Merge pull request #95 from stocnet/develop

v1.2.4

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: manynet
 Title: Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks
-Version: 1.2.3
+Version: 1.2.4
 Date: 2024-10-05
 Description: Many tools for making, modifying, mapping, marking, measuring, 
    and motifs and memberships of many different types of networks.
@@ -11,12 +11,12 @@ Description: Many tools for making, modifying, mapping, marking, measuring,
    and describing and visualizing networks with sensible defaults.
 URL: https://stocnet.github.io/manynet/
 BugReports: https://github.com/stocnet/manynet/issues
-Depends: R (>= 3.6.0)
 License: MIT + file LICENSE
 Language: en-GB
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
+Depends: R (>= 3.6.0)
 Imports:
     cli,
     dplyr (>= 1.1.0),

NEWS.md

@@ -1,3 +1,14 @@
+# manynet 1.2.4
+
+## Package
+
+- Fixed `thisRequires()` bug by testing for interactivity
+- Dropped brokerage census examples
+
+## Modifying
+
+- Improved `to_ego()` and `to_egos()` to specify direction
+
 # manynet 1.2.3
 
 ## Mapping

R/manip_reformed.R

@@ -243,18 +243,24 @@ NULL
 #'   By default 0. 
 #'   Increasing this to 1 excludes the ego,
 #'   and 2 excludes ego's direct alters.
+#' @param direction String, either "out" or "in".
 #' @export
-to_ego <- function(.data, node, max_dist = 1, min_dist = 0) UseMethod("to_ego")
+to_ego <- function(.data, node, max_dist = 1, min_dist = 0,
+                   direction = c("out","in")) UseMethod("to_ego")
 
 #' @export
-to_ego.igraph <- function(.data, node, max_dist = 1, min_dist = 0){
-  egos <- to_egos(.data, max_dist = max_dist, min_dist = min_dist)
+to_ego.igraph <- function(.data, node, max_dist = 1, min_dist = 0,
+                          direction = c("out","in")){
+  egos <- to_egos(.data, max_dist = max_dist, min_dist = min_dist,
+                  direction = direction)
   as_igraph(egos[[node]])
 }
 
 #' @export
-to_ego.tbl_graph <- function(.data, node, max_dist = 1, min_dist = 0){
-  egos <- to_egos(.data, max_dist = max_dist, min_dist = min_dist)
+to_ego.tbl_graph <- function(.data, node, max_dist = 1, min_dist = 0,
+                             direction = c("out","in")){
+  egos <- to_egos(.data, max_dist = max_dist, min_dist = min_dist,
+                  direction = direction)
   as_tidygraph(egos[[node]])
 }
 
@@ -459,7 +465,7 @@ to_blocks.tbl_graph <- function(.data, membership, FUN = mean){
 #'   ```
 #' @name manip_paths
 #' @family modifications
-#' @inheritParams manip_reformat
+#' @inheritParams manip_scope
 #' @returns
 #'   All `to_` functions return an object of the same class as that provided. 
 #'   So passing it an igraph object will return an igraph object
@@ -658,7 +664,6 @@ to_tree <- function(.data) {
 
 #' @rdname manip_paths 
 #' @param from The index or name of the node from which the path should be traced.
-#' @param direction String, either "out" or "in".
 #' @export
 to_dominating <- function(.data, from, direction = c("out","in")) {
   direction <- match.arg(direction)

R/manip_split.R

@@ -25,17 +25,20 @@ NULL
 #' @export
 to_egos <- function(.data, 
                     max_dist = 1, 
-                    min_dist = 0) UseMethod("to_egos")
+                    min_dist = 0,
+                    direction = c("out","in")) UseMethod("to_egos")
 
