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## Welcome

These are the materials for workshops on survival analysis with [tidymodels](https://www.tidymodels.org/). The tidymodels framework is a collection of packages for modeling and machine learning using [tidyverse](https://www.tidyverse.org/) principles. 

This course will teach you core tidymodels packages and their uses: data splitting/resampling with rsample, model fitting with parsnip, measuring model performance with yardstick, and basic model optimization with tune. Time permitting, you'll be introduced to pre-processing using the recipes package. You'll learn tidymodels syntax as well as the process of predictive modeling for tabular data.

## Is this workshop for me? <img src="slides/images/parsnip-flagger.jpg" align="right" height="150"/>

This workshop is for you if you:

-   are familiar with basic survival analysis such as censoring of time-to-event data, Kaplan-Meier curves, proportional hazards models
-   are familiar with the basic predictive modeling workflow such as split in train and test set, resampling, tuning via grid search
-   want to learn how to leverage the tidymodels framework for survival analysis

Intermediate or expert familiarity with modeling or machine learning is not required. 

## Preparation

The process to set up your computer for either workshop will look the same. Please join the workshop with a computer that has the following installed (all available for free):

-   A recent version of R, available at <https://cran.r-project.org/>
-   A recent version of RStudio Desktop (RStudio Desktop Open Source License, at least v2022.02), available at <https://posit.co/download/rstudio-desktop/>
-   The following R packages, which you can install from the R console:

```{r}
#| label: installs
#| eval: false
#| echo: true

# Install the packages for the workshop
pkgs <- 
  c("aorsf", "censored", "glmnet", "partykit", "pec", "rpart", "tidymodels")

install.packages(pkgs)
```

If you're a Windows user and encounter an error message during installation noting a missing Rtools installation, install Rtools using the installer linked [here](https://cran.r-project.org/bin/windows/Rtools/).

## Slides

These slides are designed to use with live teaching and are published for workshop participants' convenience. There are not meant as standalone learning materials. For that, we recommend [tidymodels.org](https://www.tidymodels.org/start/) and [*Tidy Modeling with R*](https://www.tmwr.org/).

-   01: [Introduction](slides/intro-01-introduction.html){target="_blank"}
-   02: [Your data budget](slides/intro-02-data-budget.html){target="_blank"}
-   03: [What makes a model?](slides/intro-03-what-makes-a-model.html){target="_blank"}
-   04: [Evaluating models](slides/intro-04-evaluating-models.html){target="_blank"}
-   05: [Tuning models](slides/intro-05-tuning-models.html){target="_blank"}
-   06: [Wrapping up](slides/intro-06-wrapping-up.html){target="_blank"}

There's also a page for [slide annotations](slides/annotations.html){target="_blank"}; these are extra notes for selected slides.

## Code

Quarto files for working along [are available on GitHub](https://github.com/hfrick/tidymodels-survival-workshop/tree/main/classwork). (Don't worry if you haven't used Quarto before; it will feel familiar to R Markdown users.)

## Acknowledgments {.appendix}

This website, including the slides, is made with [Quarto](https://quarto.org/). Please [submit an issue](https://github.com/hfrick/tidymodels-survival-workshop/issues) on the GitHub repo for this workshop if you find something that could be fixed or improved.

## Reuse and licensing {.appendix}

Unless otherwise noted (i.e. not an original creation and reused from another source), these educational materials are licensed under Creative Commons Attribution [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0/).