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.
The example requires several R packages, and targets
must be version 0.5.0.9000 or above.
install.packages(c("biglm", "dplyr", "ggplot2", "readr", "targets", "tidyr"))
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()
We first define some global options/functions common to all targets. The function below plots a histogram of ozone concentrations, and our histogram target will need it.
```{targets example-globals, tar_globals = TRUE} options(tidyverse.quiet = TRUE) tar_option_set(packages = c("biglm", "dplyr", "ggplot2", "readr", "tidyr")) create_plot <- function(data) { ggplot(data) + geom_histogram(aes(x = Ozone), bins = 12) + theme_gray(24) }
# 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 %>% filter(!is.na(Ozone))), tar_target(hist, create_plot(data)) )
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} biglm(Ozone ~ Wind + Temp, data)
If you ran all the {targets}
chunks in non-interactive mode, then your R scripts are set up to run the pipeline.
tar_make()
You can retrieve results from the _targets/
data store using tar_read()
or tar_load()
.
library(biglm) tar_read(fit)
tar_read(hist)
The targets
dependency graph helps your readers understand the steps of your pipeline at a high level.
tar_visnetwork()
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.
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