v1.6.0

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: manynet
-Title: Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks
-Version: 1.5.1
-Date: 2025-06-23
-Description: Many tools for making, modifying, mapping, marking, measuring, 
+Title: Many Ways to Make, Modify, Mark, and Measure Myriad Networks
+Version: 1.6.0
+Date: 2025-08-22
+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,
-   and on one-mode, two-mode (bipartite), and sometimes three-mode networks.
+   on directed, multiplex, multimodal, signed, and other networks.
    The package includes functions for importing and exporting, creating and generating networks,
    modifying networks and node and tie attributes,
-   and describing and visualizing networks with sensible defaults.
+   and describing networks with sensible defaults.
 URL: https://stocnet.github.io/manynet/
 BugReports: https://github.com/stocnet/manynet/issues
 License: MIT + file LICENSE
@@ -20,25 +20,16 @@ Depends: R (>= 3.6.0)
 Imports:
     cli,
     dplyr (>= 1.1.0),
-    ggplot2,
-    ggraph,
     igraph (>= 2.1.0),
     network,
     pillar,
     tidygraph
 Suggests:
-    BiocManager,
-    concaveman,
-    gganimate,
-    ggdendro,
-    ggforce,
-    gifski,
-    graphlayouts,
+    autograph,
     knitr,
     learnr,
     methods,
     netdiffuseR,
-    patchwork,
     readxl,
     rmarkdown,
     RSiena,
@@ -47,8 +38,6 @@ Suggests:
     tibble,
     tidyr,
     xml2
-Enhances:
-    Rgraphviz
 Authors@R: 
     c(person(given = "James",
              family = "Hollway",

