v1.3.1

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: manynet
 Title: Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks
-Version: 1.3.0
-Date: 2024-10-16
+Version: 1.3.1
+Date: 2024-10-29
 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,

NAMESPACE

@@ -252,8 +252,10 @@ S3method(to_signed,igraph)
 S3method(to_signed,matrix)
 S3method(to_signed,network)
 S3method(to_signed,tbl_graph)
+S3method(to_simplex,data.frame)
 S3method(to_simplex,igraph)
 S3method(to_simplex,matrix)
+S3method(to_simplex,network)
 S3method(to_simplex,tbl_graph)
 S3method(to_slices,igraph)
 S3method(to_slices,tbl_graph)
@@ -651,6 +653,7 @@ export(node_triad_census)
 export(node_vitality)
 export(node_walktrap)
 export(node_weak_components)
+export(over_membership)
 export(over_time)
 export(over_waves)
 export(pkg_data)
@@ -854,6 +857,7 @@ importFrom(igraph,as.undirected)
 importFrom(igraph,as_adjacency_matrix)
 importFrom(igraph,as_biadjacency_matrix)
 importFrom(igraph,as_data_frame)
+importFrom(igraph,as_directed)
 importFrom(igraph,assortativity_degree)
 importFrom(igraph,bipartite_projection)
 importFrom(igraph,cohesion)

NEWS.md

@@ -1,3 +1,27 @@
+# manynet 1.3.1
+
+## Package
+
+- Fixed miscellaneous documentation issues, re roxygen
+- Separated out the data sections in pkgdown
+
+## Modifying
+
+- Added `to_simplex.data.frame()` and `to_simplex.network()`
+
+## Marking
+
+- Fixed bug in `is_aperiodic()` where it would not work in tutorial chunks
+
+## Measuring
+
+- Added `over_membership()` for obtaining summary statistics by a membership vector
+
+## Practicing
+
+- Fixed data pointers in several tutorials
+- Added glossary items to diffusion tutorial
+
 # manynet 1.3.0
 
 ## Package

R/make_generate.R

@@ -331,7 +331,8 @@ generate_fire <- function(n, contacts = 1, their_out = 0, their_in = 1, directed
 #' @examples
 #' generate_islands(10)
 #' @export
-generate_islands <- function(n, islands = 2, p = 0.5, bridges = 1, directed = FALSE){
+generate_islands <- function(n, islands = 2, p = 0.5, bridges = 1, 
+                             directed = FALSE){
   directed <- infer_directed(n, directed)
   if(is_manynet(n)){
     m <- net_nodes(n)

R/manip_as.R

@@ -55,10 +55,17 @@
 #' @return
 #' The currently implemented coercions or translations are:
 #'
-#' ```{r, echo = FALSE, cache = TRUE} 
-#'  knitr::kable(available_methods(c("as_edgelist","as_matrix", "as_igraph", "as_tidygraph", 
-#'  "as_network", "as_siena", "as_graphAM", "as_diffusion", "as_diffnet")))
-#'  ```
+#' |             | data.frame| diff_model| diffnet| igraph| list| matrix| network| network.goldfish| siena| tbl_graph|
+#' |:------------|----------:|----------:|-------:|------:|----:|------:|-------:|----------------:|-----:|---------:|
+#' |as_diffnet   |          0|          1|       0|      0|    0|      0|       0|                0|     0|         0|
+#' |as_diffusion |          0|          1|       1|      1|    0|      0|       0|                0|     0|         0|
+#' |as_edgelist  |          1|          0|       0|      1|    0|      1|       1|                1|     1|         1|
+#' |as_graphAM   |          1|          0|       0|      1|    0|      1|       1|                1|     1|         1|
+#' |as_igraph    |          1|          1|       1|      1|    0|      1|       1|                1|     1|         1|
+#' |as_matrix    |          1|          1|       0|      1|    0|      1|       1|                1|     1|         1|
+#' |as_network   |          1|          0|       1|      1|    0|      1|       1|                1|     1|         1|
+#' |as_siena     |          0|          0|       0|      1|    0|      0|       0|                0|     0|         1|
+#' |as_tidygraph |          1|          1|       1|      1|    1|      1|       1|                1|     1|         1|
 NULL
 
