refactor!: New arpack_defaults() replaces igraph.arpack.default and arpack_defaults lists

NAMESPACE

@@ -484,7 +484,6 @@ export(hrg_tree)
 export(hub.score)
 export(hub_score)
 export(identical_graphs)
-export(igraph.arpack.default)
 export(igraph.console)
 export(igraph.drl.coarsen)
 export(igraph.drl.coarsest)

R/aaa-auto.R

@@ -371,7 +371,7 @@ personalized_pagerank_impl <- function(graph, algo=c("prpack", "arpack"), vids=V
     if (algo == 0L) {
       options <- list(niter=1000, eps=0.001)
     } else if (algo == 1L) {
-      options <- arpack_defaults
+      options <- arpack_defaults()
     } else {
       options <- NULL
     }
@@ -549,7 +549,7 @@ count_multiple_impl <- function(graph, eids=E(graph)) {
   res
 }
 
-eigenvector_centrality_impl <- function(graph, directed=FALSE, scale=TRUE, weights=NULL, options=arpack_defaults) {
+eigenvector_centrality_impl <- function(graph, directed=FALSE, scale=TRUE, weights=NULL, options=arpack_defaults()) {
   # Argument checks
   ensure_igraph(graph)
   directed <- as.logical(directed)
@@ -562,7 +562,7 @@ eigenvector_centrality_impl <- function(graph, directed=FALSE, scale=TRUE, weigh
   } else {
     weights <- NULL
   }
-  options.tmp <- arpack_defaults; options.tmp[ names(options) ] <- options ; options <- options.tmp
+  options <- modify_list(arpack_defaults(), options)
 
   on.exit( .Call(R_igraph_finalizer) )
   # Function call
@@ -573,7 +573,7 @@ eigenvector_centrality_impl <- function(graph, directed=FALSE, scale=TRUE, weigh
   res
 }
 
-hub_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults) {
+hub_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
   # Argument checks
   ensure_igraph(graph)
   scale <- as.logical(scale)
@@ -585,7 +585,7 @@ hub_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defau
   } else {
     weights <- NULL
   }
-  options.tmp <- arpack_defaults; options.tmp[ names(options) ] <- options ; options <- options.tmp
+  options <- modify_list(arpack_defaults(), options)
 
   on.exit( .Call(R_igraph_finalizer) )
   # Function call
@@ -596,7 +596,7 @@ hub_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defau
   res
 }
 
-authority_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults) {
+authority_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
   # Argument checks
   ensure_igraph(graph)
   scale <- as.logical(scale)
@@ -608,7 +608,7 @@ authority_score_impl <- function(graph, scale=TRUE, weights=NULL, options=arpack
   } else {
     weights <- NULL
   }
-  options.tmp <- arpack_defaults; options.tmp[ names(options) ] <- options ; options <- options.tmp
+  options <- modify_list(arpack_defaults(), options)
 
   on.exit( .Call(R_igraph_finalizer) )
   # Function call
@@ -772,12 +772,12 @@ centralization_closeness_tmax_impl <- function(graph=NULL, nodes=0, mode=c("out"
   res
 }
 
-centralization_eigenvector_centrality_impl <- function(graph, directed=FALSE, scale=TRUE, options=arpack_defaults, normalized=TRUE) {
+centralization_eigenvector_centrality_impl <- function(graph, directed=FALSE, scale=TRUE, options=arpack_defaults(), normalized=TRUE) {
   # Argument checks
   ensure_igraph(graph)
   directed <- as.logical(directed)
   scale <- as.logical(scale)
-  options.tmp <- arpack_defaults; options.tmp[ names(options) ] <- options ; options <- options.tmp
+  options <- modify_list(arpack_defaults(), options)
   normalized <- as.logical(normalized)
 
   on.exit( .Call(R_igraph_finalizer) )
@@ -2013,7 +2013,7 @@ scg_norm_eps_impl <- function(V, groups, mtype=c("symmetric", "laplacian", "stoc
   res
 }
 