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method("+",ggplot)
 S3method(add_nodes,igraph)
 S3method(add_nodes,network)
 S3method(add_nodes,tbl_graph)
@@ -140,6 +139,7 @@ S3method(net_dims,igraph)
 S3method(net_dims,matrix)
 S3method(net_dims,network)
 S3method(pillar_shaft,logi)
+S3method(pillar_shaft,mdate)
 S3method(print,diff_model)
 S3method(print,learn_model)
 S3method(print,mnet)
@@ -315,7 +315,6 @@ export(add_node_attribute)
 export(add_nodes)
 export(add_tie_attribute)
 export(add_ties)
-export(aes)
 export(apply_changes)
 export(arrange_ties)
 export(as_changelist)
@@ -329,9 +328,6 @@ 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)
@@ -372,14 +368,7 @@ export(generate_random)
 export(generate_scalefree)
 export(generate_smallworld)
 export(generate_utilities)
-export(ggplot)
-export(ggsave)
-export(ggtitle)
 export(gloss)
-export(graphr)
-export(graphs)
-export(grapht)
-export(guides)
 export(is.tbl_graph)
 export(is_acyclic)
 export(is_aperiodic)
@@ -408,22 +397,6 @@ export(join_ties)
 export(k_elbow)
 export(k_silhouette)
 export(k_strict)
-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)
 export(mutate_changes)
 export(mutate_net)
@@ -632,6 +605,7 @@ export(node_is_pendant)
 export(node_is_random)
 export(node_is_recovered)
 export(node_is_universal)
+export(node_kcoreness)
 export(node_kernighanlin)
 export(node_leading_eigen)
 export(node_leiden)
@@ -685,42 +659,10 @@ export(rename)
 export(rename_nodes)
 export(rename_ties)
 export(run_tute)
-export(scale_color_centres)
-export(scale_color_ethz)
-export(scale_color_iheid)
-export(scale_color_rug)
-export(scale_color_sdgs)
-export(scale_color_uzh)
-export(scale_colour_centres)
-export(scale_colour_ethz)
-export(scale_colour_iheid)
-export(scale_colour_rug)
-export(scale_colour_sdgs)
-export(scale_colour_uzh)
-export(scale_edge_color_centres)
-export(scale_edge_color_ethz)
-export(scale_edge_color_iheid)
-export(scale_edge_color_rug)
-export(scale_edge_color_sdgs)
-export(scale_edge_color_uzh)
-export(scale_edge_colour_centres)
-export(scale_edge_colour_ethz)
-export(scale_edge_colour_iheid)
-export(scale_edge_colour_rug)
-export(scale_edge_colour_sdgs)
-export(scale_edge_colour_uzh)
-export(scale_fill_centres)
-export(scale_fill_ethz)
-export(scale_fill_iheid)
-export(scale_fill_rug)
-export(scale_fill_sdgs)
-export(scale_fill_uzh)
-export(scale_size)
 export(select)
 export(select_changes)
 export(select_nodes)
 export(select_ties)
-export(set_manynet_theme)
 export(snet_abort)
 export(snet_info)
 export(snet_minor_info)
@@ -734,10 +676,6 @@ export(snet_unavailable)
 export(snet_warn)
 export(summarise_ties)
 export(table_data)
-export(theme_ethz)
-export(theme_iheid)
-export(theme_rug)
-export(theme_uzh)
 export(tie_attribute)
 export(tie_betweenness)
 export(tie_closeness)
@@ -809,8 +747,6 @@ export(write_matrix)
 export(write_nodelist)
 export(write_pajek)
 export(write_ucinet)
-export(xlab)
-export(ylab)
 importFrom(cli,cli_div)
 importFrom(cli,cli_end)
 importFrom(cli,cli_inform)
@@ -825,39 +761,12 @@ importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
-importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,tibble)
 importFrom(dplyr,ungroup)
-importFrom(ggplot2,aes)
-importFrom(ggplot2,arrow)
-importFrom(ggplot2,geom_point)
-importFrom(ggplot2,geom_segment)
-importFrom(ggplot2,geom_text)
-importFrom(ggplot2,ggplot)
-importFrom(ggplot2,ggsave)
-importFrom(ggplot2,ggtitle)
-importFrom(ggplot2,guides)
-importFrom(ggplot2,labs)
-importFrom(ggplot2,scale_alpha_manual)
-importFrom(ggplot2,scale_color_brewer)
-importFrom(ggplot2,scale_fill_brewer)
-importFrom(ggplot2,scale_size)
-importFrom(ggplot2,theme_void)
-importFrom(ggplot2,unit)
-importFrom(ggplot2,xlab)
-importFrom(ggplot2,ylab)
-importFrom(ggraph,create_layout)
-importFrom(ggraph,geom_conn_bundle)
-importFrom(ggraph,geom_edge_link)
-importFrom(ggraph,geom_node_label)
-importFrom(ggraph,geom_node_point)
-importFrom(ggraph,geom_node_text)
-importFrom(ggraph,get_con)
-importFrom(ggraph,scale_edge_width_continuous)
 importFrom(igraph,E)
 importFrom(igraph,V)
 importFrom(igraph,add_edges)
@@ -894,12 +803,10 @@ importFrom(igraph,edge_density)
 importFrom(igraph,eulerian_path)
 importFrom(igraph,feedback_arc_set)
 importFrom(igraph,fit_power_law)
-importFrom(igraph,get.edgelist)
 importFrom(igraph,graph_from_adjacency_matrix)
 importFrom(igraph,graph_from_biadjacency_matrix)
 importFrom(igraph,graph_from_data_frame)
 importFrom(igraph,graph_from_incidence_matrix)
-importFrom(igraph,gsize)
 importFrom(igraph,has_eulerian_path)
 importFrom(igraph,induced_subgraph)
 importFrom(igraph,is_bipartite)

NEWS.md

@@ -1,3 +1,45 @@
+# manynet 1.6.0
+
+## Package
+
+- Dropped viz-related dependencies: `{ggplot2}`, `{ggraph}`, `{patchwork}`, 
+`{ggdendro}`, `{concaveman}`, `{gifski}`, `{graphlayouts}`, `{ggforce}`,
+and `{BiocManager}`
+
+## Classes
+
+- Added mdate pillar shaft for pretty printing of NAs in messydate variables
+
+## Modifying
+
+- Improved `to_no_missing()` to record missing removal
+- Improved `to_no_isolates()` to record isolate removal
+- Improved `to_giant()` to record giant component scoping
+- Improved `to_matching()` to record matching
+- Fixed `to_matching()` triggering warnings from handling NAs (thanks @schochastics for fixing #109)
+- Improved `to_mentoring()` to record mentoring
+- Improved `to_eulerian()` to record Eulerian pathing
+
+## Measuring
+
+- Improved `net_core()` with method options for calculating correlation, distance, ndiff, and diff
+
+## Membership
+
+- Improved `node_coreness()` to implement Borgatti and Everett's continuous coreness algorithm
+- Moved previous functionality of `node_coreness()` to `node_kcoreness()`
+
+## Mapping
+
+- Moved `graphr()`, `graphs()`, and `grapht()` to `{autograph}`
+- Moved palette functionality to `{autograph}`
+- Moved remaining layouts to `{autograph}`
+- Moved theme functionality to `{autograph}`
+- Dropped remaining plot functions
+- Dropped or avoided using `{autograph}`-related functions in examples to
+make package lighter
+- Please see `{autograph}` for continued development of these features
+
 # manynet 1.5.1
 
