Merge pull request #94 from stocnet/develop

v1.2.3

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: manynet
 Title: Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks
-Version: 1.2.2
-Date: 2024-10-04
+Version: 1.2.3
+Date: 2024-10-05
 Description: Many tools for making, modifying, mapping, marking, measuring, 
    and motifs and memberships of many different types of networks.
    All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,

NEWS.md

@@ -1,3 +1,10 @@
+# manynet 1.2.3
+
+## Mapping
+
+- Fixed bug in `graphr()` where user not informed about `{concaveman}` dependency
+- Fixed `graphr()` examples
+
 # manynet 1.2.2
 
 ## Package

R/map_autograph.R

@@ -25,6 +25,9 @@
 #'   Lastly, `graphr()` uses `{ggplot2}`-related theme information, so
 #'   it is easy to make colour palette and fonts institution-specific and consistent.
 #'   See e.g. `theme_iheid()` for more.
+#'   
+#'   To learn more about what can be done visually,
+#'   try `run_tute("Visualisation")`.
 #' @name map_graphr
 #' @family mapping
 #' @param .data A manynet-consistent object.
@@ -97,10 +100,6 @@
 #'   mutate_ties(ecolor = rep(c("friends", "acquaintances"), times = 5)) %>%
 #'   graphr(node_color = "color", node_size = "size",
 #'          edge_size = 1.5, edge_color = "ecolor")
-#' graphr(ison_lotr, node_color = Race, node_size = node_degree(ison_lotr)*2,
-#'        edge_color = "yellow", edge_size = tie_degree(ison_lotr))
-#' graphr(ison_karateka, node_group = allegiance,
-#'        edge_size = tie_closeness(ison_karateka))
 #' @export
 graphr <- function(.data, layout, labels = TRUE,
                    node_color, node_shape, node_size, node_group,
@@ -172,6 +171,7 @@ graphr <- function(.data, layout, labels = TRUE,
   if (!is.null(node_group)) {
     x <- y <- NULL
     thisRequires("ggforce")
+    thisRequires("concaveman")
     p <- p + 
       ggforce::geom_mark_hull(ggplot2::aes(x, y, fill = node_group,
                                            label = node_group), data = lo) +
@@ -280,7 +280,7 @@ reduce_categories <- function(g, node_group) {
     toCondense <- names(which(table(node_attribute(g, node_group)) <= 2))
     out <- ifelse(node_attribute(g, node_group) %in% toCondense,
                   "Other", node_attribute(g, node_group))
-    message("The number of groups was reduced since there were groups with less than 2 nodes.")
+    mnet_info("The number of groups was reduced since there were groups with less than 2 nodes.")
   } else if (sum(table(node_attribute(g, node_group)) <= 2) == 2 &
              length(unique(node_attribute(g, node_group))) > 2) {
     limit <- stats::reorder(node_attribute(g, node_group),
@@ -293,7 +293,7 @@ reduce_categories <- function(g, node_group) {
     }
     out <- ifelse(node_attribute(g, node_group) %in% toCondense, "Other",
                   node_attribute(g, node_group))
-    message("The number of groups was reduced since there were groups with less than 2 nodes.")
+    mnet_info("The number of groups was reduced since there were groups with less than 2 nodes.")
   } else if (sum(table(node_attribute(g, node_group)) <= 2) == 1 &
              length(unique(node_attribute(g, node_group))) > 2) {
     limit <- stats::reorder(node_attribute(g, node_group),
@@ -302,11 +302,11 @@ reduce_categories <- function(g, node_group) {
     toCondense <- utils::tail(levels(limit), 2)
     out <- ifelse(node_attribute(g, node_group) %in% toCondense, "Other",
                   node_attribute(g, node_group))
-    message("The number of groups was reduced since there were groups with less than 2 nodes.")
+    mnet_info("The number of groups was reduced since there were groups with less than 2 nodes.")
   } else if (sum(table(node_attribute(g, node_group)) <= 2) == 1 &
              length(unique(node_attribute(g, node_group))) == 2) {
     out <- as.factor(node_attribute(g, node_group))
-    message("Node groups with 2 nodes or less can be cause issues for plotting ...")
+    mnet_info("Node groups with 2 nodes or less can be cause issues for plotting ...")
   } else out <- as.factor(node_attribute(g, node_group))
   out
 }
@@ -335,7 +335,7 @@ reduce_categories <- function(g, node_group) {
       } else out <- as.factor(as.character(tie_attribute(g, edge_color)))
       if (length(unique(out)) == 1) {
         out <- rep("black", net_ties(g))
