feat: remove deprecated functions before 1.0

NAMESPACE

@@ -475,6 +475,7 @@ export(head_of)
 export(head_print)
 export(hierarchical_sbm)
 export(hierarchy)
+export(hits_scores)
 export(hrg)
 export(hrg.consensus)
 export(hrg.create)

R/aaa-auto.R

@@ -298,6 +298,34 @@ turan_impl <- function(n, r) {
   res
 }
 
+erdos_renyi_game_gnp_impl <- function(n, p, directed=FALSE, loops=FALSE) {
+  # Argument checks
+  n <- as.numeric(n)
+  p <- as.numeric(p)
+  directed <- as.logical(directed)
+  loops <- as.logical(loops)
+
+  on.exit( .Call(R_igraph_finalizer) )
+  # Function call
+  res <- .Call(R_igraph_erdos_renyi_game_gnp, n, p, directed, loops)
+
+  res
+}
+
+erdos_renyi_game_gnm_impl <- function(n, m, directed=FALSE, loops=FALSE) {
+  # Argument checks
+  n <- as.numeric(n)
+  m <- as.numeric(m)
+  directed <- as.logical(directed)
+  loops <- as.logical(loops)
+
+  on.exit( .Call(R_igraph_finalizer) )
+  # Function call
+  res <- .Call(R_igraph_erdos_renyi_game_gnm, n, m, directed, loops)
+
+  res
+}
+
 forest_fire_game_impl <- function(nodes, fw.prob, bw.factor=1, ambs=1, directed=TRUE) {
   # Argument checks
   nodes <- as.numeric(nodes)
@@ -1411,52 +1439,6 @@ eigenvector_centrality_impl <- function(graph, directed=FALSE, scale=TRUE, weigh
   res
 }
 
-hub_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
-  # Argument checks
-  ensure_igraph(graph)
-  scale <- as.logical(scale)
-  if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
-    weights <- E(graph)$weight
-  }
-  if (!is.null(weights) && any(!is.na(weights))) {
-    weights <- as.numeric(weights)
-  } else {
-    weights <- NULL
-  }
-  options <- modify_list(arpack_defaults(), options)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_hub_score, graph, scale, weights, options)
-  if (igraph_opt("add.vertex.names") && is_named(graph)) {
-    names(res$vector) <- vertex_attr(graph, "name", V(graph))
-  }
-  res
-}
-
-authority_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
-  # Argument checks
-  ensure_igraph(graph)
-  scale <- as.logical(scale)
-  if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
-    weights <- E(graph)$weight
-  }
-  if (!is.null(weights) && any(!is.na(weights))) {
-    weights <- as.numeric(weights)
-  } else {
-    weights <- NULL
-  }
-  options <- modify_list(arpack_defaults(), options)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_authority_score, graph, scale, weights, options)
-  if (igraph_opt("add.vertex.names") && is_named(graph)) {
-    names(res$vector) <- vertex_attr(graph, "name", V(graph))
-  }
-  res
-}
-
 hub_and_authority_scores_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
   # Argument checks
   ensure_igraph(graph)
@@ -1475,10 +1457,10 @@ hub_and_authority_scores_impl <- function(graph, scale=TRUE, weights=NULL, optio
   # Function call
   res <- .Call(R_igraph_hub_and_authority_scores, graph, scale, weights, options)
   if (igraph_opt("add.vertex.names") && is_named(graph)) {
-    names(res$hub.vector) <- vertex_attr(graph, "name", V(graph))
+    names(res$hub) <- vertex_attr(graph, "name", V(graph))
   }
   if (igraph_opt("add.vertex.names") && is_named(graph)) {
-    names(res$authority.vector) <- vertex_attr(graph, "name", V(graph))
+    names(res$authority) <- vertex_attr(graph, "name", V(graph))
   }
   res
 }
@@ -1986,34 +1968,6 @@ random_walk_impl <- function(graph, start, steps, weights=NULL, mode=c("out", "i
   res
 }
 
-random_edge_walk_impl <- function(graph, start, steps, weights=NULL, mode=c("out", "in", "all", "total"), stuck=c("return", "error")) {
-  # Argument checks
-  ensure_igraph(graph)
-  if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
-    weights <- E(graph)$weight
-  }
-  if (!is.null(weights) && any(!is.na(weights))) {
-    weights <- as.numeric(weights)
-  } else {
-    weights <- NULL
-  }
-  start <- as_igraph_vs(graph, start)
-  if (length(start) == 0) {
-    stop("No vertex was specified")
-  }
-  mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
-  steps <- as.numeric(steps)
-  stuck <- switch(igraph.match.arg(stuck), "error" = 0L, "return" = 1L)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_random_edge_walk, graph, weights, start-1, mode, steps, stuck)
-  if (igraph_opt("return.vs.es")) {
-    res <- create_es(graph, res)
-  }
-  res
-}
-
 global_efficiency_impl <- function(graph, weights=NULL, directed=TRUE) {
   # Argument checks
   ensure_igraph(graph)
@@ -2197,24 +2151,6 @@ is_bipartite_impl <- function(graph) {
   res
 }
 
