Merge pull request #246 from snlab-ch/develop

migraph 0.12.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: migraph
 Title: Tools for Multimodal Network Analysis
-Version: 0.11.3
-Date: 2022-09-13
+Version: 0.12.0
+Date: 2022-09-23
 Description: A set of tools for analysing multimodal networks.
    All functions operate with matrices, edge lists, 
    and 'igraph', 'network', and 'tidygraph' objects,

NAMESPACE

@@ -93,12 +93,16 @@ S3method(plot,graph_test)
 S3method(plot,matrix)
 S3method(plot,netlm)
 S3method(plot,netlogit)
+S3method(plot,network_test)
 S3method(plot,node_measure)
 S3method(plot,node_member)
 S3method(plot,tie_measure)
 S3method(print,graph_measure)
 S3method(print,graph_motif)
 S3method(print,graph_test)
+S3method(print,network_measure)
+S3method(print,network_motif)
+S3method(print,network_test)
 S3method(print,node_mark)
 S3method(print,node_measure)
 S3method(print,node_member)
@@ -305,7 +309,37 @@ export(layout_tbl_graph_ladder)
 export(layout_tbl_graph_railway)
 export(layout_tbl_graph_stressgrid)
 export(mutate)
+export(network_adhesion)
+export(network_assortativity)
+export(network_balance)
+export(network_betweenness)
+export(network_closeness)
+export(network_cohesion)
+export(network_components)
+export(network_congruency)
+export(network_core)
+export(network_degree)
+export(network_density)
+export(network_diameter)
+export(network_dims)
+export(network_diversity)
+export(network_dyad_census)
+export(network_eigenvector)
+export(network_equivalency)
+export(network_factions)
+export(network_homophily)
+export(network_length)
+export(network_mixed_census)
+export(network_modularity)
+export(network_node_attributes)
+export(network_nodes)
+export(network_reciprocity)
 export(network_reg)
+export(network_smallworld)
+export(network_tie_attributes)
+export(network_ties)
+export(network_transitivity)
+export(network_triad_census)
 export(node_attribute)
 export(node_automorphic_equivalence)
 export(node_betweenness)

R/class_measures.R

@@ -9,9 +9,9 @@ make_tie_measure <- function(out, object) {
   out
 }
 
-make_graph_measure <- function(out, object) {
-  class(out) <- c("graph_measure", class(out))
-  attr(out, "mode") <- graph_dims(object)
+make_network_measure <- function(out, object) {
+  class(out) <- c("network_measure", class(out))
+  attr(out, "mode") <- network_dims(object)
   out
 }
 
@@ -41,7 +41,7 @@ print.tie_measure <- function(x, ...,
 }
 
 #' @export
-print.graph_measure <- function(x, ...,
+print.network_measure <- function(x, ...,
                                digits = 3) {
     if (length(attr(x, "mode")) == 1) {
       print(as.numeric(x), digits = digits)

R/class_motifs.R

@@ -4,9 +4,9 @@ make_node_motif <- function(out, object) {
   out
 }
 
-make_graph_motif <- function(out, object) {
-  class(out) <- c("graph_motif", class(out))
-  attr(out, "mode") <- graph_dims(object)
+make_network_motif <- function(out, object) {
+  class(out) <- c("network_motif", class(out))
+  attr(out, "mode") <- network_dims(object)
   out
 }
 
@@ -37,7 +37,7 @@ summary.node_motif <- function(object, ...,
 }
 
 #' @export
-print.graph_motif <- function(x, ...) {
+print.network_motif <- function(x, ...) {
   names <- list(names(x))
   x <- as.numeric(x)
   mat <- matrix(x, dimnames = names)

R/data_ison.R

@@ -194,7 +194,6 @@
 #'   ggsave("man/figures/isonnetworkers.png", width = 5, height = 5, dpi = "screen")
 #'   ggsave("man/figures/isonnetworkers.pdf", width = 5, height = 5)
 #'   ```
-#' \if{latex}{\figure{isonnetworkers.pdf}{options: width=7cm}}
 #' @docType data
 #' @keywords datasets
 #' @name ison_networkers

