions(+), 866 deletions(-)
Title: R Analyzer for Large-Scale Assessments
Description: Prepare and analyze data from large-scale assessments and surveys with
complex sampling and assessment design (see 'Rutkowski', 2010
<doi:10.3102/0013189X10363170>). Such studies are, for example,
international assessments like 'TIMSS', 'PIRLS' and 'PISA'. A graphical
interface is available for the non-technical user.The package includes
functions to covert the original data from 'SPSS' into 'R' data sets
keeping the user-defined missing values, merge data from different
respondents and/or countries, generate variable dictionaries, modify
data, produce descriptive statistics (percentages, means, percentiles,
benchmarks) and multivariate statistics (correlations, linear
regression, binary logistic regression). The number of supported
studies and analysis types will increase in future. For a general
presentation of the package, see 'Mirazchiyski', 2021a
(<doi:10.1186/s40536-021-00114-4>). For detailed technical aspects of the
package, see 'Mirazchiyski', 2021b (<doi:10.339 [...truncated...]
Author: Plamen V. Mirazchiyski [aut, cre],
INERI [aut]
Maintainer: Plamen V. Mirazchiyski <plamen.mirazchiyski@ineri.org>
Diff between RALSA versions 1.3.7 dated 2023-10-26 and 1.4.0 dated 2024-02-02
DESCRIPTION | 17 MD5 | 36 - NAMESPACE | 5 NEWS.md | 45 + R/RALSA.r | 6 R/common.r | 450 ++++++++++++++++ R/lsa.bench.r | 4 R/lsa.bin.log.reg.r | 1250 +++++++++++++++++++++++------------------------ R/lsa.convert.data.r | 375 +------------- R/lsa.convert.data2.r |only R/lsa.corr.r | 2 R/lsa.crosstabs.r | 25 R/lsa.lin.reg.r | 1238 +++++++++++++++++++++++----------------------- R/lsa.merge.data.r | 2 inst/shiny/GUI/server.r | 985 ++++++++++++++++++++++++++++++++++++- inst/shiny/GUI/ui.r | 450 ++++++++-------- man/RALSA.Rd | 1 man/lsa.convert.data.Rd | 2 man/lsa.convert.data2.Rd |only man/lsa.merge.data.Rd | 2 20 files changed, 3015 insertions(+), 1880 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format and has either no header or a two column header. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Jairo H Migueles [aut] ,
Severine Sabia [ctb],
Matthew R Patterson [ctb],
Zhou Fang [ctb],
Joe Heywood [ctb],
Joan Capdevila Pujol [ctb],
Lena Kushleyeva [ctb],
Mathilde Chen [ctb],
Manasa Yerramalla [ctb],
Patrick Bos [...truncated...]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 3.0-3 dated 2024-01-11 and 3.0-5 dated 2024-02-02
DESCRIPTION | 10 +- MD5 | 77 ++++++++++----------- NEWS.md | 25 +++++++ R/GGIR.R | 5 - R/HASPT.R | 21 ++++- R/check_params.R | 19 +++++ R/convertEpochData.R | 76 +++++++++++++++++---- R/g.analyse.R | 2 R/g.analyse.perday.R | 11 +-- R/g.getM5L5.R | 8 ++ R/g.part2.R | 12 +-- R/g.part3.R | 12 +++ R/g.part4.R | 6 - R/g.part5.R | 24 ++++-- R/g.part5.definedays.R | 39 +++++----- R/g.part5_analyseSegment.R | 9 ++ R/g.part5_initialise_ts.R | 40 ++++++++--- R/g.plot.R | 26 +++++-- R/g.plot5.R | 16 ++-- R/g.report.part2.R | 5 - R/g.report.part5.R | 34 ++++++++- R/g.sib.det.R | 49 ++++++++----- README.md | 2 inst/doc/CutPoints.Rmd | 47 ++++++++++--- inst/doc/CutPoints.html | 100 ++++++++++++++++++++++------ inst/doc/ExternalFunction.pdf |binary inst/doc/GGIR.Rmd | 7 + inst/doc/GGIR.html | 19 ++++- inst/doc/GGIRParameters.Rmd | 4 - inst/doc/GGIRParameters.html | 67 +++++++++++------- inst/testfiles/sensewear.xls |only man/GGIR-package.Rd | 4 - man/GGIR.Rd | 66 ++++++++++++++---- man/g.part5_initialise_ts.Rd | 6 + tests/testthat/test_chainof5parts.R | 4 - tests/testthat/test_convertExtEpochData.R | 21 +++++ tests/testthat/test_recordingEndSleepHour.R | 60 ++++++++++++++++ vignettes/CutPoints.Rmd | 47 ++++++++++--- vignettes/GGIR.Rmd | 7 + vignettes/GGIRParameters.Rmd | 4 - 40 files changed, 730 insertions(+), 261 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-09 0.5.0
2018-06-08 0.4.0
2017-10-23 0.3.2
2017-05-20 0.3.1
2017-05-03 0.3.0
2016-08-11 0.2.0
2016-06-13 0.1.0
Title: Interactive Sketches
Description: Creates static / animated / interactive visualisations embeddable
in R Markdown documents. It implements an R-to-JavaScript transpiler and
enables users to write JavaScript applications using the syntax of R.
