Improving igraph interface: current deprecations
Source:vignettes/articles/current-deprecations.Rmd
current-deprecations.RmdTo provide a more consistent interface, part of igraph functions or arguments are slowly but consistently being deprecated. You can follow along the current level of deprecations in the table below.
Please update your codebases as soon as you can, be they packages or scripts. To do that, run your code in a session where you installed the latest igraph version, possibly even the development version that you can install from R-universe:
options(
repos = c(
igraph = 'https://igraph.r-universe.dev',
CRAN = 'https://cloud.r-project.org'
)
)
install.packages('igraph')And pay attention to any message emitted through the lifecycle package.
Thank you for your cooperation! Direct any question to us in the igraph issue tracker.
| level | version | old | new |
|---|---|---|---|
| 2 – warn | 2.0.0 | graph.adjacency() | graph_from_adjacency_matrix() |
| 1 – soft | 3.0.0 | base::I(“Calling
graph_from_adjacency_matrix() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph_from_adjacency_matrix(”,base::paste(base::c(“adjmatrix”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph_from_adjacency_matrix(”,base::paste(base::c(“adjmatrix”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 1.6.0 | graph_from_adjacency_matrix(adjmatrix = ‘must be a matrix’) | |
| 2 – warn | 1.6.0 | graph_from_adjacency_matrix(adjmatrix = ‘must be symmetric with mode = "undirected"’) | Use mode = “max” to achieve the original behavior. |
| 1 – soft | 3.0.0 | base::I(“Calling from_adjacency() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: from_adjacency(”,base::paste(base::c(“adjmatrix”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: from_adjacency(”,base::paste(base::c(“adjmatrix”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 1.5.0 | ape::as.phylo() | |
| 2 – warn | 2.0.0 | assortativity.nominal() | assortativity_nominal() |
| 2 – warn | 2.0.0 | assortativity.degree() | assortativity_degree() |
| 2 – warn | 1.6.0 | assortativity(… =) | Arguments values and
values.in must be named. |
| 2 – warn | 1.6.0 | assortativity(types1 =) | assortativity(values =) |
| 2 – warn | 1.6.0 | assortativity(types2 =) | assortativity(values.in =) |
| 1 – soft | 3.0.0 | base::I(“Calling assortativity_nominal()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: assortativity_nominal(”,base::paste(base::c(“graph”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: assortativity_nominal(”,base::paste(base::c(“graph”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling assortativity_degree()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: assortativity_degree(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: assortativity_degree(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | set.vertex.attribute() | set_vertex_attr() |
| 2 – warn | 2.0.0 | set.graph.attribute() | set_graph_attr() |
| 2 – warn | 2.0.0 | set.edge.attribute() | set_edge_attr() |
| 2 – warn | 2.0.0 | remove.vertex.attribute() | delete_vertex_attr() |
| 2 – warn | 2.0.0 | remove.graph.attribute() | delete_graph_attr() |
| 2 – warn | 2.0.0 | remove.edge.attribute() | delete_edge_attr() |
| 2 – warn | 2.0.0 | list.vertex.attributes() | vertex_attr_names() |
| 2 – warn | 2.0.0 | list.graph.attributes() | graph_attr_names() |
| 2 – warn | 2.0.0 | list.edge.attributes() | edge_attr_names() |
| 2 – warn | 2.0.0 | is.weighted() | is_weighted() |
| 2 – warn | 2.0.0 | is.named() | is_named() |
| 2 – warn | 2.0.0 | is.bipartite() | is_bipartite() |
| 2 – warn | 2.0.0 | get.vertex.attribute() | vertex_attr() |
| 2 – warn | 2.0.0 | get.graph.attribute() | graph_attr() |
| 2 – warn | 2.0.0 | get.edge.attribute() | edge_attr() |
| 2 – warn | 2.0.0 | is.igraph() | is_igraph() |
| 2 – warn | 2.0.0 | bipartite.projection.size() | bipartite_projection_size() |
| 2 – warn | 2.0.0 | bipartite.projection() | bipartite_projection() |
| 2 – warn | 2.0.0 | bipartite.mapping() | bipartite_mapping() |
| 1 – soft | 3.0.0 | base::I(“Calling bipartite_projection()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: bipartite_projection(”,base::paste(base::c(“graph”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: bipartite_projection(”,base::paste(base::c(“graph”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | subgraph.centrality() | subgraph_centrality() |
| 2 – warn | 2.0.0 | page.rank() | page_rank() |
| 3 – stop | 2.0.0 | hub.score() | hits_scores() |
| 3 – stop | 2.0.0 | authority.score() | hits_scores() |
| 2 – warn | 2.0.0 | graph.strength() | strength() |
| 2 – warn | 2.0.0 | graph.eigen() | spectrum() |
| 2 – warn | 2.0.0 | graph.diversity() | diversity() |
| 2 – warn | 2.0.0 | evcent() | eigen_centrality() |
| 2 – warn | 2.0.0 | edge.betweenness() | edge_betweenness() |
| 2 – warn | 2.0.0 | bonpow() | power_centrality() |
| 2 – warn | 2.0.0 | alpha.centrality() | alpha_centrality() |
| 2 – warn | 1.6.0 | estimate_betweenness() | betweenness() |
| 1 – soft | 3.0.0 | base::I(“Calling betweenness() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: betweenness(”,base::paste(base::c(“graph”,“v”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: betweenness(”,base::paste(base::c(“graph”,“v”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling edge_betweenness() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: edge_betweenness(”,base::paste(base::c(“graph”,“e”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: edge_betweenness(”,base::paste(base::c(“graph”,“e”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 1.6.0 | estimate_edge_betweenness() | edge_betweenness() |
| 1 – soft | 3.0.0 | base::I(“Calling closeness() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: closeness(”,base::paste(base::c(“graph”,“vids”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: closeness(”,base::paste(base::c(“graph”,“vids”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 1.6.0 | estimate_closeness() | closeness() |
| 2 – warn | 1.6.0 | arpack(options = ‘must be a list’) | c(“arpack_defaults() is now a function,
use options = arpack_defaults() instead of
options = arpack_defaults.”) |
| 1 – soft | 3.0.0 | base::I(“Calling subgraph_centrality()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: subgraph_centrality(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: subgraph_centrality(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 1.6.0 | spectrum(options = ‘must be a list’) | c(“arpack_defaults() is now a function,
use options = arpack_defaults() instead of
options = arpack_defaults.”) |
| 2 – warn | 1.6.0 | eigen_centrality(options = ‘must be a list’) | c(“arpack_defaults() is now a function,
use options = arpack_defaults() instead of
options = arpack_defaults.”) |
| 2 – warn | 2.1.1 | eigen_centrality(scale) | eigen_centrality() will always behave as if scale=TRUE were used. |
| 3 – stop | 2.1.1 | eigen_centrality(scale = ‘always as if TRUE’) | Normalization is always performed |
| 1 – soft | 3.0.0 | base::I(“Calling strength() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: strength(”,base::paste(base::c(“graph”,“vids”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: strength(”,base::paste(base::c(“graph”,“vids”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling diversity() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: diversity(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: diversity(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | authority_score() | hits_scores() |
| 2 – warn | 1.6.0 | I(“arpack_defaults”) | arpack_defaults() |
| 2 – warn | 2.0.3 | hub_score() | hits_scores() |
| 2 – warn | 1.6.0 | I(“arpack_defaults”) | arpack_defaults() |
| 1 – soft | 3.0.0 | base::I(“Calling page_rank() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: page_rank(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: page_rank(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling harmonic_centrality()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: harmonic_centrality(”,base::paste(base::c(“graph”,“vids”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: harmonic_centrality(”,base::paste(base::c(“graph”,“vids”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling power_centrality() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: power_centrality(”,base::paste(base::c(“graph”,“nodes”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: power_centrality(”,base::paste(base::c(“graph”,“nodes”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling alpha_centrality() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: alpha_centrality(”,base::paste(base::c(“graph”,“nodes”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: alpha_centrality(”,base::paste(base::c(“graph”,“nodes”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | centralize.scores() | centralize() |
| 2 – warn | 2.0.0 | centralization.evcent.tmax() | centr_eigen_tmax() |
| 2 – warn | 2.0.0 | centralization.evcent() | centr_eigen() |
| 2 – warn | 2.0.0 | centralization.degree.tmax() | centr_degree_tmax() |
| 2 – warn | 2.0.0 | centralization.degree() | centr_degree() |
| 2 – warn | 2.0.0 | centralization.closeness.tmax() | centr_clo_tmax() |
| 2 – warn | 2.0.0 | centralization.closeness() | centr_clo() |
| 2 – warn | 2.0.0 | centralization.betweenness.tmax() | centr_betw_tmax() |
| 2 – warn | 2.0.0 | centralization.betweenness() | centr_betw() |
| 1 – soft | 3.0.0 | base::I(“Calling centralize() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: centralize(”,base::paste(base::c(“scores”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: centralize(”,base::paste(base::c(“scores”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling centr_degree() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: centr_degree(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: centr_degree(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 2.0.0 | centr_degree_tmax(loops = ‘must be explicit’) | The default value (currently FALSE) will
be dropped in the next release. Add an explicit value for the
loops argument. |
