test.qmd

---
title: "an educator's perspective of the tidyverse"
subtitle: "[bit.ly/tidyperspective-dagstat](https://bit.ly/tidyperspective-dagstat)"
author: "mine çetinkaya-rundel"
format:
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    theme: theme.scss
    transition: fade
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    highlight-style: ayu-mirage
code-link: true
execute:
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  freeze: auto
---

# introduction



## collaborators

-   Johanna Hardin, Pomona College
-   Benjamin S. Baumer, Smith College
-   Amelia McNamara, University of St Thomas
-   Nicholas J. Horton, Amherst College
-   Colin W. Rundel, Duke University

## setting the scene

::: columns
::: {.column width="50%" style="text-align: center;"}
![](images/icons8-code-64.png)

**Assumption 1:**

Teach authentic tools
:::

::: {.column width="50%" style="text-align: center;"}
![](images/icons8-code-R-64.png)

**Assumption 2:**

Teach R as the authentic tool
:::
:::

## takeaway

<br><br>

> The tidyverse provides an effective and efficient pathway for undergraduate students at all levels and majors to gain computational skills and thinking needed throughout the data science cycle.

::: aside
Çetinkaya-Rundel, M., Hardin, J., Baumer, B. S., McNamara, A., Horton, N. J., & Rundel, C.
(2021).
An educator's perspective of the tidyverse.
arXiv preprint arXiv:2108.03510.
[arxiv.org/abs/2108.03510](https://arxiv.org/abs/2108.03510)
:::

# principles of the tidyverse

## tidyverse

::: columns
::: {.column width="80%"}
-   meta R package that loads eight core packages when invoked and also bundles numerous other packages upon installation
-   tidyverse packages share a design philosophy, common grammar, and data structures
:::

::: {.column width="20%"}
![](images/tidyverse.png){fig-align="center"}
:::
:::

![](images/data-science.png){fig-align="center"}

## setup

**Data:** Thousands of loans made through the Lending Club, a peer-to-peer lending platform available in the **openintro** package, with a few modifications.



## start with a data frame



## tidy data

1.  Each variable forms a column
2.  Each observation forms a row
3.  Each type of observational unit forms a table

::: aside
Wickham, H.
. (2014).
Tidy Data.
*Journal of Statistical Software*, *59*(10), 1--23.
[doi.org/10.18637/jss.v059.i10](https://doi.org/10.18637/jss.v059.i10).
:::

## task: calculate a summary statistic

::: goal
Calculate the mean loan amount.
:::



. . .



. . .



## accessing a variable

**Approach 1:** With `attach()`:



. . .

<br>

*Not recommended.* What if you had another data frame you're working with concurrently called `car_loans` that also had a variable called `loan_amount` in it?


## accessing a variable

**Approach 2:** Using `$`:



. . .

<br>

**Approach 3:** Using `with()`:



## accessing a variable

**Approach 4:** The tidyverse approach:



. . .

-   More verbose
-   But also more expressive and extensible

## the tidyverse approach

::: incremental
-   tidyverse functions take a `data` argument that allows them to localize computations inside the specified data frame

-   does not muddy the concept of what is in the current environment: variables always accessed from within in a data frame without the use of an additional function (like `with()`) or quotation marks, never as a vector
:::

# teaching with the tidyverse

## task: grouped summary

::: goal
Based on the applicants' home ownership status, compute the average loan amount and the number of applicants.
Display the results in descending order of average loan amount.
:::

<br>

::: small
```{r}
#| echo: false

loans %>%
  group_by(homeownership) %>% 
  summarize(
    avg_loan_amount = mean(loan_amount),
    n_applicants = n()
    ) %>%
  arrange(desc(avg_loan_amount)) %>%
  mutate(
    n_applicants = number(n_applicants, big.mark = ","),
    avg_loan_amount = dollar(avg_loan_amount, accuracy = 1)
    ) %>%
  kable(
    col.names = c("Homeownership", "Number of applicants", "Average loan amount"),
    align = "lrr"
    )
```
:::

## break it down I

::: columns
::: {.column width="40%"}
Based on the applicants' home ownership status, compute the average loan amount and the number of applicants.
Display the results in descending order of average loan amount.
:::

::: {.column width="60%"}
```{r}
loans
```
:::
:::

## break it down II

::: columns
::: {.column width="40%"}
[Based on the applicants' home ownership status]{style="font-weight:bold;background-color:#ccddeb;"}, compute the average loan amount and the number of applicants.
Display the results in descending order of average loan amount.
:::