-bipartite_game_impl <- function(type, n1, n2, p=0.0, m=0, directed=FALSE, mode=c("all", "out", "in", "total")) {
-  # Argument checks
-  n1 <- as.numeric(n1)
-  n2 <- as.numeric(n2)
-  p <- as.numeric(p)
-  m <- as.numeric(m)
-  directed <- as.logical(directed)
-  mode <- switch(igraph.match.arg(mode), "out"=1L, "in"=2L, "all"=3L, "total"=3L)
-
-  on.exit( .Call(R_igraph_finalizer) )
-  # Function call
-  res <- .Call(R_igraph_bipartite_game, type, n1, n2, p, m, directed, mode)
-  if (igraph_opt("add.vertex.names") && is_named(graph)) {
-    names(res$types) <- vertex_attr(graph, "name", V(graph))
-  }
-  res
-}
-
 get_laplacian_impl <- function(graph, mode=c("out", "in", "all", "total"), normalization=c("unnormalized", "symmetric", "left", "right"), weights=NULL) {
   # Argument checks
   ensure_igraph(graph)

R/centrality.R

@@ -40,10 +40,25 @@ page.rank <- function(graph, algo = c("prpack", "arpack"), vids = V(graph), dire
 #' @keywords internal
 #' @export
 hub.score <- function(graph, scale = TRUE, weights = NULL, options = arpack_defaults()) { # nocov start
-  lifecycle::deprecate_soft("2.0.0", "hub.score()", "hub_score()")
+  lifecycle::deprecate_warn("2.0.0", "hub.score()", "hits_score()")
   hub_score(graph = graph, scale = scale, weights = weights, options = options)
 } # nocov end
 
+#' Kleinberg's hub and authority centrality scores.
+#'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' `authority.score()` was renamed to `authority_score()` to create a more
+#' consistent API.
+#' @inheritParams authority_score
+#' @keywords internal
+#' @export
+authority.score <- function(graph, scale = TRUE, weights = NULL, options = arpack_defaults()) { # nocov start
+  lifecycle::deprecate_warn("2.0.0", "authority.score()", "hits_score()")
+  authority_score(graph = graph, scale = scale, weights = weights, options = options)
+} # nocov end
+
 #' Strength or weighted vertex degree
 #'
 #' @description
@@ -134,21 +149,6 @@ bonpow <- function(graph, nodes = V(graph), loops = FALSE, exponent = 1, rescale
   power_centrality(graph = graph, nodes = nodes, loops = loops, exponent = exponent, rescale = rescale, tol = tol, sparse = sparse)
 } # nocov end
 
-#' Kleinberg's hub and authority centrality scores.
-#'
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' `authority.score()` was renamed to `authority_score()` to create a more
-#' consistent API.
-#' @inheritParams authority_score
-#' @keywords internal
-#' @export
-authority.score <- function(graph, scale = TRUE, weights = NULL, options = arpack_defaults()) { # nocov start
-  lifecycle::deprecate_soft("2.0.0", "authority.score()", "authority_score()")
-  authority_score(graph = graph, scale = scale, weights = weights, options = options)
-} # nocov end
-
 #' Find Bonacich alpha centrality scores of network positions
 #'
 #' @description
@@ -1105,6 +1105,7 @@ diversity <- diversity_impl
 #'   selected by the surfer.
 #' @param options A named list, to override some ARPACK options. See
 #'   [arpack()] for details.
+#' @inheritParams rlang::args_dots_empty
 #' @return A named list with members:
 #'   \item{vector}{The hub or authority scores of the vertices.}
 #'   \item{value}{The corresponding eigenvalue of the calculated
@@ -1124,36 +1125,66 @@ diversity <- diversity_impl
 #' @examples
 #' ## An in-star
 #' g <- make_star(10)
-#' hub_score(g)$vector
-#' authority_score(g)$vector
+#' hits_scores(g)
 #'
 #' ## A ring
 #' g2 <- make_ring(10)
-#' hub_score(g2)$vector
-#' authority_score(g2)$vector
+#' hits_scores(g2)
 #' @family centrality
-hub_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
+hits_scores <- function(graph, ..., scale=TRUE, weights=NULL, options=arpack_defaults()) {
 