| 1 – soft | 3.0.0 | base::I(“Calling centr_betw() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: centr_betw(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: centr_betw(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling centr_betw_tmax() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: centr_betw_tmax(”,base::paste(base::c(“graph”,“nodes”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: centr_betw_tmax(”,base::paste(base::c(“graph”,“nodes”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling centr_clo() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: centr_clo(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: centr_clo(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling centr_clo_tmax() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: centr_clo_tmax(”,base::paste(base::c(“graph”,“nodes”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: centr_clo_tmax(”,base::paste(base::c(“graph”,“nodes”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.2.0 | centr_eigen(scale = ) | The function always behaves as if
scale = TRUE. |
| The argument will be removed in the future. | |||
| 2 – warn | 2.2.0 | centr_eigen_tmax(scale = ) | The function always behaves as if
scale = TRUE. |
| The argument will be removed in the future. | |||
| 2 – warn | 2.0.0 | maximal.independent.vertex.sets() | max_ivs() |
| 2 – warn | 2.0.0 | maximal.cliques.count() | count_max_cliques() |
| 2 – warn | 2.0.0 | maximal.cliques() | max_cliques() |
| 2 – warn | 2.0.0 | largest.independent.vertex.sets() | largest_ivs() |
| 2 – warn | 2.0.0 | largest.cliques() | largest_cliques() |
| 2 – warn | 2.0.0 | independent.vertex.sets() | ivs() |
| 2 – warn | 2.0.0 | independence.number() | ivs_size() |
| 2 – warn | 2.0.0 | clique.number() | clique_num() |
| 1 – soft | 3.0.0 | base::I(“Calling count_max_cliques() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: count_max_cliques(”,base::paste(base::c(“graph”,“min”,“max”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: count_max_cliques(”,base::paste(base::c(“graph”,“min”,“max”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling weighted_cliques() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: weighted_cliques(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: weighted_cliques(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling
largest_weighted_cliques() with positional or abbreviated
arguments”) |
base::c(i=base::paste0(“Detected call: largest_weighted_cliques(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: largest_weighted_cliques(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling weighted_clique_num()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: weighted_clique_num(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: weighted_clique_num(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | maximal_ivs() | max_ivs() |
| 1 – soft | 3.0.0 | base::I(“Calling clique_size_counts() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: clique_size_counts(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: clique_size_counts(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling is_clique() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: is_clique(”,base::paste(base::c(“graph”,“candidate”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: is_clique(”,base::paste(base::c(“graph”,“candidate”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | exportPajek() | export_pajek() |
| 2 – warn | 2.0.0 | plotHierarchy() | plot_hierarchy() |
| 2 – warn | 2.0.0 | maxcohesion() | max_cohesion() |
| 2 – warn | 2.0.0 | graph.cohesion() | cohesion() |
| 2 – warn | 2.0.0 | cohesive.blocks() | cohesive_blocks() |
| 2 – warn | 2.0.0 | blockGraphs() | graphs_from_cohesive_blocks() |
| 1 – soft | 3.0.0 | base::I(“Calling cohesive_blocks() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: cohesive_blocks(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: cohesive_blocks(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling export_pajek() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: export_pajek(”,base::paste(base::c(“blocks”,“graph”,“file”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: export_pajek(”,base::paste(base::c(“blocks”,“graph”,“file”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling greedy_vertex_coloring()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: greedy_vertex_coloring(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: greedy_vertex_coloring(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | create.communities() | make_clusters() |
| 2 – warn | 2.0.0 | walktrap.community() | cluster_walktrap() |
| 2 – warn | 2.0.0 | spinglass.community() | cluster_spinglass() |
| 2 – warn | 2.0.0 | showtrace() | show_trace() |
| 2 – warn | 2.0.0 | optimal.community() | cluster_optimal() |
| 2 – warn | 2.0.0 | multilevel.community() | cluster_louvain() |
| 2 – warn | 2.0.0 | mod.matrix() | modularity_matrix() |
| 2 – warn | 2.0.0 | leading.eigenvector.community() | cluster_leading_eigen() |
| 2 – warn | 2.0.0 | label.propagation.community() | cluster_label_prop() |
| 2 – warn | 2.0.0 | is.hierarchical() | is_hierarchical() |
| 2 – warn | 2.0.0 | infomap.community() | cluster_infomap() |
| 2 – warn | 2.0.0 | fastgreedy.community() | cluster_fast_greedy() |
| 2 – warn | 2.0.0 | edge.betweenness.community() | cluster_edge_betweenness() |
| 2 – warn | 2.0.0 | dendPlot() | plot_dendrogram() |
| 2 – warn | 2.0.0 | cutat() | cut_at() |
| 2 – warn | 2.0.0 | contract.vertices() | contract() |
| 2 – warn | 2.0.0 | code.length() | code_len() |
| 1 – soft | 3.0.0 | base::I(“Calling make_clusters() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_clusters(”,base::paste(base::c(“graph”,“membership”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_clusters(”,base::paste(base::c(“graph”,“membership”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling modularity_matrix() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: modularity_matrix(”,base::paste(base::c(“graph”,“membership”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: modularity_matrix(”,base::paste(base::c(“graph”,“membership”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 2.1.0 | modularity_matrix(membership = ‘is no longer used’) | |
| 1 – soft | 3.0.0 | base::I(“Calling cluster_spinglass() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: cluster_spinglass(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: cluster_spinglass(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | cluster_leiden(resolution_parameter) | cluster_leiden(resolution) |
| 1 – soft | 3.0.0 | base::I(“Calling cluster_walktrap() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: cluster_walktrap(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: cluster_walktrap(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling
cluster_edge_betweenness() with positional or abbreviated
arguments”) |
base::c(i=base::paste0(“Detected call: cluster_edge_betweenness(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: cluster_edge_betweenness(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling cluster_fast_greedy()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: cluster_fast_greedy(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: cluster_fast_greedy(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 1.6.0 | cluster_leading_eigen(options = ‘must be a list’) | c(“arpack_defaults() is now a function,
use options = arpack_defaults() instead of
options = arpack_defaults.”) |
| 2 – warn | 1.6.0 | cluster_label_prop(… = ) | Arguments initial and fixed
must be named. |
| 1 – soft | 3.0.0 | base::I(“Calling cluster_louvain() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: cluster_louvain(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: cluster_louvain(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling cluster_optimal() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: cluster_optimal(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: cluster_optimal(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling cluster_infomap() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: cluster_infomap(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: cluster_infomap(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | no.clusters() | count_components() |
| 2 – warn | 2.0.0 | decompose.graph() | decompose() |
| 2 – warn | 2.0.0 | cluster.distribution() | component_distribution() |
| 2 – warn | 2.0.0 | biconnected.components() | biconnected_components() |
| 2 – warn | 2.0.0 | articulation.points() | articulation_points() |
| 1 – soft | 3.0.0 | base::I(“Calling decompose() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: decompose(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: decompose(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling largest_component() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: largest_component(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: largest_component(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | igraph.console() | console() |
| 3 – stop | 3.0.0 | console() | |
| 2 – warn | 2.0.0 | igraph.to.graphNEL() | as_graphnel() |
| 2 – warn | 2.0.0 | igraph.from.graphNEL() | graph_from_graphnel() |
| 2 – warn | 2.0.0 | graph.adjlist() | graph_from_adj_list() |
| 2 – warn | 2.0.0 | get.incidence() | as_biadjacency_matrix() |
| 2 – warn | 2.0.0 | get.edgelist() | as_edgelist() |
| 2 – warn | 2.0.0 | get.data.frame() | as_data_frame() |
| 2 – warn | 2.0.0 | get.adjacency() | as_adjacency_matrix() |
| 2 – warn | 2.0.0 | get.adjlist() | as_adj_list() |
| 2 – warn | 2.0.0 | get.adjedgelist() | as_adj_edge_list() |
| 1 – soft | 3.0.0 | sprintf(“%s(attr = )”,fn) | sprintf(“%s(weights = )”,fn) |
| 2 – warn | 2.1.0 | get.adjacency.dense(loops = ‘must be a character’) | sprintf(“Converting to get.adjacency.dense (loops = ‘%s’)”,loops) |
| 1 – soft | 3.0.0 | base::I(“Calling as_adjacency_matrix()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: as_adjacency_matrix(”,base::paste(base::c(“graph”,“type”,base::c(weights=“attr”,edges=“edges”,names=“names”,sparse=“sparse”)[.arg_names]),collapse=“,”),“)”),i=base::paste0(“Use instead: as_adjacency_matrix(”,base::paste(base::c(“graph”,“type”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 2.0.0 | as_adjacency_matrix(edges = ) | |
| 2 – warn | 2.1.0 | as_adj() | as_adjacency_matrix() |