::: {.column width="60%"}
::: {.fragment fragment-index="2"}
::: in-out
**\[input\]** data frame
:::
:::

::: {.fragment fragment-index="3"}
```{r}
#| code-line-numbers: "2"

loans %>%
  group_by(homeownership)
```
:::

::: {.fragment fragment-index="4"}
::: {.in-out style="text-align: right;"}
data frame **\[output\]**
:::
:::
:::
:::

## break it down III

::: columns
::: {.column width="40%"}
Based on the applicants' home ownership status, [compute the average loan amount]{style="font-weight:bold;background-color:#ccddeb;"} and the number of applicants.
Display the results in descending order of average loan amount.
:::

::: {.column width="60%"}
```{r}
#| code-line-numbers: "3-5"

loans %>%
  group_by(homeownership) %>% 
  summarize(
    avg_loan_amount = mean(loan_amount)
    )
```
:::
:::

## break it down IV

::: columns
::: {.column width="40%"}
Based on the applicants' home ownership status, compute the average loan amount and [the number of applicants]{style="font-weight:bold;background-color:#ccddeb;"}.
Display the results in descending order of average loan amount.
:::

::: {.column width="60%"}
```{r}
#| code-line-numbers: "5"

loans %>%
  group_by(homeownership) %>% 
  summarize(
    avg_loan_amount = mean(loan_amount),
    n_applicants = n()
    )
```
:::
:::

## break it down V

::: columns
::: {.column width="40%"}
Based on the applicants' home ownership status, compute the average loan amount and the number of applicants.
[Display the results in descending order of average loan amount.]{style="font-weight:bold;background-color:#ccddeb;"}
:::

::: {.column width="60%"}
```{r}
#| code-line-numbers: "7"

loans %>%
  group_by(homeownership) %>% 
  summarize(
    avg_loan_amount = mean(loan_amount),
    n_applicants = n()
    ) %>%
  arrange(desc(avg_loan_amount))
```
:::
:::

## putting it back together

::: in-out
**\[input\]** data frame
:::

```{r}
loans %>%
  group_by(homeownership) %>% 
  summarize(
    avg_loan_amount = mean(loan_amount),
    n_applicants = n()
    ) %>%
  arrange(desc(avg_loan_amount))
```

::: in-out
**\[output\]** data frame
:::

## grouped summary with `aggregate()`

```{r}
res1 <- aggregate(loan_amount ~ homeownership, 
                  data = loans, FUN = length)
res1

names(res1)[2] <- "n_applicants"
res1
```

## grouped summary with `aggregate()`

```{r}
res2 <- aggregate(loan_amount ~ homeownership, 
                  data = loans, FUN = mean)
names(res2)[2] <- "avg_loan_amount"

res2
```

. . .

```{r}
res <- merge(res1, res2)
res[order(res$avg_loan_amount, decreasing = TRUE), ]
```

## grouped summary with `aggregate()`

::: small
```{r}
#| eval: false

res1 <- aggregate(loan_amount ~ homeownership, data = loans, FUN = length)
names(res1)[2] <- "n_applicants"
res2 <- aggregate(loan_amount ~ homeownership, data = loans, FUN = mean)
names(res2)[2] <- "avg_loan_amount"
res <- merge(res1, res2)
res[order(res$avg_loan_amount, decreasing = TRUE), ]
```
:::

. . .

-   **Good:** Inputs and outputs are data frames
-   **Not so good:** Need to introduce
    -   formula syntax

    -   passing functions as arguments

    -   merging datasets

    -   square bracket notation for accessing rows

## grouped summary with `tapply()`

```{r}
sort(
  tapply(loans$loan_amount, loans$homeownership, mean),
  decreasing = TRUE
  )
```

. . .

<br>

**Not so good:**

-   passing functions as arguments
-   distinguishing between the various `apply()` functions
-   ending up with a new data structure (`array`)
-   reading nested functions

## task: data visualization

::: goal
Create side-by-side box plots that shows the relationship between loan amount and application type, faceted by homeownership.
:::

```{r}
#| echo: false
#| fig-align: center
#| fig-width: 12

ggplot(loans, 
         aes(x = application_type, y = loan_amount)) +
  geom_boxplot() +
  facet_wrap(~ homeownership) +
  theme_minimal(base_size = 18) +
  scale_y_continuous(labels = label_dollar()) +
  labs(x = "Application type", y = "Loan amount")
```

## break it down I

::: columns
::: {.column width="40%"}
[Create side-by-side box plots that shows the relationship between annual income and application type]{style="font-weight:bold;background-color:#ccddeb;"}, faceted by homeownership.
:::

