## ----setup, include = FALSE---------------------------------------------------
has_cograph <- requireNamespace("cograph", quietly = TRUE)
knitr::opts_chunk$set(collapse = TRUE, comment = "#>",
                      fig.width = 7, fig.height = 6, dpi = 100)
library(psychnets)

## ----check, echo = FALSE, results = "asis", eval = !has_cograph---------------
# cat("> `cograph` is not installed, so the cograph plotting chunks below are skipped.")

## ----fit, eval = has_cograph--------------------------------------------------
fit <- ebic_glasso(SRL_GPT)
fit

## ----default, eval = has_cograph----------------------------------------------
plot(fit)

## ----splot-default, eval = has_cograph----------------------------------------
cograph::splot(fit)

## ----layouts, eval = has_cograph, fig.width = 9, fig.height = 4.5-------------
op <- par(mfrow = c(1, 2), mar = c(1, 1, 3, 1))
cograph::splot(fit, layout = "circle", title = "circle")
cograph::splot(fit, layout = "spring", seed = 11, title = "spring")
par(op)

## ----nodes, eval = has_cograph------------------------------------------------
cograph::splot(
  fit,
  layout = "circle",
  scale_nodes_by = "strength",
  node_size_range = c(4, 12),
  node_fill = c("#4C78A8", "#F58518", "#54A24B", "#B279A2", "#E45756"),
  node_border_color = "white",
  node_border_width = 2,
  label_size = 0.9,
  title = "Node size scaled by strength"
)

## ----edges, eval = has_cograph------------------------------------------------
cograph::splot(
  fit,
  layout = "circle",
  threshold = 0.05,
  edge_width_range = c(0.5, 5),
  edge_positive_color = "#2A9D8F",
  edge_negative_color = "#E76F51",
  edge_labels = TRUE,
  edge_label_size = 0.7,
  edge_label_bg = "white",
  title = "Thresholded edge weights"
)

## ----edge-weights, eval = has_cograph, fig.width = 7, fig.height = 4.5--------
cograph::plot_edge_weights(fit)

## ----bootstrap, eval = has_cograph, fig.width = 8, fig.height = 5-------------
set.seed(1)
bs <- net_boot(SRL_GPT, method = "pcor", n_boot = 250, cores = 1)
plot(bs)

## ----edge-diff-box, eval = has_cograph, fig.width = 6.5, fig.height = 6.5-----
plot(bs, type = "edge_diff")

## ----edge-diff-forest, eval = has_cograph, fig.width = 7, fig.height = 5------
plot(difference_test(bs, type = "edge"), style = "forest")

## ----themes, eval = has_cograph, fig.width = 9, fig.height = 4.5--------------
op <- par(mfrow = c(1, 2), mar = c(1, 1, 3, 1))
cograph::splot(fit, theme = "minimal", title = "minimal")
cograph::splot(fit, theme = "colorblind", title = "colorblind")
par(op)

## ----group-data, include = FALSE----------------------------------------------
grouped_srl <- rbind(
  data.frame(SRL_GPT, source = "GPT", check.names = FALSE),
  data.frame(SRL_Claude, source = "Claude", check.names = FALSE)
)

## ----groups, eval = has_cograph, fig.width = 8, fig.height = 4.5--------------
group_fit <- psychnet(grouped_srl, group = "source", method = "glasso")
cograph::splot(group_fit, layout = "circle", psych_styling = TRUE)

## ----export, eval = FALSE-----------------------------------------------------
# cograph::splot(fit, layout = "circle", filename = "network.png",
#                width = 8, height = 8, res = 300)

