Merge pull request #90 from stocnet/develop

v1.2.0

.github/workflows/pushrelease.yml

@@ -61,18 +61,20 @@ jobs:
           path: build/
 
       - name: Calculate code coverage
+        if: runner.os == 'macOS-latest'
         run: Rscript -e "covr::codecov()"
 
   release:
     name: Bump version and release
     if: ${{ always() }}
     needs: build
+    if: github.event.pull_request.merged == true
     runs-on: ubuntu-latest
     permissions:
       contents: write
     steps:
       - name: Checkout one
-        uses: actions/checkout@master
+        uses: actions/checkout@v4
         with:
           fetch-depth: '0'
       - name: Bump version and push tag
@@ -84,24 +86,16 @@ jobs:
           DEFAULT_BUMP: patch
           RELEASE_BRANCHES: main
       - name: Checkout two
-        uses: actions/checkout@v2
-      - name: Create Release
-        id: create_release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          tag_name: ${{ steps.newtag.outputs.tag }}
-          release_name: Release ${{ steps.newtag.outputs.tag }}
-          draft: false
-          prerelease: false
+        uses: actions/checkout@v4
+
+      - name: Extract version
+        run: |
+          echo "PACKAGE_VERSION=$(grep '^Version' DESCRIPTION | sed 's/.*: *//')" >> $GITHUB_ENV
+          echo "PACKAGE_NAME=$(grep '^Package' DESCRIPTION | sed 's/.*: *//')" >> $GITHUB_ENV
 
       - name: Download binaries
         uses: actions/download-artifact@v4
 
-      - name: Display structure of downloaded files
-        run: ls -R
-
       - name: Rename binaries release
         shell: bash
         run: |
@@ -111,9 +105,9 @@ jobs:
           cp ./winOS/${{ env.PACKAGE_NAME }}_${{ env.PACKAGE_VERSION }}*.zip .
           echo "Renamed files"
           ls manynet_*
-
+       
       - name: Create Release and Upload Assets
-        id: upload_release
+        id: create_release
         uses: softprops/action-gh-release@v2
         with:
           tag_name: ${{ steps.newtag.outputs.tag }}
@@ -127,7 +121,7 @@ jobs:
             manynet_*.tar.gz
             manynet_*.zip
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
 
   pkgdown:
     name: Build and deploy website

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: manynet
 Title: Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks
-Version: 1.1.0
-Date: 2024-09-12
+Version: 1.2.0
+Date: 2024-09-28
 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,
@@ -41,7 +41,6 @@ Suggests:
     methods,
     multiplex,
     netdiffuseR,
-    oaqc,
     patchwork,
     readxl,
     rmarkdown,

