An overview of targets

In targets: Dynamic Function-Oriented 'Make'-Like Declarative Pipelines

This vignette is a high-level overview of targets and its educational materials. The goal is to summarize the major features of targets and direct users to the appropriate resources. It explains how to get started, and then it briefly describes each chapter of the user manual.

What is targets?

The targets R package is a Make-like pipeline toolkit for Statistics and data science in R. targets accelerates analysis with easy-to-configure parallel computing, enhances reproducibility, and reduces the burdens of repeated computation and manual data micromanagement. A fully up-to-date targets pipeline is tangible evidence that the output aligns with the code and data, which substantiates trust in the results.

How to get started

The top of the reference website links to a number of materials to help new users start learning targets. It lists online talks, tutorials, books, and workshops in the order that a new user should consume them. The rest of the main page outlines a more comprehensive list of resources.

The walkthrough

The user manual starts with a walkthrough chapter, a short tutorial to quickly started with targets using a simple example project. That project also has a repository with the source code and an RStudio Cloud workspace that lets you try out the workflow in a web browser. Sign up for a free RStudio Cloud account, click on the link, and try out functions tar_make() and tar_read() in the R console.

Help

The help guide explains how to best get help using targets, including reproducible examples and where to post.

Debugging

The debugging chapter describes two alternative built-in systems for troubleshooting errors. The first system uses workspaces, which let you load a target's dependencies into you R session. This way is usually preferred, especially with large pipelines on computing clusters, but it still may require some manual work. The second system launches an interactive debugger while the pipeline is actually running, which may not be feasible in some situations, but can often help you reach the problem more quickly.

Functions

targets expects users to adopt a function-oriented style of programming. User-defined R functions are essential to express the complexities of data generation, analysis, and reporting. The user manual has a whole chapter dedicated to user-defined functions for data science, and it explains why they are important and how to use them in targets-powered pipelines.

Target construction

The target construction chapter explains best practices for creating targets: what a good target should do, how much work a target should do, and guidelines for thinking about side effects and upstream dependencies (i.e. other targets and global objects).

Packages

The packages chapter explains best practices for working with packages in targets: how to load them, how to work with packages as projects, target factories inside packages, and automatically invalidating targets based on changes inside one or more packages.

Projects

The projects chapter explains best practices for working with targets-powered projects: the recommended file structure, recommended third-party tools, multi-project repositories, and interdependent projects.

Data and files

The chapter at https://books.ropensci.org/targets/data.html describes how the targets package stores data, manages memory, allows you to customize the data processing model. When a target finishes running during tar_make(), it returns an R object. Those return values, along with descriptive metadata, are saved to persistent storage so your pipeline stays up to date even after you exit R. By default, this persistent storage is a special _targets/ folder created in your working directory by tar_make(). However, you can also interact with files outside the data store and send target data to the cloud.

Literate programming

The chapter at https://books.ropensci.org/targets/literate-programming.html covers literate programming: how to render an R Markdown or Quarto report as part of a targets pipeline. A report can depend on other targets and take advantage of long computation already completed upstream.

Distributed computing

targets is capable of distributing the computation in a pipeline across multiple cores of a laptop or multiple jobs on a computing cluster. The orchestration and scaling mechanisms are automatic, and only high-level configuration is required. Visit https://books.ropensci.org/targets/crew.html to learn more. Configuration happens through the crew package: https://wlandau.github.io/crew/. The appendix at https://books.ropensci.org/targets/hpc.html describes how to use targets with legacy backends clustermq and future.

Performance

https://books.ropensci.org/targets/performance.html explains how to monitor the progress of a running pipeline and optimize your pipeline for performance. targets has easy-to-configure efficiency settings at the level of tar_target() and tar_option_set().

Dynamic branching

Sometimes, a pipeline contains more targets than a user can comfortably type by hand. For projects with hundreds of targets, branching can make the _targets.R file more concise and easier to read and maintain. Dynamic branching is a way to create new targets while the pipeline is running, and it is best suited to iterating over a larger number of very similar tasks. The dynamic branching chapter outlines this functionality, including how to create branching patterns, different ways to iterate over data, and recommendations for batching large numbers of small tasks into a comfortably small number of dynamic branches.

Static branching

Static branching is the act of defining a group of targets in bulk before the pipeline starts. Whereas dynamic branching uses last-minute dependency data to define the branches, static branching uses metaprogramming to modify the code of the pipeline up front. Whereas dynamic branching excels at creating a large number of very similar targets, static branching is most useful for smaller number of heterogeneous targets. Some users find it more convenient because they can use tar_manifest() and tar_visnetwork() to check the correctness of static branching before launching the pipeline. Read more about it in the static branching chapter.

targets documentation built on Oct. 3, 2024, 1:11 a.m.