v1.6.1

.github/pull_request_template.md

@@ -2,18 +2,12 @@
 
 # Checklist:
 
-- PR form
-  - [ ] Description above itemizes changes under subtitles, e.g. "## Data""
-  - [ ] Any closed, fixed, or related issues are referenced and explained in the description above, e.g. "Fixed #0 by adding A"
-  - [ ] Package builds on my OS without issues
-- PR checks all pass for latest commit
-  - [ ] CodeFactor check: Package improves or maintains good style
-  - [ ] Package builds on Mac
-  - [ ] Package builds on Windows
-  - [ ] Package builds on Linux
-  - [ ] CodeCov check: Package improves or maintains good test coverage
 - Documentation
-  - [ ] Any new or modified functions or data have roxygen style documentation in their .R scripts
-  - [ ] Longer functions are commented inline or broken down into helper functions so that it is easier to debug in the future
-  - [ ] PR description above and the NEWS.md file are aligned
   - [ ] DESCRIPTION file version is bumped by the appropriate increment (major, minor, patch)
+  - [ ] Date in DESCRIPTION is correct
+  - [ ] Longer functions are commented inline or broken down into helper functions to help debugging
+- PR form
+  - [ ] Title indicates expected version number
+  - [ ] PR description above and the NEWS.md file are aligned
+  - [ ] Description above itemizes changes under subsection titles, e.g. "## Data""
+  - [ ] Closed, fixed, or related issues are referenced and explained in the description above, e.g. "Fixed #0 by adding A"

.github/workflows/prchecks.yml

@@ -60,7 +60,10 @@ jobs:
           path: build/
 
       - name: Calculate code coverage
-        run: Rscript -e "covr::codecov()"
+        if: runner.os == 'macOS'
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        run: Rscript -e 'covr::codecov(token = Sys.getenv("CODECOV_TOKEN"))'
 
       - name: Lint
         run: lintr::lint_package()

.github/workflows/pushrelease.yml

@@ -61,8 +61,10 @@ jobs:
           path: build/
 
       - name: Calculate code coverage
-        if: runner.os == 'macOS-latest'
-        run: Rscript -e "covr::codecov()"
+        if: runner.os == 'macOS'
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        run: Rscript -e 'covr::codecov(token = Sys.getenv("CODECOV_TOKEN"))'
 
   release:
     name: Bump version and release

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: manynet
 Title: Many Ways to Make, Modify, Mark, and Measure Myriad Networks
-Version: 1.6.0
-Date: 2025-08-22
+Version: 1.6.1
+Date: 2025-09-12
 Description: Many tools for making, modifying, 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,
@@ -36,7 +36,6 @@ Suggests:
     sna,
     testthat (>= 3.0.0),
     tibble,
-    tidyr,
     xml2
 Authors@R: 
     c(person(given = "James",

NAMESPACE

@@ -337,6 +337,7 @@ export(cluster_hierarchical)
 export(collect_changes)
 export(create_components)
 export(create_core)
+export(create_cycle)
 export(create_degree)
 export(create_ego)
 export(create_empty)
@@ -347,6 +348,8 @@ export(create_motifs)
 export(create_ring)
 export(create_star)
 export(create_tree)
+export(create_wheel)
+export(create_windmill)
 export(delete_nodes)
 export(delete_ties)
 export(extract_tute)

NEWS.md

@@ -1,3 +1,35 @@
+# manynet 1.6.1
+
+## Package
+
+- Dropped mapping from function overview on website
+- Dropped viz tutorial, moved to `{autograph}`
+- Added CITATION
+- Improved `run_tute()` and `extract_tute()` to search for `{autograph}`
+
+## Printing
+
+- Improved `describe_changes()` to work with time as well as begin/end tie attributes
+
+## Making
+
+- Added `create_windmill()`
+- Added `create_wheel()`
+- Added `create_cycle()`
+
+## Modifying
+
+- Fixed `to_uniplex()` test so that it doesn't rely on random sampling
+
+## Marking
+
+- Improved `is_multiplex()` to recognise more tie attributes
+
+## Data
+
+- Added `irps_nuclear_discourse` for goldfish and various testing of dynamic networks
+- Added `ison_judo_moves` for judo move sequences
+
 # manynet 1.6.0
 
 ## Package

R/class_networks.R

@@ -165,6 +165,14 @@ describe_changes <- function(x){
   if(is_longitudinal(x)){
     paste(" over", max(tie_attribute(x, "wave")), "waves")
   } else if (is_dynamic(x)){
-    paste(" from", min(tie_attribute(x, "begin")), "to", max(tie_attribute(x, "end")))
+
+    if("time" %in% net_tie_attributes(x)){
+      paste(" from", min(tie_attribute(x, "time"), na.rm = TRUE), 
+            "to", max(tie_attribute(x, "time"), na.rm = TRUE))
+    } else if("begin" %in% net_tie_attributes(x)){
+      paste(" from", min(tie_attribute(x, "begin"), na.rm = TRUE), 
+            "to", max(tie_attribute(x, "end"), na.rm = TRUE))
+    }
+
   }
 }

