chore: anyDuplicated() (jarl), anyNA() (jarl), nzchar()(me)

R/attributes.R

@@ -968,7 +968,7 @@ edge.attributes <- function(graph, index = E(graph)) {
 
   if (!missing(index)) {
     index <- as_igraph_es(graph, index)
-    if (any(duplicated(index)) || any(is.na(index))) {
+    if (anyDuplicated(index) > 0 || anyNA(index)) {
       cli::cli_abort("{.arg index} contains duplicated edges or NAs.")
     }
   }
@@ -1302,7 +1302,7 @@ igraph.i.attribute.combination <- function(comb) {
   if (is.null(names(comb))) {
     names(comb) <- rep("", length(comb))
   }
-  if (any(duplicated(names(comb)))) {
+  if (anyDuplicated(names(comb)) > 0) {
     cli::cli_warn("Some attributes are duplicated")
   }
   comb <- lapply(comb, function(x) {

R/community.R

@@ -1654,21 +1654,21 @@ cluster_leiden <- function(
   if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
     weights <- E(graph)$weight
   }
-  if (!is.null(weights) && !any(is.na(weights))) {
+  if (!is.null(weights) && !anyNA(weights)) {
     weights <- as.numeric(weights)
   } else {
     weights <- NULL
   }
 
   # Parse initial_membership argument
-  if (!is.null(initial_membership) && !any(is.na(initial_membership))) {
+  if (!is.null(initial_membership) && !anyNA(initial_membership)) {
     initial_membership <- as.numeric(initial_membership)
   } else {
     initial_membership <- NULL
   }
 
   # Parse node weights argument
-  if (!is.null(vertex_weights) && !any(is.na(vertex_weights))) {
+  if (!is.null(vertex_weights) && !anyNA(vertex_weights)) {
     vertex_weights <- as.numeric(vertex_weights)
     if (objective_function == 1) {
       # Using modularity
@@ -1851,7 +1851,7 @@ cluster_walktrap <- function(
   if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
     weights <- E(graph)$weight
   }
-  if (!is.null(weights) && !any(is.na(weights))) {
+  if (!is.null(weights) && !anyNA(weights)) {
     weights <- as.numeric(weights)
   } else {
     weights <- NULL

R/conversion.R

@@ -1567,7 +1567,7 @@ graph_from_data_frame <- function(d, directed = TRUE, vertices = NULL) {
   ## Handle if some elements are 'NA' (first two columns are interpreted as from/to)
   ensure_no_na(d[, 1:2], "edge data frame")
 
-  if (!is.null(vertices) && any(is.na(vertices[, 1]))) {
+  if (!is.null(vertices) && anyNA(vertices[, 1])) {
     cli::cli_warn(
       "In {.code vertices[,1]}, {.code NA} elements were replaced with string {.str NA}."
     )
@@ -1582,7 +1582,7 @@ graph_from_data_frame <- function(d, directed = TRUE, vertices = NULL) {
       cli::cli_abort("{.arg vertices} contains no rows")
     }
     names <- as.character(vertices[, 1])
-    if (any(duplicated(names))) {
+    if (anyDuplicated(names) > 0) {
       cli::cli_abort("{.arg vertices} contains duplicated vertex names")
     }
     if (any(!names2 %in% names)) {

R/indexing.R

@@ -234,12 +234,12 @@ get_adjacency_submatrix <- function(x, i, j, attr = NULL) {
     cli::cli_abort("Cannot use {.arg from}/{.arg to} without the other")
   }
   if (!missing(from)) {
-    if ((!is.numeric(from) && !is.character(from)) || any(is.na(from))) {
+    if ((!is.numeric(from) && !is.character(from)) || anyNA(from)) {
       cli::cli_abort(
         "{.arg from} must be a numeric or character vector without NAs"
       )
     }
-    if ((!is.numeric(to) && !is.character(to)) || any(is.na(to))) {
+    if ((!is.numeric(to) && !is.character(to)) || anyNA(to)) {
       cli::cli_abort(
         "{.arg to} must be a numeric or character vector without NAs"
       )
@@ -487,12 +487,12 @@ expand.grid.unordered <- function(i, j, loops = FALSE, directed = FALSE) {
     cli::cli_abort("Logical or numeric value must be of length 1")
   }
   if (!missing(from)) {
-    if ((!is.numeric(from) && !is.character(from)) || any(is.na(from))) {
+    if ((!is.numeric(from) && !is.character(from)) || anyNA(from)) {
       cli::cli_abort(
         "{.arg from} must be a numeric or character vector without NAs"
       )
     }
-    if ((!is.numeric(to) && !is.character(to)) || any(is.na(to))) {
+    if ((!is.numeric(to) && !is.character(to)) || anyNA(to)) {
       cli::cli_abort(
         "{.arg to} must be a numeric or character vector without NAs"
       )