 # Nodelists ####

R/manip_format.R

@@ -29,10 +29,14 @@
 #'   Not all functions have methods available for all object classes.
 #'   Below are the currently implemented S3 methods:
 #'  
-#'   ```{r, echo = FALSE, cache = TRUE} 
-#'   knitr::kable(available_methods(c("to_undirected", "to_unweighted", 
-#'   "to_unsigned", "to_unnamed", "to_simplex", "to_uniplex")))
-#'   ```
+#'   |              | data.frame| igraph| matrix| network| tbl_graph|
+#'   |:-------------|----------:|------:|------:|-------:|---------:|
+#'   |to_simplex    |          1|      1|      1|       1|         1|
+#'   |to_undirected |          1|      1|      1|       1|         1|
+#'   |to_uniplex    |          1|      1|      1|       1|         1|
+#'   |to_unnamed    |          1|      1|      1|       1|         1|
+#'   |to_unsigned   |          1|      1|      1|       1|         1|
+#'   |to_unweighted |          1|      1|      1|       1|         1|
 #' @inheritParams mark_is
 #' @param threshold For a matrix, the threshold to binarise/dichotomise at.
 #' @returns
@@ -96,12 +100,12 @@ to_undirected <- function(.data) UseMethod("to_undirected")
 #' @importFrom igraph as.undirected
 #' @export
 to_undirected.igraph <- function(.data) {
-  igraph::as.undirected(.data)
+  igraph::as_undirected(.data)
 }
 
 #' @export
 to_undirected.tbl_graph <- function(.data) {
-  as_tidygraph(igraph::as.undirected(.data))
+  as_tidygraph(igraph::as_undirected(.data))
 }
 
 #' @export
@@ -249,6 +253,17 @@ to_simplex.matrix <- function(.data) {
   out
 }
 
+#' @export
+to_simplex.data.frame <- function(.data) {
+  out <- .data[.data$from != .data$to,]
+  out
+}
+
+#' @export
+to_simplex.network <- function(.data) {
+  as_network(to_simplex(as_igraph(.data)))
+}
+
 #' @rdname manip_deformat
 #' @param tie Character string naming a tie attribute to retain from a graph.
 #' @importFrom igraph delete_edges edge_attr_names delete_edge_attr
@@ -311,9 +326,12 @@ to_uniplex.matrix <- function(.data, tie){
 #'   Not all functions have methods available for all object classes.
 #'   Below are the currently implemented S3 methods:
 #'  
-#'   ```{r, echo = FALSE, cache = TRUE} 
-#'   knitr::kable(available_methods(c("to_acyclic", "to_anti", "to_redirected", "to_reciprocated")))
-#'   ```
+#'   |                | data.frame| igraph| matrix| network| tbl_graph|
+#'   |:---------------|----------:|------:|------:|-------:|---------:|
+#'   |to_acyclic      |          1|      1|      1|       1|         1|
+#'   |to_anti         |          1|      1|      1|       1|         1|
+#'   |to_reciprocated |          1|      1|      1|       1|         1|
+#'   |to_redirected   |          1|      1|      1|       1|         1|
 #' @name manip_reformat
 #' @family modifications
 #' @inheritParams mark_is
@@ -325,15 +343,15 @@ to_uniplex.matrix <- function(.data, tie){
 NULL
 
 #' @rdname manip_reformat
-#' @importFrom igraph as.directed feedback_arc_set
+#' @importFrom igraph as_directed feedback_arc_set
 #' @export
 to_acyclic <- function(.data) UseMethod("to_acyclic")
 
 #' @export
 to_acyclic.igraph <- function(.data) {
   if(is_directed(.data)){
     delete_ties(.data, igraph::feedback_arc_set(.data))
-  } else igraph::as.directed(.data, mode = "acyclic")
+  } else igraph::as_directed(.data, mode = "acyclic")
 }
 
 #' @export
@@ -436,13 +454,13 @@ to_redirected.network <- function(.data) {
 }
 
 #' @describeIn manip_reformat Returns an object where all ties are reciprocated.
-#' @importFrom igraph as.directed
+#' @importFrom igraph as_directed
 #' @export
 to_reciprocated <- function(.data) UseMethod("to_reciprocated")
 
 #' @export
 to_reciprocated.igraph <- function(.data) {
-  igraph::as.directed(.data, mode = "mutual")
+  igraph::as_directed(.data, mode = "mutual")
 }
 
 #' @export
@@ -493,10 +511,14 @@ to_reciprocated.data.frame <- function(.data) {
 #'   Not all functions have methods available for all object classes.
 #'   Below are the currently implemented S3 methods:
 #'  
-#'   ```{r, echo = FALSE, cache = TRUE} 
-#'   knitr::kable(available_methods(c("to_directed", "to_redirected", 
-#'   "to_reciprocated", "to_acyclic", "to_named", "to_simplex")))
-#'   ```
+#'   |                | data.frame| igraph| matrix| network| tbl_graph|
+#'   |:---------------|----------:|------:|------:|-------:|---------:|
+#'   |to_acyclic      |          1|      1|      1|       1|         1|
+#'   |to_directed     |          1|      1|      1|       1|         1|
+#'   |to_named        |          1|      1|      1|       1|         1|
+#'   |to_reciprocated |          1|      1|      1|       1|         1|
+#'   |to_redirected   |          1|      1|      1|       1|         1|
+#'   |to_simplex      |          0|      1|      1|       0|         1|
 #' @name manip_preformat
 #' @family modifications
 #' @inheritParams mark_is
@@ -588,7 +610,7 @@ to_directed <- function(.data) UseMethod("to_directed")
 to_directed.igraph <- function(.data) {
   if(!is_directed.igraph(.data)){
     mnet_info("Directions are assigned to existing ties at random.")
-    igraph::as.directed(.data, mode = "random")
+    igraph::as_directed(.data, mode = "random")
   } else .data
 }
 
