README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# tidylda <img src='man/figures/logo.png' align="right" height="136.5" />

<!-- badges: start -->
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06800/status.svg)](https://doi.org/10.21105/joss.06800)
[![Codecov test coverage](https://codecov.io/gh/TommyJones/tidylda/branch/main/graph/badge.svg)](https://app.codecov.io/gh/tommyjones/tidylda/branch/main)
[![R-CMD-check](https://GitHub.com/TommyJones/tidylda/actions/workflows/R-CMD-check.yaml/badge.svg)](https://GitHub.com/TommyJones/tidylda/actions/workflows/R-CMD-check.yaml)
[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
<!-- badges: end -->


Latent Dirichlet Allocation Using 'tidyverse' Conventions

`tidylda` implements an algorithm for Latent Dirichlet Allocation using style conventions from the [tidyverse](https://style.tidyverse.org/) and [tidymodels](https://tidymodels.GitHub.io/model-implementation-principles/). 
    
In addition this implementation of LDA allows you to:

* use asymmetric prior parameters alpha and eta
* use a matrix prior parameter, eta, to seed topics into a model
* use a previously-trained model as a prior for a new model
* apply LDA in a transfer-learning paradigm, updating a model's parameters with additional data (or additional iterations)


## Installation

You can install the latest CRAN release with:

``` r
install("tidylda")
```


You can install the development version from [GitHub](https://GitHub.com/) with:

``` r
install.packages("remotes")

remotes::install_GitHub("tommyjones/tidylda")
```

For a list of dependencies see the DESCRIPTION file.

# Getting started

This package is still in its early stages of development. However, some basic functionality is below. Here, we will use the `tidytext` package to create a document term matrix, fit a topic model, predict topics of unseen documents, and update the model with those new documents.

`tidylda` uses the following naming conventions for topic models:

* `theta` is a matrix whose rows are distributions of topics over documents, or P(topic|document)
* `beta` is a matrix whose rows are distributions of tokens over topics, or P(token|topic)
* `lambda` is a matrix whose rows are distributions of topics over tokens, or P(topic|token)
  `lambda` is useful for making predictions with a computationally-simple and efficient dot product and it may be interesting to analyze in its own right.
* `alpha` is the prior that tunes `theta`
* `eta` is the prior that tunes `beta`