| 1 – soft | 3.0.0 | base::I(“Calling as_edgelist() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: as_edgelist(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: as_edgelist(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling as_directed() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: as_directed(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: as_directed(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling as_adj_list() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: as_adj_list(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: as_adj_list(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling as_adj_edge_list() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: as_adj_edge_list(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: as_adj_edge_list(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling graph_from_graphnel()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph_from_graphnel(”,base::paste(base::c(“graphNEL”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph_from_graphnel(”,base::paste(base::c(“graphNEL”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling as_biadjacency_matrix()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: as_biadjacency_matrix(”,base::paste(base::c(“graph”,“types”,base::c(weights=“attr”,names=“names”,sparse=“sparse”)[.arg_names]),collapse=“,”),“)”),i=base::paste0(“Use instead: as_biadjacency_matrix(”,base::paste(base::c(“graph”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 1.6.0 | as_incidence_matrix() | as_biadjacency_matrix() |
| 1 – soft | 3.0.0 | base::I(“Calling graph_from_adj_list()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph_from_adj_list(”,base::paste(base::c(“adjlist”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph_from_adj_list(”,base::paste(base::c(“adjlist”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | as.directed() | as_directed() |
| 2 – warn | 2.1.0 | as.undirected() | as_undirected() |
| 2 – warn | 2.0.0 | graph.edgelist() | graph_from_edgelist() |
| 2 – warn | 2.0.0 | graph.data.frame() | graph_from_data_frame() |
| 1 – soft | 3.0.0 | base::I(“Calling graph_from_data_frame()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph_from_data_frame(”,base::paste(base::c(“d”,“directed”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph_from_data_frame(”,base::paste(base::c(“d”,“directed”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling graph_from_edgelist()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph_from_edgelist(”,base::paste(base::c(“el”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph_from_edgelist(”,base::paste(base::c(“el”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling find_cycle() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: find_cycle(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: find_cycle(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | is.chordal() | is_chordal() |
| 1 – soft | 3.0.0 | base::I(“Calling is_chordal() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: is_chordal(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: is_chordal(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | is.graphical.degree.sequence() | is_graphical() |
| 2 – warn | 2.0.0 | is.degree.sequence() | is_degseq() |
| 1 – soft | 3.0.0 | base::I(“Calling is_graphical() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: is_graphical(”,base::paste(base::c(“out.deg”,“in.deg”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: is_graphical(”,base::paste(base::c(“out.deg”,“in.deg”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling global_efficiency() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: global_efficiency(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: global_efficiency(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling local_efficiency() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: local_efficiency(”,base::paste(base::c(“graph”,“vids”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: local_efficiency(”,base::paste(base::c(“graph”,“vids”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling
average_local_efficiency() with positional or abbreviated
arguments”) |
base::c(i=base::paste0(“Detected call: average_local_efficiency(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: average_local_efficiency(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling embed_adjacency_matrix()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: embed_adjacency_matrix(”,base::paste(base::c(“graph”,“no”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: embed_adjacency_matrix(”,base::paste(base::c(“graph”,“no”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling embed_laplacian_matrix()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: embed_laplacian_matrix(”,base::paste(base::c(“graph”,“no”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: embed_laplacian_matrix(”,base::paste(base::c(“graph”,“no”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_sphere_surface()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_sphere_surface(”,base::paste(base::c(“dim”,“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_sphere_surface(”,base::paste(base::c(“dim”,“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_sphere_volume()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_sphere_volume(”,base::paste(base::c(“dim”,“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_sphere_volume(”,base::paste(base::c(“dim”,“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling time_bins() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: time_bins(”,base::paste(base::c(“x”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: time_bins(”,base::paste(base::c(“x”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | power.law.fit() | fit_power_law() |
| 3 – stop | 2.1.0 | fit_power_law(implementation = “cannot be \”plfit.p\““) | I(‘fit_power_law(implementation = "plfit", p.value = TRUE)’) |
| 2 – warn | 2.0.0 | vertex.disjoint.paths() | vertex_disjoint_paths() |
| 2 – warn | 2.0.0 | vertex.connectivity() | vertex_connectivity() |
| 2 – warn | 2.0.0 | stMincuts() | st_min_cuts() |
| 2 – warn | 2.0.0 | stCuts() | st_cuts() |
| 2 – warn | 2.0.0 | minimum.size.separators() | min_separators() |
| 2 – warn | 2.0.0 | minimal.st.separators() | min_st_separators() |
| 2 – warn | 2.0.0 | is.separator() | is_separator() |
| 2 – warn | 2.0.0 | is.minimal.separator() | is_min_separator() |
| 2 – warn | 2.0.0 | graph.mincut() | min_cut() |
| 2 – warn | 2.0.0 | graph.maxflow() | max_flow() |
| 2 – warn | 2.0.0 | graph.adhesion() | adhesion() |
| 2 – warn | 2.0.0 | edge.disjoint.paths() | edge_connectivity() |
| 2 – warn | 2.0.0 | edge.connectivity() | edge_connectivity() |
| 2 – warn | 2.0.0 | dominator.tree() | dominator_tree() |
| 1 – soft | 3.0.0 | base::I(“Calling min_cut() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: min_cut(”,base::paste(base::c(“graph”,“source”,“target”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: min_cut(”,base::paste(base::c(“graph”,“source”,“target”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling vertex_connectivity()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: vertex_connectivity(”,base::paste(base::c(“graph”,“source”,“target”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: vertex_connectivity(”,base::paste(base::c(“graph”,“source”,“target”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling edge_connectivity() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: edge_connectivity(”,base::paste(base::c(“graph”,“source”,“target”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: edge_connectivity(”,base::paste(base::c(“graph”,“source”,“target”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling adhesion() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: adhesion(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: adhesion(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling st_min_cuts() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: st_min_cuts(”,base::paste(base::c(“graph”,“source”,“target”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: st_min_cuts(”,base::paste(base::c(“graph”,“source”,“target”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling dominator_tree() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: dominator_tree(”,base::paste(base::c(“graph”,“root”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: dominator_tree(”,base::paste(base::c(“graph”,“root”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling max_flow() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: max_flow(”,base::paste(base::c(“graph”,“source”,“target”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: max_flow(”,base::paste(base::c(“graph”,“source”,“target”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | write.graph() | write_graph() |
| 2 – warn | 2.0.0 | read.graph() | read_graph() |
| 2 – warn | 2.0.0 | graph.graphdb() | graph_from_graphdb() |
| 1 – soft | 3.0.0 | base::I(“Calling graph_from_graphdb() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph_from_graphdb(”,base::paste(base::c(“url”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph_from_graphdb(”,base::paste(base::c(“url”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | watts.strogatz.game() | sample_smallworld() |
| 2 – warn | 2.0.0 | static.power.law.game() | sample_fitness_pl() |
| 2 – warn | 2.0.0 | static.fitness.game() | sample_fitness() |
| 2 – warn | 2.0.0 | sbm.game() | sample_sbm() |
| 2 – warn | 2.0.0 | preference.game() | sample_pref() |
| 2 – warn | 2.0.0 | lastcit.game() | sample_last_cit() |
| 2 – warn | 2.0.0 | k.regular.game() | sample_k_regular() |
| 2 – warn | 2.0.0 | interconnected.islands.game() | sample_islands() |
| 2 – warn | 2.0.0 | grg.game() | sample_grg() |
| 2 – warn | 2.0.0 | growing.random.game() | sample_growing() |
| 2 – warn | 2.0.0 | forest.fire.game() | sample_forestfire() |
| 2 – warn | 2.0.0 | establishment.game() | sample_traits() |
| 2 – warn | 2.0.0 | degree.sequence.game() | sample_degseq() |
| 2 – warn | 2.0.0 | connect.neighborhood() | connect() |
| 2 – warn | 2.0.0 | citing.cited.type.game() | sample_cit_cit_types() |
| 2 – warn | 2.0.0 | cited.type.game() | sample_cit_types() |
| 2 – warn | 2.0.0 | callaway.traits.game() | sample_traits_callaway() |
| 3 – stop | 2.0.0 | bipartite.random.game() | Use sample_bipartite_gnp() or sample_bipartite_gnm() |
| 2 – warn | 2.0.0 | barabasi.game() | sample_pa() |
| 2 – warn | 2.0.0 | ba.game() | sample_pa() |
| 2 – warn | 2.0.0 | asymmetric.preference.game() | sample_asym_pref() |
| 2 – warn | 2.0.0 | aging.barabasi.game() | sample_pa_age() |
| 2 – warn | 2.0.0 | aging.ba.game() | sample_pa_age() |
| 2 – warn | 2.0.0 | aging.prefatt.game() | sample_pa_age() |