NAMESPACE

@@ -138,8 +138,10 @@ S3method(plot,diffs_model)
 S3method(plot,learn_model)
 S3method(plot,matrix)
 S3method(plot,network_measures)
+S3method(plot,network_motif)
 S3method(plot,node_measure)
 S3method(plot,node_member)
+S3method(plot,node_motif)
 S3method(plot,tie_measure)
 S3method(print,diff_model)
 S3method(print,diffs_model)
@@ -296,6 +298,7 @@ export("%>%")
 export(.E)
 export(.G)
 export(.N)
+export(add_info)
 export(add_node_attribute)
 export(add_nodes)
 export(add_tie_attribute)
@@ -321,10 +324,12 @@ export(cluster_hierarchical)
 export(create_components)
 export(create_core)
 export(create_degree)
+export(create_ego)
 export(create_empty)
 export(create_explicit)
 export(create_filled)
 export(create_lattice)
+export(create_motifs)
 export(create_ring)
 export(create_star)
 export(create_tree)
@@ -406,6 +411,7 @@ export(net_betweenness)
 export(net_by_brokerage)
 export(net_by_dyad)
 export(net_by_mixed)
+export(net_by_quad)
 export(net_by_triad)
 export(net_change)
 export(net_closeness)
@@ -509,6 +515,7 @@ export(network_upperbound)
 export(node_adoption_time)
 export(node_alpha)
 export(node_attribute)
+export(node_authority)
 export(node_automorphic_equivalence)
 export(node_betweenness)
 export(node_bridges)
@@ -517,6 +524,7 @@ export(node_brokering)
 export(node_brokering_activity)
 export(node_brokering_exclusivity)
 export(node_by_brokerage)
+export(node_by_dyad)
 export(node_by_exposure)
 export(node_by_path)
 export(node_by_quad)
@@ -537,13 +545,15 @@ export(node_efficiency)
 export(node_effsize)
 export(node_eigenvector)
 export(node_equivalence)
+export(node_equivalency)
 export(node_exposure)
 export(node_fast_greedy)
 export(node_flow)
 export(node_fluid)
 export(node_harmonic)
 export(node_heterophily)
 export(node_hierarchy)
+export(node_hub)
 export(node_in_adopter)
 export(node_in_automorphic)
 export(node_in_betweenness)
@@ -665,6 +675,7 @@ export(scale_fill_sdgs)
 export(scale_fill_uzh)
 export(scale_size)
 export(select_ties)
+export(set_manynet_theme)
 export(summarise_ties)
 export(table_data)
 export(theme_ethz)
@@ -909,7 +920,6 @@ importFrom(stats,cor)
 importFrom(stats,cutree)
 importFrom(stats,hclust)
 importFrom(stats,median)
-importFrom(tidygraph,"%E>%")
 importFrom(tidygraph,.E)
 importFrom(tidygraph,.G)
 importFrom(tidygraph,.N)

NEWS.md

@@ -1,3 +1,61 @@
+# manynet 1.2.0
+
+## Package
+
+- Added progress updates, information, and unavailability errors to several functions
+  - These can be silenced by setting `options(manynet_verbosity ="quiet")`
+  - Where a feature is unavailable, users are directed to the Github issues page
+- Added console theme to color the startup and various warning or info messages
+
+## Making
+
+- Added `create_ego()` for collecting ego networks through interviews, including arguments for:
+  - Indicating whether a roster should be used, otherwise follows a name generator approach
+  - Indicating whether nodes should be interpreted, i.e. nodal attributes collected
+  - Indicating whether ties between alters should be requested
+- Added `create_motifs()` for creating networks that correspond to the isomorphic subgraphs of certain size and format
+
+## Modifying
+
+- Improved `print.mnet()`
+  - Prints multiplex types if available
+  - Prints both nodesets for two-mode networks
+- Added `add_info()` for adding grand info to tidygraph objects
+  - This includes the name of the network, node sets and ties, DOI, year and mode of collection
+- Fixed `to_unweighted()` so that it passes through unweighted networks correctly
+
+## Mapping
+
+- Added `set_manynet_theme()` to set theme (re #60), but not yet fully implemented
+
+## Marking
+
+- Improved `is_multiplex()` to ignore "name" tie attributes
+
+## Measuring
+
+- Added `node_authority()` and `node_hub()` centrality measures
+- Added `node_equivalency()` for calculating four-cycle closure by node
+- Extended `net_equivalency()` to one-mode networks
+
+## Members
+
+- Fixed `node_in_equivalence()` to use census directly
+
+## Motifs
+
+- Added plot methods for network_motif and node_motif classes that use `create_motifs()`
+- Added `node_by_dyad()` for node level dyad census
+- Added `net_by_quad()` for network level quad census
+- Fixed `node_by_quad()` to avoid `{oaqc}` dependency (#89), more flexible but slower
+- Fixed `print.node_motif()` to convert to tibble and add modes and names where available only upon print
+  - The underlying object is still a matrix, used for equivalence and blockmodelling
+
+## Data
+
+- Updated `ison_southern_women` with grand info
+- Updated `ison_laterals` with reordered nodes
+
 # manynet 1.1.0
 
