refactor: move optional arguments of motifs-graphlets functions behind the ellipsis

R/cycles.R

@@ -31,6 +31,7 @@
 #' a specific cycle.
 #'
 #' @param graph The input graph.
+#' @inheritParams rlang::args_dots_empty
 #' @param mode Character constant specifying how to handle directed graphs.
 #'   `out` follows edge directions, `in` follows edges in the reverse direction,
 #'   and `all` ignores edge directions. Ignored in undirected graphs.

R/glet.R

@@ -64,6 +64,7 @@ graphlets.candidate.basis <- function(graph, weights = NULL) {
 #'
 #' @param graph The input graph, edge directions are ignored. Only simple graph
 #'   (i.e. graphs without self-loops and multiple edges) are supported.
+#' @inheritParams rlang::args_dots_empty
 #' @param weights Edge weights. If the graph has a `weight` edge attribute
 #'   and this argument is `NULL` (the default), then the `weight` edge
 #'   attribute is used.
@@ -135,22 +136,76 @@ graphlets.candidate.basis <- function(graph, weights = NULL) {
 #' }
 #' @family glet
 #' @export
-graphlet_basis <- function(graph, weights = NULL) {
+graphlet_basis <- function(
+  graph,
+  ...,
+  weights = NULL
+) {
+  # BEGIN GENERATED ARG_HANDLE: graphlet_basis, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(weights = weights),
+      recover_new = c("weights"),
+      recover_old = c("weights"),
+      match_names = c("weights"),
+      match_to = c("weights"),
+      defaults = list(weights = NULL),
+      head_args = c("graph"),
+      fn_name = "graphlet_basis"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   graphlets_candidate_basis_impl(
     graph = graph,
     weights = weights
   )
 }
 
 #' @rdname graphlet_basis
+#' @inheritParams rlang::args_dots_empty
 #' @export
 graphlet_proj <- function(
   graph,
+  ...,
   weights = NULL,
   cliques,
   niter = 1000,
   Mu = rep(1, length(cliques))
 ) {
+  # BEGIN GENERATED ARG_HANDLE: graphlet_proj, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(weights = weights, niter = niter, Mu = Mu),
+      recover_new = c("weights", "cliques", "niter", "Mu"),
+      recover_old = c("weights", "cliques", "niter", "Mu"),
+      match_names = c("weights", "cliques", "niter", "Mu"),
+      match_to = c("weights", "cliques", "niter", "Mu"),
+      defaults = list(
+        weights = NULL,
+        niter = 1000,
+        Mu = rep(1, length(cliques))
+      ),
+      head_args = c("graph"),
+      fn_name = "graphlet_proj"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   # Argument checks
   ensure_igraph(graph)
   if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
@@ -228,8 +283,36 @@ function() {
 }
 
 #' @rdname graphlet_basis
+#' @inheritParams rlang::args_dots_empty
 #' @export
-graphlets <- function(graph, weights = NULL, niter = 1000) {
+graphlets <- function(
+  graph,
+  ...,
+  weights = NULL,
+  niter = 1000
+) {
+  # BEGIN GENERATED ARG_HANDLE: graphlets, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(weights = weights, niter = niter),
+      recover_new = c("weights", "niter"),
+      recover_old = c("weights", "niter"),
+      match_names = c("weights", "niter"),
+      match_to = c("weights", "niter"),
+      defaults = list(weights = NULL, niter = 1000),
+      head_args = c("graph"),
+      fn_name = "graphlets"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   graphlets_impl(
     graph = graph,
     weights = weights,