-adjacency_spectral_embedding_impl <- function(graph, no, weights=NULL, which=c("lm", "la", "sa"), scaled=TRUE, cvec=graph.strength(graph, weights=weights)/(vcount(graph)-1), options=igraph.arpack.default) {
+adjacency_spectral_embedding_impl <- function(graph, no, weights=NULL, which=c("lm", "la", "sa"), scaled=TRUE, cvec=graph.strength(graph, weights=weights)/(vcount(graph)-1), options=arpack_defaults()) {
   # Argument checks
   ensure_igraph(graph)
   no <- as.integer(no)
@@ -2028,7 +2028,7 @@ adjacency_spectral_embedding_impl <- function(graph, no, weights=NULL, which=c("
   which <- switch(igraph.match.arg(which), "lm"=0L, "la"=2L, "sa"=3L)
   scaled <- as.logical(scaled)
   cvec <- as.numeric(cvec)
-  options.tmp <- arpack_defaults; options.tmp[ names(options) ] <- options ; options <- options.tmp
+  options <- modify_list(arpack_defaults(), options)
 
   on.exit( .Call(R_igraph_finalizer) )
   # Function call
@@ -2037,7 +2037,7 @@ adjacency_spectral_embedding_impl <- function(graph, no, weights=NULL, which=c("
   res
 }
 
-laplacian_spectral_embedding_impl <- function(graph, no, weights=NULL, which=c("lm", "la", "sa"), type=c("default", "D-A", "DAD", "I-DAD", "OAP"), scaled=TRUE, options=igraph.arpack.default) {
+laplacian_spectral_embedding_impl <- function(graph, no, weights=NULL, which=c("lm", "la", "sa"), type=c("default", "D-A", "DAD", "I-DAD", "OAP"), scaled=TRUE, options=arpack_defaults()) {
   # Argument checks
   ensure_igraph(graph)
   no <- as.integer(no)
@@ -2055,7 +2055,7 @@ laplacian_spectral_embedding_impl <- function(graph, no, weights=NULL, which=c("
     "da"=0L, "d-a"=0L, "idad"=1L, "i-dad"=1L, "dad"=2L,
     "oap"=3L)
   scaled <- as.logical(scaled)
-  options.tmp <- arpack_defaults; options.tmp[ names(options) ] <- options ; options <- options.tmp
+  options <- modify_list(arpack_defaults(), options)
 
   on.exit( .Call(R_igraph_finalizer) )
   # Function call
@@ -2064,15 +2064,15 @@ laplacian_spectral_embedding_impl <- function(graph, no, weights=NULL, which=c("
   res
 }
 
-eigen_adjacency_impl <- function(graph, algorithm=c("arpack", "auto", "lapack", "comp_auto", "comp_lapack", "comp_arpack"), which=list(), options=arpack_defaults) {
+eigen_adjacency_impl <- function(graph, algorithm=c("arpack", "auto", "lapack", "comp_auto", "comp_lapack", "comp_arpack"), which=list(), options=arpack_defaults()) {
   # Argument checks
   ensure_igraph(graph)
   algorithm <- switch(igraph.match.arg(algorithm), "auto"=0, "lapack"=1,
     "arpack"=2, "comp_auto"=3, "comp_lapack"=4,
     "comp_arpack"=5)
   which.tmp <- eigen_defaults();
   which.tmp[ names(which) ] <- which ; which <- which.tmp
-  options.tmp <- arpack_defaults; options.tmp[ names(options) ] <- options ; options <- options.tmp
+  options <- modify_list(arpack_defaults(), options)
 
   on.exit( .Call(R_igraph_finalizer) )
   # Function call

R/centrality.R

@@ -318,11 +318,13 @@ closeness.estimate <- estimate_closeness
 #' @rdname arpack
 #' @family arpack
 #' @export
-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_defaults <- function() {
+  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 eigenvector calculation
 #'
@@ -431,7 +433,7 @@ arpack_defaults <- list(
 #' re-orthogonalization.} } } Please see the ARPACK documentation for
 #' additional details.
 #'
-#' @aliases arpack arpack-options igraph.arpack.default arpack.unpack.complex
+#' @aliases arpack arpack-options arpack.unpack.complex
 #' arpack_defaults
 #' @param func The function to perform the matrix-vector multiplication. ARPACK
 #'   requires to perform these by the user. The function gets the vector \eqn{x}
@@ -512,27 +514,38 @@ arpack_defaults <- list(
 #' }
 #' @family arpack
 #' @export
-arpack <- function(func, extra = NULL, sym = FALSE, options = arpack_defaults,
+arpack <- function(func, extra = NULL, sym = FALSE, options = arpack_defaults(),
                    env = parent.frame(), complex = !sym) {
+
+  eval_try <- rlang::eval_tidy(options)
+  if (is.function(options)) {
+    lifecycle::deprecate_soft(
+      "2.0.0",
+      "arpack_defaults(options = 'must be a list')",
+      details = c("`arpack_defaults()` is now a function, use `options = arpack_defaults()` instead of `options = arpack_defaults`.")
+    )
+    options <- options()
+  }
+
   if (!is.list(options) ||
     (is.null(names(options)) && length(options) != 0)) {
     stop("options must be a named list")
   }
   if (any(names(options) == "")) {
     stop("all options must be named")
   }
-  if (any(!names(options) %in% names(arpack_defaults))) {
+
+  defaults <- arpack_defaults()
+  if (any(!names(options) %in% names(defaults))) {
     stop(
       "unkown ARPACK option(s): ",
-      paste(setdiff(names(options), names(arpack_defaults)),
+      paste(setdiff(names(options), names(defaults)),
         collapse = ", "
       )
     )
   }
 