R/make_create.R

@@ -208,7 +208,7 @@ create_tree <- function(n,
 #' @export
 create_lattice <- function(n,
                            directed = FALSE) {
-  if (is_migraph(n)) n <- graph_dims(n)
+  if (is_migraph(n)) n <- network_dims(n)
   igraph::make_lattice(n, directed = directed)
 }
 
@@ -296,7 +296,7 @@ create_core <- function(n, membership = NULL) {
 # Helper functions ------------------
 
 infer_n <- function(n) {
-  if (is_migraph(n)) n <- graph_dims(n)
+  if (is_migraph(n)) n <- network_dims(n)
   if (length(n) > 2) stop(paste("`n` should be a single integer for a one-mode network or",
                              "a vector of two integers for a two-mode network."))
   n

R/make_generate.R

@@ -29,16 +29,16 @@ NULL
 #' @export
 generate_random <- function(n, p = 0.5, directed = FALSE, with_attr = TRUE) {
   if(is_migraph(n)){
-    m <- graph_ties(n)
+    m <- network_ties(n)
     directed <- is_directed(n)
     if(is_twomode(n)){
-      g <- igraph::sample_bipartite(graph_dims(n)[1], 
-                                    graph_dims(n)[2],
+      g <- igraph::sample_bipartite(network_dims(n)[1], 
+                                    network_dims(n)[2],
                                     m = m, type = "gnm",
                                     directed = directed,
                                     mode = "out")
     } else {
-      g <- igraph::sample_gnm(graph_nodes(n), 
+      g <- igraph::sample_gnm(network_nodes(n), 
                                     m = m,
                                     directed = directed)
     }
@@ -152,7 +152,7 @@ generate_permutation <- function(object, with_attr = TRUE) {
 # Helper functions ------------------
 
 r1perm <- function(m) {
-  n <- sample(1:dim(m)[1])
+  n <- sample(seq_len(dim(m)[1]))
   if(is_labelled(m)){
     p <- matrix(data = m[n, n], nrow = dim(m)[1], ncol = dim(m)[2],
                 dimnames = dimnames(m))
@@ -163,8 +163,8 @@ r1perm <- function(m) {
 }
 
 r2perm <- function(m) {
-  n <- sample(1:dim(m)[1])
-  o <- sample(1:dim(m)[2])
+  n <- sample(seq_len(dim(m)[1]))
+  o <- sample(seq_len(dim(m)[2]))
   if(is_labelled(m)){
     p <- matrix(data = m[n, o], nrow = dim(m)[1], ncol = dim(m)[2],
                 dimnames = dimnames(m))

R/manip_add.R

@@ -19,12 +19,12 @@ NULL
 #' add_node_attribute(mpn_elite_usa_advice, "wealth", 1:14)
 #' @export
 add_node_attribute <- function(object, attr_name, vector){
-  if(length(vector)!=graph_nodes(object)){
-    if(is_twomode(object) && any(length(vector) == graph_dims(object))){
-      if(length(vector) == graph_dims(object)[1]){
-        vector <- c(vector, rep(NA, graph_dims(object)[2]))
-      } else if (length(vector) == graph_dims(object)[2]){
-        vector <- c(rep(NA, graph_dims(object)[1]), vector)
+  if(length(vector)!=network_nodes(object)){
+    if(is_twomode(object) && any(length(vector) == network_dims(object))){
+      if(length(vector) == network_dims(object)[1]){
+        vector <- c(vector, rep(NA, network_dims(object)[2]))
+      } else if (length(vector) == network_dims(object)[2]){
+        vector <- c(rep(NA, network_dims(object)[1]), vector)
       }
     } else 
       stop("Attribute vector must be same length as nodes in object.")
@@ -49,7 +49,7 @@ add_tie_attribute <- function(object, attr_name, vector){
 #' @describeIn add Copies node attributes from a given graph into specified graph
 #' @export
 copy_node_attributes <- function(object, object2){
-  if(graph_nodes(object) != graph_nodes(object2)) 
+  if(network_nodes(object) != network_nodes(object2)) 
     stop("Objects need to be of compatible dimensions.")
   object <- as_igraph(object)
   object2 <- as_igraph(object2)