Author: Chun Fung Kwok [aut, cre] ,
Kate Saunders [ctb]
Maintainer: Chun Fung Kwok <jkwok@svi.edu.au>
Diff between sketch versions 1.1.19 dated 2022-10-23 and 1.1.20.3 dated 2024-02-02
DESCRIPTION | 8 MD5 | 26 +- R/assets-Asset_list_class.R | 8 R/assets-to_shiny_tag.R | 2 R/core-components.R | 50 ++-- R/core-rewrite.R | 4 R/ext-annotate_expr.R | 4 R/ext-components.R | 2 R/ext-source_map.R | 2 R/interface-compile.R | 2 build/vignette.rds |binary inst/doc/introduction.html | 544 +++++++++++++++++++++++++++++++------------- inst/js.tar.gz |binary man/to_shiny_tag.Rd | 2 14 files changed, 448 insertions(+), 206 deletions(-)
Title: Calculation of IBD Probabilities
Description: For biparental, three and four-way crosses Identity by Descent
(IBD) probabilities can be calculated using Hidden Markov Models and
inheritance vectors following Lander and Green
(<https://www.jstor.org/stable/29713>) and Huang
(<doi:10.1073/pnas.1100465108>). One of a series of statistical genetic
packages for streamlining the analysis of typical plant breeding experiments
developed by Biometris.
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
,
Wenhao Li [ctb] ,
Johannes Kruisselbrink [ctb]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between statgenIBD versions 1.0.6 dated 2023-08-30 and 1.0.7 dated 2024-02-02
DESCRIPTION | 13 - MD5 | 39 +-- NAMESPACE | 1 NEWS.md | 10 R/IBDprob.R | 38 ++- R/allGenoPlot.R | 40 ++- R/meanProbsPlot.R | 25 +- R/reexport.R |only R/singleGenoPlot.R | 2 R/totalCoveragePlot.R | 4 R/utils.R | 2 R/writeIBDs.R | 16 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/IBDCalculations.R | 5 inst/doc/IBDCalculations.Rmd | 11 inst/doc/IBDCalculations.html | 478 +++++++++++++++++++++--------------------- inst/doc/IBDFileFormat.R | 4 inst/doc/IBDFileFormat.html | 4 man/plot.IBDprob.Rd | 30 +- vignettes/IBDCalculations.Rmd | 11 21 files changed, 414 insertions(+), 319 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.1.4 dated 2024-01-26 and 1.1.5 dated 2024-02-02
DESCRIPTION | 14 ++++++++------ MD5 | 8 ++++---- NEWS.md | 4 ++++ R/forestcox.R | 49 +++++++++++++++++++++++++++++-------------------- inst/doc/jstable.html | 30 +++++++++++++++--------------- 5 files changed, 60 insertions(+), 45 deletions(-)
Title: Linear p-Wasserstein Projections
Description: Performs Wasserstein projections from the predictive distributions of any model into the space of predictive distributions of linear models. We utilize L1 penalties to also reduce the complexity of the model space. This package employs the methods as described in Dunipace, Eric and Lorenzo Trippa (2020) <arXiv:2012.09999>.
