---
title: "An Introduction to stoRy"
author:
  - Paul Sheridan
  - Oshan Modi
  - Mikael Onsjö
date: "`r format(Sys.time(), '%B %d, %Y')`"
bibliography: assets/stoRy_refs.bib
output: rmarkdown::html_vignette
description: This vignette introduces stoRy package functions for downloading,
  exploring, and analyzing Literary Theme Ontology (LTO) data. Familiarity
  with LTO themes and the related collaborative system of story thematic
  annotation is helpful, but not absolutely necessary for working through this
  vignette.
vignette: >
  %\VignetteIndexEntry{stoRy}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```


## Background

The *Theme Ontology Project* is an open access, community-based fiction
studies undertaking to
* define common literary themes (or "themes" for short),
* classify defined themes into a hierarchically structured
controlled-vocabulary, and
* annotate works of fiction with the themes within a collaborative framework.
The LTO refers to the hierarchically structured collection of literary themes
[@Sheridan2019b]. The current developmental version of the LTO contains over
3,000 carefully defined themes. To date over 3,000 stories (e.g., films,
novels, TV series episodes, video game plots, etc.) have been annotated with
LTO themes. All data is hosted on the Theme Ontology GitHub repository
[theming](https://github.com/theme-ontology/theming). It can be explored on
the Theme Ontology [website](https://www.themeontology.org/). The `stoRy`
package is used to perform various statistical analyses on the data. These
tells us interesting things about the kind of stories we humans invent.


## Installation

The package is hosted on CRAN and can be installed by running the command

```{r setup}
library(stoRy)
```

The developmental version is hosted on GitHub and can be installed using the
devtools package:


```{r}
# install.packages("devtools")
# devtools::install_github("theme-ontology/stoRy")
```

Once installed, the package can be loaded by running the standard library
command

```{r}
library(stoRy)
```


## Accessing Documentation

Each function in the package is documented. The command

```{r}
help(package = "stoRy")
```

gives a cursory overview of the package and a complete list of package
functions.

Help with using functions is obtained in the usual R manner. For instance,
the documentation for the `get_similar_stories` function can be accessed
with the command

```{r}
?get_similar_stories
```

The command

```{r}
citation("stoRy")
```

prints to console everything needed to cite the package in a publication.


## Quick Start: The Twilight Zone Franchise Demo Data

This section is a good starting point for first time users. Included in the
package is a toy dataset, extracted from the latest LTO version, comprising
some 2,872 LTO themes and 335 thematically annotated *The Twilight Zone*
American media franchise stories [@Wikipedia2021].

The themes are hierarchically arranged into four domains descended from an
abstract root theme:
```
literary thematic entity
├── the human condition
├── society
├── the pursuit of knowledge
└── speculative fiction theme
```

Contained in the demo data are the following *Twilight Zone* thematically
annotated stories:

* 156 *The Twilight Zone* (1959) television series episodes

* 3 *Twilight Zone: The Movie* (1983) film sub-stories

* 110 *The Twilight Zone* (1985) television series episodes

* 3 *Twilight Zone: Rod Serling's Lost Classics* (1994) film sub-stories

* 43 *The Twilight Zone* (2002) television series episodes

* 20 *The Twilight Zone* (2019) television series episodes

Users may avail themselves of the demo data to experiment with package
functions without having to download any official LTO version data to their
local machine.


To begin check that the `demo` LTO version is active
```{r}
which_lto()
```

Should it be that another LTO version is actively loaded, switch to the `demo`
version 
```{r}
set_lto(version = "demo")
```

Print LTO `demo` version summary information to console 
```{r}
print_lto()
```

A detailed description of the demo data included in the package can be viewed
by running the command

```{r}
?`lto-demo`
```

**Pro Tip**: The demo data, and LTO version data more generally, is internally
stored in such a way that prohibits users from modifying it. The following
sequence of commands, however, clones the data:

```{r}
demo_metadata_tbl <- clone_active_metadata_tbl()
demo_themes_tbl <- clone_active_themes_tbl()
demo_stories_tbl <- clone_active_stories_tbl()
demo_collections_tbl <- clone_active_collections_tbl()
```

See `?lto-demo` for more details on exploring the output tibble contents.


