Merge pull request #18 from MHenderson/chapter2

corrections to chapter 2

R/one_factorisation_plot.R

@@ -2,8 +2,28 @@ one_factorisation_plot <- function() {
 
   g <- igraph::make_full_graph(6)
 
-  ggraph::ggraph(g, layout = 'circle') +
-    ggraph::geom_edge_link() +
-    ggraph::geom_node_point()
-
-} 
+  gt <- tidygraph::as_tbl_graph(g)
+
+  gtc <- gt %>%
+    tidygraph::activate(edges) %>%
+    dplyr::mutate(
+      f = c(1, 4, 2, 5, 3, 2, 5, 3, 4, 3, 1, 5, 4, 1, 2)
+    )
+
+  ggraph::ggraph(gtc, layout = 'circle') +
+    ggraph::geom_node_point(size = 4) +
+    ggraph::geom_edge_link(
+           mapping = ggplot2::aes(label = f, edge_colour = f),
+       show.legend = FALSE,
+        angle_calc = 'along',
+       label_dodge = ggplot2::unit(3.5, 'mm'),
+        label_push = ggplot2::unit(-6.0, 'mm'),
+         start_cap = ggraph::circle(4, 'mm'),
+           end_cap = ggraph::circle(4, 'mm'),
+      label_colour = "blue", 
+        edge_width = 2,
+        label_size = 6
+    ) +
+    ggraph::facet_edges(~f)
+
+} 

R/orthogonal_one_factorisation_plot.R

@@ -1,36 +1,65 @@
 orthogonal_one_factorisation_plot <- function() {
 
-  g <- igraph::make_full_graph(6)
+  g <- igraph::make_full_graph(8)
 
-  igraph::V(g)$name <- LETTERS[1:6]
-  igraph::E(g)$name <- 1:15
+  gt <- tidygraph::as_tbl_graph(g)
 
-  f1 <- c(1, 11, 14)
-  f2 <- c(3, 6, 15)
-  f3 <- c(5, 8, 10)
-  f4 <- c(2, 9, 13)
-  f5 <- c(4, 7, 12)
+  gtc1 <- gt %>%
+    tidygraph::activate(edges) %>%
+    dplyr::mutate(
+      f = c(1, 2, 3, 4, 5, 6, 7,
+            3, 2, 5, 4, 7, 6,
+            1, 6, 7, 4, 5,
+            7, 6, 5, 4,
+            1, 2, 3,
+            3, 2,
+            1)
+    )
 
-  igraph::E(g)[f1]$onefactor <- "red"
-  igraph::E(g)[f2]$onefactor <- "blue"
-  igraph::E(g)[f3]$onefactor <- "green"
-  igraph::E(g)[f4]$onefactor <- "orange"
-  igraph::E(g)[f5]$onefactor <- "black"
+  gtc2 <- gt %>%
+    tidygraph::activate(edges) %>%
+    dplyr::mutate(
+      f = c(4, 6, 3, 5, 7, 1, 2,
+            7, 2, 1, 3, 5, 6,
+            5, 2, 1, 4, 3,
+            7, 4, 6, 1,
+            6, 3, 4,
+            2, 5,
+            7)
+    )
 
-  p1 <- ggraph::ggraph(g, layout = 'kk') + 
-    ggraph::geom_node_text(ggplot2::aes(label = name), size = 4) +
-    ggraph::geom_edge_link(ggplot2::aes(label = name, edge_colour = onefactor),
-                           show.legend = FALSE,
-                           angle_calc = 'along',
-                           label_dodge = ggplot2::unit(2.5, 'mm'),
-                           label_push = ggplot2::unit(-6.0, 'mm'),
-                           start_cap = ggraph::circle(4, 'mm'),
-                           end_cap = ggraph::circle(4, 'mm'),
-                           label_colour = "blue") +
-    ggraph::theme_graph(foreground = 'steelblue', fg_text_colour = 'white')
+  p1 <- ggraph::ggraph(gtc1, layout = 'circle') +
+    ggraph::geom_node_point(size = 4) +
+    ggraph::geom_edge_link(
+      mapping = ggplot2::aes(label = f, edge_colour = f),
+      show.legend = FALSE,
+      angle_calc = 'along',
+      label_dodge = ggplot2::unit(3.5, 'mm'),
+      label_push = ggplot2::unit(-6.0, 'mm'),
+      start_cap = ggraph::circle(4, 'mm'),
+      end_cap = ggraph::circle(4, 'mm'),
+      label_colour = "blue", 
+      edge_width = 2,
+      label_size = 6
+    ) +
+    ggraph::facet_edges(~f)
 