Author: Eric Dunipace [aut, cre] ,
Clemens Schmid [ctb] ,
Espen Bernton [ctb] ,
Mathieu Gerber [ctb] ,
Pierre Jacob [ctb] ,
Bin Dai [ctb] ,
Jared Huling [ctb] ,
Yixuan Qiu [ctb] ,
Dominic Schuhmacher [ctb] ,
Nicolas Bonneel [ctb]
Maintainer: Eric Dunipace <edunipace@mail.harvard.edu>
Diff between WpProj versions 0.2 dated 2024-01-22 and 0.2.1 dated 2024-02-02
DESCRIPTION | 14 MD5 | 79 ++-- NAMESPACE | 1 NEWS.md | 12 R/HC.R | 6 R/WPVI.R | 4 R/WP_rsquared.R | 8 R/WpProj-package.R | 3 R/WpProj.R | 6 R/distanceCompare.R | 5 R/ridgePlot.R | 4 R/transport_plan.R | 13 man/HC.Rd | 4 man/WPR2.Rd | 1 man/WPVI.Rd | 1 man/WpProj-package.Rd | 9 man/WpProj.Rd | 5 man/combine.WPR2.Rd | 3 man/distCompare.Rd | 3 man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/ridgePlot.Rd | 3 src/Makevars | 2 src/Makevars.win | 2 src/SufficientStatistics.cpp | 4 src/oem_xtx.cpp | 3 src/sort.cpp | 12 src/trans_hilbert.cpp | 2 src/trans_rank.cpp | 2 src/trans_sinkhorn.cpp | 4 src/trans_univariate.cpp | 2 src/trans_univariate_approx_pwr.cpp | 4 tests/testthat/test-W2L1.R | 19 tests/testthat/test-WPL1.R | 8 tests/testthat/test-WPR2.R | 14 tests/testthat/test-sufficientStatistics.R | 554 ++++++++++++++--------------- tests/testthat/test-transport_plan.R | 10 tests/testthat/test-wasserstein.R | 18 45 files changed, 459 insertions(+), 385 deletions(-)
Title: Various R Programming Tools for Plotting Data
Description: Various R programming tools for plotting data, including:
- calculating and plotting locally smoothed summary function as
('bandplot', 'wapply'),
- enhanced versions of standard plots ('barplot2', 'boxplot2',
'heatmap.2', 'smartlegend'),
- manipulating colors ('col2hex', 'colorpanel', 'redgreen',
'greenred', 'bluered', 'redblue', 'rich.colors'),
- calculating and plotting two-dimensional data summaries ('ci2d',
'hist2d'),
- enhanced regression diagnostic plots ('lmplot2', 'residplot'),
- formula-enabled interface to 'stats::lowess' function ('lowess'),
- displaying textual data in plots ('textplot', 'sinkplot'),
- plotting a matrix where each cell contains a dot whose size
reflects the relative magnitude of the elements ('balloonplot'),
- plotting "Venn" diagrams ('venn'),
- displaying Open-Office style plots ('ooplot'),
- plotting multiple data on same region, with separate axes
('overplot'),
- plotting means and confidence intervals ('plotCI', 'plotmeans'),
- spacing points in an x-y [...truncated...]
Author: Gregory R. Warnes [aut],
Ben Bolker [aut],
Lodewijk Bonebakker [aut],
Robert Gentleman [aut],
Wolfgang Huber [aut],
Andy Liaw [aut],
Thomas Lumley [aut],
Martin Maechler [aut],
Arni Magnusson [aut],
Steffen Moeller [aut],
Marc Schwartz [aut],
Bill Ve [...truncated...]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between gplots versions 3.1.3 dated 2022-04-25 and 3.1.3.1 dated 2024-02-02
DESCRIPTION | 6 +++--- MD5 | 3 ++- R/00.R |only 3 files changed, 5 insertions(+), 4 deletions(-)
Title: Summarize CRAN Check Results in the Terminal
Description: The CRAN check results and where your package stands in the
CRAN submission queue in your R terminal.
Author: Francois Michonneau [aut, cre],
Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between foghorn versions 1.5.1 dated 2022-10-24 and 1.5.2 dated 2024-02-02
DESCRIPTION | 11 +- MD5 | 40 +++---- NAMESPACE | 6 - NEWS.md | 10 + R/cran_check_table.R | 3 R/cran_files.R | 11 +- R/cran_flavors.R | 4 R/cran_queue.R | 2 R/cran_results.R | 9 + R/foghorn-package.R | 8 + R/foghorn.R | 13 +- README.md | 76 +++++++------- build/vignette.rds |binary inst/doc/foghorn.Rmd | 77 +++++--------- inst/doc/foghorn.html | 179 +++++++++++++++++---------------- man/cran_details.Rd | 14 -- man/cran_results.Rd | 14 -- man/foghorn.Rd | 25 ++++ man/n_cran_flavors.Rd | 4 tests/testthat/test-n_cran_platforms.R | 2 vignettes/foghorn.Rmd | 77 +++++--------- 21 files changed, 312 insertions(+), 273 deletions(-)
Title: Gene by Environment Interaction and Conditional Gene Tests for
Nuclear Families
Description: Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.
