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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   new
# 6:     predict       x         fit   new
# -------------------------------------
# <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   new
# 6:     predict       x         fit   new
# -------------------------------------
# <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 [2026-10-15 11:21:26.315 UTC]: Starting run of pipeflow 'preprocess-model'
# info [2026-10-15 11:21:26.315 UTC]: Step 1/6 data
# info [2026-10-15 11:21:26.316 UTC]: Step 2/6 prep
# info [2026-10-15 11:21:26.318 UTC]: Step 3/6 standardize
# info [2026-10-15 11:21:26.319 UTC]: Step 4/6 data2
# info [2026-10-15 11:21:26.320 UTC]: Step 5/6 fit
# info [2026-10-15 11:21:26.321 UTC]: Step 6/6 predict
# info [2026-10-15 11:21:26.322 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 [2026-10-15 11:21:26.513 UTC]: Starting run of pipeflow 'preprocess-model'
# info [2026-10-15 11:21:26.514 UTC]: Step 1/6 data - skipping done step
# info [2026-10-15 11:21:26.519 UTC]: Step 2/6 prep - skipping done step
# info [2026-10-15 11:21:26.520 UTC]: Step 3/6 standardize - skipping done step
# info [2026-10-15 11:21:26.520 UTC]: Step 4/6 data2 - skipping done step
# info [2026-10-15 11:21:26.520 UTC]: Step 5/6 fit
# info [2026-10-15 11:21:26.522 UTC]: Step 6/6 predict
# info [2026-10-15 11:21:26.524 UTC]: Finished run of pipeflow 'preprocess-model'
pip[["predict", "out"]]
# [1] "pred: 12" "pred: 18" "pred: 24" "pred: 30" "pred: 36"

Saving and restoring pipelines

A pipeline, like the combined one above, can be built once and reused later, also in another R session. To this end, it can be saved to a file with saveRDS() and read back with readRDS()4.

file <- tempfile(fileext = ".rds")
saveRDS(pip, file)

pip_restored <- readRDS(file)
pip_restored
# <pipeflow> preprocess-model (6 steps)
# -------------------------------------
#           step  params     depends state                                          out
# 1:        data       x              done                                    1,2,3,4,5
# 2:        prep       x        data  done                                    2,3,4,5,6
# 3: standardize x,scale        prep  done                                4, 6, 8,10,12
# 4:       data2       x standardize  done                                4, 6, 8,10,12
# 5:         fit   x,k,b       data2  done                               12,18,24,30,36
# 6:     predict       x         fit  done pred: 12,pred: 18,pred: 24,pred: 30,pred: 36
# -------------------------------------
# <ready> last run: 2026-10-15 11:21:26

The restored pipeline has all steps, parameters, outputs and states of the saved one. That is, it can be modified and run right away, and only the steps that need an update are run again:

pip_set_params(pip_restored, params = list(k = 4))
pip_run(pip_restored)
# info [2026-10-15 11:21:26.667 UTC]: Starting run of pipeflow 'preprocess-model'
# info [2026-10-15 11:21:26.667 UTC]: Step 1/6 data - skipping done step
# info [2026-10-15 11:21:26.667 UTC]: Step 2/6 prep - skipping done step
# info [2026-10-15 11:21:26.667 UTC]: Step 3/6 standardize - skipping done step
# info [2026-10-15 11:21:26.668 UTC]: Step 4/6 data2 - skipping done step
# info [2026-10-15 11:21:26.668 UTC]: Step 5/6 fit
# info [2026-10-15 11:21:26.669 UTC]: Step 6/6 predict
# info [2026-10-15 11:21:26.669 UTC]: Finished run of pipeflow 'preprocess-model'

pip_restored[["predict", "out"]]
# [1] "pred: 16" "pred: 24" "pred: 32" "pred: 40" "pred: 48"

Both the saved and the restored pipelines are independent of each other, so the original pip still uses the multiplier k = 3:

pip_get_params(pip)$k
# [1] 3

For more details see also the section “Saving pipelines” in the help of pip_new().

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.