README.qmd

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# quartets: Datasets to help teach statistics <img src="man/figures/logo.png" align="right" height="138" />

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**Authors:** [Lucy D'Agostino McGowan](https://www.lucymcgowan.com/)<br/>
**License:** [MIT](https://opensource.org/license/mit/)

The quartets package is a collection of datasets aimed to help data analysis practitioners and students learn key statistical insights in a hands-on manner. It contains:

* [Anscombe's Quartet](#anscombes-quartet)
* [Causal Quartet](#causal-quartet)
* [Datasaurus Dozen](#datasaurus-dozen)
* [Interaction Triptych](#interaction-triptych)
* [Rashomon Quartet](#rashomon-quartet)
* [Gelman Variation and Heterogeneity Causal Quartets](#gelman-variation-and-heterogenity-causal-quartets)

## Installation 

You can install the quartets package from CRAN as follows:

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

Or the development version of quartets like so:

``` r
devtools::install_github("r-causal/quartets")
```

## Anscombe's Quartet 

The goal of the `anscombe_quartet` data set is to help drive home the point that visualizing your data is important. Francis Anscombe generated these four datasets to demonstrate that statistical summary measures alone cannot capture the full relationship between two variables (here, `x` and `y`). Anscombe emphasized the importance of visualizing data prior to calculating summary statistics.

* Dataset 1 has a linear relationship between `x` and `y`  
* Dataset 2 has shows a nonlinear relationship between `x` and `y`    
* Dataset 3 has a linear relationship between `x` and `y` with a single outlier    
* Dataset 4 has shows no relationship between `x` and `y` with a single outlier that serves as a high-leverage point.    

In each of the datasets the following statistical summaries hold:

* mean of `x`: 9    
* variance of `x`: 11   
* mean of `y`: 7.5    
* variance of y: 4.125    
* correlation between `x` and `y`: 0.816    
* linear regression between `x` and `y`: `y = 3 + 0.5x`   
* $R^2$ for the regression: 0.67    

## Example

```{r}
#| message: false
#| warning: false
library(tidyverse)
library(quartets)

ggplot(anscombe_quartet, aes(x = x, y = y)) +
  geom_point() + 
  geom_smooth(method = "lm", formula = "y ~ x") +
  facet_wrap(~dataset)

anscombe_quartet |>
  group_by(dataset) |>
  summarise(mean_x = mean(x),
            var_x = var(x),
            mean_y = mean(y),
            var_y = var(y),
            cor = cor(x, y)) |>
  knitr::kable(digits = 2)
```

## Causal Quartet 

The goal of the `causal_quartet` data set is to help drive home the point that when presented with an exposure, outcome, and some measured factors, statistics alone, whether summary statistics or data visualizations, are not sufficient to determine the appropriate causal estimate. Additional information about the data generating mechanism is needed in order to draw the correct conclusions. See [this paper](https://github.com/LucyMcGowan/writing-quartet/blob/main/manuscript.pdf) for details.


## Example

```{r}
#| message: false
#| warning: false

ggplot(causal_quartet, aes(x = exposure, y = outcome)) +
  geom_point() + 
  geom_smooth(method = "lm", formula = "y ~ x") +
  facet_wrap(~dataset)
```

```{r}
causal_quartet |>
  nest_by(dataset) |>
  mutate(`Y ~ X` = round(coef(lm(outcome ~ exposure, data = data))[2], 2),
         `Y ~ X + Z` = round(coef(lm(outcome ~ exposure + covariate, data = data))[2], 2),
         `Correlation of X and Z` = round(cor(data$exposure, data$covariate), 2)) |>
  select(-data, `Data generating mechanism` = dataset) |>
  knitr::kable()
```

## Datasaurus Dozen

Similar to Anscombe's Quartet, the Datasaurus Dozen has additional data sets where the mean, variance, and Pearson's correlation are identical, but visualizations demonstrate the large difference between datasets. This dataset is re-exported from the [datasauRus](https://CRAN.R-project.org/package=datasauRus) R package.

## Example

```{r}
#| message: false
#| warning: false

ggplot(datasaurus_dozen, aes(x = x, y = y)) +
  geom_point() + 
  geom_smooth(method = "lm", formula = "y ~ x") +
  facet_wrap(~dataset)

datasaurus_dozen |>
  group_by(dataset) |>
  summarise(mean_x = mean(x),
            var_x = var(x),
            mean_y = mean(y),
            var_y = var(y),
            cor = cor(x, y)) |>
  knitr::kable(digits = 2)
```

## Interaction Triptych

This set of 3 datasets demonstrating that while the slopes estimated by a simple linear interaction model may be the same, the underlying data-generating mechanisms can be vastly different.

```{r}
ggplot(interaction_triptych, aes(x, y)) +
  geom_point(shape = "o") +
  geom_smooth(method = "lm", formula = "y ~ x") + 
  facet_grid(dataset ~ moderator)
```

