Nothing
## ----include=FALSE------------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE,
comment = "#>",
out.width = "50%",
dpi = 72,
fig.align = "center")
## ----'setup', echo=FALSE------------------------------------------------------
library("chessboard")
library("ggplot2")
library("patchwork")
## ----'fictitious-data', echo=FALSE--------------------------------------------
sites <- expand.grid("transect" = 1:9, "quadrat" = 1:9)
nodes <- create_node_labels(data = sites,
transect = "transect",
quadrat = "quadrat")
focus <- "5-5"
transects_quadrats <- expand.grid("transect" = 1:3,
"quadrat" = 1:5)
transects_only <- data.frame("transect" = 1:3)
quadrats_only <- data.frame("quadrat" = 1:5)
nodes_transects_quadrats <- create_node_labels(data = transects_quadrats,
transect = "transect",
quadrat = "quadrat")
nodes_transects_only <- create_node_labels(data = transects_only,
transect = "transect")
nodes_quadrats_only <- create_node_labels(data = quadrats_only,
quadrat = "quadrat")
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# pawn(nodes, focus = "5-5", degree = 4, ...)
## ----'cb-pawn', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 1. Moves of the **Pawn** (with degree = 4)", out.width='100%'----
pawn_1 <-
gg_chessboard(nodes, "A. Undirected network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, pawn(nodes, focus, degree = 4, directed = FALSE,
reverse = FALSE))
pawn_2 <-
gg_chessboard(nodes, "B. Directed network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, pawn(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE))
pawn_3 <-
gg_chessboard(nodes, "C. Directed network (reverse)", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, pawn(nodes, focus, degree = 4, directed = TRUE,
reverse = TRUE))
(pawn_1 | pawn_2 | pawn_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# create_edge_list(nodes, method = "pawn", degree = 4, ...)
## ----'cb-pawn-mat', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 2. Connectivity matrices of the **Pawn** (with degree = 4)", out.width='100%'----
nb_1 <- create_edge_list(nodes,
method = "pawn",
degree = 4,
directed = FALSE,
reverse = FALSE)
pawn_1 <- gg_matrix(connectivity_matrix(nb_1), "A. Undirected network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_2 <- create_edge_list(nodes,
method = "pawn",
degree = 4,
directed = TRUE,
reverse = FALSE)
pawn_2 <- gg_matrix(connectivity_matrix(nb_2), "B. Directed network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_3 <- create_edge_list(nodes,
method = "pawn",
degree = 4,
directed = TRUE,
reverse = TRUE)
pawn_3 <- gg_matrix(connectivity_matrix(nb_3), "C. Directed network (reverse)") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
(pawn_1 | pawn_2 | pawn_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# fool(nodes, focus = "5-5", degree = 4, ...)
## ----'cb-fool', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 3. Moves of the **Fool** (with degree = 4)", out.width='100%'----
fool_1 <-
gg_chessboard(nodes, "A. Undirected network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, fool(nodes, focus, degree = 4, directed = FALSE,
reverse = FALSE))
fool_2 <-
gg_chessboard(nodes, "B. Directed network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, fool(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE))
fool_3 <-
gg_chessboard(nodes, "C. Directed network (reverse)", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, fool(nodes, focus, degree = 4, directed = TRUE,
reverse = TRUE))
(fool_1 | fool_2 | fool_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# create_edge_list(nodes, method = "fool", degree = 4, ...)
## ----'cb-fool-mat', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 4. Connectivity matrices of the **Fool** (with degree = 4)", out.width='100%'----
nb_1 <- create_edge_list(nodes,
method = "fool",
degree = 4,
directed = FALSE,
reverse = FALSE)
fool_1 <- gg_matrix(connectivity_matrix(nb_1), "A. Undirected network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_2 <- create_edge_list(nodes,
method = "fool",
degree = 4,
directed = TRUE,
reverse = FALSE)
fool_2 <- gg_matrix(connectivity_matrix(nb_2), "B. Directed network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_3 <- create_edge_list(nodes,
method = "fool",
degree = 4,
directed = TRUE,
reverse = TRUE)
fool_3 <- gg_matrix(connectivity_matrix(nb_3), "C. Directed network (reverse)") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
(fool_1 | fool_2 | fool_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# rook(nodes, focus = "5-5", degree = 4, ...)
