More renaming, #553

igraph · Oct 1, 2014 · cbd5dec · cbd5dec
1 parent 2e2ec2c
commit cbd5dec
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Showing 172 changed files with 1,644 additions and 1,338 deletions.
diff --git a/interfaces/R/NAMESPACE.in b/interfaces/R/NAMESPACE.in
@@ -292,9 +292,17 @@ S3method(time_bins, sir)
 export(add_edges)
 export(add_shape)
 export(add_vertices)
+export(adhesion)
+export(adj)
+export(adj_edge_list)
+export(adj_eigen)
+export(adj_list)
+export(any_multiple)
+export(arpack_defaults)
 export(articulation_points)
-export(avg_path_len)
+export(automorphisms)
 
+export(bfs)
 export(biconn_comps)
 export(bip_map)
 export(bip_proj)
@@ -303,24 +311,52 @@ export(bip_proj_size)
 export(canon_perm)
 export(clique_num)
 export(code_len)
+export(cohesion)
+S3method(cohesion, igraph)
+S3method(cohesion, cohesiveBlocks)
 export(cohesive_blocks)
+export(comp_dist)
+export(complementer)
+export(compose)
 export(comps)
+export(console)
 export(connect)
 export(contract)
 export(convex_hull)
+export(coreness)
+export(count_comps)
+export(count_motifs)
 export(count_multiple)
 export(count_triangles)
 export(cut_at)
 
 export(decompose)
+export(delete_edge_attr)
+export(delete_graph_attr)
+export(delete_vertex_attr)
 export(delete_edges)
 export(delete_vertices)
 export(dend_plot)
 S3method(dend_plot, communities)
 S3method(dend_plot, igraphHRG)
+export(dfs)
+export(difference)
+export(disjoint_union)
+export(distance_table)
+export(distances)
+export(diversity)
 export(dominator_tree)
 export(dyad_census)
 
+export(edge_attr)
+export(edge_attr_names)
+export(edge_conn)
+export(edge_disjoint_paths)
+export(edgelist)
+export(ego)
+export(ego_size)
+export(eigen_defaults)
+
 export(g_adj_matrix)
 export(g_atlas)
 export(g_bip)
@@ -343,7 +379,7 @@ export(g_grg)
 export(g_growing)
 export(g_incidence)
 export(g_islands)
-export(g_isoclass)
+export(g_iso_class)
 export(g_k_reg)
 export(g_kautz)
 export(g_last_cit)
@@ -364,8 +400,22 @@ export(g_star)
 export(g_traits)
 export(g_traits_callaway)
 export(g_tree)
-
+export(graph_attr)
+export(graph_attr_names)
+export(graphlet_basis)
+export(graphlet_proj)
+
+export(igraph_demo)
+export(igraph_test)
+export(igraph_version)
+export(incidence)
+export(ivs)
+export(ivs_size)
+export(induced_subgraph)
 export(is_connected_to)
+export(iso_class)
+
+export(knn)
 
 export(l_auto)
 export(l_bip)
@@ -387,7 +437,67 @@ export(l_sphere)
 export(l_star)
 export(l_sugiyama)
 export(l_tree)
+export(laplacian)
+export(largest_cliques)
+export(largest_ivs)
 
 export(make_curves)
+export(max_bip_match)
+export(max_cardinality)
+export(max_cliques)
+export(max_flow)
+export(maximal_ivs)
+export(mean_distance)
+export(min_cut)
+export(min_size_sep)
+export(min_st_sep)
+export(motifs)
+export(mst)
+
+export(num_max_cliques)
+
+export(permute)
+export(pl_fit)
+export(plot_hierarchy)
+
+export(read_graph)
+export(running_mean)
+
+export(sample_motifs)
+export(sample_seq)
+export(scg_group)
+export(scg_eps)
+export(scg_semi_proj)
+export(set_edge_attr)
+export(set_graph_attr)
+export(set_vertex_attr)
+export(show_trace)
+export(st_cuts)
+export(st_min_cuts)
+export(stochastic)
+export(strength)
+
+export(tk_canvas)
+export(tk_center)
+export(tk_close)
+export(tk_postscript)
+export(tk_fit)
+export(tk_coords)
+export(tk_off)
+export(tk_reshape)
+export(tk_rotate)
+export(tk_set_coords)
+export(topo_sort)
+export(triad_census)
+
+export(unfold_tree)
+export(union)
+
+export(vertex_attr)
+export(vertex_attr_names)
+export(vertex_conn)
+export(vertex_disjoint_paths)
+
+export(write_graph)
 
