In-class_Ex08

Loading packages and data

Code chunk:

pacman::p_load(igraph, tidygraph, ggraph, 
               visNetwork, lubridate, clock,
               tidyverse, graphlayouts)

GAStech_nodes <- read_csv("data/GAStech_email_node.csv")

Rows: 54 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (3): label, Department, Title
dbl (1): id

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

GAStech_edges <- read_csv("data/GAStech_email_edge-v2.csv")

Rows: 9063 Columns: 8
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr  (5): SentDate, Subject, MainSubject, sourceLabel, targetLabel
dbl  (2): source, target
time (1): SentTime

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Data Wrangling

GAStech_edges <- GAStech_edges %>%
  mutate(SendDate = dmy(SentDate)) %>%
  mutate(Weekday = wday(SentDate,
                        label = TRUE,
                        abbr = FALSE))

GAStech_edges_aggregated <- GAStech_edges %>%
  filter(MainSubject == "Work related") %>%
  group_by(source, target, Weekday) %>%
    summarise(Weight = n()) %>%
  filter(source!=target) %>%
  filter(Weight > 1) %>%
  ungroup()

`summarise()` has grouped output by 'source', 'target'. You can override using
the `.groups` argument.

Create network objects

GAStech_graph <- tbl_graph(nodes = GAStech_nodes,
                           edges = GAStech_edges_aggregated, 
                           directed = TRUE)

GAStech_graph %>%
  activate(edges) %>%
  arrange(desc(Weight))

# A tbl_graph: 54 nodes and 1372 edges
#
# A directed multigraph with 1 component
#
# Edge Data: 1,372 × 4 (active)
   from    to Weekday  Weight
  <int> <int> <ord>     <int>
1    40    41 Saturday     13
2    41    43 Monday       11
3    35    31 Tuesday      10
4    40    41 Monday       10
5    40    43 Monday       10
6    36    32 Sunday        9
# … with 1,366 more rows
#
# Node Data: 54 × 4
     id label           Department     Title           
  <dbl> <chr>           <chr>          <chr>           
1     1 Mat.Bramar      Administration Assistant to CEO
2     2 Anda.Ribera     Administration Assistant to CFO
3     3 Rachel.Pantanal Administration Assistant to CIO
# … with 51 more rows

ggraph(GAStech_graph) +
  geom_edge_link() +
  geom_node_point()

Using "stress" as default layout

Warning: Using the `size` aesthetic in this geom was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` in the `default_aes` field and elsewhere instead.

g <- ggraph(GAStech_graph, 
            layout = "fr") +
  geom_edge_link(aes()) +
  geom_node_point(aes())

g + theme_graph()

g <- ggraph(GAStech_graph, 
            layout = "nicely") + 
  geom_edge_link(aes()) +
  geom_node_point(aes(colour = Department, 
                      size = 3))

g + theme_graph()

Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family not
found in Windows font database

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Facet weekdays

set_graph_style()

g <- ggraph(GAStech_graph, 
            layout = "nicely") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = Department), 
                  size = 2)

g + facet_edges(~Weekday)

Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family not
found in Windows font database

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Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
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g <- GAStech_graph %>%
  mutate(betweenness_centrality = centrality_betweenness()) %>%
  ggraph(layout = "fr") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = Department,
            size=betweenness_centrality))
g + theme_graph()

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
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g <- GAStech_graph %>%
  ggraph(layout = "fr") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = Department, 
                      size = centrality_betweenness()))
g + theme_graph()

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
family not found in Windows font database

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
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g <- GAStech_graph %>%
  mutate(community = as.factor(group_edge_betweenness(weights = Weight, directed = TRUE))) %>%
  ggraph(layout = "fr") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = community))  

Warning in cluster_edge_betweenness(graph = .G(), weights = weights, directed =
directed): At core/community/edge_betweenness.c:492 : Membership vector will be
selected based on the highest modularity score.

Warning in cluster_edge_betweenness(graph = .G(), weights = weights, directed
= directed): At core/community/edge_betweenness.c:497 : Modularity calculation
with weighted edge betweenness community detection might not make sense --
modularity treats edge weights as similarities while edge betwenness treats them
as distances.

g + theme_graph()

Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : font
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Interactive Network graph

GAStech_edges_aggregated <- GAStech_edges %>%
  left_join(GAStech_nodes, by = c("sourceLabel" = "label")) %>%
  rename(from = id) %>%
  left_join(GAStech_nodes, by = c("targetLabel" = "label")) %>%
  rename(to = id) %>%
  filter(MainSubject == "Work related") %>%
  group_by(from, to) %>%
    summarise(weight = n()) %>%
  filter(from!=to) %>%
  filter(weight > 1) %>%
  ungroup()

`summarise()` has grouped output by 'from'. You can override using the
`.groups` argument.

visNetwork(GAStech_nodes, 
           GAStech_edges_aggregated)

visNetwork(GAStech_nodes,
           GAStech_edges_aggregated) %>%
  visIgraphLayout(layout = "layout_with_fr") 

visNetwork(GAStech_nodes,
           GAStech_edges_aggregated) %>%
  visIgraphLayout(layout = "layout_with_fr") %>%
  visLegend() %>%
  visLayout(randomSeed = 123)

visNetwork(GAStech_nodes,
           GAStech_edges_aggregated) %>%
  visIgraphLayout(layout = "layout_with_fr") %>%
  visEdges(arrows = "to", 
           smooth = list(enabled = TRUE, 
                         type = "curvedCW")) %>%
  visLegend() %>%
  visLayout(randomSeed = 123)