Author: Thomas Hoffmann <tjhoffm@gmail.com>
Maintainer: Thomas Hoffmann <tjhoffm@gmail.com>
Diff between fbati versions 1.0-8 dated 2023-12-13 and 1.0-9 dated 2024-02-02
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- R/fbatcStrategyStep.R | 6 +++--- R/fbatge.R | 2 +- R/fbatgeAll.R | 4 ++-- R/fbatgeInterface.R | 2 +- R/fbatmeev.R | 4 ++-- man/fbatcStrategyStep.Rd | 8 ++++---- 8 files changed, 26 insertions(+), 26 deletions(-)
Title: Bayesian Ammi Model for Continuous Data
Description: Flexible multi-environment trials analysis via MCMC method for Additive Main Effects and Multiplicative Model (AMMI) for continuous data.
Biplot with the averages and regions of confidence can be generated. The chains run in parallel on Linux systems and run serially on Windows.
Author: Luciano A. Oliveira [aut],
Carlos P. Silva [aut],
Cristian T. E. Mendes [aut],
Alessandra Q. Silva [aut],
Joel J. Nuvunga [aut],
Marcio Balestre [ths],
Julio S. S. Bueno-Filho [ths],
Fabio M. Correa [aut, cre]
Maintainer: Fabio M. Correa <fmcron@protonmail.com>
Diff between ammiBayes versions 1.0-1 dated 2022-03-14 and 1.0-2 dated 2024-02-02
ammiBayes-1.0-1/ammiBayes/data/ammiData.RData |only ammiBayes-1.0-2/ammiBayes/ChangeLog | 3 +++ ammiBayes-1.0-2/ammiBayes/DESCRIPTION | 14 +++++++------- ammiBayes-1.0-2/ammiBayes/MD5 | 12 ++++++------ ammiBayes-1.0-2/ammiBayes/R/main.R | 4 ++-- ammiBayes-1.0-2/ammiBayes/build/vignette.rds |binary ammiBayes-1.0-2/ammiBayes/data/ammiData.rda |only ammiBayes-1.0-2/ammiBayes/inst/CITATION | 4 ++-- 8 files changed, 20 insertions(+), 17 deletions(-)
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.2-8 dated 2023-10-23 and 3.2-10 dated 2024-02-02
DESCRIPTION | 12 ++++++------ MD5 | 39 ++++++++++++++++++++------------------- NAMESPACE | 24 ++++++++++++++++++++++++ NEWS | 35 +++++++++++++++++++++++++++++++++++ R/diagnoseppm.R | 14 ++++++++++---- R/getglmfit.R |only R/mppm.R | 20 +++++++++++++++++++- R/ppmclass.R | 30 ++++++++++++++++++------------ R/slrm.R | 18 +++++++++++++++++- R/sysdata.rda |binary R/update.ppm.R | 1 + R/vcov.kppm.R | 38 ++++++++++++++++++++++++++++++++------ R/vcov.ppm.R | 37 ++++++++++++++++++++++--------------- inst/doc/packagesizes.txt | 2 ++ man/ppm.ppp.Rd | 24 ++++++++++++++++++++---- man/spatstat.model-internal.Rd | 30 +++++++++++++++++++++++++++--- man/vcov.kppm.Rd | 2 +- man/vcov.ppm.Rd | 4 +++- tests/testsD.R | 3 ++- tests/testsEtoF.R | 16 +++++++++++++++- tests/testsNtoO.R | 2 +- 21 files changed, 275 insertions(+), 76 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: Simple Component Analysis
Description: Simple Component Analysis (SCA) often provides much more
interpretable components than Principal Components (PCA) while still
representing much of the variability in the data.
Author: Valentin Rousson <rousson@ifspm.unizh.ch> and Martin Maechler
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sca versions 0.9-1 dated 2023-01-14 and 0.9-2 dated 2024-02-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/sca.R | 11 ++--------- build/partial.rdb |binary 4 files changed, 9 insertions(+), 16 deletions(-)
Title: Fit Models Derived from Point Processes to Species Distributions
using 'inlabru'
Description: Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models.
Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking.
We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them.
There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions.
An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Author: Philip Mostert [aut, cre],
Bob O'hara [aut]
Maintainer: Philip Mostert <philip.s.mostert@ntnu.no>
Diff between PointedSDMs versions 1.3.1 dated 2023-10-10 and 1.3.2 dated 2024-02-02
DESCRIPTION | 6 MD5 | 54 +++--- NEWS.md | 15 + R/bruSDM_outputs.R | 17 +- R/bruSDM_predict.R | 44 +++++ R/data2ENV.R | 11 + R/dataOrganize.R | 88 +++++++++-- R/dataSDM.R | 263 +++++++++++++++++++++++++++------ R/dataSet.R | 14 + R/datasetOut.R | 18 +- R/fitISDM.R | 9 - R/intModel.R | 46 +++++ R/makeLhoods.R | 7 build/vignette.rds |binary inst/doc/Marked_Point_Process.html | 4 inst/doc/Setophaga.html | 4 inst/doc/Solitary_tinamou.R | 14 - inst/doc/Solitary_tinamou.Rmd | 14 - inst/doc/Solitary_tinamou.html | 21 +- inst/doc/Spatiotemporal_example.html | 4 man/dataOrganize.Rd | 8 - man/dataSDM.Rd | 7 man/intModel.Rd | 8 - tests/testthat/testthat_dataOrganize.R | 105 ++++++++++--- tests/testthat/testthat_dataSDM.R | 5 tests/testthat/testthat_dataSet.R | 4 tests/testthat/testthat_fitISDM.R | 2 vignettes/Solitary_tinamou.Rmd | 14 - 28 files changed, 632 insertions(+), 174 deletions(-)
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.
Author: Sinnwell JP, Schaid DJ
Maintainer: Jason P. Sinnwell <sinnwell.jason@mayo.edu>
Diff between haplo.stats versions 1.9.5 dated 2023-12-11 and 1.9.5.1 dated 2024-02-02
DESCRIPTION | 6 +++--- MD5 | 3 ++- R/00.R |only 3 files changed, 5 insertions(+), 4 deletions(-)
Title: Animation of Multiple Trajectories with Uncertainty
Description: Animation of observed trajectories using spline-based interpolation (see for example, Buderman, F. E., Hooten, M. B., Ivan, J. S. and Shenk, T. M. (2016), <doi:10.1111/2041-210X.12465> "A functional model for characterizing long-distance movement behaviour". Methods Ecol Evol). Intended to be used exploratory data analysis, and perhaps for preparation of presentations.
Author: Henry Scharf [aut, cre],
Kristine Dinh [aut],
Rosales Hugo [aut],
Rivera Angelica [aut]
Maintainer: Henry Scharf <hscharf@arizona.edu>
Diff between anipaths versions 0.10.2 dated 2023-01-16 and 0.10.3 dated 2024-02-02
DESCRIPTION | 20 +-- MD5 | 40 +++--- NAMESPACE | 13 -- NEWS | 9 + R/animate_paths.R | 93 ++++----------- R/animation_expression.R | 52 +++----- R/blur.R | 8 - R/crawl_interpolation.R | 38 +++--- R/gam_interpolation.R | 2 build/vignette.rds |binary inst/doc/anipaths.R | 12 +- inst/doc/anipaths.Rmd | 12 +- inst/doc/anipaths.html | 253 ++++++++++++++++++++++--------------------- inst/doc/anipaths_crawl.html | 125 +++++++++++---------- inst/doc/anipaths_gam.R | 10 - inst/doc/anipaths_gam.Rmd | 11 - inst/doc/anipaths_gam.html | 147 ++++++++++++------------ man/animate_paths.Rd | 10 - man/crawl_interpolation.Rd | 4 vignettes/anipaths.Rmd | 12 +- vignettes/anipaths_gam.Rmd | 11 - 21 files changed, 421 insertions(+), 461 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Lightweight parallel code execution and distributed computing.
Designed for simplicity, a 'mirai' evaluates an R expression asynchronously,
on local or network resources, resolving automatically upon completion.
Efficient scheduling over fast inter-process communications or secure TLS
connections over TCP/IP, built on 'nanonext' and 'NNG' (Nanomsg Next Gen).