-  options.tmp <- arpack_defaults
-  options.tmp[names(options)] <- options
-  options <- options.tmp
+  options <- modify_list(defaults, options)
 
   if (sym && complex) {
     complex <- FALSE
@@ -692,7 +705,24 @@ subgraph_centrality <- function(graph, diag = FALSE) {
 #'
 #' @family centrality
 #' @export
-spectrum <- eigen_adjacency_impl
+spectrum <- function(graph, algorithm=c("arpack", "auto", "lapack", "comp_auto", "comp_lapack", "comp_arpack"), which=list(), options=arpack_defaults()) {
+  eval_try <- rlang::eval_tidy(options)
+  options_value <- rlang::call_args(rlang::current_call())[["options"]]
+  if (is(eval_try, "function") && as.character(options_value) == "arpack_defaults") {
+    lifecycle::deprecate_soft(
+      "1.5.0",
+      I("arpack_defaults"),
+      "arpack_defaults()",
+      details = c("So the function arpack_defaults(), not an object called arpack_defaults.")
+    )
+    options <- arpack_defaults()
+  }
+
+  eigen_adjacency_impl(graph,
+                       algorithm = algorithm,
+                       which = which,
+                       options = options)
+}
 
 eigen_defaults <- function() {
   list(
@@ -787,8 +817,30 @@ eigen_defaults <- function() {
 #' eigen_centrality(g)
 #' @family centrality
 #' @export
-eigen_centrality <- eigenvector_centrality_impl
+eigen_centrality <- function(graph,
+                             directed = FALSE,
+                             scale = TRUE,
+                             weights = NULL,
+                             options = arpack_defaults()) {
+
+    eval_try <- rlang::eval_tidy(options)
+  options_value <- rlang::call_args(rlang::current_call())[["options"]]
+  if (is(eval_try, "function") && as.character(options_value) == "arpack_defaults") {
+    lifecycle::deprecate_soft(
+      "1.5.0",
+      I("arpack_defaults"),
+      "arpack_defaults()",
+      details = c("So the function arpack_defaults(), not an object called arpack_defaults.")
+    )
+    options <- arpack_defaults()
+  }
 
+  eigenvector_centrality_impl(graph = graph,
+                              directed = directed,
+                              scale = scale,
+                              weights = weights,
+                              options = options)
+}
 
 #' Strength or weighted vertex degree
 #'
@@ -927,16 +979,49 @@ diversity <- diversity_impl
 #' hub_score(g2)$vector
 #' authority_score(g2)$vector
 #' @family centrality
-hub_score <- hub_score_impl
+hub_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
 
+  eval_try <- rlang::eval_tidy(options)
+  options_value <- rlang::call_args(rlang::current_call())[["options"]]
+  if (is(eval_try, "function") && as.character(options_value) == "arpack_defaults") {
+    lifecycle::deprecate_soft(
+      "1.5.0",
+      I("arpack_defaults"),
+      "arpack_defaults()",
+      details = c("So the function arpack_defaults(), not an object called arpack_defaults.")
+    )
+    options <- arpack_defaults()
+  }
+
+  hub_score_impl(graph = graph,
+                 scale = scale,
+                 weights = weights,
+                 options = options)
+}
 