| 1 – soft | 3.0.0 | base::I(“Calling sample_pa() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_pa(”,base::paste(base::c(“n”,“power”,“m”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_pa(”,base::paste(base::c(“n”,“power”,“m”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling pa() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: pa(”,base::paste(base::c(“n”,“power”,“m”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: pa(”,base::paste(base::c(“n”,“power”,“m”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_gnp() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_gnp(”,base::paste(base::c(“n”,“p”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_gnp(”,base::paste(base::c(“n”,“p”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling gnp() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: gnp(”,base::paste(base::c(“n”,“p”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: gnp(”,base::paste(base::c(“n”,“p”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_gnm() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_gnm(”,base::paste(base::c(“n”,“m”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_gnm(”,base::paste(base::c(“n”,“m”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling gnm() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: gnm(”,base::paste(base::c(“n”,“m”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: gnm(”,base::paste(base::c(“n”,“m”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 0.8.0 | erdos.renyi.game() | sample_gnp() |
| 2 – warn | 0.8.0 | erdos.renyi.game() | sample_gnm() |
| 2 – warn | 0.8.0 | random.graph.game() | sample_gnp() |
| 2 – warn | 0.8.0 | random.graph.game() | sample_gnm() |
| 1 – soft | 3.0.0 | base::I(“Calling sample_degseq() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_degseq(”,base::paste(base::c(“out.deg”,“in.deg”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_degseq(”,base::paste(base::c(“out.deg”,“in.deg”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 2.1.0 | sample_degseq(method = ‘must be configuration instead of simple’) | |
| 3 – stop | 2.1.0 | sample_degseq(method = ‘must be fast.heur.simple instead of simple.no.multiple’) | |
| 3 – stop | 2.1.0 | sample_degseq(method = ‘must be configuration.simple instead of simple.no.multiple.uniform’) | |
| 1 – soft | 3.0.0 | base::I(“Calling sample_pa_age() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_pa_age(”,base::paste(base::c(“n”,“pa.exp”,“aging.exp”,“m”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_pa_age(”,base::paste(base::c(“n”,“pa.exp”,“aging.exp”,“m”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling pa_age() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: pa_age(”,base::paste(base::c(“n”,“pa.exp”,“aging.exp”,“m”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: pa_age(”,base::paste(base::c(“n”,“pa.exp”,“aging.exp”,“m”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_traits_callaway()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_traits_callaway(”,base::paste(base::c(“nodes”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_traits_callaway(”,base::paste(base::c(“nodes”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling traits_callaway() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: traits_callaway(”,base::paste(base::c(“nodes”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: traits_callaway(”,base::paste(base::c(“nodes”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_traits() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_traits(”,base::paste(base::c(“nodes”,“types”,“k”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_traits(”,base::paste(base::c(“nodes”,“types”,“k”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling traits() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: traits(”,base::paste(base::c(“nodes”,“types”,“k”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: traits(”,base::paste(base::c(“nodes”,“types”,“k”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_grg() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_grg(”,base::paste(base::c(“nodes”,“radius”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_grg(”,base::paste(base::c(“nodes”,“radius”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling grg() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: grg(”,base::paste(base::c(“nodes”,“radius”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: grg(”,base::paste(base::c(“nodes”,“radius”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_pref() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_pref(”,base::paste(base::c(“nodes”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_pref(”,base::paste(base::c(“nodes”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling pref() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: pref(”,base::paste(base::c(“nodes”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: pref(”,base::paste(base::c(“nodes”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_asym_pref() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_asym_pref(”,base::paste(base::c(“nodes”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_asym_pref(”,base::paste(base::c(“nodes”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling asym_pref() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: asym_pref(”,base::paste(base::c(“nodes”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: asym_pref(”,base::paste(base::c(“nodes”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling connect() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: connect(”,base::paste(base::c(“graph”,“order”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: connect(”,base::paste(base::c(“graph”,“order”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_smallworld() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_smallworld(”,base::paste(base::c(“dim”,“size”,“nei”,“p”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_smallworld(”,base::paste(base::c(“dim”,“size”,“nei”,“p”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling smallworld() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: smallworld(”,base::paste(base::c(“dim”,“size”,“nei”,“p”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: smallworld(”,base::paste(base::c(“dim”,“size”,“nei”,“p”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_last_cit() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_last_cit(”,base::paste(base::c(“n”,“edges”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_last_cit(”,base::paste(base::c(“n”,“edges”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling last_cit() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: last_cit(”,base::paste(base::c(“n”,“edges”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: last_cit(”,base::paste(base::c(“n”,“edges”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_cit_types() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_cit_types(”,base::paste(base::c(“n”,“edges”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_cit_types(”,base::paste(base::c(“n”,“edges”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling cit_types() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: cit_types(”,base::paste(base::c(“n”,“edges”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: cit_types(”,base::paste(base::c(“n”,“edges”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_cit_cit_types()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_cit_cit_types(”,base::paste(base::c(“n”,“edges”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_cit_cit_types(”,base::paste(base::c(“n”,“edges”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling cit_cit_types() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: cit_cit_types(”,base::paste(base::c(“n”,“edges”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: cit_cit_types(”,base::paste(base::c(“n”,“edges”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.2.0 | sample_bipartite() | sample_bipartite_gnp() |
| 2 – warn | 2.2.0 | sample_bipartite() | sample_bipartite_gnm() |
| 2 – warn | 2.1.3 | bipartite() | bipartite_gnp() |
| 2 – warn | 2.1.3 | bipartite() | bipartite_gnm() |
| 1 – soft | 3.0.0 | base::I(“Calling sample_sbm() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_sbm(”,base::paste(base::c(“n”,“pref.matrix”,“block.sizes”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_sbm(”,base::paste(base::c(“n”,“pref.matrix”,“block.sizes”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sbm() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sbm(”,base::paste(base::c(“n”,“pref.matrix”,“block.sizes”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sbm(”,base::paste(base::c(“n”,“pref.matrix”,“block.sizes”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_dot_product() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_dot_product(”,base::paste(base::c(“vecs”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_dot_product(”,base::paste(base::c(“vecs”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling dot_product() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: dot_product(”,base::paste(base::c(“vecs”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: dot_product(”,base::paste(base::c(“vecs”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_k_regular() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_k_regular(”,base::paste(base::c(“no.of.nodes”,“k”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_k_regular(”,base::paste(base::c(“no.of.nodes”,“k”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_fitness() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_fitness(”,base::paste(base::c(“no.of.edges”,“fitness.out”,“fitness.in”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_fitness(”,base::paste(base::c(“no.of.edges”,“fitness.out”,“fitness.in”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_fitness_pl() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_fitness_pl(”,base::paste(base::c(“no.of.nodes”,“no.of.edges”,“exponent.out”,“exponent.in”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_fitness_pl(”,base::paste(base::c(“no.of.nodes”,“no.of.edges”,“exponent.out”,“exponent.in”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_forestfire() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_forestfire(”,base::paste(base::c(“nodes”,“fw.prob”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_forestfire(”,base::paste(base::c(“nodes”,“fw.prob”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_correlated_gnp()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_correlated_gnp(”,base::paste(base::c(“old.graph”,“corr”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_correlated_gnp(”,base::paste(base::c(“old.graph”,“corr”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | graphlets.project() | graphlet_proj() |