-  p2 <- p1 + ggraph::facet_edges(~factor)
+  p2 <- ggraph::ggraph(gtc2, layout = 'circle') +
+    ggraph::geom_node_point(size = 4) +
+    ggraph::geom_edge_link(
+      mapping = ggplot2::aes(label = f, edge_colour = f),
+      show.legend = FALSE,
+      angle_calc = 'along',
+      label_dodge = ggplot2::unit(3.5, 'mm'),
+      label_push = ggplot2::unit(-6.0, 'mm'),
+      start_cap = ggraph::circle(4, 'mm'),
+      end_cap = ggraph::circle(4, 'mm'),
+      label_colour = "blue", 
+      edge_width = 2,
+      label_size = 6
+    ) +
+    ggraph::facet_edges(~f)
 
-  p1
+  p1 / p2 
 
 }

R/two_one_factors_plot.R

@@ -1,20 +1,23 @@
 two_one_factors_plot <- function() {
 
-  gm <- matrix( c(1, 2, 3, 4), nc = 2, byrow = TRUE)
-  hm <- matrix( c(1, 3, 2, 4), nc = 2, byrow = TRUE)
+  g <- tidygraph::tbl_graph(nodes = tibble::tibble(name = c(1, 2, 3, 4)),
+                 edges = tibble::tibble(from = c(1, 3), to = c(2, 4)))
 
-  g <- igraph::graph_from_edgelist(gm, directed = FALSE)
-  h <- igraph::graph_from_edgelist(hm, directed = FALSE)
+  h <- tidygraph::tbl_graph(nodes = tibble::tibble(name = c(1, 2, 3, 4)),
+                 edges = tibble::tibble(from = c(1, 2), to = c(3, 4)))
 
   gp <- ggraph::ggraph(g, layout = 'circle') +
     ggraph::geom_edge_link() +
-    ggraph::geom_node_point()
+    ggraph::geom_node_point() +
+    ggraph::geom_node_label(aes(label = name))
 
   hp <- ggraph::ggraph(h, layout = 'circle') +
     ggraph::geom_edge_link() +
-    ggraph::geom_node_point()
+    ggraph::geom_node_point() +
+    ggraph::geom_node_label(aes(label = name))
 
   gp + hp
 
 }
 
+

_targets.R

@@ -30,18 +30,34 @@ list(
     name = complete_graph_fig,
     command = complete_graph_plot()
   ),
+  tar_target(
+    name = complete_graph_fig_file,
+    command = ggplot2::ggsave("figure/complete_graph.pdf", plot = complete_graph_fig, width = 2, height = 2)
+  ),
   tar_target(
     name = two_one_factors_fig,
     command = two_one_factors_plot()
   ),
+  tar_target(
+    name = two_one_factors_fig_file,
+    command = ggplot2::ggsave("figure/two_one_factors.pdf", plot = two_one_factors_fig, width = 6, height = 3)
+  ),
   tar_target(
     name = one_factorisation_fig,
     command = one_factorisation_plot()
   ),
+  tar_target(
+    name = one_factorisation_fig_file,
+    command = ggplot2::ggsave("figure/one_factorisation.pdf", plot = one_factorisation_fig, width = 5, height = 4)
+  ),
   tar_target(
     name = orthogonal_one_factorisation_fig,
     command = orthogonal_one_factorisation_plot()
   ),
+  tar_target(
+    name = orthogonal_one_factorisation_fig_file,
+    command = ggplot2::ggsave("figure/orthogonal_one_factorisation.pdf", plot = orthogonal_one_factorisation_fig, width = 8, height = 8)
+  ),
   tar_knit(
     name = room_tex,
     path = "room.Rnw"

