knitr::opts_chunk$set( collapse = TRUE, comment = "#>", eval = requireNamespace("parsnip", quietly = TRUE) )
library(butcher) library(parsnip)
One of the benefits of working in R is the ease with which you can implement complex models and implement challenging data analysis pipelines. Take, for example, the parsnip package; with the installation of a few associated libraries and a few lines of code, you can fit something as sophisticated as a boosted tree:
fitted_model <- boost_tree(mode = "regression") %>% fit(mpg ~ ., data = mtcars)
Yet, while this code is compact, the underlying fitted result may not be. Since parsnip works as a wrapper for many modeling packages, its fitted model objects inherit the same properties as those that arise from the original modeling package. A straightforward example is the lm()
function from the base stats
package. Whether you leverage parsnip or not, you get the same result:
parsnip_lm <- linear_reg() %>% fit(mpg ~ ., data = mtcars) parsnip_lm
Using just lm()
:
old_lm <- lm(mpg ~ ., data = mtcars) old_lm
Let's say we take this familiar old_lm
approach in building a custom in-house modeling pipeline. Such a pipeline might entail wrapping lm()
in other function, but in doing so, we may end up carrying around some unnecessary junk.
in_house_model <- function() { some_junk_in_the_environment <- runif(1e6) # we didn't know about lm(mpg ~ ., data = mtcars) }
The linear model fit that exists in our custom modeling pipeline is then:
library(lobstr) obj_size(in_house_model())
But it is functionally the same as our old_lm
, which only takes up:
obj_size(old_lm)
Ideally, we want to avoid saving this new in_house_model()
on disk, when we could have something like old_lm
that takes up less memory. But what the heck is going on here? We can examine possible issues with a fitted model object using the butcher package:
big_lm <- in_house_model() weigh(big_lm, threshold = 0, units = "MB")
The problem here is in the terms
component of big_lm
. Because of how lm()
is implemented in the base stats
package (relying on intermediate forms of the data from model.frame
and model.matrix
) the environment in which the linear fit was created is carried along in the model output.
We can see this with the env_print()
function from the rlang package:
library(rlang) env_print(big_lm$terms)
To avoid carrying possible junk around in our production pipeline, whether it be associated with an lm()
model (or something more complex), we can leverage axe_env()
from the butcher package:
cleaned_lm <- axe_env(big_lm, verbose = TRUE)
Comparing it against our old_lm
, we find:
weigh(cleaned_lm, threshold = 0, units = "MB")
And now it takes the same memory on disk:
weigh(old_lm, threshold = 0, units = "MB")
Axing the environment, however, is not the only functionality of butcher. This package provides five S3 generics that include:
axe_call()
: Remove the call object. axe_ctrl()
: Remove the controls fixed for training.axe_data()
: Remove the original data.axe_env()
: Replace inherited environments with empty environments. axe_fitted()
: Remove fitted values.In our case here with lm()
, if we are only interested in prediction as the end product of our modeling pipeline, we could free up a lot of memory if we execute all the possible axe functions at once. To do so, we simply run butcher()
:
butchered_lm <- butcher(big_lm) predict(butchered_lm, mtcars[, 2:11])
Alternatively, we can pick and choose specific axe functions, removing only those parts of the model object that we are no longer interested in characterizing.
butchered_lm <- big_lm %>% axe_env() %>% axe_fitted() predict(butchered_lm, mtcars[, 2:11])
The butcher package provides tooling to axe parts of the fitted output that are no longer needed, without sacrificing much functionality from the original model object.
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