 #' @rdname hub_score
 #' @aliases authority.score
 #' @param options A named list, to override some ARPACK options. See
 #'   [arpack()] for details.
 #' @export
-authority_score <- authority_score_impl
+authority_score <- function(graph, scale=TRUE, weights=NULL, options=arpack_defaults()) {
+  eval_try <- rlang::eval_tidy(options)
+  options_value <- rlang::call_args(rlang::current_call())[["options"]]
+  if (is(eval_try, "function") && as.character(options_value) == "arpack_defaults") {
+    lifecycle::deprecate_soft(
+      "1.5.0",
+      I("arpack_defaults"),
+      "arpack_defaults()",
+      details = c("So the function arpack_defaults(), not an object called arpack_defaults.")
+    )
+    options <- arpack_defaults()
+  }
 
+  authority_score_impl(graph = graph,
+                       scale = scale,
+                       weights = weights,
+                       options = options)
+}
 
 #' The Page Rank algorithm
 #'

R/community.R

@@ -1621,9 +1621,22 @@ igraph.i.levc.arp <- function(externalP, externalE) {
 #'
 cluster_leading_eigen <- function(graph, steps = -1, weights = NULL,
                                   start = NULL,
-                                  options = arpack_defaults,
+                                  options = arpack_defaults(),
                                   callback = NULL, extra = NULL,
                                   env = parent.frame()) {
+
+  eval_try <- rlang::eval_tidy(options)
+  options_value <- rlang::call_args(rlang::current_call())[["options"]]
+  if (is(eval_try, "function") && as.character(options_value) == "arpack_defaults") {
+    lifecycle::deprecate_soft(
+      "1.5.0",
+      I("arpack_defaults"),
+      "arpack_defaults()",
+      details = c("So the function arpack_defaults(), not an object called arpack_defaults.")
+    )
+    options <- arpack_defaults()
+  }
+
   # Argument checks
   ensure_igraph(graph)
 
@@ -1639,9 +1652,8 @@ cluster_leading_eigen <- function(graph, steps = -1, weights = NULL,
   if (!is.null(start)) {
     start <- as.numeric(start) - 1
   }
-  options.tmp <- arpack_defaults
-  options.tmp[names(options)] <- options
-  options <- options.tmp
+
+  options <- modify_list(arpack_defaults(), options)
 
   on.exit(.Call(R_igraph_finalizer))
   # Function call

R/embedding.R

@@ -65,7 +65,7 @@
 #'   graph. This vector is added to the diagonal of the adjacency matrix.
 #' @param options A named list containing the parameters for the SVD
 #'   computation algorithm in ARPACK. By default, the list of values is assigned
-#'   the values given by [igraph.arpack.default].
+#'   the values given by [arpack_defaults()].
 #' @return A list containing with entries: \item{X}{Estimated latent positions,
 #'   an `n` times `no` matrix, `n` is the number of vertices.}
 #'   \item{Y}{`NULL` for undirected graphs, the second half of the latent
@@ -203,7 +203,7 @@ dim_select <- dim_select_impl
 #'   returned instead of \eqn{X} and \eqn{Y}.
 #' @param options A named list containing the parameters for the SVD
 #'   computation algorithm in ARPACK. By default, the list of values is assigned
-#'   the values given by [igraph.arpack.default].
+#'   the values given by [arpack_defaults()].
 #' @return A list containing with entries: \item{X}{Estimated latent positions,
 #'   an `n` times `no` matrix, `n` is the number of vertices.}
 #'   \item{Y}{`NULL` for undirected graphs, the second half of the latent

R/layout.R

@@ -1517,7 +1517,20 @@ layout.lgl <- function(..., params = list()) {
 #' l <- layout_with_mds(g)
 #' plot(g, layout = l, vertex.label = NA, vertex.size = 3)
 layout_with_mds <- function(graph, dist = NULL, dim = 2,
-                            options = arpack_defaults) {
+                            options = arpack_defaults()) {
+
+  eval_try <- rlang::eval_tidy(options)
+  options_value <- rlang::call_args(rlang::current_call())[["options"]]
+  if (is(eval_try, "function") && as.character(options_value) == "arpack_defaults") {
+    lifecycle::deprecate_soft(
+      "1.5.0",
+      I("arpack_defaults"),
+      "arpack_defaults()",
+      details = c("So the function arpack_defaults(), not an object called arpack_defaults.")
+    )
+    options <- arpack_defaults()
+  }
+
   # Argument checks
   ensure_igraph(graph)
   if (!is.null(dist)) dist <- structure(as.double(dist), dim = dim(dist))