agenda.qmd

---
title: "Agenda"
bibliography: packages.bib
embed-resources: true
---

## Intro

The course will alternate between face-to-face presentations and exercises (15-20 minute each) on the covered topics. Next, the instructor will provide the "official" answer to the challenge. That not only offers a comparative learning experience but also sets the stage for the next topic. Each new chapter begins in a collaborative environment, with the official solution to the previous challenge implemented, ensuring a smooth transition and cohesive learning path.

At the end of each day, participants will have the option to tackle an longer hands-on exercise covering the day's topics; the solution will be discussed and presented in the first half-hour of the next class.

At the end of the course, we will suggest a comprehensive exercise to be done independently at home. We will also send a questionnaire to participants to assess the retention of the concepts presented in the course.

The whole course will be conducted using the R programming languages [@R-base], and it will introduce the main **Tidyverse** [@tidyverse2019] R-package ecosystem and philosophy for a uniform, composable, functional, and human-first design utilities to do data science. In particular, the following packages will be introduced and used during the course:

-   the `{tidyverse}` [@R-tidyverse] to activate the ecosystem on the R session

-   the RStudio projects, and the `{renv}` [@R-renv], and `{here}` [@R-here] packages for project management, reproducibility, and portability. On their side, there will be introduced the native *pipe*, with only mentioning the {magrittr} \[\@R-magrittr\], to pipe instructions in an easy-to-write/read/understand way.

-   `{ggplot2}` [@R-ggplot2] for graphics production

-   the `{rio}` [@R-rio] for data reading/import and writing/export

-   `{janitor}` [@R-janitor], and `{tidyr}` [@R-tidyr] for data cleaning at import level, and the `{dplyr}` [@R-dplyr], `{forcats}` [@R-forcats], `{lubridate}` [@R-lubridate], and (optionally at teh end of teh course) `{stringr}` [@R-stringr], and `{glue}` [@R-glue] for post-import data sets and type-specific data manipulation and management.

-   `{gtsummary}` [@R-gtsummary] to create summary tables for data and models and to include table data in a report's narrative text sections directly, i.e., without copy-pasting them by hand.[^1]

[^1]: The `{flextable}` [@R-flextable] package will be not introduced explicitly because `{gtsummary}` can now manage MS Word tables as well. On the other side, it will be explained how to convert a `gtsummary` table on other formats, `flextable` included.

<!-- -->

-   R Markdown [@R-rmarkdown], `{knitr}` [@R-knitr], and Quarto [@R-quarto] to create reproducible, dynamic documents such as reports, articles, slides, and much more.

```{r}
#| include: false
knitr::write_bib(c(.packages(), "tidyverse", "ggplot2", "readr", "readxl", "writexl", "haven",  "rio", "tidyr", "janitor", "dplyr", "forcats", "glue", "magrittr", "lubridate", "stringr", "renv", "here", "gtsummary", "flextable", "rmarkdown", "knitr", "quarto"), "packages.bib")
```

## Agenda

[240' each day]{.aside}

::: panel-tabset
## Day 1

### \[60'\] Intros:

-   Course's objectives and philosophy

-   Ts/TAs presentation

-   Course organization, teaching materials, and personalized assistance

-   R/RStudio

-   Posit RStudio Cloud IDE presentation and setup

### EXERCISE \[15'\]

::: {.callout-note appearance="minimal"}
\[10'\] `BREAK`{=html}
:::

### \[20'\] Basic R and RStudio:

-   R basics

-   Packages

-   Tidyverse

### EXERCISE \[15'\]

### SOLUTION \[5'\]

### \[30'\] Infrastructures[^2]

-   R projects

-   `{here}`

-   Files organization (dev/ folder)

### EXERCISE \[20'\]

### SOLUTION \[5'\]

::: {.callout-note appearance="minimal"}
\[10'\] `BREAK`{=html}
:::

### \[20'\] Import and cleaning

-   `rio`[^3] [^4]

### EXERCISE \[15'\]

### SOLUTION \[5'\]

::: {.callout-note appearance="minimal"}
\[10'\] Recap & Assignments
:::

## Day 2

::: {.callout-note appearance="minimal"}
\[10'\] Recap & Solutions
:::