| 2 – warn | 2.0.0 | graphlets.candidate.basis() | graphlet_basis() |
| 1 – soft | 3.0.0 | base::I(“Calling graphlet_basis() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graphlet_basis(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graphlet_basis(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling graphlet_proj() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graphlet_proj(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graphlet_proj(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling graphlets() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graphlets(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graphlets(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | hrg.predict() | predict_edges() |
| 2 – warn | 2.0.0 | hrg.fit() | fit_hrg() |
| 2 – warn | 2.0.0 | hrg.game() | sample_hrg() |
| 2 – warn | 2.0.0 | hrg.dendrogram() | hrg_tree() |
| 2 – warn | 2.0.0 | hrg.create() | hrg() |
| 2 – warn | 2.0.0 | hrg.consensus() | consensus_tree() |
| 1 – soft | 3.0.0 | base::I(“Calling fit_hrg() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: fit_hrg(”,base::paste(base::c(“graph”,“hrg”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: fit_hrg(”,base::paste(base::c(“graph”,“hrg”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling consensus_tree() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: consensus_tree(”,base::paste(base::c(“graph”,“hrg”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: consensus_tree(”,base::paste(base::c(“graph”,“hrg”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling predict_edges() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: predict_edges(”,base::paste(base::c(“graph”,“hrg”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: predict_edges(”,base::paste(base::c(“graph”,“hrg”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | graph.incidence() | graph_from_biadjacency_matrix() |
| 1 – soft | 3.0.0 | base::I(“Calling
graph_from_biadjacency_matrix() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph_from_biadjacency_matrix(”,base::paste(base::c(“incidence”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph_from_biadjacency_matrix(”,base::paste(base::c(“incidence”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 1.6.0 | graph_from_incidence_matrix() | graph_from_biadjacency_matrix() |
| 2 – warn | 1.6.0 | graph_from_incidence_matrix() | graph_from_biadjacency_matrix() |
| 2 – warn | 2.0.0 | is.directed() | is_directed() |
| 2 – warn | 2.0.0 | delete.vertices() | delete_vertices() |
| 2 – warn | 2.0.0 | delete.edges() | delete_edges() |
| 2 – warn | 2.0.0 | add.vertices() | add_vertices() |
| 2 – warn | 2.0.0 | add.edges() | add_edges() |
| 1 – soft | 3.0.0 | base::I(“Calling neighbors() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: neighbors(”,base::paste(base::c(“graph”,“v”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: neighbors(”,base::paste(base::c(“graph”,“v”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling incident() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: incident(”,base::paste(base::c(“graph”,“v”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: incident(”,base::paste(base::c(“graph”,“v”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling ends() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: ends(”,base::paste(base::c(“graph”,“es”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: ends(”,base::paste(base::c(“graph”,“es”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 2.1.5 | get_edge_ids(vp = ‘is not allowed to be a 2 times 2 matrix’) | |
| 3 – stop | 2.1.5 | get_edge_ids(vp = ‘supplied as a matrix should be a n times 2 matrix, not 2 times n’) | either transpose the matrix with t() or convert it to a data.frame with two columns. |
| 1 – soft | 3.0.0 | base::I(“Calling get_edge_ids() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: get_edge_ids(”,base::paste(base::c(“graph”,“vp”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: get_edge_ids(”,base::paste(base::c(“graph”,“vp”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 2.0.0 | get.edge.ids(multi = ) | |
| 2 – warn | 2.0.0 | get.edge.ids(multi = ) | |
| 2 – warn | 2.1.0 | get.edge.ids() | get_edge_ids() |
| 1 – soft | 3.0.0 | base::I(“Calling adjacent_vertices() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: adjacent_vertices(”,base::paste(base::c(“graph”,“v”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: adjacent_vertices(”,base::paste(base::c(“graph”,“v”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling incident_edges() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: incident_edges(”,base::paste(base::c(“graph”,“v”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: incident_edges(”,base::paste(base::c(“graph”,“v”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling identical_graphs() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: identical_graphs(”,base::paste(base::c(“g1”,“g2”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: identical_graphs(”,base::paste(base::c(“g1”,“g2”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling E() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: E(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: E(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 2.1.0 | nei() | .nei() |
| 3 – stop | 2.1.0 | innei() | .innei() |
| 3 – stop | 2.1.0 | outnei() | .outnei() |
| 3 – stop | 2.1.0 | inc() | .inc() |
| 3 – stop | 2.1.0 | adj() | .inc() |
| 3 – stop | 2.1.0 | from() | .from() |
| 3 – stop | 2.1.0 | to() | .to() |
| 3 – stop | 2.1.0 | adj() | .inc() |
| 3 – stop | 2.1.0 | inc() | .inc() |
| 3 – stop | 2.1.0 | from() | .from() |
| 3 – stop | 2.1.0 | to() | .to() |
| 2 – warn | 2.0.0 | piecewise.layout() | layout_components() |
| 2 – warn | 2.0.0 | layout.sugiyama() | layout_with_sugiyama() |
| 2 – warn | 2.0.0 | layout.star() | layout_as_star() |
| 2 – warn | 2.0.0 | layout.norm() | norm_coords() |
| 2 – warn | 2.0.0 | layout.merge() | merge_coords() |
| 2 – warn | 2.0.0 | layout.mds() | layout_with_mds() |
| 2 – warn | 2.0.0 | layout.grid() | layout_on_grid() |
| 2 – warn | 2.0.0 | layout.graphopt() | layout_with_graphopt() |
| 2 – warn | 2.0.0 | layout.gem() | layout_with_gem() |
| 2 – warn | 2.0.0 | layout.davidson.harel() | layout_with_dh() |
| 2 – warn | 2.0.0 | layout.bipartite() | layout_as_bipartite() |
| 2 – warn | 2.0.0 | layout.auto() | layout_nicely() |
| 1 – soft | 3.0.0 | base::I(“Calling layout_as_bipartite()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_as_bipartite(”,base::paste(base::c(“graph”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_as_bipartite(”,base::paste(base::c(“graph”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling layout_as_star() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_as_star(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_as_star(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling layout_as_tree() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_as_tree(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_as_tree(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | layout.reingold.tilford() | layout_as_tree() |
| 2 – warn | 2.1.0 | layout.circle() | layout_in_circle() |
| 1 – soft | 3.0.0 | base::I(“Calling layout_on_grid() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_on_grid(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_on_grid(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | layout.sphere() | layout_on_sphere() |
| 1 – soft | 3.0.0 | base::I(“Calling layout_randomly() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_randomly(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_randomly(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | layout.random() | layout_randomly() |
| 1 – soft | 3.0.0 | base::I(“Calling layout_with_dh() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_with_dh(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_with_dh(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling layout_with_fr() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_with_fr(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_with_fr(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 0.8.0 | layout_with_fr(coolexp = ) | |
| 3 – stop | 0.8.0 | layout_with_fr(maxdelta = ) | |
| 3 – stop | 0.8.0 | layout_with_fr(area = ) | |
| 3 – stop | 0.8.0 | layout_with_fr(repulserad = ) | |
| 2 – warn | 2.1.0 | layout.fruchterman.reingold() | layout_with_fr() |
| 1 – soft | 3.0.0 | base::I(“Calling layout_with_gem() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_with_gem(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_with_gem(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling layout_with_graphopt()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_with_graphopt(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_with_graphopt(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling layout_with_kk() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_with_kk(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_with_kk(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 0.8.0 | layout_with_kk(niter = ) | |
| 3 – stop | 0.8.0 | layout_with_kk(sigma = ) | |
| 3 – stop | 0.8.0 | layout_with_kk(initemp = ) | |
| 3 – stop | 0.8.0 | layout_with_kk(coolexp = ) | |
| 2 – warn | 2.1.0 | layout.kamada.kawai() | layout_with_kk() |
| 1 – soft | 3.0.0 | base::I(“Calling layout_with_lgl() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_with_lgl(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_with_lgl(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | layout.lgl() | layout_with_lgl() |
| 2 – warn | 1.6.0 | layout_with_mds(options = ‘must be a list’) | c(“arpack_defaults() is now a function,
use options = arpack_defaults() instead of
options = arpack_defaults.”) |