## ----'cb-rook', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 5. Moves of the **Rook** (with degree = 4)", out.width='100%'----
rook_1 <-
gg_chessboard(nodes, "A. Undirected network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, rook(nodes, focus, degree = 4, directed = FALSE,
reverse = FALSE))
rook_2 <-
gg_chessboard(nodes, "B. Directed network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, rook(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE))
rook_3 <-
gg_chessboard(nodes, "C. Directed network (reverse)", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, rook(nodes, focus, degree = 4, directed = TRUE,
reverse = TRUE))
(rook_1 | rook_2 | rook_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# create_edge_list(nodes, method = "rook", degree = 4, ...)
## ----'cb-rook-mat', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 6. Connectivity matrices of the **Rook** (with degree = 4)", out.width='100%'----
nb_1 <- create_edge_list(nodes,
method = "rook",
degree = 4,
directed = FALSE,
reverse = FALSE)
rook_1 <- gg_matrix(connectivity_matrix(nb_1), "A. Undirected network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_2 <- create_edge_list(nodes,
method = "rook",
degree = 4,
directed = TRUE,
reverse = FALSE)
rook_2 <- gg_matrix(connectivity_matrix(nb_2), "B. Directed network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_3 <- create_edge_list(nodes,
method = "rook",
degree = 4,
directed = TRUE,
reverse = TRUE)
rook_3 <- gg_matrix(connectivity_matrix(nb_3), "C. Directed network (reverse)") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
(rook_1 | rook_2 | rook_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# bishop(nodes, focus = "5-5", degree = 4, ...)
## ----'cb-bishop', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 7. Moves of the **Bishop** (with degree = 4)", out.width='100%'----
bishop_1 <-
gg_chessboard(nodes, "A. Undirected network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, bishop(nodes, focus, degree = 4, directed = FALSE,
reverse = FALSE))
bishop_2 <-
gg_chessboard(nodes, "B. Directed network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, bishop(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE))
bishop_3 <-
gg_chessboard(nodes, "C. Directed network (reverse)", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, bishop(nodes, focus, degree = 4, directed = TRUE,
reverse = TRUE))
(bishop_1 | bishop_2 | bishop_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# create_edge_list(nodes, method = "bishop", degree = 4, ...)
## ----'cb-bishop-mat', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 8. Connectivity matrices of the **Bishop** (with degree = 4)", out.width='100%'----
nb_1 <- create_edge_list(nodes,
method = "bishop",
degree = 4,
directed = FALSE,
reverse = FALSE)
bishop_1 <- gg_matrix(connectivity_matrix(nb_1), "A. Undirected network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_2 <- create_edge_list(nodes,
method = "bishop",
degree = 4,
directed = TRUE,
reverse = FALSE)
bishop_2 <- gg_matrix(connectivity_matrix(nb_2), "B. Directed network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_3 <- create_edge_list(nodes,
method = "bishop",
degree = 4,
directed = TRUE,
reverse = TRUE)
bishop_3 <- gg_matrix(connectivity_matrix(nb_3), "C. Directed network (reverse)") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
(bishop_1 | bishop_2 | bishop_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# knight(nodes, focus = "5-5", degree = 4, ...)
## ----'cb-knight', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 9. Moves of the **Knight** (with degree = 4)", out.width='100%'----
knight_1 <-
gg_chessboard(nodes, "A. Undirected network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, knight(nodes, focus, degree = 4, directed = FALSE,
reverse = FALSE))
knight_2 <-
gg_chessboard(nodes, "B. Directed network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, knight(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE))
knight_3 <-
gg_chessboard(nodes, "C. Directed network (reverse)", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, knight(nodes, focus, degree = 4, directed = TRUE,
reverse = TRUE))
(knight_1 | knight_2 | knight_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# create_edge_list(nodes, method = "knight", degree = 4, ...)
## ----'cb-knight-mat', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 10. Connectivity matrices of the **Knight** (with degree = 4)", out.width='100%'----
nb_1 <- create_edge_list(nodes,
method = "knight",
degree = 4,
directed = FALSE,
reverse = FALSE)
knight_1 <- gg_matrix(connectivity_matrix(nb_1), "A. Undirected network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_2 <- create_edge_list(nodes,
method = "knight",
degree = 4,
directed = TRUE,
reverse = FALSE)
knight_2 <- gg_matrix(connectivity_matrix(nb_2), "B. Directed network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_3 <- create_edge_list(nodes,
method = "knight",
degree = 4,
directed = TRUE,
reverse = TRUE)
knight_3 <- gg_matrix(connectivity_matrix(nb_3), "C. Directed network (reverse)") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
(knight_1 | knight_2 | knight_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# queen(nodes, focus = "5-5", degree = 4, ...)