::: {.column width="60%"}
```{r}
#| code-line-numbers: "1"

ggplot(loans)
```
:::
:::

## break it down II

::: columns
::: {.column width="40%"}
[Create side-by-side box plots that shows the relationship between annual income and application type]{style="font-weight:bold;background-color:#ccddeb;"}, faceted by homeownership.
:::

::: {.column width="60%"}
```{r}
#| code-line-numbers: "2"

ggplot(loans, 
       aes(x = application_type))
```
:::
:::

## break it down III

::: columns
::: {.column width="40%"}
[Create side-by-side box plots that shows the relationship between annual income and application type]{style="font-weight:bold;background-color:#ccddeb;"}, faceted by homeownership.
:::

::: {.column width="60%"}
```{r}
#| code-line-numbers: "3"

ggplot(loans, 
       aes(x = application_type,
           y = loan_amount))
```
:::
:::

## break it down IV

::: columns
::: {.column width="40%"}
[Create side-by-side box plots that shows the relationship between annual income and application type]{style="font-weight:bold;background-color:#ccddeb;"}, faceted by homeownership.
:::

::: {.column width="60%"}
```{r}
#| code-line-numbers: "4"

ggplot(loans, 
       aes(x = application_type,
           y = loan_amount)) +
  geom_boxplot()
```
:::
:::

## break it down IV

::: columns
::: {.column width="40%"}
Create side-by-side box plots that shows the relationship between annual income and application type, [faceted by homeownership.]{style="font-weight:bold;background-color:#ccddeb;"}
:::

::: {.column width="60%"}
```{r}
#| code-line-numbers: "5"

ggplot(loans, 
       aes(x = application_type,
           y = loan_amount)) +
  geom_boxplot() +
  facet_wrap(~ homeownership)
```
:::
:::

## plotting with `ggplot()`

```{r}
#| eval: false

ggplot(loans, 
       aes(x = application_type, y = loan_amount)) +
  geom_boxplot() +
  facet_wrap(~ homeownership)
```

. . .

-   Each layer produces a valid plot
-   Faceting by a third variable takes only one new function

## plotting with `boxplot()`

```{r}
levels <- sort(unique(loans$homeownership))
levels

loans1 <- loans[loans$homeownership == levels[1],]
loans2 <- loans[loans$homeownership == levels[2],]
loans3 <- loans[loans$homeownership == levels[3],]
```

## plotting with `boxplot()`

```{r}
par(mfrow = c(1, 3))

boxplot(loan_amount ~ application_type, 
        data = loans1, main = levels[1])
boxplot(loan_amount ~ application_type, 
        data = loans2, main = levels[2])
boxplot(loan_amount ~ application_type, 
        data = loans3, main = levels[3])
```

## visualizing a different relationship

::: goal
Visualize the relationship between interest rate and annual income, conditioned on whether the applicant had a bankruptcy.
:::

```{r}
#| echo: false
#| fig-align: center
#| fig-width: 12

ggplot(loans, 
       aes(y = interest_rate, x = annual_income, 
           color = bankruptcy)) +
  geom_point(alpha = 0.1) + 
  geom_smooth(method = "lm", linewidth = 2, se = FALSE) + 
  scale_x_log10(labels = scales::label_dollar()) +
  scale_y_continuous(labels = scales::label_percent(scale = 1)) +
  scale_color_OkabeIto() +
  labs(x = "Annual Income", y = "Interest Rate", 
       color = "Previous\nBankruptcy") +
  theme_minimal(base_size = 18)
```

## plotting with `ggplot()`

```{r}
#| fig-align: center
#| fig-width: 12
#| code-line-numbers: "|4|5|6"

ggplot(loans, 
       aes(y = interest_rate, x = annual_income, 
           color = bankruptcy)) +
  geom_point(alpha = 0.1) + 
  geom_smooth(method = "lm", linewidth = 2, se = FALSE) + 
  scale_x_log10()
```

## further customizing `ggplot()`

```{r}
#| fig-align: center
#| fig-width: 12
#| code-line-numbers: "|6|7|8|9,10|11"

ggplot(loans, 
       aes(y = interest_rate, x = annual_income, 
           color = bankruptcy)) +
  geom_point(alpha = 0.1) + 
  geom_smooth(method = "lm", linewidth = 2, se = FALSE) + 
  scale_x_log10(labels = scales::label_dollar()) +
  scale_y_continuous(labels = scales::label_percent(scale = 1)) +
  scale_color_OkabeIto() +
  labs(x = "Annual Income", y = "Interest Rate", 
       color = "Previous\nBankruptcy") +
  theme_minimal(base_size = 18)
```

