## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>",
                      fig.width = 8, fig.height = 5, out.width = "100%")

## ----setup--------------------------------------------------------------------
library(transitiontrees)
data(trajectories)
set.seed(1)

tree   <- context_tree(trajectories, max_depth = 3L, min_count = 5L)
pruned <- prune_tree(tree, criterion = "G2", alpha = 0.05)
pruned

## ----horizontal, fig.width = 14, fig.height = 8-------------------------------
plot(pruned, style = "horizontal")

## ----horizontal-sized, fig.width = 14, fig.height = 8-------------------------
plot(pruned, style = "horizontal",
     point_size_range = c(3, 12), edge_size_range = c(0.4, 3.5))

## ----dendrogram, fig.height = 6-----------------------------------------------
plot(pruned, style = "dendrogram")

## ----icicle, fig.height = 6---------------------------------------------------
plot(pruned, style = "icicle")

## ----heatmap-count, fig.height = 5.5------------------------------------------
plot_pathways(pruned, top = 12, sort_by = "count")        # the highways

## ----heatmap-div, fig.height = 5.5--------------------------------------------
plot_pathways(pruned, top = 12, sort_by = "divergence")   # the informative ones

## ----divergence, fig.height = 5-----------------------------------------------
plot_divergence(pruned, top = 12, min_count = 5)

## ----distributions, fig.height = 5.5------------------------------------------
plot_distributions(pruned, top = 6)

## ----pruning, fig.width = 9, fig.height = 4.5---------------------------------
plot_pruning(tree, "Active -> Active -> Average")

## ----predictive-logloss, fig.height = 4.5-------------------------------------
plot_predictive(pruned, trajectories, type = "logloss")

## ----predictive-ecdf, fig.height = 4.5----------------------------------------
plot_predictive(pruned, trajectories, type = "ecdf")

## ----traj-fit-----------------------------------------------------------------
data(ai_long)
tree_ai   <- context_tree(ai_long, actor = "project", session = "session_id",
                         action = "code", max_depth = 3L, min_count = 10L)
pruned_ai <- prune_tree(tree_ai)

## ----traj-freq, fig.width = 11, fig.height = 7--------------------------------
plot_trajectories(tree_ai, measure = "frequency", min_count = 20L)

## ----traj-pred, fig.width = 11, fig.height = 7--------------------------------
plot_trajectories(pruned_ai, measure = "predictability", min_count = 20L)

## ----boot-plot, fig.height = 5.5----------------------------------------------
boot <- bootstrap_pathways(pruned, iter = 100L, seed = 1L)
plot(boot)

## ----boot-resamples, fig.height = 4.5-----------------------------------------
plot_pathway_resamples(boot, stat = "divergence", top = 6)

## ----compare-plot, fig.height = 4.5-------------------------------------------
data(group_regulation_long)
grp_reg <- context_tree(group_regulation_long,
                       actor = "Actor", time = "Time", action = "Action",
                       group = "Achiever", max_depth = 2L, min_count = 10L)
cmp <- compare_trees(prune_tree(grp_reg), iter = 199L, seed = 1L)
plot(cmp)

## ----tune-plot, fig.height = 5------------------------------------------------
tg <- tune_tree(trajectories, max_depth = 1L:4L, folds = 5L, seed = 1L)
plot(tg)

## ----difference, fig.height = 5-----------------------------------------------
plot_difference(grp_reg, depth = 1L)