v2.1.2

DESCRIPTION

@@ -1,8 +1,7 @@
 Package: manynet
-Title: Many Ways to Make, Modify, Mark, and Measure Myriad Networks
-Version: 2.1.1
-Description: Many tools for making, modifying, marking, measuring, 
-   and motifs and memberships of many different types of networks.
+Title: Many Ways to Make, Manipulate, and Modify Myriad Networks
+Version: 2.1.2
+Description: Many tools for making, manipulating, and modifying many different types of networks.
    All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects,
    on directed, multiplex, multimodal, signed, and other networks.
    The package includes functions for importing and exporting, creating and generating networks,

NAMESPACE

@@ -117,6 +117,7 @@ S3method(as_tidygraph,siena)
 S3method(as_tidygraph,stocnet)
 S3method(as_tidygraph,tbl_graph)
 S3method(bind_changes,default)
+S3method(bind_changes,igraph)
 S3method(bind_changes,stocnet)
 S3method(bind_changes,tbl_graph)
 S3method(bind_nodes,default)
@@ -142,6 +143,8 @@ S3method(filter_nodes,default)
 S3method(filter_nodes,stocnet)
 S3method(filter_nodes,tbl_graph)
 S3method(filter_ties,default)
+S3method(filter_ties,igraph)
+S3method(filter_ties,stocnet)
 S3method(filter_ties,tbl_graph)
 S3method(from_ties,stocnet)
 S3method(from_ties,tbl_graph)
@@ -394,6 +397,7 @@ S3method(to_components,matrix)
 S3method(to_components,network)
 S3method(to_components,tbl_graph)
 S3method(to_correlation,default)
+S3method(to_correlation,matrix)
 S3method(to_correlation,tbl_graph)
 S3method(to_cosine,default)
 S3method(to_cosine,matrix)
@@ -776,51 +780,11 @@ export(node_heterophily)
 export(node_hierarchy)
 export(node_homophily)
 export(node_hub)
-export(node_in_adopter)
-export(node_in_automorphic)
-export(node_in_betweenness)
-export(node_in_brokering)
-export(node_in_community)
-export(node_in_component)
-export(node_in_core)
-export(node_in_eigen)
-export(node_in_equivalence)
-export(node_in_fluid)
-export(node_in_greedy)
-export(node_in_infomap)
-export(node_in_leiden)
-export(node_in_louvain)
-export(node_in_optimal)
-export(node_in_partition)
-export(node_in_regular)
-export(node_in_roulette)
-export(node_in_spinglass)
-export(node_in_strong)
-export(node_in_structural)
-export(node_in_walktrap)
-export(node_in_weak)
 export(node_indegree)
 export(node_induced)
 export(node_infomap)
 export(node_information)
-export(node_is_core)
-export(node_is_cutpoint)
-export(node_is_exposed)
-export(node_is_fold)
-export(node_is_independent)
-export(node_is_infected)
-export(node_is_isolate)
-export(node_is_latent)
-export(node_is_max)
-export(node_is_mean)
-export(node_is_mentor)
-export(node_is_min)
 export(node_is_mode)
-export(node_is_neighbor)
-export(node_is_pendant)
-export(node_is_random)
-export(node_is_recovered)
-export(node_is_universal)
 export(node_kcoreness)
 export(node_kernighanlin)
 export(node_leading_eigen)
@@ -904,21 +868,6 @@ export(tie_closeness)
 export(tie_cohesion)
 export(tie_degree)
 export(tie_eigenvector)
-export(tie_is_bridge)
-export(tie_is_cyclical)
-export(tie_is_feedback)
-export(tie_is_imbalanced)
-export(tie_is_loop)
-export(tie_is_max)
-export(tie_is_min)
-export(tie_is_multiple)
-export(tie_is_path)
-export(tie_is_random)
-export(tie_is_reciprocated)
-export(tie_is_simmelian)
-export(tie_is_transitive)
-export(tie_is_triangular)
-export(tie_is_triplet)
 export(tie_is_twomode)
 export(tie_signs)
 export(tie_weights)

NEWS.md

@@ -1,3 +1,33 @@
+# manynet 2.1.2
+
+## Package
+
+- Updated title/description text
+- Updated README
+  - Updated TOC to include new wrangling section
+  - Added package migration note to README
+- Updated startup messages with migration notesand links to `{autograph}`, `{netrics}`, and `{migraph}`
+- Removed a set of defunct wrappers for moved/retired functions
+
+## Making
+
+- Fixed reference formatting of DOI and citation text
+
+## Coercion
+
+- Improved `expect_nodes()`/`expect_ties()` and introduces internal active-context helpers
+- Fixed `as_diffusion.igraph()` to derive diffusion events from changelists
+
+## Manipulating
+
+- Added `filter_ties.igraph()` and `filter_ties.stocnet()`
+- Improved active context inference across `mutate_nodes.stocnet()`, `mutate_ties.stocnet()`, `filter_nodes.stocnet()`, and `filter_ties.stocnet()`
+- Added `bind_changes.igraph()` and delegated 'tbl_graph' method to it
+
+## Modifying
+
+- Added `to_correlation.matrix()` S3 method
+
 # manynet 2.1.1
 