## Example

```{r example}
library(tidytext)
library(dplyr)
library(ggplot2)
library(tidyr)
library(tidylda)
library(Matrix)

### Initial set up ---
# load some documents
docs <- nih_sample 

# tokenize using tidytext's unnest_tokens
tidy_docs <- docs %>% 
  select(APPLICATION_ID, ABSTRACT_TEXT) %>% 
  unnest_tokens(output = word, 
                input = ABSTRACT_TEXT,
                stopwords = stop_words$word,
                token = "ngrams",
                n_min = 1, n = 2) %>% 
  count(APPLICATION_ID, word) %>% 
  filter(n>1) #Filtering for words/bigrams per document, rather than per corpus

tidy_docs <- tidy_docs %>% # filter words that are just numbers
  filter(! stringr::str_detect(tidy_docs$word, "^[0-9]+$"))

# append observation level data 
colnames(tidy_docs)[1:2] <- c("document", "term")


# turn a tidy tbl into a sparse dgCMatrix 
# note tidylda has support for several document term matrix formats
d <- tidy_docs %>% 
  cast_sparse(document, term, n)

# let's split the documents into two groups to demonstrate predictions and updates
d1 <- d[1:50, ]

d2 <- d[51:nrow(d), ]

# make sure we have different vocabulary for each data set to simulate the "real world"
# where you get new tokens coming in over time
d1 <- d1[, colSums(d1) > 0]

d2 <- d2[, colSums(d2) > 0]

### fit an intial model and inspect it ----
set.seed(123)

lda <- tidylda(
  data = d1,
  k = 10,
  iterations = 200, 
  burnin = 175,
  alpha = 0.1, # also accepts vector inputs
  eta = 0.05, # also accepts vector or matrix inputs
  optimize_alpha = FALSE, # experimental
  calc_likelihood = TRUE,
  calc_r2 = TRUE, # see https://arxiv.org/abs/1911.11061
  return_data = FALSE
)

# did the model converge?
# there are actual test stats for this, but should look like "yes"
qplot(x = iteration, y = log_likelihood, data = lda$log_likelihood, geom = "line") + 
    ggtitle("Checking model convergence")

# look at the model overall
glance(lda)

print(lda)

# it comes with its own summary matrix that's printed out with print(), above
lda$summary


# inspect the individual matrices
tidy_theta <- tidy(lda, matrix = "theta")

tidy_theta

tidy_beta <- tidy(lda, matrix = "beta")

tidy_beta

tidy_lambda <- tidy(lda, matrix = "lambda")

tidy_lambda

# append observation-level data
augmented_docs <- augment(lda, data = tidy_docs)

augmented_docs

### predictions on held out data ---
# two methods: gibbs is cleaner and more technically correct in the bayesian sense
p_gibbs <- predict(lda, new_data = d2[1, ], iterations = 100, burnin = 75)

# dot is faster, less prone to error (e.g. underflow), noisier, and frequentist
p_dot <- predict(lda, new_data = d2[1, ], method = "dot")

# pull both together into a plot to compare
tibble(topic = 1:ncol(p_gibbs), gibbs = p_gibbs[1,], dot = p_dot[1, ]) %>%
  pivot_longer(cols = gibbs:dot, names_to = "type") %>%
  ggplot() + 
  geom_bar(mapping = aes(x = topic, y = value, group = type, fill = type), 
           stat = "identity", position="dodge") +
  scale_x_continuous(breaks = 1:10, labels = 1:10) + 
  ggtitle("Gibbs predictions vs. dot product predictions")

### Augment as an implicit prediction using the 'dot' method ----
# Aggregating over terms results in a distribution of topics over documents
# roughly equivalent to using the "dot" method of predictions.
augment_predict <- 
  augment(lda, tidy_docs, "prob") %>%
  group_by(document) %>% 
  select(-c(document, term)) %>% 
  summarise_all(function(x) sum(x, na.rm = T))

# reformat for easy plotting
augment_predict <- 
  as_tibble(t(augment_predict[, -c(1,2)]), .name_repair = "minimal")

colnames(augment_predict) <- unique(tidy_docs$document)

augment_predict$topic <- 1:nrow(augment_predict) %>% as.factor()

compare_mat <- 
  augment_predict %>%
  select(
    topic,
    augment = matches(rownames(d2)[1])
  ) %>%
  mutate(
    augment = augment / sum(augment), # normalize to sum to 1
    dot = p_dot[1, ]
  ) %>%
  pivot_longer(cols = c(augment, dot))

ggplot(compare_mat) + 
  geom_bar(aes(y = value, x = topic, group = name, fill = name), 
           stat = "identity", position = "dodge") +
  labs(title = "Prediction using 'augment' vs 'predict(..., method = \"dot\")'")

# Not shown: aggregating over documents results in recovering the "tidy" lambda.

### updating the model ----
# now that you have new documents, maybe you want to fold them into the model?
lda2 <- refit(
  object = lda, 
  new_data = d, # save me the trouble of manually-combining these by just using d
  iterations = 200, 
  burnin = 175,
  calc_likelihood = TRUE,
  calc_r2 = TRUE
)

# we can do similar analyses
# did the model converge?
qplot(x = iteration, y = log_likelihood, data = lda2$log_likelihood, geom = "line") +
  ggtitle("Checking model convergence")

# look at the model overall
glance(lda2)

print(lda2)


# how does that compare to the old model?
print(lda)
```

There are several vignettes available in [/vignettes](https://GitHub.com/TommyJones/tidylda/tree/main/vignettes). They can be compiled using `knitr` or you can view [PDF versions on CRAN](https://CRAN.R-project.org/package=tidylda).

See NEWS.md for a changelog, including changes from the CRAN release to the development version on GitHub.

See the "Issues" tab on GitHub to see planned features as well as bug fixes.

# Contributions

If you would like to contribute to this package, please start by opening an issue on GitHub. Direct contributions via merge requests are discouraged unless invited to do so. 

If you have any suggestions for additional functionality, changes to functionality, changes to arguments or other aspects of the API please let me know by opening an issue on GitHub or sending me an email: jones.thos.w at gmail.com.

## Code of Conduct

Please note that the tidylda project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.