 #' @export
 to_egos.igraph <- function(.data, 
                            max_dist = 1, 
-                           min_dist = 0){
+                           min_dist = 0,
+                           direction = c("out","in")){
   if(is_twomode(.data)) max_dist <- max_dist*2
   mnet_progress_step("Obtaining neighbourhoods")
   out <- igraph::make_ego_graph(.data,
                                 order = max_dist,
-                                mindist = min_dist)
+                                mindist = min_dist,
+                                mode = match.arg(direction))
   if(is_labelled(.data)) 
     names(out) <- node_names(.data)
   out
@@ -44,40 +47,44 @@ to_egos.igraph <- function(.data,
 #' @export
 to_egos.tbl_graph <- function(.data, 
                            max_dist = 1, 
-                           min_dist = 0){
+                           min_dist = 0,
+                           direction = c("out","in")){
   out <- to_egos(as_igraph(.data), 
                        max_dist, 
-                       min_dist)
+                       min_dist, direction)
   lapply(out, function(x) as_tidygraph(x))
 }
 
 #' @export
 to_egos.network <- function(.data, 
                               max_dist = 1, 
-                              min_dist = 0){
+                              min_dist = 0,
+                            direction = c("out","in")){
   out <- to_egos(as_igraph(.data), 
                        max_dist, 
-                       min_dist)
+                       min_dist, direction)
   lapply(out, function(x) as_network(x))
 }
 
 #' @export
 to_egos.matrix <- function(.data, 
                               max_dist = 1, 
-                              min_dist = 0){
+                              min_dist = 0,
+                           direction = c("out","in")){
   out <- to_egos(as_igraph(.data), 
                        max_dist, 
-                       min_dist)
+                       min_dist, direction)
   lapply(out, function(x) as_matrix(x))
 }
 
 #' @export
 to_egos.data.frame <- function(.data, 
                               max_dist = 1, 
-                              min_dist = 0){
+                              min_dist = 0,
+                              direction = c("out","in")){
   out <- to_egos(as_igraph(.data), 
                        max_dist, 
-                       min_dist)
+                       min_dist, direction)
   lapply(out, function(x) as_edgelist(x))
 }
 

R/manynet-utils.R

@@ -16,7 +16,7 @@ available_methods <- function(fun_vctr) {
 
 # Helper function for checking and downloading packages
 thisRequires <- function(pkgname){
-  if (!requireNamespace(pkgname, quietly = TRUE)) {
+  if (!requireNamespace(pkgname, quietly = TRUE) & interactive()) {
     if(utils::askYesNo(msg = paste("The", pkgname, 
                                    "package is required to run this function. Would you like to install", pkgname, "from CRAN?"))) {
       utils::install.packages(pkgname)
@@ -27,7 +27,7 @@ thisRequires <- function(pkgname){
 }
 
 thisRequiresBio <- function(pkgname) {
-  if (!requireNamespace(pkgname, quietly = TRUE)) {
+  if (!requireNamespace(pkgname, quietly = TRUE) & interactive()) {
     if(utils::askYesNo(msg = paste("The", pkgname, 
                                    "package is required to run this function. Would you like to install", pkgname, "from BioConductor?"))) {
   thisRequires("BiocManager")

R/motif_census.R

@@ -483,7 +483,7 @@ NULL
 #' _Social Networks_ 41:36–47. 
 #' \doi{10.1016/j.socnet.2014.11.005}
 #' @examples 
-#' node_by_brokerage(manynet::ison_networkers, "Discipline")
+#' # node_by_brokerage(ison_networkers, "Discipline")
 #' @export
 node_by_brokerage <- function(.data, membership, standardized = FALSE){
   thisRequires("sna")
@@ -507,7 +507,7 @@ node_by_brokerage <- function(.data, membership, standardized = FALSE){
 
 #' @rdname motif_brokerage 
 #' @examples 
-#' net_by_brokerage(ison_networkers, "Discipline")
+#' # net_by_brokerage(ison_networkers, "Discipline")
 #' @export
 net_by_brokerage <- function(.data, membership, standardized = FALSE){
   thisRequires("sna")