Merge pull request #101 from stocnet/develop

v1.3.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: manynet
 Title: Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks
-Version: 1.2.6
-Date: 2024-10-05
+Version: 1.3.0
+Date: 2024-10-16
 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,
@@ -39,7 +39,6 @@ Suggests:
     knitr,
     learnr,
     methods,
-    multiplex,
     netdiffuseR,
     patchwork,
     readxl,

NAMESPACE

@@ -50,6 +50,7 @@ S3method(as_network,network)
 S3method(as_network,network.goldfish)
 S3method(as_network,siena)
 S3method(as_network,tbl_graph)
+S3method(as_nodelist,tbl_graph)
 S3method(as_siena,igraph)
 S3method(as_siena,tbl_graph)
 S3method(as_tidygraph,data.frame)
@@ -158,6 +159,8 @@ S3method(print,tie_measure)
 S3method(summary,diff_model)
 S3method(summary,diffs_model)
 S3method(summary,learn_model)
+S3method(summary,network_measure)
+S3method(summary,network_motif)
 S3method(summary,node_measure)
 S3method(summary,node_member)
 S3method(summary,node_motif)
@@ -244,6 +247,11 @@ S3method(to_redirected,igraph)
 S3method(to_redirected,matrix)
 S3method(to_redirected,network)
 S3method(to_redirected,tbl_graph)
+S3method(to_signed,data.frame)
+S3method(to_signed,igraph)
+S3method(to_signed,matrix)
+S3method(to_signed,network)
+S3method(to_signed,tbl_graph)
 S3method(to_simplex,igraph)
 S3method(to_simplex,matrix)
 S3method(to_simplex,tbl_graph)
@@ -294,6 +302,9 @@ S3method(to_waves,data.frame)
 S3method(to_waves,diff_model)
 S3method(to_waves,igraph)
 S3method(to_waves,tbl_graph)
+S3method(to_weighted,igraph)
+S3method(to_weighted,network)
+S3method(to_weighted,tbl_graph)
 export("%>%")
 export(.E)
 export(.G)
@@ -312,14 +323,17 @@ export(as_graphAM)
 export(as_igraph)
 export(as_matrix)
 export(as_network)
+export(as_nodelist)
 export(as_siena)
 export(as_tidygraph)
 export(autographd)
 export(autographr)
 export(autographs)
 export(bind_node_attributes)
 export(bind_ties)
+export(clear_glossary)
 export(cluster_concor)
+export(cluster_cosine)
 export(cluster_hierarchical)
 export(create_components)
 export(create_core)
@@ -356,6 +370,7 @@ export(generate_utilities)
 export(ggplot)
 export(ggsave)
 export(ggtitle)
+export(gloss)
 export(graphr)
 export(graphs)
 export(grapht)
@@ -391,12 +406,16 @@ export(labs)
 export(layout_tbl_graph_alluvial)
 export(layout_tbl_graph_concentric)
 export(layout_tbl_graph_configuration)
+export(layout_tbl_graph_dyad)
+export(layout_tbl_graph_hexad)
 export(layout_tbl_graph_hierarchy)
 export(layout_tbl_graph_ladder)
 export(layout_tbl_graph_lineage)
 export(layout_tbl_graph_multilevel)
+export(layout_tbl_graph_pentad)
 export(layout_tbl_graph_quad)
 export(layout_tbl_graph_railway)
+export(layout_tbl_graph_tetrad)
 export(layout_tbl_graph_triad)
 export(many_palettes)
 export(mutate)
@@ -412,6 +431,7 @@ export(net_by_brokerage)
 export(net_by_dyad)
 export(net_by_mixed)
 export(net_by_quad)
+export(net_by_tetrad)
 export(net_by_triad)
 export(net_change)
 export(net_closeness)
@@ -528,6 +548,7 @@ export(node_by_dyad)
 export(node_by_exposure)
 export(node_by_path)
 export(node_by_quad)
+export(node_by_tetrad)
 export(node_by_tie)
 export(node_by_triad)
 export(node_closeness)
@@ -558,6 +579,7 @@ 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_eigen)
 export(node_in_equivalence)
@@ -591,6 +613,8 @@ export(node_is_max)
 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_kernighanlin)
@@ -624,6 +648,7 @@ export(node_thresholds)
 export(node_tie_census)
 export(node_transitivity)
 export(node_triad_census)
+export(node_vitality)
 export(node_walktrap)
 export(node_weak_components)
 export(over_time)
@@ -633,6 +658,7 @@ export(play_diffusion)
 export(play_diffusions)
 export(play_learning)
 export(play_segregation)
+export(print_glossary)
 export(read_cran)
 export(read_dynetml)
 export(read_edgelist)
@@ -695,6 +721,7 @@ export(tie_is_bridge)
 export(tie_is_cyclical)
 export(tie_is_feedback)
 export(tie_is_forbidden)
+export(tie_is_imbalanced)
 export(tie_is_loop)
 export(tie_is_max)
 export(tie_is_min)
@@ -713,12 +740,12 @@ export(to_anti)
 export(to_blocks)
 export(to_components)
 export(to_correlation)
+export(to_cosine)
 export(to_directed)
 export(to_dominating)
 export(to_ego)
 export(to_egos)
 export(to_eulerian)
-export(to_galois)
 export(to_giant)
 export(to_matching)
 export(to_mentoring)
@@ -731,6 +758,7 @@ export(to_onemode)
 export(to_permuted)
 export(to_reciprocated)
 export(to_redirected)
+export(to_signed)
 export(to_simplex)
 export(to_slices)
 export(to_subgraph)
@@ -744,6 +772,7 @@ export(to_unnamed)
 export(to_unsigned)
 export(to_unweighted)
 export(to_waves)
+export(to_weighted)
 export(with_graph)
 export(write_edgelist)
 export(write_graphml)