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 0.12.0 dated 2024-01-12 and 0.12.1 dated 2024-02-02
DESCRIPTION | 8 +-- MD5 | 84 +++++++++++++++++++------------------- NAMESPACE | 4 - NEWS.md | 9 ++++ R/daemon.R | 26 +++++------ R/daemons.R | 107 +++++++++++++++++++++++++------------------------ R/dispatcher.R | 27 ++++++------ R/launchers.R | 33 ++++++++------- R/mirai-package.R | 25 +++-------- R/mirai.R | 65 +++++++++++++++-------------- R/next.R | 12 ++--- R/parallel.R | 10 ++-- README.md | 10 ++-- inst/doc/mirai.Rmd | 82 ++++++++++++++++++------------------- inst/doc/mirai.html | 82 ++++++++++++++++++------------------- inst/doc/parallel.Rmd | 6 +- inst/doc/parallel.html | 6 +- inst/doc/plumber.Rmd | 32 +++++++------- inst/doc/plumber.html | 32 +++++++------- inst/doc/shiny.R | 19 ++++++-- inst/doc/shiny.Rmd | 25 ++++++++--- inst/doc/shiny.html | 25 ++++++++--- inst/doc/torch.Rmd | 42 +++++++++---------- inst/doc/torch.html | 42 +++++++++---------- man/call_mirai.Rd | 3 - man/daemon.Rd | 16 +++---- man/daemons.Rd | 5 -- man/dispatcher.Rd | 4 - man/dot-daemon.Rd | 3 - man/everywhere.Rd | 8 +-- man/is_mirai_error.Rd | 6 +- man/launch_local.Rd | 3 - man/mirai-package.Rd | 15 +++--- man/mirai.Rd | 8 +-- man/nextstream.Rd | 13 ++--- man/remote_config.Rd | 7 +-- man/saisei.Rd | 3 - tests/tests.R | 7 +-- vignettes/mirai.Rmd | 82 ++++++++++++++++++------------------- vignettes/parallel.Rmd | 6 +- vignettes/plumber.Rmd | 32 +++++++------- vignettes/shiny.Rmd | 25 ++++++++--- vignettes/torch.Rmd | 42 +++++++++---------- 43 files changed, 573 insertions(+), 528 deletions(-)
Title: Multi-Site Stochastic Models for Daily Precipitation and
Temperature
Description: Application of multi-site models for daily precipitation and temperature data.
This package is designed for an application to 105 precipitation and 26 temperature gauges located in Switzerland.
It applies fitting procedures and provides weather generators described in the following references:
- Evin, G., A.-C. Favre, and B. Hingray. (2018) <doi:10.5194/hess-22-655-2018>.
- Evin, G., A.-C. Favre, and B. Hingray. (2018) <doi:10.1007/s00704-018-2404-x>.
Author: Guillaume Evin [aut, cre]
Maintainer: Guillaume Evin <guillaume.evin@inrae.fr>
Diff between GWEX versions 1.1.2 dated 2023-11-08 and 1.1.3 dated 2024-02-02
DESCRIPTION | 8 ++-- MD5 | 4 +- R/GWexTemp_lib.r | 110 +++++++++++++++++++++++++++---------------------------- 3 files changed, 61 insertions(+), 61 deletions(-)
Title: NASA POWER API Client
Description: An API client for NASA POWER global meteorology, surface solar
energy and climatology data API. POWER (Prediction Of Worldwide Energy
Resources) data are freely available for download with varying spatial
resolutions dependent on the original data and with several temporal
resolutions depending on the POWER parameter and community. This work is
funded through the NASA Earth Science Directorate Applied Science Program.
For more on the data themselves, the methodologies used in creating, a web-
based data viewer and web access, please see <https://power.larc.nasa.gov/>.
Author: Adam H. Sparks [aut, cre] ,
Scott Chamberlain [rev] ,
Hazel Kavili [rev] ,
Alison Boyer [rev] ,
Fernando Miguez [ctb] ,
Maelle Salmon [ctb] ,
Phillip D. Alderman [ctb] ` must use `I` for literal data as of
vroom 1.5.0.', see
<https://github.com/ropen [...truncated...]