 ######################## REST IS GENERATED BY stimulus
diff --git a/interfaces/R/igraph/R/attributes.R b/interfaces/R/igraph/R/attributes.R
@@ -33,15 +33,15 @@
 ## e(graph)$weight[1:10]           # get edge attribute
 ##
 
-get.graph.attribute <- function(graph, name) {
+graph_attr <- function(graph, name) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
   .Call("R_igraph_mybracket2", graph, 9L, 2L,
         PACKAGE="igraph")[[as.character(name)]]
 }
 
-set.graph.attribute <- function(graph, name, value) {
+set_graph_attr <- function(graph, name, value) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
@@ -71,7 +71,7 @@ graph.attributes <- function(graph) {
         PACKAGE="igraph")
 }
 
-get.vertex.attribute <- function(graph, name, index=V(graph)) {
+vertex_attr <- function(graph, name, index=V(graph)) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
@@ -81,7 +81,7 @@ get.vertex.attribute <- function(graph, name, index=V(graph)) {
   myattr[index]
 }
 
-set.vertex.attribute <- function(graph, name, index=V(graph), value) {
+set_vertex_attr <- function(graph, name, index=V(graph), value) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
@@ -124,7 +124,7 @@ vertex.attributes <- function(graph) {
         PACKAGE="igraph")
 }
 
-get.edge.attribute <- function(graph, name, index=E(graph)) {
+edge_attr <- function(graph, name, index=E(graph)) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
@@ -135,7 +135,7 @@ get.edge.attribute <- function(graph, name, index=E(graph)) {
   myattr[index]
 }
 
-set.edge.attribute <- function(graph, name, index=E(graph), value) {
+set_edge_attr <- function(graph, name, index=E(graph), value) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
@@ -179,7 +179,7 @@ edge.attributes <- function(graph) {
         PACKAGE="igraph")
 }
 
-list.graph.attributes <- function(graph) {
+graph_attr_names <- function(graph) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
@@ -188,7 +188,7 @@ list.graph.attributes <- function(graph) {
   res
 }
 
-list.vertex.attributes <- function(graph) {
+vertex_attr_names <- function(graph) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
@@ -198,7 +198,7 @@ list.vertex.attributes <- function(graph) {
   res
 }
 
-list.edge.attributes <- function(graph) {
+edge_attr_names <- function(graph) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
@@ -207,12 +207,12 @@ list.edge.attributes <- function(graph) {
   res
 }
 
-remove.graph.attribute <- function(graph, name) {
+delete_graph_attr <- function(graph, name) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
   name <- as.character(name)
-  if (!name %in% list.graph.attributes(graph)) {
+  if (!name %in% graph_attr_names(graph)) {
     stop("No such graph attribute: ", name)
   }
 
@@ -222,12 +222,12 @@ remove.graph.attribute <- function(graph, name) {
   .Call("R_igraph_mybracket2_set", graph, 9L, 2L, gattr, PACKAGE="igraph")
 }
 
-remove.vertex.attribute <- function(graph, name) {
+delete_vertex_attr <- function(graph, name) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
   name <- as.character(name)
-  if (!name %in% list.vertex.attributes(graph)) {
+  if (!name %in% vertex_attr_names(graph)) {
     stop("No such vertex attribute: ", name)
   }
 
@@ -237,12 +237,12 @@ remove.vertex.attribute <- function(graph, name) {
   .Call("R_igraph_mybracket2_set", graph, 9L, 3L, vattr, PACKAGE="igraph")
 }
 
-remove.edge.attribute <- function(graph, name) {
+delete_edge_attr <- function(graph, name) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
   name <- as.character(name)
-  if (!name %in% list.edge.attributes(graph)) {
+  if (!name %in% edge_attr_names(graph)) {
     stop("No such edge attribute: ", name)
   }
 
@@ -289,7 +289,7 @@ is.named <- function(graph) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
-  "name" %in% list.vertex.attributes(graph)
+  "name" %in% vertex_attr_names(graph)
 }
 