R/interface.R

@@ -145,7 +145,7 @@ add_edges <- function(graph, edges, ..., attr = list()) {
   attrs <- list(...)
   attrs <- append(attrs, attr)
   nam <- names(attrs)
-  if (length(attrs) != 0 && (is.null(nam) || any(nam == ""))) {
+  if (length(attrs) != 0 && (is.null(nam) || any(!nzchar(nam)))) {
     cli::cli_abort("All attributes must be named.")
   }
 
@@ -212,7 +212,7 @@ add_vertices <- function(graph, nv, ..., attr = list()) {
   attrs <- list(...)
   attrs <- append(attrs, attr)
   nam <- names(attrs)
-  if (length(attrs) != 0 && (is.null(nam) || any(nam == ""))) {
+  if (length(attrs) != 0 && (is.null(nam) || any(!nzchar(nam)))) {
     cli::cli_abort("All attributes must be named.")
   }
 

R/iterators.R

@@ -401,7 +401,7 @@ create_es <- function(graph, idx, na_ok = FALSE) {
 
 simple_vs_index <- function(x, i, na_ok = FALSE) {
   res <- unclass(x)[i]
-  if (!na_ok && any(is.na(res))) {
+  if (!na_ok && anyNA(res)) {
     cli::cli_abort("Unknown vertex selected.")
   }
   class(res) <- "igraph.vs"
@@ -842,7 +842,7 @@ simple_es_index <- function(x, i, na_ok = FALSE) {
   } else {
     res <- unclass(x)[i]
   }
-  if (!na_ok && any(is.na(res))) {
+  if (!na_ok && anyNA(res)) {
     cli::cli_abort("Unknown edge selected")
   }
   attr(res, "env") <- attr(x, "env")
@@ -1562,7 +1562,7 @@ as_igraph_vs <- function(graph, v, na.ok = FALSE) {
   }
   if (is.character(v) && "name" %in% vertex_attr_names(graph)) {
     v <- as.numeric(match(v, V(graph)$name))
-    if (!na.ok && any(is.na(v))) {
+    if (!na.ok && anyNA(v)) {
       cli::cli_abort("Invalid vertex names")
     }
     v
@@ -1574,7 +1574,7 @@ as_igraph_vs <- function(graph, v, na.ok = FALSE) {
     } else {
       res <- as.numeric(v)
     }
-    if (!na.ok && any(is.na(res))) {
+    if (!na.ok && anyNA(res)) {
       cli::cli_abort("Invalid vertex name(s)")
     }
     res
@@ -1617,7 +1617,7 @@ as_igraph_es <- function(graph, e) {
   } else {
     res <- as.numeric(e)
   }
-  if (any(is.na(res))) {
+  if (anyNA(res)) {
     cli::cli_abort("Invalid edge names")
   }
   res

R/layout.R

@@ -2867,7 +2867,7 @@ layout_with_drl <- function(
   if (is.null(weights) && "weight" %in% edge_attr_names(graph)) {
     weights <- E(graph)$weight
   }
-  if (!is.null(weights) && !any(is.na(weights))) {
+  if (!is.null(weights) && !anyNA(weights)) {
     weights <- as.numeric(weights)
   } else {
     weights <- NULL

R/make.R

@@ -695,7 +695,7 @@ graph.bipartite <- function(types, edges, directed = FALSE) {
       )
     }
     edges <- match(edges, vertex.names)
-    if (any(is.na(edges))) {
+    if (anyNA(edges)) {
       cli::cli_abort(
         "edge vector contains a vertex name that is not found in {.arg types}"
       )
@@ -2672,7 +2672,7 @@ make_bipartite_graph <- function(types, edges, directed = FALSE) {
       )
     }
     edges <- match(edges, vertex.names)
-    if (any(is.na(edges))) {
+    if (anyNA(edges)) {
       cli::cli_abort(
         "edge vector contains a vertex name that is not found in {.arg types}"
       )

R/operators.R

@@ -261,7 +261,7 @@ disjoint_union <- function(...) {
   }
   vertex.attributes(res) <- attr
 
-  if ("name" %in% names(attr) && any(duplicated(attr$name))) {
+  if ("name" %in% names(attr) && anyDuplicated(attr$name) > 0) {
     cli::cli_warn("Duplicate vertex names in disjoint union.")
   }
 