## ----'cb-queen', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 11. Moves of the **Queen** (with degree = 4)", out.width='100%'----
queen_1 <-
gg_chessboard(nodes, "A. Undirected network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, queen(nodes, focus, degree = 4, directed = FALSE,
reverse = FALSE))
queen_2 <-
gg_chessboard(nodes, "B. Directed network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, queen(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE))
queen_3 <-
gg_chessboard(nodes, "C. Directed network (reverse)", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, queen(nodes, focus, degree = 4, directed = TRUE,
reverse = TRUE))
(queen_1 | queen_2 | queen_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# create_edge_list(nodes, method = "queen", degree = 4, ...)
## ----'cb-queen-mat', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 12. Connectivity matrices of the **Queen** (with degree = 4)", out.width='100%'----
nb_1 <- create_edge_list(nodes,
method = "queen",
degree = 4,
directed = FALSE,
reverse = FALSE)
queen_1 <- gg_matrix(connectivity_matrix(nb_1), "A. Undirected network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_2 <- create_edge_list(nodes,
method = "queen",
degree = 4,
directed = TRUE,
reverse = FALSE)
queen_2 <- gg_matrix(connectivity_matrix(nb_2), "B. Directed network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_3 <- create_edge_list(nodes,
method = "queen",
degree = 4,
directed = TRUE,
reverse = TRUE)
queen_3 <- gg_matrix(connectivity_matrix(nb_3), "C. Directed network (reverse)") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
(queen_1 | queen_2 | queen_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# wizard(nodes, focus = "5-5", degree = 4, ...)
## ----'cb-wizard', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 13. Moves of the **Wizard** (with degree = 4)", out.width='100%'----
wizard_1 <-
gg_chessboard(nodes, "A. Undirected network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, wizard(nodes, focus, degree = 4, directed = FALSE,
reverse = FALSE))
wizard_2 <-
gg_chessboard(nodes, "B. Directed network", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, wizard(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE))
wizard_3 <-
gg_chessboard(nodes, "C. Directed network (reverse)", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, wizard(nodes, focus, degree = 4, directed = TRUE,
reverse = TRUE))
(wizard_1 | wizard_2 | wizard_3)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# create_edge_list(nodes, method = "wizard", degree = 4, ...)
## ----'cb-wizard-mat', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 14. Connectivity matrices of the **Wizard** (with degree = 4)", out.width='100%'----
nb_1 <- create_edge_list(nodes,
method = "wizard",
degree = 4,
directed = FALSE,
reverse = FALSE)
wizard_1 <- gg_matrix(connectivity_matrix(nb_1), "A. Undirected network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_2 <- create_edge_list(nodes,
method = "wizard",
degree = 4,
directed = TRUE,
reverse = FALSE)
wizard_2 <- gg_matrix(connectivity_matrix(nb_2), "B. Directed network") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
nb_3 <- create_edge_list(nodes,
method = "wizard",
degree = 4,
directed = TRUE,
reverse = TRUE)
wizard_3 <- gg_matrix(connectivity_matrix(nb_3), "C. Directed network (reverse)") +
theme(axis.text = element_blank(), axis.text.x = element_blank(),
plot.caption = ggplot2::element_text(family = "mono", size = 12,
face = "bold", hjust = 0.5))
(wizard_1 | wizard_2 | wizard_3)
## ----'cb-custom', eval=TRUE, fig.height=4.3, fig.width=12, echo=FALSE, fig.cap="Figure 15. Custom moves", out.width='100%'----
wizard_1 <-
gg_chessboard(nodes, "Pawn & Bishop", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, pawn(nodes, focus, degree = 3, directed = TRUE,
reverse = FALSE)) +
geom_neighbors(nodes, bishop(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE))
wizard_2 <-
gg_chessboard(nodes, "Knight L & Bishop L", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, knight_left(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE)) +
geom_neighbors(nodes, bishop_left(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE))
wizard_3 <-
gg_chessboard(nodes, "Knight L, Bishop L, Pawn & Fool", "") +
geom_node(nodes, focus) +
geom_neighbors(nodes, knight_left(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE)) +
geom_neighbors(nodes, bishop_left(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE)) +
geom_neighbors(nodes, pawn(nodes, focus, degree = 4, directed = TRUE,
reverse = FALSE)) +
geom_neighbors(nodes, fool(nodes, focus, degree = 4, directed = TRUE,
reverse = TRUE))
(wizard_1 | wizard_2 | wizard_3)
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