_targets/meta/meta

@@ -1,11 +1,14 @@
 name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error
-complete_graph_fig|stem|d7f756a1837c813d|51e25aae93e5c254|e9000e4f304f30b7|-103651696||t19486.6920742588s|54ef969d5ea32844|91088|rds|local|vector|||0.037||
-complete_graph_figure|function|a480007d61cb4b10|||||||||||||||
+complete_graph_fig|stem|b99248a09b239f9d|51e25aae93e5c254|e9000e4f304f30b7|-103651696||t19487.7107360239s|2406450afc03cd2b|91087|rds|local|vector|||0.047||
+complete_graph_fig_file|stem|06cb0c0f0eca3613|a6e5114b998faa03|4c6c8db2bf0e1aec|-1692498324||t19487.7107473203s|dff9495c51b724c1|77|rds|local|vector|||0.283||
 complete_graph_plot|function|a480007d61cb4b10|||||||||||||||
-one_factorisation_fig|stem|aa6939de52207209|1fee88e3d0b170a8|e1e06292af9ba234|-1429099058||t19486.6920752773s|542062d09a35de2f|86133|rds|local|vector|||0.02||
-one_factorisation_plot|function|790fdd285708dd6b|||||||||||||||
-orthogonal_one_factorisation_fig|stem|5a198482c41f2197|e0293d63f58739dd|569490652f1e00cc|-1045084297||t19486.6920712958s|8a3557bdef044ce5|151981|rds|local|vector|||0.825||
-orthogonal_one_factorisation_plot|function|96cb8e792f30a898|||||||||||||||
-room_tex|stem|432d48f4610f8646|d16ca72643af0c32|e686f1d9d75ea008|-23973361|room.tex*room.Rnw|t19487.3554344618s|86b3ee2b5d760fea|198349|file|local|vector|||1.565||
-two_one_factors_fig|stem|62dd37e48ddfc46a|f0979edb2f66a5ac|ee00e06580ba06e1|346093151||t19486.6920730551s|6ca6e3393dbb23e8|90585|rds|local|vector|||0.053||
-two_one_factors_plot|function|43c7d164ec277730|||||||||||||||
+one_factorisation_fig|stem|84d0239cd9b30827|1fee88e3d0b170a8|1abff12a869d6d87|-1429099058||t19488.4449005607s|257ad5f68254e5b7|142989|rds|local|vector|||0.046||
+one_factorisation_fig_file|stem|6ff76b4a23152265|f87cd30b4d121e6a|d853e8f783ef2f03|-1709970623||t19488.4449515332s|6281f79619f6778a|80|rds|local|vector|||0.49||
+one_factorisation_plot|function|d64d0ccec9eaa6a2|||||||||||||||
+orthogonal_one_factorisation_fig|stem|050a62f87feca6a6|e0293d63f58739dd|b87cd1cfddc5ee8d|-1045084297||t19488.4448983385s|59c0883c7cdd4600|151364|rds|local|vector|||0.849||
+orthogonal_one_factorisation_fig_file|stem|8ce309d1de9ee57d|24d4057c9dbebd8e|8ff8ee9b649b8360|-678393291||t19488.4449156534s|e961a0bcff3caad6|91|rds|local|vector|||1.297|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.|
+orthogonal_one_factorisation_plot|function|dcfe9e030d4e0bb4|||||||||||||||
+room_tex|stem|bccb328361466968|1ad8de4483c80f15|4577a5eaaa618f60|-23973361|room.tex*room.Rnw|t19488.4481137253s|14469f93f2512bc3|198301|file|local|vector|||0.966||
+two_one_factors_fig|stem|0aa569881d7161eb|f0979edb2f66a5ac|fba3863c64269ef4|346093151||t19487.7107347276s|2a4504ccf4b024bc|96128|rds|local|vector|||0.081||
+two_one_factors_fig_file|stem|908f9011dd2e1f04|17167c0ed623ae6b|41f5107a467f936c|-202751565||t19487.710743987s|c852eab37a726e04|78|rds|local|vector|||0.533|1m22mUsing the size aesthetic in this geom was deprecated in ggplot2 3.4.0.36mℹ39m Please use linewidth in the default_aes field and elsewhere instead.|
+two_one_factors_plot|function|66584c000622211f|||||||||||||||

chapters/01_introduction.Rnw

@@ -11,7 +11,6 @@ Fifteen young ladies of a school walk out three abreast for seven days in succes
 In solving this problem Kirkman discovered the following square array, which he observed was a ``very curious arrangement''.
 
 \begin{equation}
-  \label{eq:roomsquare}
   \begin{bmatrix}
        &    &    & hi & kl & mn & op \\
        & il & mo &    & np & hk &    \\
@@ -21,6 +20,7 @@ In solving this problem Kirkman discovered the following square array, which he
     ho & km &    & ln &    & ip &    \\
     kn & hp &    &    & io &    & lm 
   \end{bmatrix}
+  \label{eq:roomsquare}
 \end{equation}
 
 The curiosity of this square is that each of the letters