 ## Package
@@ -98,7 +156,7 @@
 - `table_data()` can now report on data from multiple packages
   - `{manynet}` and `{migraph}` are included by default,
   and if any are not installed they are just ignored
-- `tabe_data()` can now filter by any reported formats,
+- `table_data()` can now filter by any reported formats,
 such as 'directed' or 'twomode'
 
 ## Website
@@ -198,7 +256,7 @@ including force-directed, layered, circular, spectral, and grid layouts
 existing network was incorrect
 - Added `generate_configuration()` for generating configuration models
 (including for two-mode networks)
-- `play_diffuson()` now includes an explicit contact argument to control the
+- `play_diffusion()` now includes an explicit contact argument to control the
 basis of exposure
 
 ## Marking
@@ -277,7 +335,7 @@ and `node_is_infected()` (closes #71)
   `net_balance()`, `net_change()`, and `net_stability()`
 - Updated properties from mapping to measuring
 - Updated attributes from mapping to measuring
-    - Renamed `node_mode()` (deprecated) to node_is_mode() since it returns a
+    - Renamed `node_mode()` (deprecated) to `node_is_mode()` since it returns a
     logical vector
     - Updated `node_attribute()` and `tie_attribute()` to return measures
     when the output is numeric

R/class_motifs.R

@@ -1,6 +1,7 @@
 make_node_motif <- function(out, .data) {
   class(out) <- c("node_motif", class(out))
-  attr(out, "mode") <- node_is_mode(.data)
+  if(is_twomode(.data)) attr(out, "mode") <- node_is_mode(.data)
+  if(is_labelled(.data)) attr(out, "dimnames")[[1]] <- node_names(.data)
   out
 }
 
@@ -14,17 +15,55 @@ make_network_motif <- function(out, .data) {
 print.node_motif <- function(x, ...,
                          n = 6,
                          digits = 3) {
-  if(!is.null(attr(x, "dimnames")[[1]])){
-    x <- data.frame(names = attr(x, "dimnames")[[1]], x)
-  }
   if (any(attr(x, "mode"))) {
-    print(dplyr::tibble(as.data.frame(x)[!attr(x, "mode")]), n = n)
-    print(dplyr::tibble(as.data.frame(x)[attr(x, "mode")]), n = n)
+    y <- as.data.frame(x[!attr(x, "mode"),])
+    z <- as.data.frame(x[attr(x, "mode"),])
+    if(!is.null(attr(x, "dimnames")[[1]])){
+      y <- data.frame(names = attr(x, "dimnames")[[1]][!attr(x, "mode")], y)
+      z <- data.frame(names = attr(x, "dimnames")[[1]][attr(x, "mode")], z)
+    } 
+    print(dplyr::tibble(y), n = n)
+    print(dplyr::tibble(z), n = n)
   } else {
-    print(dplyr::tibble(as.data.frame(x)), n = n)
+    if(!is.null(attr(x, "dimnames")[[1]])){
+      x <- data.frame(names = attr(x, "dimnames")[[1]], x)
+    } else x <- as.data.frame(x)
+    print(dplyr::tibble(x), n = n)
   }
 }
 
+#' @export
+plot.node_motif <- function(x, ...) {
+  motifs <- dimnames(x)[[2]]
+  if("X4" %in% motifs){
+    graphs(create_motifs(4), waves = 1:11)
+  } else if("021D" %in% motifs){
+    graphs(create_motifs(3, directed = TRUE), waves = 1:16)
+  } else if("102" %in% motifs){
+    graphs(create_motifs(3), waves = 1:4)
+  } else if("Asymmetric" %in% motifs){
+    graphs(create_motifs(2, directed = TRUE), waves = 1:3)
+  } else if("Mutual" %in% motifs){
+    graphs(create_motifs(2), waves = 1:2)
+  } else mnet_unavailable("Cannot plot these motifs yet, sorry.")
+}
+
+#' @export
+plot.network_motif <- function(x, ...) {
+  motifs <- dimnames(x)[[2]]
+  if("X4" %in% motifs){
+    graphs(create_motifs(4), waves = 1:11)
+  } else if("021D" %in% motifs){
+    graphs(create_motifs(3, directed = TRUE), waves = 1:16)
+  } else if("102" %in% motifs){
+    graphs(create_motifs(3), waves = 1:4)
+  } else if("Asymmetric" %in% motifs){
+    graphs(create_motifs(2, directed = TRUE), waves = 1:3)
+  } else if("Mutual" %in% motifs){
+    graphs(create_motifs(2), waves = 1:2)
+  } else mnet_unavailable("Cannot plot these motifs yet, sorry.")
+}
+
 # summary(node_by_triad(mpn_elite_mex),
 #         membership = node_regular_equivalence(mpn_elite_mex, "elbow"))
 #' @export