R/motifs.R

@@ -132,6 +132,7 @@ dyad.census <- function(graph) {
 #' @param graph Graph object, the input graph.
 #' @param size The size of the motif, currently sizes 3 and 4 are supported in
 #'   directed graphs and sizes 3 to 6 in undirected graphs.
+#' @inheritParams rlang::args_dots_empty
 #' @param cut.prob Numeric vector giving the probabilities that the search
 #'   graph is cut at a certain level. Its length should be the same as the size
 #'   of the motif (the `size` argument).
@@ -171,7 +172,35 @@ dyad.census <- function(graph) {
 #'   count <<- count + 1
 #'   count < 5  # stop after 5 motifs
 #' })
-motifs <- function(graph, size = 3, cut.prob = NULL, callback = NULL) {
+motifs <- function(
+  graph,
+  size = 3,
+  ...,
+  cut.prob = NULL,
+  callback = NULL
+) {
+  # BEGIN GENERATED ARG_HANDLE: motifs, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(cut.prob = cut.prob, callback = callback),
+      recover_new = c("cut.prob", "callback"),
+      recover_old = c("cut.prob", "callback"),
+      match_names = c("cut.prob", "callback"),
+      match_to = c("cut.prob", "callback"),
+      defaults = list(cut.prob = NULL, callback = NULL),
+      head_args = c("graph", "size"),
+      fn_name = "motifs"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   if (!is.null(cut.prob) && length(cut.prob) != size) {
     cli::cli_abort("{.arg cut.prob} must be the same length as {.arg size}")
   }
@@ -208,6 +237,7 @@ motifs <- function(graph, size = 3, cut.prob = NULL, callback = NULL) {
 #'
 #' @param graph Graph object, the input graph.
 #' @param size The size of the motif.
+#' @inheritParams rlang::args_dots_empty
 #' @param cut.prob Numeric vector giving the probabilities that the search
 #'   graph is cut at a certain level. Its length should be the same as the size
 #'   of the motif (the `size` argument).
@@ -223,7 +253,34 @@ motifs <- function(graph, size = 3, cut.prob = NULL, callback = NULL) {
 #' motifs(g, 3)
 #' count_motifs(g, 3)
 #' sample_motifs(g, 3)
-count_motifs <- function(graph, size = 3, cut.prob = NULL) {
+count_motifs <- function(
+  graph,
+  size = 3,
+  ...,
+  cut.prob = NULL
+) {
+  # BEGIN GENERATED ARG_HANDLE: count_motifs, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(cut.prob = cut.prob),
+      recover_new = c("cut.prob"),
+      recover_old = c("cut.prob"),
+      match_names = c("cut.prob"),
+      match_to = c("cut.prob"),
+      defaults = list(cut.prob = NULL),
+      head_args = c("graph", "size"),
+      fn_name = "count_motifs"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   ensure_igraph(graph)
 
   if (!is.null(cut.prob) && length(cut.prob) != size) {
@@ -248,6 +305,7 @@ count_motifs <- function(graph, size = 3, cut.prob = NULL) {
 #' @param graph Graph object, the input graph.
 #' @param size The size of the motif, currently size 3 and 4 are supported
 #'   in directed graphs and sizes 3-6 in undirected graphs.
+#' @inheritParams rlang::args_dots_empty
 #' @param cut.prob Numeric vector giving the probabilities that the search
 #'   graph is cut at a certain level. Its length should be the same as the size
 #'   of the motif (the `size` argument).
@@ -272,10 +330,41 @@ count_motifs <- function(graph, size = 3, cut.prob = NULL) {
 sample_motifs <- function(
   graph,
   size = 3,
+  ...,
   cut.prob = rep(0, size),
   sample.size = NULL,
   sample = NULL
 ) {
+  # BEGIN GENERATED ARG_HANDLE: sample_motifs, do not edit, see tools/generate-migrations.R
+  if (...length() > 0L) {
+    .arg_handle <- migrate_recover_args(
+      list(...),
+      current = list(
+        cut.prob = cut.prob,
+        sample.size = sample.size,
+        sample = sample
+      ),
+      recover_new = c("cut.prob", "sample.size", "sample"),
+      recover_old = c("cut.prob", "sample.size", "sample"),
+      match_names = c("cut.prob", "sample.size", "sample"),
+      match_to = c("cut.prob", "sample.size", "sample"),
+      defaults = list(
+        cut.prob = rep(0, size),
+        sample.size = NULL,
+        sample = NULL
+      ),
+      head_args = c("graph", "size"),
+      fn_name = "sample_motifs"
+    )
+    list2env(.arg_handle$values, environment())
+    lifecycle::deprecate_soft(
+      "3.0.0",
+      what = I(.arg_handle$what),
+      details = .arg_handle$details
+    )
+  }
+  # END GENERATED ARG_HANDLE
+
   ensure_igraph(graph)
 
   if (!is.null(cut.prob) && length(cut.prob) != size) {