R/data_ison.R

@@ -84,6 +84,50 @@
 #'   ```
 "ison_karateka"
 
+## Judo moves ####
+
+#' One-mode judo moves network (Bastazini 2025)
+#'
+#' @description
+#'   Judo is a martial art with a long history and many different techniques.
+#'   It involves a dynamic 'chess match' of throws, holds, locks, 
+#'   submission techniques, and other maneuvers.
+#'   The techniques are often combined in sequences to create fluid and 
+#'   effective combinations to score points or achieve victory.
+#'   As the author of this network describes,
+#'   "While individual techniques (called waza) are foundational,
+#'   the real artistry lies in how they are chained together --
+#'   through renraku-waza (combination techniques) and 
+#'   renzoku-waza (continuous combination techniques)"
+#'   This network describes the relationships between 33 individual judo moves,
+#'   as recognised by the Kodokan (the official international governing body of judo),
+#'   where an arc indicates that one move can be followed by another.
+#' @docType data
+#' @keywords datasets
+#' @name ison_judo_moves
+#' @usage data(ison_judo_moves)
+#' @references
+#'   Bastazini, Vinicius. 2025. 
+#'   "The Dynamics of the “Gentle Way”: Exploring Judo Attack Combinations as Networks in R",
+#'   https://geekcologist.wordpress.com/2025/05/27/the-dynamics-of-the-gentle-way-exploring-judo-attack-combinations-as-networks-in-r/
+#'   
+#'   Kashiwazaki, Katsuhiko, and Hidetoshi Nakanishi. 1995. 
+#'   _Attacking Judo: A Guide to Combinations and Counters_. 
+#'   Ippon Books.
+#'   
+#'   Kawaishi, Mikinosuke. 1963. 
+#'   _Standing judo: The combinations and counter-attacks_. 
+#'   Budoworks.
+#'   
+#'   van Haesendonck, F.M. 1968. 
+#'   _Judo: Ecyclopédie par l’Image_. 
+#'   Éditions Erasme: Anvers-Bruxelles.
+#' @format
+#'   ```{r, echo = FALSE}
+#'   ison_judo_moves
+#'   ```
+"ison_judo_moves"
+
 ## Koenigsberg ####
 
 #' One-mode Seven Bridges of Koenigsberg network (Euler 1741)
@@ -837,5 +881,31 @@
 #'   ```
 "irps_revere"
 
+## Nuclear Discourse ####
+
+#' Two-mode dynamic discourse network of Germany's nuclear energy phase-out (Haunss and Hollway 2023)
+#'
+#' @description
+#'   Following the 11 March 2011 Fukushima nuclear disaster in Japan,
+#'   there was a vigorous public debate in Germany about the future of nuclear energy.
+#'   This network captures the discourse established by 337 actors,
+#'   including individual politicians, experts, parties, and the media,
+#'   and their claims about nuclear energy and German nuclear energy policy.
+#'   These claims were with respect to 54 concepts coded,
+#'   and could be supportive or critical, and could also be repeated.
+#' @docType data
+#' @keywords datasets
+#' @name irps_nuclear_discourse
+#' @usage data(irps_nuclear_discourse)
+#' @references
+#'   Haunss Sebastian, James Hollway. 2023.
+#'   "Multimodal mechanisms of political discourse dynamics and the case of Germany’s nuclear energy phase-out". 
+#'   _Network Science_, 11(2):205-223. 
+#'   \doi{10.1017/nws.2022.31}
+#' @format
+#'   ```{r, echo = FALSE}
+#'   irps_nuclear_discourse
+#'   ```
+"irps_nuclear_discourse"
 
 

R/make_create.R

@@ -736,6 +736,161 @@ create_core <- function(n, directed = FALSE, mark = NULL) {
   }
 }
 