R/class_networks.R

@@ -6,22 +6,23 @@
 print.mnet <- function(x, ..., n = 6) {
   arg_list <- list(...)
   arg_list[['useS4']] <- NULL
+  if(is_grand(x) && !is.null(igraph::graph_attr(x, "grand")$name)) 
+    cli::cli_text("# {igraph::graph_attr(x, 'grand')$name}")
   graph_desc <- describe_graph(x)
+  tie_desc <- describe_ties(x)
+  node_desc <- describe_nodes(x)
+  cli::cli_text("# {graph_desc} network of {node_desc} and {tie_desc}")  
   top <- dplyr::as_tibble(tidygraph::activate(x, "nodes"))
   bottom <- dplyr::as_tibble(tidygraph::activate(x, "edges"))
-  if(is.null(igraph::graph_attr(x, "grand"))) node_name <- "nodes" else
-    node_name <- igraph::graph_attr(x, "grand")$vertex1
-  if(is.null(igraph::graph_attr(x, "grand"))) 
-    tie_name <- ifelse(is_directed(x), "arcs", "ties") else
-      tie_name <- paste(igraph::graph_attr(x, "grand")$edge.pos,
-                        ifelse(is_directed(x), "arcs", "ties"))
-  cat('#', graph_desc, 'network of', igraph::gorder(x), node_name, 'and',
-      igraph::gsize(x), tie_name, '\n', sep = ' ')  
   if (ncol(top)>0) print(top, n = n)
   if (ncol(bottom)>0) print(bottom, n = n, max_footer_lines = 1)
   invisible(x)
 }
 
+is_grand <- function(.data){
+  !is.null(igraph::graph_attr(.data, "grand"))
+}
+
 describe_graph <- function(x) {
   paste0("A ",
          ifelse(is_dynamic(x), "dynamic, ", ""),
@@ -35,3 +36,26 @@ describe_graph <- function(x) {
                 ifelse(is_directed(x), "directed", "undirected"))
   )
 }
+
+describe_nodes <- function(x){
+  nd <- net_dims(x)
+  if(!is.null(igraph::graph_attr(x, "grand")$vertex1)){
+    node_name <- paste(nd[1], igraph::graph_attr(x, "grand")$vertex1)
+    if(length(nd)==2 && !is.null(igraph::graph_attr(x, "grand")$vertex2))
+      node_name <- c(node_name, paste(nd[2], igraph::graph_attr(x, "grand")$vertex2))
+  } else node_name <- paste(sum(nd), "nodes")
+  node_name
+}
+
+describe_ties <- function(x){
+  nt <- net_ties(x)
+  tie_name <- ifelse(is_directed(x), "arcs", "ties") 
+  if(!is.null(igraph::graph_attr(x, "grand")$edge.pos)){
+    tie_name <- paste(igraph::graph_attr(x, "grand")$edge.pos,
+                      tie_name)
+  } else if(!is.null(tie_attribute(x, "type"))){
+    tie_name <- paste(cli::ansi_collapse(unique(tie_attribute(x, "type"))), 
+          tie_name)
+  } 
+  paste(nt, tie_name)
+}