@@ -710,9 +732,11 @@ to_weighted.network <- function(.data, measure = NULL){
 #'   Not all functions have methods available for all object classes.
 #'   Below are the currently implemented S3 methods:
 #'  
-#'   ```{r, echo = FALSE, cache = TRUE} 
-#'   knitr::kable(available_methods(c("to_onemode", "to_twomode", "to_multilevel")))
-#'   ```
+#'   |              | igraph| matrix| network| tbl_graph|
+#'   |:-------------|------:|------:|-------:|---------:|
+#'   |to_multilevel |      1|      1|       0|         1|
+#'   |to_onemode    |      1|      1|       0|         1|
+#'   |to_twomode    |      1|      0|       1|         1|
 #' @name manip_levels
 #' @family modifications
 #' @inheritParams mark_is

R/manip_nodes.R

@@ -18,9 +18,10 @@
 #'   Not all functions have methods available for all object classes.
 #'   Below are the currently implemented S3 methods:
 #'  
-#'   ```{r, echo = FALSE, cache = TRUE} 
-#'   knitr::kable(available_methods(c("add_nodes", "delete_nodes", "add_node_attribute")))
-#'   ```
+#'   |             | igraph| network| tbl_graph|
+#'   |:------------|------:|-------:|---------:|
+#'   |add_nodes    |      1|       1|         1|
+#'   |delete_nodes |      1|       1|         1|
 #' @family modifications
 #' @inheritParams mark_is
 #' @param attribute A named list to be added as tie or node attributes.

R/manip_reformed.R

@@ -15,9 +15,11 @@
 #'   Not all functions have methods available for all object classes.
 #'   Below are the currently implemented S3 methods:
 #'  
-#'    ```{r, echo = FALSE, cache = TRUE} 
-#'  knitr::kable(available_methods(c("to_mode1", "to_mode2", "to_ties")))
-#'  ```
+#'  |         | data.frame| igraph| matrix| network| tbl_graph|
+#'  |:--------|----------:|------:|------:|-------:|---------:|
+#'  |to_mode1 |          1|      1|      1|       1|         1|
+#'  |to_mode2 |          1|      1|      1|       1|         1|
+#'  |to_ties  |          1|      1|      1|       1|         1|
 #' @name manip_project
 #' @family modifications
 #' @inheritParams manip_reformat
@@ -222,9 +224,13 @@ to_ties.matrix <- function(.data){
 #'   Not all functions have methods available for all object classes.
 #'   Below are the currently implemented S3 methods:
 #'  
-#'    ```{r, echo = FALSE, cache = TRUE} 
-#'  knitr::kable(available_methods(c("to_ego", "to_giant", "to_no_isolates", "to_subgraph", "to_blocks")))
-#'  ```
+#'  |               | data.frame| igraph| list| matrix| network| tbl_graph|
+#'  |:--------------|----------:|------:|----:|------:|-------:|---------:|
+#'  |to_blocks      |          1|      1|    0|      1|       1|         1|
+#'  |to_ego         |          0|      1|    0|      0|       0|         1|
+#'  |to_giant       |          1|      1|    0|      1|       1|         1|
+#'  |to_no_isolates |          1|      1|    1|      1|       1|         1|
+#'  |to_subgraph    |          1|      1|    0|      1|       1|         1|
 #' @name manip_scope
 #' @family modifications
 #' @inheritParams manip_reformat
@@ -460,9 +466,11 @@ to_blocks.tbl_graph <- function(.data, membership, FUN = mean){
 #'   Not all functions have methods available for all object classes.
 #'   Below are the currently implemented S3 methods:
 #'  
-#'   ```{r, echo = FALSE, cache = TRUE} 
-#'   knitr::kable(available_methods(c("to_matching", "to_mentoring", "to_eulerian", "to_tree")))
-#'   ```
+#'  |             | data.frame| igraph| matrix| network| tbl_graph|
+#'  |:------------|----------:|------:|------:|-------:|---------:|
+#'  |to_eulerian  |          0|      1|      0|       0|         1|
+#'  |to_matching  |          1|      1|      1|       1|         1|
+#'  |to_mentoring |          0|      1|      0|       0|         1|
 #' @name manip_paths
 #' @family modifications
 #' @inheritParams manip_scope