| 1 – soft | 3.0.0 | base::I(“Calling layout_with_sugiyama()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_with_sugiyama(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_with_sugiyama(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling merge_coords() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: merge_coords(”,base::paste(base::c(“graphs”,“layouts”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: merge_coords(”,base::paste(base::c(“graphs”,“layouts”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling norm_coords() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: norm_coords(”,base::paste(base::c(“layout”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: norm_coords(”,base::paste(base::c(“layout”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 2.1.0 | layout.spring() | layout_with_fr() |
| 3 – stop | 2.1.0 | layout.svd() | layout_with_fr() |
| 3 – stop | 2.1.0 | layout.fruchterman.reingold.grid() | layout_with_fr() |
| 2 – warn | 2.0.0 | layout.drl() | layout_with_drl() |
| 1 – soft | 3.0.0 | base::I(“Calling layout_with_drl() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: layout_with_drl(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: layout_with_drl(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | graph() | make_graph() |
| 2 – warn | 2.1.0 | graph.famous() | make_graph() |
| 2 – warn | 2.1.0 | line.graph() | make_line_graph() |
| 2 – warn | 2.1.0 | graph.ring() | make_ring() |
| 2 – warn | 2.1.0 | graph.tree() | make_tree() |
| 2 – warn | 2.1.0 | graph.star() | make_star() |
| 2 – warn | 2.1.0 | graph.lcf() | graph_from_lcf() |
| 2 – warn | 2.1.0 | graph.lattice() | make_lattice() |
| 2 – warn | 2.0.3 | graph.lattice(circular = ‘use periodic argument instead’) | c(“circular is now deprecated, use
periodic instead.”) |
| 2 – warn | 2.1.0 | graph.kautz() | make_kautz_graph() |
| 2 – warn | 2.1.0 | graph.full.citation() | make_full_citation_graph() |
| 2 – warn | 2.1.0 | graph.full.bipartite() | make_full_bipartite_graph() |
| 2 – warn | 2.1.0 | graph.full() | make_full_graph() |
| 2 – warn | 2.1.0 | graph.formula() | graph_from_literal() |
| 2 – warn | 2.1.0 | graph.extended.chordal.ring() | make_chordal_ring() |
| 2 – warn | 2.1.0 | graph.empty() | make_empty_graph() |
| 2 – warn | 2.1.0 | graph.de.bruijn() | make_de_bruijn_graph() |
| 2 – warn | 2.1.0 | graph.bipartite() | make_bipartite_graph() |
| 2 – warn | 2.1.0 | graph.atlas() | graph_from_atlas() |
| 2 – warn | 2.1.0 | graph_() | c(“Please use constructors directly, for instance graph_from_edgelist().”,“graph_() will be removed in a future version of igraph.”) |
| 1 – soft | 3.0.0 | base::I(“Calling make_empty_graph() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_empty_graph(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_empty_graph(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling empty_graph() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: empty_graph(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: empty_graph(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling make_star() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_star(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_star(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling star() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: star(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: star(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling make_full_graph() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_full_graph(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_full_graph(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling full_graph() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: full_graph(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: full_graph(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.3 | make_lattice(circular = ‘use periodic argument instead’) | c(“circular is now deprecated, use
periodic instead.”) |
| 1 – soft | 3.0.0 | base::I(“Calling make_ring() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_ring(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_ring(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling ring() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: ring(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: ring(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling make_tree() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_tree(”,base::paste(base::c(“n”,“children”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_tree(”,base::paste(base::c(“n”,“children”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_tree() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_tree(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_tree(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling make_chordal_ring() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_chordal_ring(”,base::paste(base::c(“n”,“w”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_chordal_ring(”,base::paste(base::c(“n”,“w”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling chordal_ring() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: chordal_ring(”,base::paste(base::c(“n”,“w”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: chordal_ring(”,base::paste(base::c(“n”,“w”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling make_circulant() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_circulant(”,base::paste(base::c(“n”,“shifts”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_circulant(”,base::paste(base::c(“n”,“shifts”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling circulant() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: circulant(”,base::paste(base::c(“n”,“shifts”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: circulant(”,base::paste(base::c(“n”,“shifts”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling
make_full_bipartite_graph() with positional or abbreviated
arguments”) |
base::c(i=base::paste0(“Detected call: make_full_bipartite_graph(”,base::paste(base::c(“n1”,“n2”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_full_bipartite_graph(”,base::paste(base::c(“n1”,“n2”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling full_bipartite_graph()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: full_bipartite_graph(”,base::paste(base::c(“n1”,“n2”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: full_bipartite_graph(”,base::paste(base::c(“n1”,“n2”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling make_bipartite_graph()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_bipartite_graph(”,base::paste(base::c(“types”,“edges”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_bipartite_graph(”,base::paste(base::c(“types”,“edges”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling bipartite_graph() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: bipartite_graph(”,base::paste(base::c(“types”,“edges”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: bipartite_graph(”,base::paste(base::c(“types”,“edges”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling make_full_multipartite()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_full_multipartite(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_full_multipartite(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling full_multipartite() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: full_multipartite(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: full_multipartite(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling
make_full_citation_graph() with positional or abbreviated
arguments”) |
base::c(i=base::paste0(“Detected call: make_full_citation_graph(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_full_citation_graph(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling full_citation_graph()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: full_citation_graph(”,base::paste(base::c(“n”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: full_citation_graph(”,base::paste(base::c(“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling realize_degseq() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: realize_degseq(”,base::paste(base::c(“out.deg”,“in.deg”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: realize_degseq(”,base::paste(base::c(“out.deg”,“in.deg”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling migration_fixture() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: migration_fixture(”,base::paste(base::c(“graph”,“n”,base::c(weights=“weight”,type=“kind”,directed=“directed”)[.arg_names]),collapse=“,”),“)”),i=base::paste0(“Use instead: migration_fixture(”,base::paste(base::c(“graph”,“n”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling
migration_fixture_prefix() with positional or abbreviated
arguments”) |
base::c(i=base::paste0(“Detected call: migration_fixture_prefix(”,base::paste(base::c(“dimvector”,“p”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: migration_fixture_prefix(”,base::paste(base::c(“dimvector”,“p”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling
migration_fixture_shadow() with positional or abbreviated
arguments”) |
base::c(i=base::paste0(“Detected call: migration_fixture_shadow(”,base::paste(base::c(“graph”,base::c(weights=“attr”,names=“names”,c=“c”)[.arg_names]),collapse=“,”),“)”),i=base::paste0(“Use instead: migration_fixture_shadow(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | minimum.spanning.tree() | mst() |
| 2 – warn | 2.0.0 | triad.census() | triad_census() |
| 2 – warn | 2.0.0 | graph.motifs.no() | count_motifs() |
| 2 – warn | 2.0.0 | graph.motifs.est() | sample_motifs() |
| 2 – warn | 2.0.0 | graph.motifs() | motifs() |
| 2 – warn | 2.0.0 | dyad.census() | dyad_census() |
| 1 – soft | 3.0.0 | base::I(“Calling motifs() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: motifs(”,base::paste(base::c(“graph”,“size”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: motifs(”,base::paste(base::c(“graph”,“size”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling count_motifs() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: count_motifs(”,base::paste(base::c(“graph”,“size”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: count_motifs(”,base::paste(base::c(“graph”,“size”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_motifs() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_motifs(”,base::paste(base::c(“graph”,“size”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_motifs(”,base::paste(base::c(“graph”,“size”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | graph.intersection() | intersection() |
| 2 – warn | 2.0.0 | graph.union() | union.igraph() |