R/manip_as.R

@@ -474,7 +474,7 @@ as_igraph.siena <- function(object, twomode = NULL) {
         }
       } else {
         # add names for one-mode y
-        y <- add_node_attribute(y, "name", as.character(seq_len(graph_nodes(y))))
+        y <- add_node_attribute(y, "name", as.character(seq_len(network_nodes(y))))
         # join ties
         if (isTRUE(is_twomode(x))) { # x is twomode but y is onemode
           y <- as_edgelist(y)
@@ -510,7 +510,7 @@ as_igraph.siena <- function(object, twomode = NULL) {
   # Add in first network as base and add names
   out <- object$depvars[[ddvs[1]]][,,1] # first wave
   if (is_twomode(out) == FALSE) {
-    out <- add_node_attribute(out, "name", as.character(seq_len(graph_nodes(out))))
+    out <- add_node_attribute(out, "name", as.character(seq_len(network_nodes(out))))
   } else {
     rownames(out) <- as.character(seq_len(nrow(out)))
     colnames(out) <- as.character(paste0("N", seq_len(ncol(out))))

R/manip_grab.R

@@ -4,7 +4,7 @@
 #'   from given network data.
 #'   They are also useful as helpers within other functions.
 #'   
-#'   `graph_*()` functions always relate to the overall graph or network,
+#'   `network_*()` functions always relate to the overall graph or network,
 #'   usually returning a scalar.
 #'   `node_*()` and `tie_*()` always return vectors the same length
 #'   as the number of nodes or edges in the network, respectively.
@@ -30,7 +30,7 @@ node_mode <- function(object){
   if(is_twomode(object)){
     out <- igraph::get.vertex.attribute(as_igraph(object), "type")
   } else{
-    out <- rep(FALSE, graph_nodes(object))
+    out <- rep(FALSE, network_nodes(object))
   }
   # cannot use make_node_mark here because then eternal loop
   class(out) <- c("node_mark", class(out))
@@ -63,7 +63,7 @@ tie_attribute <- function(object, attribute){
 tie_weights <- function(object){
   object <- as_igraph(object)
   out <- igraph::get.edge.attribute(object, "weight")
-  if(is.null(out)) out <- rep(1, graph_ties(object))
+  if(is.null(out)) out <- rep(1, network_ties(object))
   out
 }
 
@@ -74,33 +74,33 @@ tie_weights <- function(object){
 tie_signs <- function(object){
   object <- as_igraph(object)
   out <- igraph::get.edge.attribute(object, "sign")
-  if(is.null(out)) out <- rep(1, graph_ties(object))
+  if(is.null(out)) out <- rep(1, network_ties(object))
   out
 }
 
 #' @describeIn grab Returns the total number of nodes (of any mode) in a network.
 #' @examples
-#' graph_nodes(ison_southern_women)
+#' network_nodes(ison_southern_women)
 #' @export
-graph_nodes <- function(object){
+network_nodes <- function(object){
   igraph::vcount(as_igraph(object))
 }
 
 #' @describeIn grab Returns the number of edges in a network.
 #' @examples
-#' graph_ties(ison_southern_women)
+#' network_ties(ison_southern_women)
 #' @export
-graph_ties <- function(object){
+network_ties <- function(object){
   igraph::ecount(as_igraph(object))
 }
 
 #' @describeIn grab Returns the dimensions of a network in a vector
 #'   as long as the number of modes in the network.
 #' @examples
-#' graph_dims(ison_southern_women)
-#' graph_dims(to_mode1(ison_southern_women))
+#' network_dims(ison_southern_women)
+#' network_dims(to_mode1(ison_southern_women))
 #' @export
-graph_dims <- function(object){
+network_dims <- function(object){
   if(is_twomode(object)){
     c(sum(!igraph::V(as_igraph(object))$type),
       sum(igraph::V(as_igraph(object))$type))
@@ -112,17 +112,17 @@ graph_dims <- function(object){
 #' @describeIn grab Returns a vector of nodal attributes in a network
 #' @importFrom igraph list.vertex.attributes
 #' @examples
-#' graph_node_attributes(mpn_elite_mex)
+#' network_node_attributes(mpn_elite_mex)
 #' @export
-graph_node_attributes <- function(object){
+network_node_attributes <- function(object){
   igraph::list.vertex.attributes(as_igraph(object))
 }
 