+  rlang::check_dots_empty()
+
+  hub_and_authority_scores_impl(graph = graph,
+    scale = scale,
+    weights = weights,
+    options = options)
+}
+
+#' @title Kleinberg's authority centrality scores.
+#' @rdname hub_score
+#' @param options A named list, to override some ARPACK options. See
+#'   [arpack()] for details.
+#' @export
+authority_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
+  lifecycle::deprecate_soft("2.0.4", "authority_score()", "hits_scores()")
   if (is.function(options)) {
     lifecycle::deprecate_soft(
       "1.6.0",
-      "hub_score(options = 'must be a list')",
-      details = c("`arpack_defaults()` is now a function, use `options = arpack_defaults()` instead of `options = arpack_defaults`.")
+      I("arpack_defaults"),
+      "arpack_defaults()",
+      details = c("So the function arpack_defaults(), not an object called arpack_defaults.")
     )
-    options <- options()
+    options <- arpack_defaults()
   }
 
-  hub_score_impl(graph = graph,
-                 scale = scale,
-                 weights = weights,
-                 options = options)
+  scores <- hits_scores(
+    graph = graph,
+    scale = scale,
+    weights = weights,
+    options = options)
+  scores$hub <- NULL
+  rlang::set_names(scores, c("vector", "value", "options"))
 }
 
+#' @title Kleinberg's hub centrality scores.
 #' @rdname hub_score
+#' @param graph The input graph.
+#' @param scale Logical scalar, whether to scale the result to have a maximum
+#'   score of one. If no scaling is used then the result vector has unit length
+#'   in the Euclidean norm.
+#' @param weights Optional positive weight vector for calculating weighted
+#'   scores. If the graph has a `weight` edge attribute, then this is used
+#'   by default.
+#'   This function interprets edge weights as connection strengths. In the
+#'   random surfer model, an edge with a larger weight is more likely to be
+#'   selected by the surfer.
 #' @param options A named list, to override some ARPACK options. See
 #'   [arpack()] for details.
+#' @family centrality
 #' @export
-authority_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
+hub_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
+  lifecycle::deprecate_soft("2.0.3", "hub_score()", "hits_scores()")
   if (is.function(options)) {
     lifecycle::deprecate_soft(
       "1.6.0",
@@ -1164,10 +1195,13 @@ authority_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defa
     options <- arpack_defaults()
   }
 
-  authority_score_impl(graph = graph,
-                       scale = scale,
-                       weights = weights,
-                       options = options)
+  scores <- hits_scores(
+    graph = graph,
+    scale = scale,
+    weights = weights,
+    options = options)
+  scores$authority <- NULL
+  rlang::set_names(scores, c("vector", "value", "options"))
 }
 
 #' The Page Rank algorithm

R/games.R

@@ -596,7 +596,7 @@ sample_gnp <- function(n, p, directed = FALSE, loops = FALSE) {
 
   on.exit(.Call(R_igraph_finalizer))
   res <- .Call(
-    R_igraph_erdos_renyi_game, as.numeric(n), as.numeric(type1),
+    R_igraph_erdos_renyi_game_gnp, as.numeric(n),
     as.numeric(p), as.logical(directed), as.logical(loops)
   )
 
@@ -651,7 +651,7 @@ sample_gnm <- function(n, m, directed = FALSE, loops = FALSE) {
 
   on.exit(.Call(R_igraph_finalizer))
   res <- .Call(
-    R_igraph_erdos_renyi_game, as.numeric(n), as.numeric(type1),
+    R_igraph_erdos_renyi_game_gnm, as.numeric(n),
     as.numeric(m), as.logical(directed), as.logical(loops)
   )
 
@@ -716,16 +716,19 @@ gnm <- function(...) constructor_spec(sample_gnm, ...)
 erdos.renyi.game <- function(n, p.or.m, type = c("gnp", "gnm"),
                              directed = FALSE, loops = FALSE) {
   type <- igraph.match.arg(type)
-  type1 <- switch(type,
-    "gnp" = 0,
-    "gnm" = 1
-  )
 
   on.exit(.Call(R_igraph_finalizer))
-  res <- .Call(
-    R_igraph_erdos_renyi_game, as.numeric(n), as.numeric(type1),
-    as.numeric(p.or.m), as.logical(directed), as.logical(loops)
-  )
+  if (type == "gnp") {
+    res <- .Call(
+      R_igraph_erdos_renyi_game_gnp, as.numeric(n),
+      as.numeric(p.or.m), as.logical(directed), as.logical(loops)
+    )
+  } else if (type == "gnm") {
+    res <- .Call(
+      R_igraph_erdos_renyi_game_gnm, as.numeric(n),
+      as.numeric(p.or.m), as.logical(directed), as.logical(loops)
+    )
+  }
 
   if (igraph_opt("add.params")) {
     res$name <- sprintf("Erdos-Renyi (%s) graph", type)