---
title: "An Introduction to the RSTr Package"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{An Introduction to the RSTr Package}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(comment = "#>", collapse = TRUE)
library(RSTr)
library(ggplot2)
is_cran <- identical(Sys.getenv("NOT_CRAN"), "false")
if (Sys.getenv("NOT_CRAN") == "") is_cran <- TRUE
```

## Overview
The RSTr package is a tool that provides a host of Bayesian spatiotemporal models in conjunction with C++ to quickly and easily generate spatially-smoothed age-standardized estimates for your spatial data. This vignette introduces you to the basics of the RSTr package and shows you how to apply the basic functions to the included example data to get small area estimates.

## Models
The models provided in the RSTr package are based on the [Besag, York, and Mollié (1991)](https://link.springer.com/article/10.1007/bf00116466) Conditional Autoregressive (CAR) model, which spatially smooths data by incorporating information such as event and population counts from neighboring geographic units (counties, census tracts, etc.). The degree of spatial smoothing is determined by a spatial region's respective population size. The CAR model can be extended to several levels of complexity, depending on the input data:

-   BYM CAR (CAR): Spatially smooths across geographies;

-   Restricted CAR (RCAR): Spatially smooths across geographies and prevents over-smoothing;

-   Multivariate CAR (MCAR): Spatially smooths across geographies and sociodemographic groups; and

-   Multivariate Spatiotemporal CAR (MSTCAR): Spatially smooths across geographies, sociodemographic groups, and time periods.

For this vignette, we will demonstrate RSTr's functionality with an MSTCAR model.

### Restricted models to prevent over-smoothing

A problem with CAR models pointed out by [Quick, et al. (2021)](https://pubmed.ncbi.nlm.nih.gov/33980402/) is that of over-smoothing due to the informativeness of the BYM model. The RSTr package provides enhancements to the CAR models for both Poisson- and binomial-distributed data that prevent over-smoothing by restricting model informativeness through the `rcar()` function. Enhancements for the MCAR and MSTCAR models are under progress, and will be incorporated into the RSTr package as they are developed.

To learn more about restricted CAR models, read `vignette("RSTr-informativeness")`.

## Datasets

RSTr comes with three main datasets: `miheart`, `miadj`, and `mishp`. `miheart` and `miadj` are related to the necessary components of our models, and `mishp` is a shapefile that helps map your results. To run an MSTCAR model, two components are necessary:

-   Event counts for a parameter of interest, stratified by region, group, and time period, and its corresponding population counts. These data may be binomial- or Poisson-distributed. The example dataset is binomial-distributed myocardial infarction deaths in six age groups from 1979-1988 in Michigan. Reference `miheart` to see how this data looks or `?miheart` for more information on the dataset. For more information on preparing your event data, read `vignette("RSTr-event")`.

-   An adjacency structure for your data. This is a `list` that tells RSTr which regions are neighbors of one other based on their region index (i.e., the order they appear in the dataset). Reference `miadj` for an example adjacency structure list. For more information on preparing your adjacency data, read `vignette("RSTr-adjacency")`.

Some quick notes about data setup:

-   Event/population data must be organized in a very specific manner. RSTr's models can accept up to three-dimensional arrays: in the MSTCAR model, for example, spatial regions must be on the rows, socio/demographic groups must be on the columns, and time periods must be on the matrix slices. Additionally, your event data's regions should be listed in the same order in your adjacency structure data.

-   Every region must have at least one neighbor. The adjacency structures must be listed in the same order as your count data.

## Functions

RSTr comes with a set of functions to generate small area estimates from your dataset. Here is a brief overview of the basic functions and their purpose:

-   `*car()`: Inputs data and model specifics and creates a local folder with all associated files to prepare for sample generation;
-   `age_standardize()`: Generates age-standardized estimates based on user-specified age groups;
-   `suppress_estimates()`: Suppresses estimates based on reliability criteria; and
-   `get_estimates()`: Creates a long `table` containing information on each region/group/time in the model.

## Example Model

### `mstcar()`

With an understanding of the example datasets and the functions, we can start running our first model. The example datasets are set up to run out-of-the-box:

```{r, eval = !is_cran, results = "hide", fig.keep = "last"}
mod_mst <- mstcar(
  name = "my_test_model",
  data = miheart,
  adjacency = miadj,
  dir = tempdir(),
  seed = 1234
)
```