## plotting with `plot()`

```{r}
#| label: base-r-viz-extend
#| fig-show: hide

# From the OkabeIto palette
cols = c(No = "#e6a003", Yes = "#57b4e9")

plot(
  loans$annual_income,
  loans$interest_rate,
  pch = 16,
  col = adjustcolor(cols[loans$bankruptcy], alpha.f = 0.1),
  log = "x",
  xlab = "Annual Income ($)",
  ylab = "Interest Rate (%)",
  xaxp = c(1000, 10000000, 1)
)

lm_b_no = lm(
  interest_rate ~ log10(annual_income), 
  data = loans[loans$bankruptcy == "No",]
)
lm_b_yes = lm(
  interest_rate ~ log10(annual_income), 
  data = loans[loans$bankruptcy == "Yes",]
)

abline(lm_b_no, col = cols["No"], lwd = 3)
abline(lm_b_yes, col = cols["Yes"], lwd = 3)

legend(
  "topright", 
  legend = c("Yes", "No"), 
  title = "Previous\nBankruptcy", 
  col = cols[c("Yes", "No")], 
  pch = 16, lwd = 1
)
```

## plotting with `plot()`

```{r}
#| ref.label: base-r-viz-extend
#| echo: false
```

## beyond wrangling, summaries, visualizations

Modeling and inference with **tidymodels**:

-   A unified interface to modeling functions available in a large variety of packages

-   Sticking to the data frame in / data frame out paradigm

-   Guardrails for methodology

# pedagogical strengths of the tidyverse

## consistency

-   No matter which approach or tool you use, you should strive to be consistent in the classroom whenever possible

-   tidyverse offers consistency, something we believe to be of the utmost importance, allowing students to move knowledge about function arguments to their long-term memory

## teaching consistently

-   Challenge: Google and Stack Overflow can be less useful -- demo problem solving

-   Counter-proposition: teach *all* (or multiple) syntaxes at once -- trying to teach two (or more!) syntaxes at once will slow the pace of the course, introduce unnecessary syntactic confusion, and make it harder for students to complete their work.

-   "Disciplined in what we teach, liberal in what we accept"

::: aside
Postel, J.
(1980).
DoD standard internet protocol.
ACM SIGCOMM Computer Communication Review, 10(4), 12-51.
[datatracker.ietf.org/doc/html/rfc760](https://datatracker.ietf.org/doc/html/rfc760)
:::

## mixability

-   Mix with base R code or code from other packages

-   In fact, you can't not mix with base R code!

## scalability

Adding a new variable to a visualization or a new summary statistic doesn't require introducing a numerous functions, interfaces, and data structures

## user-centered design

-   Interfaces designed with user experience (and learning) in mind

-   Continuous feedback collection and iterative improvements based on user experiences improve functions' and packages' usability (and learnability)

## readability

Interfaces that are designed to produce readable code

## community

-   The encouraging and inclusive tidyverse community is one of the benefits of the paradigm

-   Each package comes with a website, each of these websites are similarly laid out, and results of example code are displayed, and extensive vignettes describe how to use various functions from the package together

## shared syntax

Get SQL for free with **dplyr** verbs!

# final thoughts

## building a curriculum

-   Start with `library(tidyverse)`

-   Teach by learning goals, not packages

## keeping up with the tidyverse

-   Blog posts highlight updates, along with the reasoning behind them and worked examples

-   [Lifecycle stages](https://lifecycle.r-lib.org/articles/stages.html) and badges

    ![](images/lifecycle.png)

## coda {.smaller}

::: columns
::: {.column width="60%"}
> We are all converts to the tidyverse and have made a conscious choice to use it in our research and our teaching.
> We each learned R without the tidyverse and have all spent quite a few years teaching without it at a variety of levels from undergraduate introductory statistics courses to graduate statistical computing courses.
> This paper is a synthesis of the reasons supporting our tidyverse choice, along with benefits and challenges associated with teaching statistics with the tidyverse.
:::

::: {.column width="40%"}
![](images/paper.png)
:::
:::

::: aside
Çetinkaya-Rundel, M., Hardin, J., Baumer, B. S., McNamara, A., Horton, N. J., & Rundel, C.
(2021).
An educator's perspective of the tidyverse.
arXiv preprint arXiv:2108.03510.
[arxiv.org/abs/2108.03510](https://arxiv.org/abs/2108.03510)
:::

# thank you!

[bit.ly/tidyperspective-dagstat](https://bit.ly/tidyperspective-dagstat)