R/manip_split.R

@@ -7,9 +7,13 @@
 #'   Not all functions have methods available for all object classes.
 #'   Below are the currently implemented S3 methods:
 #'  
-#'    ```{r, echo = FALSE, cache = TRUE} 
-#'    knitr::kable(available_methods(c("to_egos", "to_subgraphs", "to_components", "to_waves", "to_slices")))
-#'    ```
+#'   |              | data.frame| diff_model| igraph| matrix| network| tbl_graph|
+#'   |:-------------|----------:|----------:|------:|------:|-------:|---------:|
+#'   |to_components |          1|          0|      1|      1|       1|         1|
+#'   |to_egos       |          1|          0|      1|      1|       1|         1|
+#'   |to_slices     |          0|          0|      1|      0|       0|         1|
+#'   |to_subgraphs  |          0|          0|      1|      0|       1|         1|
+#'   |to_waves      |          1|          1|      1|      0|       0|         1|
 #' @name manip_split
 #' @family modifications
 #' @inheritParams manip_scope
@@ -21,7 +25,7 @@ NULL
 #' @importFrom igraph make_ego_graph
 #' @examples
 #'   to_egos(ison_adolescents)
-#'   #autographs(to_egos(ison_adolescents,2))
+#'   # graphs(to_egos(ison_adolescents,2))
 #' @export
 to_egos <- function(.data, 
                     max_dist = 1, 
@@ -265,7 +269,7 @@ cumulative_ties <- function(x, attribute) {
       }
     }
   } else {
-    message("Cummulative ties were added based on order of appearance for attribute.")
+    mnet_info("Cummulative ties were added based on order of appearance for attribute.")
     a <- list()
     for (k in unique(ties$order)) {
       if (k != 1) {

R/manynet-tutorials.R

@@ -19,8 +19,6 @@
 NULL
 
 #' @rdname tutorials 
-#' @examples
-#' #run_tute("tutorial2")
 #' @export
 run_tute <- function(tute) {
   thisRequires("learnr")
@@ -61,8 +59,6 @@ run_tute <- function(tute) {
 }
 
 #' @rdname tutorials 
-#' @examples
-#' #extract_tute("tutorial2")
 #' @export
 extract_tute <- function(tute) {
   if (missing(tute)) {
@@ -216,17 +212,22 @@ clear_glossary <- function(){
 
 glossies <- list(
   acyclic = "An acyclic network is a network without any cycles.",
+  aperiodic = "An aperiodic network is a network where the greatest common divisor of the lengths of its cycles is one.",
   adhesion = "The minimum number of ties to remove to increase the number of components.",
   blockmodel = "A blockmodel reduces a network to a smaller comprehensible structure of the roles positions take with respect to one another.",
   bridge = "A bridge is a tie whose deletion increases the number of components.",
   cohesion = "The minimum number of nodes to remove to increase the number of components.",
   component = "A component is a connected subgraph not part of a larger connected subgraph.",
+  connected = "A connected network is one with a single (strong) component.",
   cutpoint = "A cutpoint or articulation point is a node whose deletion increases the number of components.",
   degree = "A node's degree is the number of connections it has.",
   giant = "The giant component is the component that includes the most nodes in the network.",
   graphlet = "A graphlet is a small, connected, induced, non-isomorphic subgraphs.",
+  hit = "A herd immunity threshold is the proportion of the population that would need to be immune for a disease to cease being endemic.",
   induced = "An induced subgraph comprises all ties in a subset of the nodes in a network.",
+  intervention = "A network intervention is a process to accelerate behavioural change or improve performance in a network.",
   lattice = "A network that can be drawn as a regular tiling.",
+  LTM = "A linear threshold model is a diffusion model where nodes are resistant to activation up to some threshold.",
   motif = "A subgraph that is exceptional or significant compared to a null model.",
   neighborhood = "A node's neighborhood is the set of other nodes to which that node is connected.",
   network = "A network comprises a set of nodes/vertices and a set of ties/edges among them.",
@@ -235,6 +236,7 @@ glossies <- list(
   reduced = "A reduced graph is a representation of the ties within and between blocks in the network.",
   subgraph = "A subgraph comprises a subset of the nodes and ties in a network.",
   transitivity = "Triadic closure is where if the connections A-B and A-C exist among three nodes, there is a tendency for B-C also to be formed.",
+  threshold = "A threshold is a limit over which behaviour is expected to vary.",
   undirected = "An undirected network is one in which tie direction is undefined."
 )