### Example: Initialize a Theme

The social phenomenon of dangers, be they real or imagined, spreading through
a community as a result of rumors and fear is explored in numerous works of
fiction, including several *Twilight Zone* episodes.

The LTO captures hysteria of this kind with the theme
[mass hysteria](https://themeontology.org/theme.php?name=mass%20hysteria). To
explore "mass hysteria" theme ("demo" version) initialize the `Theme` class
object
```{r}
theme <- Theme$new(theme_name = "mass hysteria")
```

The theme entry can be printed to console in two ways
```{r}
# Print stylized text:
theme

# Print in plain text .th.txt file format:
theme$print(canonical = TRUE)
```

Story thematic annotations are stored as a tibble
```{r}
theme$annotations()
```

See `?Theme` for more on `Theme` class objects.

**A Note on Finding Themes**: LTO developmental themes are easily explored
using the [theme search box](https://themeontology.org/themes) on the project
website. Chances are that any theme found in the developmental version will
also exist in the demo version. So searching for themes on the website offers
a practical approach to finding interesting themes to initialize in an R
session.

**Pro Tip**: Demo version themes are explorable in tibble format. For example,
here is one way to search for "mass hysteria" directly in the demo themes:
```{r}
# install.packages("dplyr")
suppressMessages(library(dplyr))
# install.packages("stringr")
library(stringr)
demo_themes_tbl <- clone_active_themes_tbl()
demo_themes_tbl %>% filter(str_detect(theme_name, "mass"))
```
Notice that all themes containing the substring `"mass"` are returned. The
`dplyr` package is required to run the `%>%` mediated pipeline.


### Example: Initialize a Story

Thematically annotated stories are initialized by story ID. For example, run
```{r}
story <- Story$new(story_id = "tz1959e1x22")
```
to initialize a `Story` class object representing the "mass hysteria"
featuring classic *Twilight Zone* (1959) television series episode *The
Monsters Are Due on Maple Street*.

Story thematic annotations along with episode identifying metadata can be
printed to console
```{r}
# In stylized text format:
story

# In plain text .st.txt file format:
story$print(canonical = TRUE)
```

A tibble of thematic annotations is obtained by running
```{r}
themes <- story$themes()
themes
```

See `?Theme` for more on `Theme` class objects.

**A Note on Finding Story IDs**: The project website
[story search box](https://themeontology.org/stories) offers a
quick-and-dirty way of locating LTO developmental version story IDs of
interest. Since story IDs are stable, developmental version *The Twilight
Zone* story IDs can be expected to agree with their demo data counterparts.

**Pro Tip**: A demo data story ID is directly obtained from an episode title
as follows:
```{r}
title <- "The Monsters Are Due on Maple Street"
demo_stories_tbl <- clone_active_stories_tbl()
story_id <- demo_stories_tbl %>% filter(title == !!title) %>% pull(story_id)
story_id
```
The `dplyr` package is again required to run the `%>%` mediated pipeline.


### Example: Initialize a Collection

Each story belongs to at least one collection (i.e. a set of related stories).
*The Monsters Are Due on Maple Street*, for instance, belongs to the two
collections
```{r}
story$collections()
```

To initialize a `Collection` class object for *The Twilight Zone* (1959)
television series, of which *The Monsters Are Due on Maple Street* is an
episode, run:
```{r}
collection <- Collection$new(collection_id = "Collection: tvseries: The Twilight Zone (1959)")
```

Collection info is printed to console in the same way as with themes and
stories
```{r}
# Print stylized text:
collection

# Print in plain text .st.txt file format:
collection$print(canonical = TRUE)
```

**A Note on Finding Collection IDs**: As with stories, LTO developmental
version collections can be explored from the project website
[story search box](https://themeontology.org/stories). Developmental and demo
version collection IDs should generally match up. This is in particular the
case with *Twilight Zone* collection IDs.