NEWS.md

@@ -1,3 +1,94 @@
+# manynet 1.3.0
+
+## Package
+
+- Improved user information in the console
+  - manynet cli functions now inherit parent frame
+  - Added manynet cli functions for success and progress along, seq, and nodes
+- Improved testing architecture
+  - Moving to nested testthats
+  - Added custom testthat function for expecting values and ignoring dimension names
+
+## Making
+
+- Added some names to created networks (`create_ego()`, `create_empty()`, 
+`create_filled()`, `create_ring()`, `create_star()`, `create_lattice()`)
+
+## Modifying
+
+- Fixed how `as_matrix()` handles signed networks
+- Added `as_nodelist()` for extracting nodelists from networks into tibbles
+- Added `to_cosine()`
+- Dropped `to_galois()` until it can be refactored
+- Split reformatting documentation into format, reformat, and deformat groups of functions
+  - Added `to_signed()` for adding signs to networks
+  - Added `to_weighted()` for adding weights to networks
+
+## Mapping
+
+- Fixed default color ordering so that red is the highlight
+- Fixed bug in `graphr()` where line types were inferred incorrectly
+- Improved `graphr()` so that layouts can now be `snap`ped to a grid,
+mileage may vary
+- Improved theme handling so that it is set globally (WIP)
+  - Added highlight themes
+  - Added background themes
+  - Added categorical themes
+- Improved configurational layouts
+  - Added dyad, pentad, and hexad layouts to configurational layouts
+  - Renamed quad layout to tetrad layout
+
+## Marking
+
+- Added `node_is_pendant()` for identifying pendant nodes
+- Added `node_is_neighbor()` for identifying adjacent nodes
+- Added `tie_is_imbalanced()` for identifying ties in imbalanced configurations
+
+## Measuring
+
+- Added `summary.network_measure()` to return z-scores and p-values for measures
+- Added `node_vitality()` for measuring closeness vitality centrality
+- Fixed #98 by dropping scale and normalization for `node_eigenvector()`
+
+## Memberships
+
+- Improved community detection options for new users
+  - Community detection algorithms now reformat networks as necessary or suggest that it be used on only the giant component
+  - Added `node_in_community()` which runs through most salient community detection algorithms to find and return the one with the highest modularity
+  - Updated documentation on resolution parameters
+- Improved `node_in_regular()` to inform user which census is being used
+- Renamed `node_by_quad()` to `node_by_tetrad()` to be more consistent with Greek origins
+  - Restored and updated documentation about the various configurations
+- Added `summary.network_motif()` which returns the z-scores for the motif scores based on random or configurational networks, traces progress
+- Fixed bug in `plot.network_motif()` where motif names were not identified correctly, internal make_network_motif now inherits call information
+
+## Modelling
+
+- Added `cluster_cosine()` for another equivalence option
+- Added internal documentation for depth_first_recursive_search
+
+## Practicing
+
+- Improved how `run_tute()` fuzzy matched so that insertions are not as costly
+- Improved tutorials with glossary architecture
+  - Added `gloss()`, `clear_glossary()`, and `print_glossary()` for adding glossaries to tutorials
+- Updated tutorials
+  - Updated community, position, and topology tutorials with glossaries, free play sections, and gifs
+  - Fixed miscellaneous issues in these tutorials
+  - Added faction section to community tutorial
+
+## Data
+
+- Added `irps_wwi`, a dynamic, signed network
+- Renamed `ison_blogs` to `irps_blogs`, added info
+- Renamed `ison_books` to `irps_books`, added info
+- Renamed `ison_usstates` to `irps_usgeo`, added info
+- Renamed `ison_friends` to `fict_friends`, added info and fixed directed issue
+- Renamed `ison_greys` to `fict_greys`, added info
+- Renamed `ison_lotr` to `fict_lotr`, added info
+- Renamed `ison_thrones` to `fict_thrones`, added info and some additional nodal attributes
+- Renamed `ison_potter` to `fict_potter`, added info and combined waves into single object
+
 # manynet 1.2.6
 