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between nasapower versions 4.1.0 dated 2023-12-05 and 4.2.0 dated 2024-02-02
DESCRIPTION | 34 MD5 | 63 NAMESPACE | 2 NEWS.md | 22 R/get_power.R | 223 +- R/internal_functions.R | 147 + R/query_groupings.R |only R/query_parameters.R | 93 R/query_surfaces.R |only R/sysdata.rda |binary README.md | 6 inst/WORDLIST | 4 inst/doc/nasapower.Rmd | 1668 ----------------- inst/doc/nasapower.html | 1667 ---------------- man/get_power.Rd | 34 man/nasapower-package.Rd | 4 man/query_groupings.Rd |only man/query_parameters.Rd | 32 man/query_surfaces.Rd |only tests/fixtures/adjusted_air_pressure.json | 2 tests/fixtures/adjusted_wind_elevation.json | 2 tests/fixtures/climatology_ag_point.json | 2 tests/fixtures/daily_ag_point.json | 2 tests/fixtures/daily_sb_point_LST.json | 2 tests/fixtures/daily_sb_point_UTC.json | 2 tests/fixtures/query_groupings.json |only tests/fixtures/query_groupings_global.json |only tests/fixtures/query_parameters_comm&temporal_api.json |only tests/fixtures/query_surfaces_all.json |only tests/fixtures/query_surfaces_seaice.json |only tests/testthat.R | 8 tests/testthat/test-get_power.R | 47 tests/testthat/test-internal_functions.R | 48 tests/testthat/test-query_groupings.R |only tests/testthat/test-query_parameters.R | 71 tests/testthat/test-query_surfaces.R |only vignettes/nasapower.Rmd | 1668 ----------------- vignettes/nasapower.Rmd.orig | 11 38 files changed, 620 insertions(+), 5244 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for
the complete machine learning life cycle, see <https://mlflow.org/>.
This package supports installing 'MLflow', tracking experiments,
creating and running projects, and saving and serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] ,
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 2.9.2 dated 2023-12-20 and 2.10.0 dated 2024-02-02
DESCRIPTION | 6 +++--- MD5 | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-)
Title: Import and Analyse Ego-Centered Network Data
Description: Tools for importing, analyzing and visualizing ego-centered
network data. Supports several data formats, including the export formats of
'EgoNet', 'EgoWeb 2.0' and 'openeddi'. An interactive (shiny) app for the
intuitive visualization of ego-centered networks is provided. Also included
are procedures for creating and visualizing Clustered Graphs
(Lerner 2008 <DOI:10.1109/PACIFICVIS.2008.4475458>).
Author: Till Krenz [aut, cre],
Pavel N. Krivitsky [aut],
Raffaele Vacca [aut],
Michal Bojanowski [aut] ,
Markus Gamper [ctb],
Andreas Herz [aut],
Christopher McCarty [ctb]
Maintainer: Till Krenz <egor@tillt.net>
Diff between egor versions 1.23.3 dated 2023-03-16 and 1.24.2 dated 2024-02-02
DESCRIPTION | 8 MD5 | 36 - NAMESPACE | 6 NEWS.md | 8 R/count_dyads.R | 2 R/dplyr_methods.R | 60 ++ R/read.egonet.R | 6 R/rotate.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/check_and_release.R | 3 inst/doc/egor_allbus.html | 198 ++++----- inst/doc/qualtrics.R | 2 inst/doc/qualtrics.html | 228 +++++------ inst/doc/using_egor.html | 721 ++++++++++++++++++------------------ man/rotate_to_equilibrium.Rd | 2 man/wide.dyads.to.edgelist.Rd | 6 man/wide.to.long.Rd | 8 tests/testthat/test-dplyr_methods.R | 67 +++ 19 files changed, 750 insertions(+), 613 deletions(-)
Title: Fit Dynamic Structural Equation Models
Description: Applies dynamic structural equation models to time-series data
with generic and simplified specification for simultaneous and lagged
effects. Methods are described in Thorson et al. (In press)
"Dynamic structural equation models synthesize ecosystem dynamics
constrained by ecological mechanisms."
Author: James Thorson [aut, cre]
Maintainer: James Thorson <James.Thorson@noaa.gov>
Diff between dsem versions 1.0.1 dated 2024-01-17 and 1.0.2 dated 2024-02-02
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Title: NPMLE for Logistic-Cox Cure-Rate Model
Description: Expectation-Maximization (EM) algorithm for point estimation and variance estimation to
the nonparametric maximum likelihood estimator (NPMLE) for
logistic-Cox cure-rate model with left truncation and right-
censoring. See Hou, Chambers and Xu (2017) <doi:10.1007/s10985-017-9415-2>.
Author: Jue Hou, Evan Ren
Maintainer: Jue (Marquis) Hou <hou00123@umn.edu>
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