| 2 – warn | 2.0.0 | graph.difference() | difference() |
| 2 – warn | 2.0.0 | graph.disjoint.union() | disjoint_union() |
| 2 – warn | 2.0.0 | graph.compose() | compose() |
| 2 – warn | 2.0.0 | graph.complementer() | complementer() |
| 1 – soft | 3.0.0 | base::I(“Calling complementer() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: complementer(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: complementer(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling compose() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: compose(”,base::paste(base::c(“g1”,“g2”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: compose(”,base::paste(base::c(“g1”,“g2”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | running.mean() | running_mean() |
| 2 – warn | 2.0.0 | igraph.sample() | sample_seq() |
| 2 – warn | 2.0.0 | convex.hull() | convex_hull() |
| 2 – warn | 2.0.0 | igraph.options() | igraph_options() |
| 2 – warn | 2.0.0 | getIgraphOpt() | igraph_opt() |
| 1 – soft | 3.0.0 | base::I(“Calling igraph_opt() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: igraph_opt(”,base::paste(base::c(“x”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: igraph_opt(”,base::paste(base::c(“x”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | path.length.hist() | distance_table() |
| 2 – warn | 2.0.0 | maximum.cardinality.search() | max_cardinality() |
| 2 – warn | 2.0.0 | is.dag() | is_dag() |
| 1 – soft | 3.0.0 | base::I(“Calling all_simple_paths() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: all_simple_paths(”,base::paste(base::c(“graph”,“from”,“to”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: all_simple_paths(”,base::paste(base::c(“graph”,“from”,“to”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | eccentricity(… =) | The argument mode must be named. |
| 2 – warn | 2.1.0 | radius(… =) | The argument mode must be named. |
| 1 – soft | 3.0.0 | base::I(“Calling distance_table() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: distance_table(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: distance_table(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | autocurve.edges() | curve_multiple() |
| 1 – soft | 3.0.0 | base::I(“Calling curve_multiple() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: curve_multiple(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: curve_multiple(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | igraph.shape.noplot() | shape_noplot() |
| 2 – warn | 2.0.0 | igraph.shape.noclip() | shape_noclip() |
| 2 – warn | 2.0.0 | vertex.shapes() | shapes() |
| 2 – warn | 2.0.0 | add.vertex.shape() | add_shape() |
| 1 – soft | 3.0.0 | base::I(“Calling add_shape() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: add_shape(”,base::paste(base::c(“shape”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: add_shape(”,base::paste(base::c(“shape”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling random_walk() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: random_walk(”,base::paste(base::c(“graph”,“start”,“steps”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: random_walk(”,base::paste(base::c(“graph”,“start”,“steps”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling random_edge_walk() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: random_edge_walk(”,base::paste(base::c(“graph”,“start”,“steps”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: random_edge_walk(”,base::paste(base::c(“graph”,“start”,“steps”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling each_edge() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: each_edge(”,base::paste(base::c(“prob”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: each_edge(”,base::paste(base::c(“prob”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling similarity() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: similarity(”,base::paste(base::c(“graph”,“vids”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: similarity(”,base::paste(base::c(“graph”,“vids”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | similarity.jaccard() | similarity(method) |
| 2 – warn | 2.1.0 | similarity.dice() | similarity(method) |
| 2 – warn | 2.1.0 | similarity.invlogweighted() | similarity(method) |
| 2 – warn | 2.0.0 | is.simple() | is_simple() |
| 1 – soft | 3.0.0 | base::I(“Calling sir() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sir(”,base::paste(base::c(“graph”,“beta”,“gamma”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sir(”,base::paste(base::c(“graph”,“beta”,“gamma”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | get.stochastic() | stochastic_matrix() |
| 1 – soft | 3.0.0 | base::I(“Calling stochastic_matrix() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: stochastic_matrix(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: stochastic_matrix(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | get.shortest.paths() | shortest_paths() |
| 2 – warn | 2.0.0 | get.all.shortest.paths() | all_shortest_paths() |
| 2 – warn | 2.0.0 | get.diameter() | get_diameter() |
| 2 – warn | 2.0.0 | unfold.tree() | unfold_tree() |
| 2 – warn | 2.0.0 | topological.sort() | topo_sort() |
| 2 – warn | 2.0.0 | shortest.paths() | distances() |
| 2 – warn | 2.0.0 | neighborhood.size() | ego_size() |
| 2 – warn | 2.0.0 | maximum.bipartite.matching() | max_bipartite_match() |
| 2 – warn | 2.0.0 | is.mutual() | which_mutual() |
| 2 – warn | 2.0.0 | is.multiple() | which_multiple() |
| 2 – warn | 2.0.0 | is.maximal.matching() | is_max_matching() |
| 2 – warn | 2.0.0 | is.matching() | is_matching() |
| 2 – warn | 2.0.0 | is.loop() | which_loop() |
| 2 – warn | 2.0.0 | is.connected() | is_connected() |
| 2 – warn | 2.0.0 | induced.subgraph() | induced_subgraph() |
| 2 – warn | 2.0.0 | has.multiple() | any_multiple() |
| 2 – warn | 2.0.0 | graph.neighborhood() | make_ego_graph() |
| 2 – warn | 2.0.0 | graph.laplacian() | laplacian_matrix() |
| 2 – warn | 2.0.0 | graph.knn() | knn() |
| 2 – warn | 2.0.0 | graph.dfs() | dfs() |
| 2 – warn | 2.0.0 | graph.density() | edge_density() |
| 2 – warn | 2.0.0 | graph.coreness() | coreness() |
| 2 – warn | 2.0.0 | graph.bfs() | bfs() |
| 2 – warn | 2.0.0 | farthest.nodes() | farthest_vertices() |
| 2 – warn | 2.0.0 | degree.distribution() | degree_distribution() |
| 2 – warn | 2.0.0 | count.multiple() | count_multiple() |
| 2 – warn | 2.0.0 | clusters() | components() |
| 2 – warn | 2.0.0 | average.path.length() | mean_distance() |
| 1 – soft | 3.0.0 | base::I(“Calling diameter() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: diameter(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: diameter(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling get_diameter() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: get_diameter(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: get_diameter(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling farthest_vertices() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: farthest_vertices(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: farthest_vertices(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling mean_distance() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: mean_distance(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: mean_distance(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling degree() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: degree(”,base::paste(base::c(“graph”,“v”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: degree(”,base::paste(base::c(“graph”,“v”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling mean_degree() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: mean_degree(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: mean_degree(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling distances() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: distances(”,base::paste(base::c(“graph”,“v”,“to”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: distances(”,base::paste(base::c(“graph”,“v”,“to”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling shortest_paths() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: shortest_paths(”,base::paste(base::c(“graph”,“from”,“to”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: shortest_paths(”,base::paste(base::c(“graph”,“from”,“to”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling all_shortest_paths() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: all_shortest_paths(”,base::paste(base::c(“graph”,“from”,“to”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: all_shortest_paths(”,base::paste(base::c(“graph”,“from”,“to”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling subcomponent() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: subcomponent(”,base::paste(base::c(“graph”,“v”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: subcomponent(”,base::paste(base::c(“graph”,“v”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling induced_subgraph() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: induced_subgraph(”,base::paste(base::c(“graph”,“vids”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: induced_subgraph(”,base::paste(base::c(“graph”,“vids”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling subgraph_from_edges()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: subgraph_from_edges(”,base::paste(base::c(“graph”,“eids”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: subgraph_from_edges(”,base::paste(base::c(“graph”,“eids”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.1.0 | subgraph.edges() | subgraph_from_edges() |