 #' @describeIn grab Returns a vector of edge attributes in a network
 #' @importFrom igraph list.edge.attributes
 #' @examples
-#' graph_tie_attributes(mpn_elite_mex)
+#' network_tie_attributes(mpn_elite_mex)
 #' @export
-graph_tie_attributes <- function(object){
+network_tie_attributes <- function(object){
   igraph::list.edge.attributes(as_igraph(object))
 }

R/manip_to.R

@@ -318,7 +318,7 @@ to_named.tbl_graph <- function(object, names = NULL) {
     object <- object %>% mutate(name = names)
   } else {
     object <- object %>% mutate(name = sample(baby_names,
-                                              graph_nodes(object)))
+                                              network_nodes(object)))
   }
   object
 }
@@ -329,7 +329,7 @@ to_named.igraph <- function(object, names = NULL) {
     igraph::V(object)$name  <- names
   } else {
     igraph::V(object)$name  <- sample(baby_names,
-                                      graph_nodes(object))
+                                      network_nodes(object))
   }
   object
 }
@@ -341,17 +341,17 @@ to_named.data.frame <- function(object, names = NULL) {
     object[,2]  <- names[as.numeric(object[,2])]
   } else {
     object[,1]  <- sample(baby_names, 
-                          graph_nodes(object))[as.numeric(object[,1])]
+                          network_nodes(object))[as.numeric(object[,1])]
     object[,2]  <- sample(baby_names, 
-                          graph_nodes(object))[as.numeric(object[,2])]
+                          network_nodes(object))[as.numeric(object[,2])]
   }
   object
 }
 
 #' @export
 to_named.matrix <- function(object, names = NULL) {
   if(is.null(names)) names <- sample(baby_names, 
-                                     graph_nodes(object))
+                                     network_nodes(object))
   if(is_twomode(object)){
     rownames(object)  <- names[seq_len(nrow(object))]
     colnames(object)  <- names[(nrow(object)+1):length(names)]

R/mark_is.R

@@ -169,8 +169,8 @@ is_directed <- function(object) UseMethod("is_directed")
 
 #' @export
 is_directed.data.frame <- function(object) {
-  !(graph_reciprocity(object) == 0 |
-    graph_reciprocity(object) == 1)
+  !(network_reciprocity(object) == 0 |
+    network_reciprocity(object) == 1)
 }
 
 #' @export
@@ -322,13 +322,13 @@ is_multiplex.matrix <- function(object){
 #' @export
 is_multiplex.tbl_graph <- function(object){
   igraph::any_multiple(object) |
-    length(graph_tie_attributes(object)) > 1
+    length(network_tie_attributes(object)) > 1
 }
 
 #' @export
 is_multiplex.igraph <- function(object){
   igraph::any_multiple(object) |
-    length(graph_tie_attributes(object)) > 1
+    length(network_tie_attributes(object)) > 1
 }
 
 #' @export

R/mark_nodes.R

@@ -31,7 +31,7 @@ node_is_cutpoint <- function(object){
            "names")
     names(out) <- node_names(object)
   } else {
-    out <- 1:graph_nodes(object) %in% 
+    out <- 1:network_nodes(object) %in% 
       igraph::articulation_points(as_igraph(object))
   }
   make_node_mark(out, object)

R/mark_ties.R

@@ -49,7 +49,7 @@ tie_is_reciprocated <- function(object){
 #' @export
 tie_is_bridge <- function(object){
   num_comp <- length( igraph::decompose(as_igraph(object)) )
-  out <- vapply(seq_len(graph_ties(object)), function(x){
+  out <- vapply(seq_len(network_ties(object)), function(x){
     length( igraph::decompose(igraph::delete.edges(object, x)) ) > num_comp
   }, FUN.VALUE = logical(1))
   if(is_labelled(object))