 ## Package

R/make_generate.R

@@ -53,8 +53,8 @@ NULL
 #' _Publicationes Mathematicae_. 6: 290–297.
 #' @importFrom igraph sample_bipartite sample_gnp sample_gnm
 #' @examples
-#' graphr(generate_random(12, 0.4))
-#' # graphr(generate_random(c(6, 6), 0.4))
+#' generate_random(12, 0.4)
+#' # generate_random(c(6, 6), 0.4)
 #' @export
 generate_random <- function(n, p = 0.5, directed = FALSE, with_attr = TRUE) {
   if(is_manynet(n)){
@@ -243,8 +243,8 @@ NULL
 #' \doi{10.1038/30918}.
 #' @importFrom igraph sample_smallworld
 #' @examples
-#' graphr(generate_smallworld(12, 0.025))
-#' graphr(generate_smallworld(12, 0.25))
+#' generate_smallworld(12, 0.025)
+#' generate_smallworld(12, 0.25)
 #' @export
 generate_smallworld <- function(n, p = 0.05, directed = FALSE, width = 2) {
   directed <- infer_directed(n, directed)
@@ -270,8 +270,8 @@ generate_smallworld <- function(n, p = 0.05, directed = FALSE, width = 2) {
 #' _Science_ 286(5439):509–12. 
 #' \doi{10.1126/science.286.5439.509}.
 #' @examples
-#' graphr(generate_scalefree(12, 0.25))
-#' graphr(generate_scalefree(12, 1.25))
+#' generate_scalefree(12, 0.25)
+#' generate_scalefree(12, 1.25)
 #' @export
 generate_scalefree <- function(n, p = 1, directed = FALSE) {
   directed <- infer_directed(n, directed)

R/make_play.R

@@ -146,8 +146,6 @@ NULL
 #'   original network.
 #' @examples 
 #'   smeg <- generate_smallworld(15, 0.025)
-#'   plot(play_diffusion(smeg, recovery = 0.4))
-#'   #graphr(play_diffusion(ison_karateka))
 #' @export
 play_diffusion <- function(.data, 
                            seeds = 1,
@@ -406,9 +404,6 @@ play_learning <- function(.data,
 #'   latticeEg <- add_node_attribute(latticeEg, "startValues", startValues)
 #'   latticeEg
 #'   play_segregation(latticeEg, "startValues", 0.5)
-#'   # graphr(latticeEg, node_color = "startValues", node_size = 5) + 
-#'   # graphr(play_segregation(latticeEg, "startValues", 0.2), 
-#'   #            node_color = "startValues", node_size = 5)
 #' @export
 play_segregation <- function(.data, 
                              attribute,

R/make_read.R

@@ -707,8 +707,6 @@ write_graphml <- function(.data,
 #' @examples
 #' # mnet <- read_cran()
 #' # mnet <- to_ego(mnet, "manynet", max_dist = 2)
-#' # graphr(mnet, layout = "hierarchy", 
-#' #        edge_color = "type", node_color = "Compilation")
 #' @export
 read_cran <- function(pkg = "all"){
   snet_progress_step("Downloading data about available packages from CRAN")

R/manip_correlation.R

@@ -74,9 +74,6 @@ NULL
 #' @param with_attr Logical whether any attributes of the object
 #'   should be retained. 
 #'   By default TRUE. 
-#' @examples
-#' graphr(ison_adolescents, node_size = 4)
-#' graphr(to_permuted(ison_adolescents), node_size = 4)
 #' @export
 to_permuted <- function(.data, with_attr = TRUE) {
   out <- as_matrix(.data)

R/manip_format.R

@@ -378,7 +378,6 @@ to_acyclic.network <- function(.data) {
 #' @importFrom igraph complementer
 #' @examples
 #' to_anti(ison_southern_women)
-#' #graphr(to_anti(ison_southern_women))
 #' @export
 to_anti <- function(.data) UseMethod("to_anti")