+#' @rdname make_create
+#' @examples
+#'   create_windmill(6)
+#' @export
+create_windmill <- function(n) {
+  total_nodes <- n
+
+  if (length(total_nodes) == 1) {
+
+    if (total_nodes < 3) {
+      snet_abort("At least 3 nodes required to form a windmill graph.")
+    }
+
+    # Find all valid (k, n) pairs
+    valid_pairs <- list()
+    for (k in 1:(total_nodes - 2)) {
+      n_candidate <- (total_nodes - 1) / k + 1
+      if (n_candidate == floor(n_candidate) && n_candidate >= 2) {
+        valid_pairs[[length(valid_pairs) + 1]] <- list(k = k, n = as.integer(n_candidate))
+      }
+    }
+
+    if (length(valid_pairs) == 0) {
+      snet_abort("No valid (k, n) pair found for a windmill graph with given number of nodes.")
+    }
+
+    # Choose the pair with minimal |k - n|
+    best_pair <- valid_pairs[[which.min(sapply(valid_pairs, function(p) abs(p$k - p$n)))]]
+    k <- best_pair$k
+    n <- best_pair$n
+    snet_info("Using k = {k} groups of n = {n} nodes (including universal node)")
+
+    total_nodes <- 1 + k * (n - 1)
+    g <- igraph::make_empty_graph(n = total_nodes, directed = FALSE)
+
+    universal_node <- 1
+    current_node <- 2
+
+    for (i in 1:k) {
+      group_nodes <- current_node:(current_node + n - 2)
+
+      group_edges <- utils::combn(group_nodes, 2, simplify = FALSE)
+      universal_edges <- lapply(group_nodes, function(x) c(universal_node, x))
+
+      g <- igraph::add_edges(g, unlist(c(group_edges, universal_edges), recursive = FALSE))
+      current_node <- current_node + n - 1
+    }
+
+    return(g)
+
+  } else if (length(total_nodes) == 2) {
+
+    a <- total_nodes[1]  # Mode A
+    b <- total_nodes[2]  # Mode B
+
+    if (a < 2 || b < 1) {
+      snet_abort("Need at least 2 Mode A nodes and 1 Mode B node.")
+    }
+
+    k <- a - 1  # Number of blades/groups
+    if (b %% k != 0) {
+      snet_abort("Mode B nodes must divide evenly across Mode A groups (excluding universal node).")
+    }
+
+    group_size <- b / k
+    mode_A_nodes <- 1:a
+    mode_B_nodes <- (a + 1):(a + b)
+
+    edges <- list()
+    current_B <- a + 1
+
+    for (i in 1:k) {
+      group_B_nodes <- current_B:(current_B + group_size - 1)
+
+      for (b_node in group_B_nodes) {
+        # Connect to universal node (Mode A node 1)
+        edges[[length(edges) + 1]] <- c(1, b_node)
+        # Connect to group-specific Mode A node
+        edges[[length(edges) + 1]] <- c(i + 1, b_node)
+      }
+
+      current_B <- current_B + group_size
+    }
+
+    g <- igraph::make_empty_graph(n = a + b, directed = FALSE)
+    g <- igraph::add_edges(g, unlist(edges))
+    g <- igraph::set_vertex_attr(g, "type", value = c(rep(TRUE, a), rep(FALSE, b)))  # Bipartite flag
+
+    return(g)
+
+  } else snet_abort("Sorry, that's not possible.")
+
+}
+
+#' @rdname make_create
+#' @examples
+#'   create_cycle(6)
+#' @export
+create_cycle <- function(n){
+  # Helper: Create edge list for unimodal cycle
+  unimodal_cycle <- function(n_nodes) {
+    edges <- data.frame(
+      from = 1:n_nodes,
+      to = c(2:n_nodes, 1)
+    )
+    as_tidygraph(edges)
+  }
+
+  # Helper: Create edge list for bimodal cycle
+  bimodal_cycle <- function(n_modes) {
+    if(n_modes[1] != n_modes[2]){
+      snet_abort("Two-mode cycles require equal number of nodes in each mode.")
+    }
+    unimodal_cycle(sum(n_modes)) %>% 
+      mutate_nodes(type = rep_len(c(F,T), sum(n_modes)))
+  }
+
+  # Main logic
+  if (length(n) == 1) {
+    # Unimodal cycle
+    net <- unimodal_cycle(n)
+  } else if (length(n) == 2) {
+    # Bimodal cycle
+    net <- bimodal_cycle(n)
+  } else {
+    snet_abort("Argument 'n' must be a scalar or a vector of length 2.")
+  }
+  return(net)
+}
+
+#' @rdname make_create
+#' @examples
+#'   create_wheel(6)
+#' @export
+create_wheel <- function(n) {
+  if (length(n) == 1) {
+    if (n < 4) {
+      stop("At least 4 nodes required to form a wheel graph.")
+    }
+    center_node <- 1
+    rim_nodes <- 2:n
+    # Create the cycle (rim)
+    rim_cycle <- cbind(rim_nodes, c(rim_nodes[-1], rim_nodes[1]))
+    # Connect center to each rim node
+    center_edges <- cbind(center_node, rim_nodes)
+    edges <- rbind(rim_cycle, center_edges)
+    g <- igraph::graph_from_edgelist(edges, directed = FALSE)
+    return(g)
+  } else if (length(n) == 2) {
+    snet_abort("Wheel graphs are undefined for two-mode networks",
+               "because the rim nodes cannot be adjacent to both neighbouring",
+               "rim nodes and the dominant node in the centre.")
+  } else stop("Argument 'n' must be a scalar or vector of length 2.")
+}
+
 # #' @rdname create
 # #' @details Creates a nested two-mode network.
 # #' Will construct an affiliation matrix,