In cjvanlissa/worcs: Workflow for Open Reproducible Code in Science

knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

Target Markdown is a powerful R Markdown interface for reproducible analysis pipelines, and the chapter at https://books.ropensci.org/targets/markdown.html walks through it in detail. This R Markdown report the example from the chapter. Try it out in both interactive and non-interactive modes, either by running the code chunks in different ways or setting the tar_interactive chunk option.

Setup

If you are using old versions of targets (<= 0.7.0) and/or knitr (<= 1.33), you will need to load the targets package in the R Markdown document in order for Target Markdown code chunks to work.

library(targets)

Near the top of the document, you may also wish to remove the _targets_r directory previously written by non-interactive runs of the report. Otherwise, your pipeline may contain superfluous targets.

library(targets)
tar_unscript()

Targets

Our first target borrows the airquality dataset built into base R.

```{targets raw-data} tar_target(raw_data, airquality)

Our next targets preprocess the data, make a histogram, and fit a model.

```{targets downstream-targets}
list(
  tar_target(data, {raw_data[complete.cases(airquality), ]}),
  tar_target(hist, hist(data$Ozone))
)

Set the tar_simple chunk option to TRUE to define a single target with the command in the code chunk. The chunk below only contains biglm(Ozone ~ Wind + Temp, data) in the source, but because tar_simple is TRUE, it is shorthand for tar_target(name = fit, command = biglm(Ozone ~ Wind + Temp, data)). All other arguments to tar_target() are set to their default values (configurable with tar_option_set()).

```{targets fit, tar_simple = TRUE} lm(Ozone ~ Wind + Temp, data)

# Pipeline

If you ran all the `{targets}` chunks in non-interactive mode, then your R scripts are set up to run the pipeline.

```r
tar_make()

Output

You can retrieve results from the _targets/ data store using tar_read() or tar_load().

tar_read(fit)

tar_read(hist)

At this point, you can go back and run {targets} chunks in interactive mode without interfering with the code or data of the non-interactive pipeline.

cjvanlissa/worcs documentation built on Nov. 7, 2024, 1:20 p.m.