 ## Package

R/class_measures.R

@@ -24,6 +24,7 @@ make_tie_measure <- function(out, .data) {
 make_network_measure <- function(out, .data) {
   class(out) <- c("network_measure", class(out))
   attr(out, "mode") <- net_dims(.data)
+  attr(out, "call") <- deparse(sys.calls())
   out
 }
 
@@ -101,6 +102,30 @@ summary.node_measure <- function(object, ...,
   out
 }
 
+#' @export
+summary.network_measure <- function(object, ...,
+                                  null = c("random","configuration"), 
+                                  times = 500) {
+  null <- paste0("generate_", match.arg(null))
+  callItems <- trimws(strsplit(unlist(attr(object, "call")), 
+                               split = "\\(|\\)|,")[[1]])
+  idFun <- which(grepl("^net_", callItems))[1]
+  fun <- callItems[idFun]
+  dat <- callItems[idFun+1]
+  nulls <- vapply(mnet_progress_seq(times), function(r){
+    suppressMessages(get(fun)(get(null)(get(dat))))
+  }, FUN.VALUE = numeric(1))
+  out <- (object - mean(nulls))/stats::sd(nulls)
+  out[is.nan(out)] <- 0
+  p <- 2 * stats::pnorm(out, 
+             mean = mean(nulls), sd = stats::sd(nulls), 
+             lower.tail = ifelse(out>0, FALSE, TRUE))
+  cli::cli_text(cli::style_bold(round(object,3)), 
+                "  (z = ", cli::style_italic(round(out,2)),
+                ", p = ", cli::style_italic(round(p,3)),
+                ")")
+}
+
 # Plotting ####
 #' @export
 plot.node_measure <- function(x, type = c("h", "d"), ...) {

R/class_motifs.R

@@ -8,6 +8,7 @@ make_node_motif <- function(out, .data) {
 make_network_motif <- function(out, .data) {
   class(out) <- c("network_motif", class(out))
   attr(out, "mode") <- net_dims(.data)
+  attr(out, "call") <- deparse(sys.calls())
   out
 }
 
@@ -50,7 +51,7 @@ plot.node_motif <- function(x, ...) {
 
 #' @export
 plot.network_motif <- function(x, ...) {
-  motifs <- dimnames(x)[[2]]
+  motifs <- attr(x, "names")
   if("X4" %in% motifs){
     graphs(create_motifs(4), waves = 1:11)
   } else if("021D" %in% motifs){
@@ -87,3 +88,23 @@ print.network_motif <- function(x, ...) {
   out <- as.data.frame(mat)
   print(dplyr::tibble(out))
 }
+
+#' @export
+summary.network_motif <- function(object, ...,
+                               null = c("random","configuration"), 
+                               times = 500) {
+  null <- paste0("generate_", match.arg(null))
+  callItems <- trimws(strsplit(unlist(attr(object, "call")), 
+                               split = "\\(|\\)|,")[[1]])
+  idFun <- which(grepl("net_by_", callItems))[1]
+  fun <- callItems[idFun]
+  dat <- callItems[idFun+1]
+  nulls <- t(vapply(mnet_progress_seq(times), function(r){
+    suppressMessages(get(fun)(get(null)(get(dat))))
+  }, FUN.VALUE = numeric(length(object))))
+  out <- (object - colMeans(nulls))/apply(nulls, 2, stats::sd)
+  out[is.nan(out)] <- 0
+  out
+}
+
+