## Rashomon Quartet

This dataset demonstrates that model diagnostics alone (such as $R^2$ and RMSE) do not tell the full story of a prediction model. Here, there are three predictors and one outcome. Models fit using a regression tree, linear regression, random forest, and neural network all yield the same $R^2$ and RMSE, but are finding different relationships between the predictors, as evidenced by the below partial dependence plots. 

```{r}
#| message: false
#| warning: false
set.seed(1568)
library(tidymodels)
library(DALEXtra)
```

```{r}
#| cache: true
rec <- recipe(y ~ ., data = rashomon_quartet_train)

## Regression Tree

wf_tree <- workflow() |>
  add_recipe(rec) |>
  add_model(
    decision_tree(mode = "regression", engine = "rpart",
                  tree_depth = 3, min_n = 250)
  )

tree <- fit(wf_tree, rashomon_quartet_train)
exp_tree <- explain_tidymodels(
  tree, 
  data = rashomon_quartet_test[, -1], 
  y = rashomon_quartet_test[, 1],
  verbose = FALSE, 
  label = "decision tree")

## Linear Model

wf_linear <- wf_tree |>
  update_model(linear_reg())

lin <- fit(wf_linear, rashomon_quartet_train)
exp_lin <- explain_tidymodels(
  lin, 
  data = rashomon_quartet_test[, -1], 
  y = rashomon_quartet_test[, 1],
  verbose = FALSE, 
  label = "linear regression")

## Random Forest

wf_rf <- wf_tree |>
  update_model(rand_forest(mode = "regression", 
                           engine = "randomForest", 
                           trees = 100))

rf <- fit(wf_rf, rashomon_quartet_train)
exp_rf <- explain_tidymodels(
  rf, 
  data = rashomon_quartet_test[, -1], 
  y = rashomon_quartet_test[, 1],
  verbose = FALSE, 
  label = "random forest")

## Neural Network

library(neuralnet)
nn <- neuralnet(
  y ~ ., 
  data = rashomon_quartet_train, 
  hidden = c(8, 4), 
  threshold = 0.05)

exp_nn <- explain_tidymodels(
  nn, 
  data = rashomon_quartet_test[, -1], 
  y = rashomon_quartet_test[, 1],
  verbose = FALSE, 
  label = "neural network")

```

We can see that each of these models "perform" the same.

```{r}
mp <- map(list(exp_tree, exp_lin, exp_rf, exp_nn), model_performance)
tibble(
  model = c("Decision tree", "Linear regression", "Random forest", "Neural network"),
  R2 = map_dbl(mp, ~.x$measures$r2),
  RMSE = map_dbl(mp, ~.x$measures$rmse)
  ) |>
  knitr::kable(digits = 2)
```

But the way they fit to the actual predictors is quite different: 

```{r}
#| cache: true
pd_tree <- model_profile(exp_tree, N=NULL)
pd_lin <- model_profile(exp_lin, N=NULL)
pd_rf <- model_profile(exp_rf, N=NULL)
pd_nn <- model_profile(exp_nn, N=NULL)
plot(pd_tree, pd_nn, pd_rf, pd_lin)
```

## Gelman Variation and Heterogeneity Causal Quartets

The first set of data `variation_causal_quartet` demonstrates that you can get the same average treatment effect despite variability across some pre-treatment characteristic (here called `covariate`).

```{r}
ggplot(variation_causal_quartet, aes(x = covariate, y = outcome, color = factor(exposure))) + 
  geom_point(alpha = 0.5) + 
  facet_wrap(~ dataset) + 
  labs(color = "exposure group")

variation_causal_quartet |>
  nest_by(dataset) |>
  mutate(ATE = round(coef(lm(outcome ~ exposure, data = data))[2], 2)) |>
  select(-data, dataset) |>
  knitr::kable()
```

The `heterogeneous_causal_quartet` demonstrates how you can observe the same causal effect under different patterns of treatment heterogeneity.

```{r}
ggplot(heterogeneous_causal_quartet, aes(x = covariate, y = outcome, color = factor(exposure))) + 
  geom_point(alpha = 0.5) + 
  facet_wrap(~ dataset) + 
  labs(color = "exposure group")

heterogeneous_causal_quartet |>
  nest_by(dataset) |>
  mutate(ATE = round(coef(lm(outcome ~ exposure, data = data))[2], 2)) |>
  select(-data, dataset) |>
  knitr::kable()
```


## References

Anscombe, F. J. (1973). "Graphs in Statistical Analysis". American Statistician. 27 (1): 17–21. doi:10.1080/00031305.1973.10478966. JSTOR 2682899.

Biecek P, Baniecki H, Krzyziński M, Cook D (2023). Performance is not enough: the story of Rashomon’s quartet. Preprint arXiv:2302.13356v2.

Lucy D’Agostino McGowan, Travis Gerke & Malcolm Barrett (2023) Causal inference is not just a statistics problem, Journal of Statistics and Data Science Education, DOI: 10.1080/26939169.2023.2276446

Davies R, Locke S, D'Agostino McGowan L (2022). _datasauRus: Datasets from the Datasaurus Dozen_. R package version 0.1.6, <https://CRAN.R-project.org/package=datasauRus>.

Gelman, A., Hullman, J., & Kennedy, L. (2023). Causal quartets: Different ways to attain the same average treatment effect. arXiv preprint arXiv:2302.12878.

Hullman J (2023). _causalQuartet: Create Causal Quartets for Interrogating Average Treatment Effects_. R package version 0.0.0.9000.

Matejka, J., & Fitzmaurice, G. (2017). Same Stats, Different Graphs: Generating Datasets with Varied Appearance and Identical Statistics through Simulated Annealing. CHI 2017 Conference proceedings: ACM SIGCHI Conference on Human Factors in Computing Systems. Retrieved from https://www.autodesk.com/research/publications/same-stats-different-graphs

Rohrer, Julia M., and Ruben C. Arslan. "Precise answers to vague questions: Issues with interactions." Advances in Methods and Practices in Psychological Science 4.2 (2021): 25152459211007368.