Skip to contents

Combine pipelines

Source: vignettes/v03a-combine-pipelines.Rmd
v03a-combine-pipelines.Rmd

The possibility to combine pipelines basically allows to modularize the pipeline creation process. This is especially useful when you have a set of pipelines that are used in different contexts and you want to avoid code duplication1.

Two pipelines

Let’s define one pipeline that is used for data preprocessing and one that does the modelling2.

library(pipeflow)

pip1 <- pip_new("preprocess") |>
    pip_add("data", \(x = 1:5) x) |>
    pip_add("prep", \(x = ~data) x + 1) |>
    pip_add("standardize", \(x = ~prep, scale = 2) x * scale)
pip2 <- pip_new("model") |>
    pip_add("data", \(x = 1:5) x) |>
    pip_add("fit", \(x = ~data, k = 2, b = 0) x * k + b) |>
    pip_add("predict", \(x = ~fit) paste0("pred: ", x))

Combined pipeline

Next we combine the two pipelines using rbind().

pip <- rbind(pip1, pip2)

pip
# <pipeflow> preprocess-model (6 steps)
# -------------------------------------
#           step  params depends state
# 1:        data       x           new
# 2:        prep       x    data   new
# 3: standardize x,scale    prep   new
# 4:       data2       x           new
# 5:         fit   x,k,b   data2   new
# 6:     predict       x     fit   new
# -------------------------------------
# <ready> last run: never

Note that the data step of the second pipeline has been renamed to data2 in both the step and the depends columns (see line 4 above). That is, when “rbinding” pipelines, {pipeflow} automatically ensures that all step names stay unique by renaming any duplicates accordingly.

As is also visible from the graphical representation of the pipeline,

library(visNetwork)
do.call(visNetwork, args = pip_graph(pip)) |>
    visHierarchicalLayout(direction = "LR")

the two pipelines are not yet connected. To make sense of the combined pipeline, we want to use the output of the standardize step as the input of the data2 step, which we can do by applying the replace function, which was introduced in the previous vignette modify the pipeline, as follows:

pip |> pip_replace("data2", \(x = ~standardize) x)

pip
# <pipeflow> preprocess-model (6 steps)
# -------------------------------------
#           step  params     depends    state
# 1:        data       x                  new
# 2:        prep       x        data      new
# 3: standardize x,scale        prep      new
# 4:       data2       x standardize      new
# 5:         fit   x,k,b       data2 outdated
# 6:     predict       x         fit outdated
# -------------------------------------
# <ready> last run: never

The data2 step points to the output of the standardize step, so that both pipelines are now connected.

Relative indexing

Since the name of the re-routed step might not always be known3, the {pipeflow} package also provides a relative position indexing mechanism, which allows to rewrite the above command using a number (instead of the step name standardize) while having the same effect as above.

pip |> pip_replace("data2", \(x = ~ -1) x)

pip
# <pipeflow> preprocess-model (6 steps)
# -------------------------------------
#           step  params     depends    state
# 1:        data       x                  new
# 2:        prep       x        data      new
# 3: standardize x,scale        prep      new
# 4:       data2       x standardize      new
# 5:         fit   x,k,b       data2 outdated
# 6:     predict       x         fit outdated
# -------------------------------------
# <ready> last run: never

The relative indexing mechanism allows to refer to steps positioned above the current step. The index ~-1 can be interpreted as “go one step back”, ~-2 as “go two steps back”, and so on.

Combined pipeline results

Let’s now run the combined pipeline and inspect the results of the final step.

pip_run(pip)
# info [2026-10-02 18:37:24.322 UTC]: Starting run of pipeflow 'preprocess-model'
# info [2026-10-02 18:37:24.322 UTC]: Step 1/6 data
# info [2026-10-02 18:37:24.323 UTC]: Step 2/6 prep
# info [2026-10-02 18:37:24.324 UTC]: Step 3/6 standardize
# info [2026-10-02 18:37:24.325 UTC]: Step 4/6 data2
# info [2026-10-02 18:37:24.326 UTC]: Step 5/6 fit
# info [2026-10-02 18:37:24.327 UTC]: Step 6/6 predict
# info [2026-10-02 18:37:24.328 UTC]: Finished run of pipeflow 'preprocess-model'
pip[["predict", "out"]]
# [1] "pred: 8"  "pred: 12" "pred: 16" "pred: 20" "pred: 24"

As we can see, the outputs of the preprocessing pipeline flow into the modelling pipeline. We can now go ahead and for example change the multiplier of the fit step and rerun the pipeline.

pip_set_params(pip, params = list(k = 3))
pip_run(pip)
# info [2026-10-02 18:37:24.562 UTC]: Starting run of pipeflow 'preprocess-model'
# info [2026-10-02 18:37:24.562 UTC]: Step 1/6 data - skipping done step
# info [2026-10-02 18:37:24.562 UTC]: Step 2/6 prep - skipping done step
# info [2026-10-02 18:37:24.562 UTC]: Step 3/6 standardize - skipping done step
# info [2026-10-02 18:37:24.562 UTC]: Step 4/6 data2 - skipping done step
# info [2026-10-02 18:37:24.562 UTC]: Step 5/6 fit
# info [2026-10-02 18:37:24.563 UTC]: Step 6/6 predict
# info [2026-10-02 18:37:24.564 UTC]: Finished run of pipeflow 'preprocess-model'
pip[["predict", "out"]]
# [1] "pred: 12" "pred: 18" "pred: 24" "pred: 30" "pred: 36"

Whether you combine them or not, in practice pipelines can get long quickly. The next vignette shows how you can easily focus on certain parts of your entire analysis workflow by Pipeline views.