Merge pull request #280 from snlab-ch/develop

v1.1.5

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: migraph
 Title: Multimodal Network Analysis and More
-Version: 1.1.4
-Date: 2023-11-01
+Version: 1.1.5
+Date: 2023-11-02
 Description: A set of tools for analysing multimodal networks.
    It includes functions for measuring 
    centrality, centralization, cohesion, closure, constraint and diversity,

NEWS.md

@@ -1,3 +1,15 @@
+# migraph 1.1.5
+
+2023-11-02
+
+## Members
+
+- Fixed documentation issue with `summary.node_member()`
+
+## Motifs
+
+- Fixed documentation issue with `node_census()`
+
 # migraph 1.1.4
 
 2023-11-01

R/class_members.R

@@ -25,31 +25,29 @@ print.node_member <- function(x, ..., n = NULL) {
 summary.node_member <- function(object, ...,
                                n = 6,
                                digits = 3) {
-  if (any(attr(x, "mode"))) {
-    for (i in names(table(x))) {
-      if (i == names(table(x))[1]) cat(i, "\n")
+  if (any(attr(object, "mode"))) {
+    for (i in names(table(object))) {
+      if (i == names(table(object))[1]) cat(i, "\n")
       else cat("\n", i, "\n")
-      if (!is.null(names(x))) {
-        y <- paste(names(x[x == i & attr(x, "mode")]), collapse = ", ")
-        z <- paste(names(x[x == i & !attr(x, "mode")]), collapse = ", ")
+      if (!is.null(names(object))) {
+        y <- paste(names(object[object == i & attr(object, "mode")]), collapse = ", ")
+        z <- paste(names(object[object == i & !attr(object, "mode")]), collapse = ", ")
       } else {
-        y <- paste(which(x == i & attr(x, "mode")), collapse = ", ")
-        z <- paste(which(x == i & !attr(x, "mode")), collapse = ", ")
+        y <- paste(which(object == i & attr(object, "mode")), collapse = ", ")
+        z <- paste(which(object == i & !attr(object, "mode")), collapse = ", ")
       }
       cat("  ", y, "\n")
       cat("  ", z)
     }
   } else {
-    for (i in names(table(x))) {
+    for (i in names(table(object))) {
       cat(pillar::style_subtle(paste0("Class ", i, ":")))
-      # if (i == names(table(x))[1]) cat("Class ", i, ":", sep = "")
-      # else cat("Class ", i, ":", sep = "")
-      if (!is.null(names(x)))
-        y <- paste(names(x[x == i]), collapse = ", ")
+      if (!is.null(names(object)))
+        y <- paste(names(object[object == i]), collapse = ", ")
       else
-        y <- paste(which(x == i), collapse = ", ")
+        y <- paste(which(object == i), collapse = ", ")
       cat(" ", y)
-      if (i != names(table(x))[length(table(x))]) cat("\n")
+      if (i != names(table(object))[length(table(object))]) cat("\n")
     }
   }
 }

R/motif_census.R

@@ -154,37 +154,37 @@ node_quad_census <- function(.data){
   }
 }
 
-#' #' @export
-#' node_bmotif_census <- function(.data, normalized = FALSE){
-#'   if (!("bmotif" %in% rownames(utils::installed.packages()))) {
-#'     message("Please install package `{bmotif}`.")
-#'     out <- bmotif::node_positions(manynet::as_matrix(.data), 
-#'                                   weights_method = ifelse(manynet::is_weighted(.data),
-#'                                                           'mean_motifweights', 'none'),
-#'                                   normalisation = ifelse(normalized, 
-#'                                                          'levelsize_NAzero', 'none'))
-#'     make_node_motif(out, .data)
-#'   }
-#' }
-#' 
-#' #' @export
-#' node_igraph_census <- function(.data, normalized = FALSE){
-#'     out <- igraph::motifs(manynet::as_igraph(.data), 4)
-#'     if(manynet::is_labelled(.data))
-#'       rownames(out) <- manynet::node_names(.data)
-#'     colnames(out) <- c("co-K4",
-#'                        "co-diamond",
-#'                        "co-C4",
-#'                        "co-paw",
-#'                        "co-claw",
-#'                        "P4",
-#'                        "claw",
-#'                        "paw",
-#'                        "C4",
-#'                        "diamond",
-#'                        "K4")
-#'     make_node_motif(out, .data)
-#' }
+# #' @export
+# node_bmotif_census <- function(.data, normalized = FALSE){
+#   if (!("bmotif" %in% rownames(utils::installed.packages()))) {
+#     message("Please install package `{bmotif}`.")
+#     out <- bmotif::node_positions(manynet::as_matrix(.data), 
+#                                   weights_method = ifelse(manynet::is_weighted(.data),
+#                                                           'mean_motifweights', 'none'),
+#                                   normalisation = ifelse(normalized, 
+#                                                          'levelsize_NAzero', 'none'))
+#     make_node_motif(out, .data)
+#   }
+# }
+# 
+# #' @export
+# node_igraph_census <- function(.data, normalized = FALSE){
+#     out <- igraph::motifs(manynet::as_igraph(.data), 4)
+#     if(manynet::is_labelled(.data))
+#       rownames(out) <- manynet::node_names(.data)
+#     colnames(out) <- c("co-K4",
+#                        "co-diamond",
+#                        "co-C4",
+#                        "co-paw",
+#                        "co-claw",
+#                        "P4",
+#                        "claw",
+#                        "paw",
+#                        "C4",
+#                        "diamond",
+#                        "K4")
+#     make_node_motif(out, .data)
+# }
 
 #' @describeIn node_census Returns the shortest path lengths
 #'   of each node to every other node in the network.

cran-comments.md

@@ -1,12 +1,12 @@
 ## Test environments
 
-* local R installation, x86_64-apple-darwin20, R 4.3.0
-* Mac OS X 12.6.5 (on Github), R 4.3.0
-* Microsoft Windows Server 2022 10.0.20348 (on Github), R 4.3.0
-* Ubuntu 22.04.2 (on Github), R 4.3.0
-* R-hub builder (https://builder.r-hub.io)
-  - Windows Server 2022 R-devel, 64 bit
+* local R installation, x86_64-apple-darwin20, R 4.3.1
+* Mac OS X 12.6.9 (on Github), R 4.3.2
+* Microsoft Windows Server 2022 10.0.20348 (on Github), R 4.3.2
+* Ubuntu 22.04.3 (on Github), R 4.3.2
 
 ## R CMD check results
 
 0 errors | 0 warnings | 0 notes
+
+- Fixed documentation issues from previous submission