 ## Package

R/coerce_graph.R

@@ -846,6 +846,16 @@ as_diffusion.mnet <- function(.data, twomode = FALSE, events) {
 #' @export
 as_diffusion.igraph <- function(.data, twomode = FALSE, events) {
   net <- as_tidygraph(.data)
+  if (missing(events)) {
+    events <- as_changelist(.data)
+  }
+  events <- events |>
+    dplyr::filter(var == "diffusion") |>
+    dplyr::transmute(
+      t = time,
+      nodes = node,
+      event = value
+    )
   event <- NULL
   sumchanges <- events |> dplyr::group_by(t) |> 
     dplyr::reframe(I_new = sum(event == "I"),

R/make_generate.R

@@ -313,7 +313,7 @@ generate_smallworld <- function(n, p = 0.05, directed = FALSE, width = 2) {
 #' Barabasi, Albert-Laszlo, and Reka Albert. 1999. 
 #' “Emergence of Scaling in Random Networks.” 
 #' _Science_ 286(5439):509–12. 
-#' \doi{10.1126/science.286.5439.509}.
+#' \doi{10.1126/science.286.5439.509}
 #' @examples
 #' generate_scalefree(12, 0.25)
 #' generate_scalefree(12, 1.25)
@@ -348,8 +348,9 @@ generate_scalefree <- function(n, p = 1, directed = FALSE) {
 #' @references
 #' ## On the forest-fire model
 #' Leskovec, Jure, Jon Kleinberg, and Christos Faloutsos. 2007. 
-#' "\href{https://www.cs.cmu.edu/~jure/pubs/powergrowth-tkdd.pdf}{Graph evolution: Densification and shrinking diameters}". 
+#' "Graph evolution: Densification and shrinking diameters". 
 #' _ACM transactions on Knowledge Discovery from Data_, 1(1): 2-es.
+#' \doi{10.1145/1217299.1217301}
 #' @examples
 #' generate_fire(10)
 #' @export

R/manip_changes.R

@@ -93,6 +93,11 @@ bind_changes.default <- function(.data, changes, var, ...){
 
 #' @export
 bind_changes.tbl_graph <- function(.data, changes, var, ...){
+  as_tidygraph(bind_changes.igraph(.data, changes, var, ...))
+}
+
+#' @export
+bind_changes.igraph <- function(.data, changes, var, ...){
   out <- .data
   if(length(names(changes)) == 4){
 
@@ -139,7 +144,7 @@ bind_changes.tbl_graph <- function(.data, changes, var, ...){
   }
 
   igraph::graph_attr(out)$changes <- changes
-  as_tidygraph(out)
+  out
 }
 
 .check_changevars <- function(changes){

R/manip_nodes.R

@@ -110,7 +110,8 @@ filter_nodes.tbl_graph <- function(.data, ..., .by = NULL){
 
 #' @export
 filter_nodes.stocnet <- function(.data, ..., .by = NULL){
-  if(is.null(.data$nodes) || nrow(.data$nodes) == 0) return(.data)
+  with_active_context(.data, "nodes", {
+    if(is.null(.data$nodes) || nrow(.data$nodes) == 0) return(.data)
 
   node_df <- dplyr::mutate(.data$nodes, .orig_id = dplyr::row_number())
   kept_nodes <- dplyr::filter(node_df, ..., .by = dplyr::all_of(.by))
@@ -134,6 +135,7 @@ filter_nodes.stocnet <- function(.data, ..., .by = NULL){
 
   make_stocnet(nodes = out_nodes, ties = out_ties, changes = out_changes,
               global = .data$global, info = .data$info)
+  })
 }
 
 #' @rdname manip_nodes_num
@@ -279,10 +281,13 @@ mutate_nodes.network <- function(.data, ...){
 
 #' @export
 mutate_nodes.stocnet <- function(.data, ...){
-  out <- .data
-  out$nodes <- out$nodes |> 
-    dplyr::mutate(...)
-  out
+  with_active_context(.data, "nodes", {
+    if (is.null(.data$nodes) || nrow(.data$nodes) == 0) return(.data)
+    out <- .data
+    out$nodes <- out$nodes |> 
+      dplyr::mutate(...)
+    out
+  })
 }
 
 #' @rdname manip_nodes_attr

R/manip_ties.R

@@ -194,13 +194,31 @@ filter_ties.default <- function(.data, ...){
   as_input(.data, filter_ties, ...)
 }
 
+#' @export
+filter_ties.igraph <- function(.data, ...){
+  as_tidygraph(.data) |> tidygraph::activate(edges) |> 
+    tidygraph::filter(...) |> 
+    tidygraph::activate(nodes) |> 
+    as_igraph()
+}
+
 #' @export
 filter_ties.tbl_graph <- function(.data, ...){
   .data |> tidygraph::activate(edges) |> 
     dplyr::filter(...) |> 
     tidygraph::activate(nodes)
 }
 
+#' @export
+filter_ties.stocnet <- function(.data, ...){
+  with_active_context(.data, "edges", {
+    if (is.null(.data$ties) || nrow(.data$ties) == 0) return(.data)
+    out <- .data
+    out$ties <- out$ties |> dplyr::filter(...)
+    out
+  })
+}
+
 # Manipulating ties attributes ####
 
 #' Manipulating tie attributes
@@ -271,10 +289,13 @@ mutate_ties.tbl_graph <- function(.data, ...){
 
 #' @export
 mutate_ties.stocnet <- function(.data, ...){
-  out <- .data
-  out$ties <- out$ties |> 
-    dplyr::mutate(...)
-  out
+  with_active_context(.data, "edges", {
+    if (is.null(.data$ties) || nrow(.data$ties) == 0) return(.data)
+    out <- .data
+    out$ties <- out$ties |> 
+      dplyr::mutate(...)
+    out
+  })
 }
 
 #' @rdname manip_ties_attr