```{r, eval = is_cran}
# For computational reasons, full model fitting is not run during CRAN checks.
# When building on CRAN, this vignette loads a pre-fitted example model included with the package.
# The pkgdown website shows the full model-fitting workflow.
example_dir <- system.file("extdata", package = "RSTr")
mod_mst <- load_model("mstcar_example", example_dir)
```

Here, we use the `mstcar()` function to specify our model. `mstcar()` accepts a few different arguments in this case:

-   The `name` argument specifies the folder where the model data lives;
-   The `data` argument specifies event/population data;
-   The `adjacency` argument specifies our adjacency structure;
-   The `dir` argument specifies the directory where to save the folder; and
-   The `seed` argument specifies a random seed for replicability purposes.

`mstcar()` creates a folder named `my_test_model` in R's temporary directory containing folders that will hold batches of outputs for each parameter update. Additionally, an `RSTr` object which holds all information associated with the model (aside from samples) is created in the R environment and in the temporary directory. No samples are saved in the R environment because, given a sufficiently large dataset, MSTCAR models can become so large that it's impossible to hold all the model samples in RAM. Therefore, all of the samples are saved locally. Should you want to save your model somewhere besides the temporary directory for future use, you can specify a folder with the `dir` argument.

Note that `mstcar()` accepts more arguments than are used here, but these are the only ones needed to get started. Priors and initial values, for example, can be specified manually, but this is outside the scope of this vignette. There will also be checks performed on the input data: if something is wrong, warnings and error messages will tell you what is wrong and how to fix it. For a list of diagnostic errors and what they mean, read `vignette("RSTr-troubleshooting")`.

The RSTr package works by generating samples in batches and saving them locally inside of the model directory to be retrieved once the model is finished running. Generating samples in batches helps facilitate the tuning of the underlying MCMC algorithm and helps avoid computational burden by only holding a fraction of the total samples in memory at any given time. RSTr runs 6,000 iterations split into 60 batches of size 100 each. All batches are thinned for every 10 iterations by default, as the `lambdas` (a.k.a., the rate estimates) tend to exhibit autocorrelation. Moreover, thinning saves space when writing samples to the hard drive, as batches from larger models can balloon to gigabytes of size before thinning. 

Console outputs will show the current batch number, the progress within that batch, and the elapsed time. The model `Rds` file will be updated as the sampler progresses in case you need to reload your model at a later date. If the model crashes for any reason or R closes while the model is being run, the model `Rds` file will keep track of the current batch and pick back up where it left off when re-run. While `mstcar()` is running, the R plot window will show traceplots from a selection of estimates to check stability and diagnose any potential issues.

If you want to learn more about `mstcar()` and the other model functions, read `vignette("RSTr-car")`.

### `get_estimates()`

`mstcar()` takes care of the vast majority of model preparation: within the function, the model is set up, samples are generated, and our medians are estimated. Once the function finishes, we can get an overview of our model:

```{r}
mod_mst
```

Here, we get a birds-eye-view of the model, including the model we used (MSTCAR), the data likelihood type, the number of geographic units, and whether our estimates have been age-standardized or suppressed along reliability criteria. With the `get_estimates()` function, we can get a more detailed look at our estimates. For this type of mortality data, it is common to observe the rates per 100,000 population, so we set the `rates_per` argument in `get_estimates()` to 1e5:

```{r}
mst_estimates <- get_estimates(mod_mst, rates_per = 1e5)
head(mst_estimates)
```

The `mst_estimates` object contains in-depth information about our model estimates, including the medians, the credible intervals, the relative precisions, and the event/population counts; region, group, and time period columns are also provided.

### `age_standardize()`

One of the most important features of the RSTr package is the ability to easily generate age-standardized estimates. Let's say we want to get age-standardized estimates for the 35-64 age group; for our model, we use the `age_standardize()` function, then specify the groups of interest, their associated standard populations, and the name we want to give them. Since we are using data from 1979-1988, we can use 1980 standard populations from [NIH](https://seer.cancer.gov/stdpopulations/stdpop.19ages.html) to generate a `std_pop` standard population vector:

```{r}
std_pop <- c(68775, 34116, 9888)
mod_mst <- age_standardize(mod_mst, std_pop, new_name = "35-64", groups = c("35-44", "45-54", "55-64"))
mod_mst
```

Notice now that the `mod_mst` object indicates we have age-standardized our estimates and the names of our age-standardized groups.