-        message("Please indicate a variable with more than one value or level when mapping edge colors.")
+        mnet_info("Please indicate a variable with more than one value or level when mapping edge colors.")
       }
     } else {
       out <- edge_color
@@ -397,12 +397,12 @@ check_edge_variables <- function(g, edge_color, edge_size) {
   if (!is.null(edge_color)) {
     if (any(!tolower(edge_color) %in% tolower(igraph::edge_attr_names(g))) &
         any(!edge_color %in% grDevices::colors())) {
-      message("Please make sure you spelled `edge_color` variable correctly.")
+      mnet_info("Please make sure you spelled `edge_color` variable correctly.")
     } 
   }
   if (!is.null(edge_size)) {
     if (!is.numeric(edge_size) & any(!tolower(edge_size) %in% tolower(igraph::edge_attr_names(g)))) {
-      message("Please make sure you spelled `edge_size` variable correctly.")
+      mnet_info("Please make sure you spelled `edge_size` variable correctly.")
     } 
   }
 }
@@ -505,7 +505,7 @@ map_edges <- function(p, g, out) {
       } else out <- as.factor(as.character(node_attribute(g, node_color)))
       if (length(unique(out)) == 1) {
         out <- rep("black", net_nodes(g))
-        message("Please indicate a variable with more than one value or level when mapping node colors.")
+        mnet_info("Please indicate a variable with more than one value or level when mapping node colors.")
       }
     } else out <- node_color
   } else {
@@ -518,12 +518,12 @@ check_node_variables <- function(g, node_color, node_size) {
   if (!is.null(node_color)) {
     if (any(!tolower(node_color) %in% tolower(igraph::vertex_attr_names(g))) &
         any(!node_color %in% grDevices::colors())) {
-      message("Please make sure you spelled `node_color` variable correctly.")
+      mnet_info("Please make sure you spelled `node_color` variable correctly.")
     } 
   }
   if (!is.null(node_size)) {
     if (!is.numeric(node_size) & any(!tolower(node_size) %in% tolower(igraph::vertex_attr_names(g)))) {
-      message("Please make sure you spelled `node_size` variable correctly.")
+      mnet_info("Please make sure you spelled `node_size` variable correctly.")
     }
   }
 }
@@ -713,7 +713,7 @@ graphs <- function(netlist, waves,
   if (missing(waves)) {
     if (length(netlist) > 4) {
       netlist <- netlist[c(1, length(netlist))]
-      message("Plotting first and last waves side-by-side. \nTo set the waves plotted use the 'waves = ' argument.")
+      mnet_info("Plotting first and last waves side-by-side. \nTo set the waves plotted use the 'waves = ' argument.")
     }
   } else if (!missing(waves)) {
     if (length(waves) == 1) netlist <- netlist[c(1:waves)] else 
@@ -746,7 +746,7 @@ graphs <- function(netlist, waves,
         graphr(netlist[[i]], layout = "star", center = names(netlist)[[i]], ...) + 
           ggtitle(names(netlist)[i]))
     } else {
-      message("Layouts were not standardised since not all nodes appear across waves.")  
+      mnet_info("Layouts were not standardised since not all nodes appear across waves.")  
       gs <- lapply(1:length(netlist), function(i)
         graphr(netlist[[i]], ...) + ggtitle(names(netlist)[i]))
     }
@@ -830,7 +830,7 @@ grapht <- function(tlist, keep_isolates = TRUE,
                    node_colour, edge_colour) {
   thisRequires("gganimate")
   thisRequires("gifski")
-  thisRequires("png")
+  # thisRequires("png")
   x <- y <- name <- status <- frame <- NULL
   # Check arguments
   if (missing(layout)) {
@@ -922,7 +922,7 @@ grapht <- function(tlist, keep_isolates = TRUE,
   } else {
     if (nrow(nodes_out)/length(unique(nodes_out$frame)) > 30 &
         any(unlist(lapply(tlist, node_is_isolate)) == TRUE)) {
-      message("Please considering deleting isolates to improve visualisation.")
+      mnet_info("Please considering deleting isolates to improve visualisation.")
     } 
     nodes_out$status <- TRUE
   }

cran-comments.md

@@ -10,4 +10,5 @@
 0 errors | 0 warnings | 0 notes
 
 * Re errors on CRAN, this version fixes errors on Linux versions for which the {oaqc} package is not available
-* Re previous submission, this version fixes a DOI and avoids an issue with {igraph}
+* Re previous submission, this version fixes a DOI and avoids an issue with {igraph}
+* Fixed error in examples