| 1 – soft | 3.0.0 | base::I(“Calling transitivity() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: transitivity(”,base::paste(base::c(“graph”,“type”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: transitivity(”,base::paste(base::c(“graph”,“type”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling constraint() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: constraint(”,base::paste(base::c(“graph”,“nodes”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: constraint(”,base::paste(base::c(“graph”,“nodes”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling reciprocity() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: reciprocity(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: reciprocity(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling edge_density() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: edge_density(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: edge_density(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling ego_size() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: ego_size(”,base::paste(base::c(“graph”,“order”,“nodes”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: ego_size(”,base::paste(base::c(“graph”,“order”,“nodes”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling ego() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: ego(”,base::paste(base::c(“graph”,“order”,“nodes”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: ego(”,base::paste(base::c(“graph”,“order”,“nodes”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling make_ego_graph() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: make_ego_graph(”,base::paste(base::c(“graph”,“order”,“nodes”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: make_ego_graph(”,base::paste(base::c(“graph”,“order”,“nodes”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling coreness() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: coreness(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: coreness(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling topo_sort() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: topo_sort(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: topo_sort(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling feedback_arc_set() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: feedback_arc_set(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: feedback_arc_set(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling feedback_vertex_set()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: feedback_vertex_set(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: feedback_vertex_set(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling girth() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: girth(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: girth(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 3 – stop | 1.3.0 | bfs(neimode = ) | bfs(mode = ) |
| 3 – stop | 2.2.0 | bfs(father = ) | bfs(parent = ) |
| 3 – stop | 1.3.0 | dfs(neimode = ) | dfs(mode = ) |
| 3 – stop | 2.2.0 | dfs(father = ) | dfs(parent = ) |
| 1 – soft | 3.0.0 | base::I(“Calling components() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: components(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: components(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling is_connected() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: is_connected(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: is_connected(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling count_components() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: count_components(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: count_components(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling count_reachable() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: count_reachable(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: count_reachable(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling unfold_tree() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: unfold_tree(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: unfold_tree(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.3 | make_lattice(normalized = ‘provide normalization instead’) | c(“normalized is now deprecated, use
normalization instead.”) |
| 1 – soft | 3.0.0 | base::I(“Calling max_bipartite_match()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: max_bipartite_match(”,base::paste(base::c(“graph”,“types”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: max_bipartite_match(”,base::paste(base::c(“graph”,“types”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling which_mutual() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: which_mutual(”,base::paste(base::c(“graph”,“eids”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: which_mutual(”,base::paste(base::c(“graph”,“eids”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling knn() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: knn(”,base::paste(base::c(“graph”,“vids”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: knn(”,base::paste(base::c(“graph”,“vids”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | are.connected() | are_adjacent() |
| 2 – warn | 2.0.0 | tkplot.setcoords() | tk_set_coords() |
| 2 – warn | 2.0.0 | tkplot.rotate() | tk_rotate() |
| 2 – warn | 2.0.0 | tkplot.reshape() | tk_reshape() |
| 2 – warn | 2.0.0 | tkplot.off() | tk_off() |
| 2 – warn | 2.0.0 | tkplot.getcoords() | tk_coords() |
| 2 – warn | 2.0.0 | tkplot.fit.to.screen() | tk_fit() |
| 2 – warn | 2.0.0 | tkplot.export.postscript() | tk_postscript() |
| 2 – warn | 2.0.0 | tkplot.close() | tk_close() |
| 2 – warn | 2.0.0 | tkplot.center() | tk_center() |
| 2 – warn | 2.0.0 | tkplot.canvas() | tk_canvas() |
| 3 – stop | 3.0.0 | tkplot() | |
| 1 – soft | 3.0.0 | base::I(“Calling tk_close() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: tk_close(”,base::paste(base::c(“tkp.id”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: tk_close(”,base::paste(base::c(“tkp.id”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling tk_fit() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: tk_fit(”,base::paste(base::c(“tkp.id”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: tk_fit(”,base::paste(base::c(“tkp.id”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling tk_coords() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: tk_coords(”,base::paste(base::c(“tkp.id”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: tk_coords(”,base::paste(base::c(“tkp.id”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling tk_rotate() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: tk_rotate(”,base::paste(base::c(“tkp.id”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: tk_rotate(”,base::paste(base::c(“tkp.id”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | permute.vertices() | permute() |
| 2 – warn | 2.0.0 | graph.isocreate() | graph_from_isomorphism_class() |
| 2 – warn | 2.0.0 | graph.automorphisms() | count_automorphisms() |
| 2 – warn | 2.0.0 | canonical.permutation() | canonical_permutation() |
| 2 – warn | 2.0.0 | automorphisms() | count_automorphisms() |
| 1 – soft | 3.0.0 | base::I(“Calling graph.subisomorphic.lad()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph.subisomorphic.lad(”,base::paste(base::c(“pattern”,“target”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph.subisomorphic.lad(”,base::paste(base::c(“pattern”,“target”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling graph.isomorphic.bliss()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph.isomorphic.bliss(”,base::paste(base::c(“graph1”,“graph2”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph.isomorphic.bliss(”,base::paste(base::c(“graph1”,“graph2”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling graph.isomorphic.vf2()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph.isomorphic.vf2(”,base::paste(base::c(“graph1”,“graph2”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph.isomorphic.vf2(”,base::paste(base::c(“graph1”,“graph2”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling graph.subisomorphic.vf2()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph.subisomorphic.vf2(”,base::paste(base::c(“graph1”,“graph2”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph.subisomorphic.vf2(”,base::paste(base::c(“graph1”,“graph2”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling
graph.count.isomorphisms.vf2() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph.count.isomorphisms.vf2(”,base::paste(base::c(“graph1”,“graph2”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph.count.isomorphisms.vf2(”,base::paste(base::c(“graph1”,“graph2”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling
graph.count.subisomorphisms.vf2() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph.count.subisomorphisms.vf2(”,base::paste(base::c(“graph1”,“graph2”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph.count.subisomorphisms.vf2(”,base::paste(base::c(“graph1”,“graph2”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling
graph_from_isomorphism_class() with positional or
abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: graph_from_isomorphism_class(”,base::paste(base::c(“size”,“number”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: graph_from_isomorphism_class(”,base::paste(base::c(“size”,“number”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling canonical_permutation()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: canonical_permutation(”,base::paste(base::c(“graph”,“colors”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: canonical_permutation(”,base::paste(base::c(“graph”,“colors”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling count_automorphisms()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: count_automorphisms(”,base::paste(base::c(“graph”,“colors”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: count_automorphisms(”,base::paste(base::c(“graph”,“colors”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling automorphism_group() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: automorphism_group(”,base::paste(base::c(“graph”,“colors”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: automorphism_group(”,base::paste(base::c(“graph”,“colors”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling is_tree() with positional
or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: is_tree(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: is_tree(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling is_forest() with
positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: is_forest(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: is_forest(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 1 – soft | 3.0.0 | base::I(“Calling sample_spanning_tree()
with positional or abbreviated arguments”) |
base::c(i=base::paste0(“Detected call: sample_spanning_tree(”,base::paste(base::c(“graph”,.arg_names),collapse=“,”),“)”),i=base::paste0(“Use instead: sample_spanning_tree(”,base::paste(base::c(“graph”,base::paste0(.arg_names,” = “)),collapse=”, “),”)“)) |
| 2 – warn | 2.0.0 | adjacent.triangles() | count_triangles() |
| 2 – warn | 2.0.0 | igraph.version() | igraph_version() |