**Pro Tip**: Demo version collections can be directly explored in the usual
way
```{r}
demo_collections_tbl <- clone_active_collections_tbl()
demo_collections_tbl
```


### Example: Find the Topmost Featured Themes in a Collection

To view the top 10 most featured themes in the *The Twilight Zone* (1959)
series run:
```{r}
collection <- Collection$new(collection_id = "Collection: tvseries: The Twilight Zone (1959)")
result_tbl <- get_featured_themes(collection)
result_tbl
```

To view the top 10 most featured themes in the demo data as a whole run
```{r}
result_tbl <- get_featured_themes()
result_tbl
```

### Example: Find the Topmost Enriched Themes in a Collection

To view the top 10 most enriched, or over-represented themes in *The Twilight
Zone* (1959) series with all *The Twilight Zone* stories as background run
```{r}
test_collection <- Collection$new(collection_id = "Collection: tvseries: The Twilight Zone (1959)")
result_tbl <- get_enriched_themes(test_collection)
result_tbl
```

To run the same analysis not counting *minor* level themes run
```{r}
result_tbl <- get_enriched_themes(test_collection, weights = list(choice = 1, major = 1, minor = 0))
result_tbl
```

The theory and methods implemented in the `get_enriched_themes` function
are described in [@Onsjo2020].


### Example: Find Similar Stories to a Story of Interest

To view the top 10 most thematically similar *Twilight Zone* franchise
stories to *The Monsters Are Due on Maple Street* run
```{r}
query_story <- Story$new(story_id = "tz1959e1x22")
result_tbl <- get_similar_stories(query_story)
result_tbl
``` 

The theory and methods implemented in the `get_enriched_themes` function
are described in [@Sheridan2019a].


### Example : Find Clusters of Similar Stories

Cluster *The Twilight Zone* franchise stories according to thematic
similarity by running
```{r, eval = FALSE}
set.seed(123)
result_tbl <- get_story_clusters()
result_tbl
```
The command `set.seed(123)` is run here for the purpose of reproducibility.

Explore a cluster of stories related to traveling back in time
```{r, eval = FALSE}
cluster_id <- 3
pull(result_tbl, stories)[[cluster_id]]
pull(result_tbl, themes)[[cluster_id]]
```

Explore a cluster of stories related to mass panics
```{r, eval = FALSE}
cluster_id <- 5
pull(result_tbl, stories)[[cluster_id]]
pull(result_tbl, themes)[[cluster_id]]
```

Explore a cluster of stories related to executions
```{r, eval = FALSE}
cluster_id <- 7
pull(result_tbl, stories)[[cluster_id]]
pull(result_tbl, themes)[[cluster_id]]
```

Explore a cluster of stories related to space aliens
```{r, eval = FALSE}
cluster_id <- 10
pull(result_tbl, stories)[[cluster_id]]
pull(result_tbl, themes)[[cluster_id]]
```

Explore a cluster of stories related to old people wanting to be young
```{r, eval = FALSE}
cluster_id <- 11
pull(result_tbl, stories)[[cluster_id]]
pull(result_tbl, themes)[[cluster_id]]
```

Explore a cluster of stories related to wish making
```{r, eval = FALSE}
cluster_id <- 13
pull(result_tbl, stories)[[cluster_id]]
pull(result_tbl, themes)[[cluster_id]]
```

## Download and Configure LTO Version Data

The package works with data from these LTO versions
```{r, eval = FALSE}
lto_version_statuses()
```

### Example: Download and Configure the Latest LTO Version

To download and cache the latest versioned LTO release run
```{r, eval = FALSE}
configure_lto(version = "latest")
```
This can take awhile.

Load the newly configured LTO version as the active version in the R session:
```{r, eval = FALSE}
set_lto(version = "latest")
```

To double check that it has been loaded successfully run
```{r, eval = FALSE}  
which_lto()
```

Now that the latest LTO version is loaded into the R session, its stories and
themes can be analyzed in the same way as with the "demo" LTO version data as
shown above.


## References