```{r}
mst_estimates_as <- get_estimates(mod_mst)
head(mst_estimates_as)
```

Now, `get_estimates(mod_mst)` shows the age-standardized estimates. Should you want to see those instead, you can set the argument `standardized = FALSE`.

### `suppress_estimates()`

While the main benefit of RSTr is generating reliable estimates from small-population areas, we cannot guarantee that all estimates generated by `mstcar()` will be reliable. Therefore, it is prudent to suppress estimates that are deemed unreliable. For MSTCAR models, we can use two criteria to test for reliability: relative precision (i.e., the ratio of the median estimate to the width of its credible interval) and population count. For relative precisions, we aim for a value of at least 1 (i.e., the median is larger than the width of its credible interval), and for myocardial infarction death rates, we typically aim for a population threshold of at least 1,000. Using the `suppress_estimates()` function, we can generate suppressed estimates for our age-standardized rates:

```{r}
mod_mst <- suppress_estimates(mod_mst, threshold = 1e3)
mod_mst
mst_estimates_as <- get_estimates(mod_mst)
head(mst_estimates_as)
```

`mod_mst` now shows us that our estimates are suppressed and indicates the number of reliable rates.

If you want to learn more about `get_estimates()`, `age_standardize()`, and `suppress_estimates()`, read `vignette("RSTr-estimates")`.

## Illustrative Example: Mapping Estimates

We can get a better picture of the geographic patterns in our data with a map. Using `ggplot` (or your favorite mapping package), Let's see how the (non-age-standardized) estimates were smoothed:

```{r, eval = !is_cran}
# Original Myocardial Infarction Death Rates in MI, Ages 35-64, 1988
estimates_88 <- mst_estimates_as[mst_estimates_as$year == "1988", ]
estimates_3564 <- estimates_88[estimates_88$group == "35-64", ]
raw_3564 <- (estimates_3564$events / estimates_3564$population * 1e5)
ggplot(mishp) +
  geom_sf(aes(fill = raw_3564)) +
  labs(
    title = "Raw Myocardial Infarction Death Rates in MI, Ages 65 and up, 1988",
    fill = "Deaths per 100,000"
  ) +
  scale_fill_viridis_c() +
  theme_void()
# Spatially Smoothed MI Death Rates in MI
est_3564 <- estimates_3564$medians
ggplot(mishp) +
  geom_sf(aes(fill = est_3564)) +
  labs(
    title = "Smoothed Myocardial Infarction Death Rates in MI, Ages 35-64, 1988",
    fill = "Deaths per 100,000"
  ) +
  scale_fill_viridis_c() +
  theme_void()
```

```{r, eval = is_cran, echo = FALSE}
# Mapping examples are shown on the RSTr pkgdown website.
NULL
```

This map helps us see how RSTr smooths rates. First, notice how the range of the two plots are different: the smoothed map has a smaller range because RSTr stabilizes high and low extreme values which are usually caused by low population counts. Also, notice how the transitions between high-rate and low-rate regions are more gradual on the smoothed map. This is a consequence of using neighboring regions to inform and stabilize estimates.

From here, we can get a better idea of how these maps contrast. For example, on the first map, the largest region of interest is the middle portion of the Lower Peninsula (LP), but on the smoothed map, much of this area has attenuated rates. On the flip side, many areas in the Upper Peninsula (UP) have relatively lower rates on the first map, but we can see on the smoothed map that the highest rate in the state is in the UP. The higher-rate areas on the LP are focused around counties on Saginaw Bay in the east, indicating that these areas may require more attention than previously thought. These are the kinds of inferences that can be made using estimates generated by the RSTr package and the main motivation for running this spatiotemporal model.

## Closing Thoughts

This vignette introduces you to inputting data into the `mstcar()` function, extracting estimates with the `get_estimates()` function, age-standardizing estimates with the `age_standardize()` function, suppressing estimates with the `suppress_estimates()` function, and finally making a map with estimates gathered from `get_estimates()` function. What we've discussed here is just scratching the surface of the RSTr package. Other package vignettes will dive deeper into the intricacies of each component of the package. All of these things together will ensure you get the most out of using RSTr.