 
@@ -325,7 +325,7 @@ is.weighted <- function(graph) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
-  "weight" %in% list.edge.attributes(graph)
+  "weight" %in% edge_attr_names(graph)
 }
 
 #' @rdname g_bip
@@ -334,7 +334,7 @@ is.bipartite <- function(graph) {
   if (!is.igraph(graph)) {
     stop("Not a graph object")
   }
-  "type" %in% list.vertex.attributes(graph)
+  "type" %in% vertex_attr_names(graph)
 }
 
 #############

diff --git a/interfaces/R/igraph/R/bipartite.R b/interfaces/R/igraph/R/bipartite.R
@@ -92,7 +92,7 @@ bip_proj <- function(graph, types=NULL,
                                  remove.type=TRUE) {
   # Argument checks
   if (!is.igraph(graph)) { stop("Not a graph object") }
-  if (is.null(types) && "type" %in% list.vertex.attributes(graph)) { 
+  if (is.null(types) && "type" %in% vertex_attr_names(graph)) { 
   types <- V(graph)$type 
   } 
   if (!is.null(types)) {
@@ -123,10 +123,10 @@ bip_proj <- function(graph, types=NULL,
                as.integer(probe1), which, PACKAGE="igraph")
   if (remove.type) {
     if (is.igraph(res[[1]])) {
-      res[[1]] <- remove.vertex.attribute(res[[1]], "type")
+      res[[1]] <- delete_vertex_attr(res[[1]], "type")
     }
     if (is.igraph(res[[2]])) {
-      res[[2]] <- remove.vertex.attribute(res[[2]], "type")
+      res[[2]] <- delete_vertex_attr(res[[2]], "type")
     }
   }
   if (which == 0L) {

diff --git a/interfaces/R/igraph/R/centrality.R b/interfaces/R/igraph/R/centrality.R
@@ -19,11 +19,11 @@
 #
 ###################################################################
 
-igraph.arpack.default <- list(bmat="I", n=0, which="XX", nev=1, tol=0.0,
+arpack_defaults <- list(bmat="I", n=0, which="XX", nev=1, tol=0.0,
                               ncv=3, ldv=0, ishift=1, maxiter=3000, nb=1,
                               mode=1, start=0, sigma=0.0, sigmai=0.0)
 
-arpack <- function(func, extra=NULL, sym=FALSE, options=igraph.arpack.default,
+arpack <- function(func, extra=NULL, sym=FALSE, options=arpack_defaults,
                    env=parent.frame(), complex=!sym) {
 
   if (!is.list(options) ||
@@ -33,13 +33,13 @@ arpack <- function(func, extra=NULL, sym=FALSE, options=igraph.arpack.default,
   if (any(names(options) == "")) {
     stop("all options must be named")
   }
-  if (any(! names(options) %in% names(igraph.arpack.default))) {
+  if (any(! names(options) %in% names(arpack_defaults))) {
     stop("unkown ARPACK option(s): ",
-         paste(setdiff(names(options), names(igraph.arpack.default)),
+         paste(setdiff(names(options), names(arpack_defaults)),
                        collapse=", "))
   }
 
-  options.tmp <- igraph.arpack.default
+  options.tmp <- arpack_defaults
   options.tmp[ names(options) ] <- options
   options <- options.tmp
 
@@ -111,16 +111,16 @@ arpack <- function(func, extra=NULL, sym=FALSE, options=igraph.arpack.default,
 #' cor(degree(g), sc)
 #' 
 subgraph.centrality <- function(graph, diag=FALSE) {
-  A <- get.adjacency(graph)
+  A <- adj(graph)
   if (!diag) { diag(A) <- 0 }
   eig <- eigen(A)
   res <- as.vector(eig$vectors^2 %*% exp(eig$values))
   if (getIgraphOpt("add.vertex.names") && is.named(graph)) { 
-    names(res) <- get.vertex.attribute(graph, "name") 
+    names(res) <- vertex_attr(graph, "name") 
   }
   res
 }
 
-igraph.eigen.default <- list(pos="LM", howmany=1L, il=-1L, iu=-1L,
+eigen_defaults <- list(pos="LM", howmany=1L, il=-1L, iu=-1L,
                              vl=-Inf, vu=Inf, vestimate=0L,
                              balance="none")