### \[40'\] local environments

-   `{renv}`

### EXERCISE \[25'\]

### SOLUTION \[5'\]

::: {.callout-note appearance="minimal"}
\[10'\] `BREAK`{=html}
:::

### \[30'\] R Data Structures

-   Base data structures

-   Subsetting and Extractions

### EXERCISE \[25'\]

### SOLUTION \[5'\]

### \[30'\] Pipe

-   Pipe

### EXERCISE \[20'\]

### SOLUTION \[5'\]

::: {.callout-note appearance="minimal"}
\[10'\] `BREAK`{=html}
:::

### \[30'\] (cleaning (Optional if time allows))

-   Headers, variables' names, and missing data

### EXERCISE \[25'\]

### SOLUTION \[5'\]

::: {.callout-note appearance="minimal"}
\[10'\] Recap & Assignments
:::







## Day 3

::: {.callout-note appearance="minimal"}
\[10'\] Recap & Solutions
:::

### \[30'\] Transform shape of dataset [^5] [^6]

-   Tidy format

-   `select` (all_of...)

-   `filter`

### EXERCISE \[15'\]

### SOLUTION \[5'\]

::: {.callout-note appearance="minimal"}
\[10'\] BREAK
:::

### \[30'\] Transform -- manage dataset[^7]

-   mutate (across) data contents row-by-row

-   mutate and summarize data by groups

::: {.callout-note appearance="minimal"}
\[10'\] BREAK
:::

### EXERCISE \[25'\]

### SOLUTION \[5'\]

### \[50'\] Modeling (summary statistics tables)[^8]

-   Summary tables

    -   descriptive statistics

### EXERCISE \[25'\]

### SOLUTION \[5'\]

```         
- cross-tables
- saving tables
```

### EXERCISE \[20'\]

### SOLUTION \[5'\]

::: {.callout-note appearance="minimal"}
\[10'\] RECAP & assignments
:::






## Day 4

::: {.callout-note appearance="minimal"}
\[10'\] RECAP & solutions
:::

### \[85'\] Visualization [^9]

-   Intro to `{ggplot2}`

    -   Tidy data, and the layered grammar of graphics.

    -   Base template (data, aesthetics, and geometries)

### EXERCISE \[20'\]

### SOLUTION \[5'\]

::: {.callout-note appearance="minimal"}
\[10'\] `BREAK`{=html}
:::

### \[10'\] Visualization [^10]

-   Intro to `{ggplot2}`

    -   Scales, Facets, Labels, and Themes
    -   Saving plots

::: {.callout-note appearance="minimal"}
\[10'\] BREAK
:::

### \[30'\] Transform -- manage main types[^11]

-   factors

-   dates/datetimes

-   (strings (optional if time allows))

<!-- ### 7. \[60'\] Communicate (tools: R markdown and Quarto)[^11] -->

<!-- -   \[20'\] (Visual) Quarto document structure -->

<!--     -   \[10'\] types & creating -->

<!--     -   \[5'\] header -->

<!--     -   \[5'\] content -->

<!-- -   \[15'\] Base Markdown syntax -->

<!-- -   \[20'\] chunks, inline code, and inline tables content -->

<!-- -   \[5'\] chunk options -->

::: {.callout-note appearance="minimal"}
\[10'\] BREAK
:::

::: {.callout-note appearance="minimal"}
\[10'\] RECAP & final assignments
:::

::: {.callout-note appearance="minimal"}
\[25'\] finale w/ OVERALL RECAP, next-month assignment, support access instructions, and final survey
:::
:::

[^2]: pkg: {renv}, {here}

[^3]: pkgs: {readr}, {readxl}, {writexl}, {haven}

[^4]: pkg: {rio}

[^5]: pkgs: {janitor}, {tidyr}

[^6]: pkgs: {dplyr}

[^7]: pkgs: {dplyr}

[^8]: pkgs: {dplyr}, {gtsummary}

[^9]: pkg: {magrittr}, {ggplot2}

[^10]: pkg: {magrittr}, {ggplot2}

[^11]: pkgs: {dplyr}, {lubridate}, {stringr}, {glue}

<!-- [^11]: The *Communicate* section is flexible. Topics from this section can be omitted to allow for more in-depth discussion on earlier sections, if needed, based on the time available. -->

## Bibliography