@@ -690,7 +690,7 @@ difference.igraph <- function(big, small, byname = "auto", ...) {
       snames <- V(small)$name
     }
     perm <- match(bnames, snames)
-    if (any(is.na(perm))) {
+    if (anyNA(perm)) {
       perm[is.na(perm)] <- seq(from = vcount(small) + 1, to = vcount(big))
     }
     big <- permute(big, perm)
@@ -969,7 +969,7 @@ vertex <- function(...) {
 
   # Check for duplicate named arguments
   if (!is.null(arg_names)) {
-    named_args <- arg_names[arg_names != ""]
+    named_args <- arg_names[nzchar(arg_names)]
     if (anyDuplicated(named_args)) {
       duplicates <- unique(named_args[duplicated(named_args)])
       cli::cli_abort(
@@ -1142,8 +1142,8 @@ path <- function(...) {
       toadd <- unlist(e2, recursive = FALSE)
       attr <- list()
     } else {
-      toadd <- unlist(e2[names(e2) == ""])
-      attr <- e2[names(e2) != ""]
+      toadd <- unlist(e2[!nzchar(names(e2))])
+      attr <- e2[nzchar(names(e2))]
     }
     res <- add_edges(e1, as_igraph_vs(e1, toadd), attr = attr)
   } else if ("igraph.vertex" %in% class(e2)) {
@@ -1167,8 +1167,8 @@ path <- function(...) {
       to_add <- unlist(e2, recursive = FALSE)
       attr <- list()
     } else {
-      to_add <- unlist(e2[names(e2) == ""])
-      attr <- e2[names(e2) != ""]
+      to_add <- unlist(e2[!nzchar(names(e2))])
+      attr <- e2[nzchar(names(e2))]
     }
     to_add <- as_igraph_vs(e1, to_add)
     lt <- length(to_add)

R/other.R

@@ -162,7 +162,7 @@ handle_vertex_type_arg <- function(types, graph, required = T) {
       cli::cli_warn("vertex types converted to logical.")
     }
     types <- as.logical(types)
-    if (any(is.na(types))) {
+    if (anyNA(types)) {
       cli::cli_abort("`NA' is not allowed in vertex types")
     }
   }

R/plot.R

@@ -1700,7 +1700,7 @@ rglplot.igraph <- function(x, ...) {
   rgl::text3d(x, y, z, labels, col = label.color, adj = 0)
 
   edge.labels[is.na(edge.labels)] <- ""
-  if (any(edge.labels != "")) {
+  if (any(nzchar(edge.labels))) {
     x0 <- layout[, 1][el[, 1]]
     x1 <- layout[, 1][el[, 2]]
     y0 <- layout[, 2][el[, 1]]

R/plot.common.R

@@ -589,7 +589,7 @@ i.parse.plot.params <- function(graph, params) {
       }
     }
     if (!is.function(p[[type]][[name]])) {
-      if (any(is.na(p[[type]][[name]]))) {
+      if (anyNA(p[[type]][[name]])) {
         if (name != "label") {
           cli::cli_warn(
             "{type} attribute {name} contains NAs. Replacing with default value {i.default.values[[type]][[name]]

R/print.R

@@ -87,16 +87,16 @@
   cat(title, "\n", sep = "")
 
   atxt <- .get.attr.codes(object)
-  atxt <- paste(atxt[atxt != ""], collapse = ", ")
-  if (atxt != "") {
+  atxt <- paste(atxt[nzchar(atxt)], collapse = ", ")
+  if (nzchar(atxt)) {
     atxt <- strwrap(
       paste(sep = "", "+ attr: ", atxt),
       prefix = "| ",
       initial = ""
     )
     cat(atxt, sep = "\n")
   }
-  1 + if (length(atxt) == 1 && atxt == "") 0 else length(atxt)
+  1 + if (length(atxt) == 1 && !nzchar(atxt)) 0 else length(atxt)
 }
 
 #' @importFrom utils capture.output

R/sparsedf.R

@@ -28,8 +28,8 @@ sdf <- function(..., row.names = NULL, NROW = NULL) {
 
   if (
     is.null(names(cols)) ||
-      any(names(cols) == "") ||
-      any(duplicated(names(cols)))
+      any(!nzchar(names(cols))) ||
+      anyDuplicated(names(cols)) > 0
   ) {
     cli::cli_abort("Columns must be have (unique) names.")
   }

tests/testthat/test-cliques.R

@@ -158,7 +158,7 @@ test_that("max_cliques() work", {
           } else {
             numeric()
           }
-          if (any(duplicated(PX$PX))) {
+          if (anyDuplicated(PX$PX) > 0) {
             cli::cli_abort("foo2")
           }
         }