Forging data for predictions

library(hardhat)
library(modeldata)
#> Warning: package 'modeldata' was built under R version 4.0.2

data(penguins)
penguins <- na.omit(penguins)

Introduction

The counterpart to mold() (which you can read all about in vignette("mold", "hardhat")), is forge(). Where mold() is used to preprocess your training data, forge() is used to preprocess new data that you are going to use to generate predictions from your model.

Like mold(), forge() is not intended to be used interactively. Instead, it should be called from the predict() method for your model. To learn more about using forge() in a modeling package, see vignette("package", "hardhat"). The rest of this vignette will be focused on the many features that forge() offers.

Connection with mold()

When mold() is used, one of the returned objects is an blueprint. This is the key to preprocessing new data with forge(). For instance, assume you’ve called mold() like so:

penguin_train <- penguins[1:300,]
penguin_test  <- penguins[-(1:300),]
penguin_form <- mold(
  log(body_mass_g) ~ species + bill_length_mm, 
  penguin_train, 
  blueprint = default_formula_blueprint(indicators = "none")
)

formula_eng <- penguin_form$blueprint

formula_eng
#> Formula blueprint: 
#>  
#> # Predictors: 2 
#>   # Outcomes: 1 
#>    Intercept: FALSE 
#> Novel Levels: FALSE 
#>  Composition: tibble 
#>   Indicators: none

A formula blueprint is returned here, which knows about the predictors and outcomes that were used at training time, and knows that you don’t want to expand species into dummy variables by setting indicators = "none".

When it is time to predict() on new data, that data is passed on to forge() along with the blueprint we just created.

forge(penguin_test, formula_eng)
#> $predictors
#> # A tibble: 33 x 2
#>    bill_length_mm species  
#>             <dbl> <fct>    
#>  1           47.5 Chinstrap
#>  2           47.6 Chinstrap
#>  3           52   Chinstrap
#>  4           46.9 Chinstrap
#>  5           53.5 Chinstrap
#>  6           49   Chinstrap
#>  7           46.2 Chinstrap
#>  8           50.9 Chinstrap
#>  9           45.5 Chinstrap
#> 10           50.9 Chinstrap
#> # … with 23 more rows
#> 
#> $outcomes
#> NULL
#> 
#> $extras
#> $extras$offset
#> NULL

Note that in predictors, species was not expanded because the blueprint knew about the preprocessing options that were set when mold() was called.

forge() always returns three things, and they should look familiar to you if you have used mold().

Outcomes

Generally when generating predictions you only need to know about the new predictors. However, when performing resampling you will need to have the processed outcomes as well so you can compute cross validated performance statistics and decide between multiple models, or choose between hyperparameters.

You can easily request the outcomes as well with outcomes = TRUE. Just like with the predictors, these get processed using the same steps as done to the outcomes at fit time.

forge(penguin_test, formula_eng, outcomes = TRUE)
#> $predictors
#> # A tibble: 33 x 2
#>    bill_length_mm species  
#>             <dbl> <fct>    
#>  1           47.5 Chinstrap
#>  2           47.6 Chinstrap
#>  3           52   Chinstrap
#>  4           46.9 Chinstrap
#>  5           53.5 Chinstrap
#>  6           49   Chinstrap
#>  7           46.2 Chinstrap
#>  8           50.9 Chinstrap
#>  9           45.5 Chinstrap
#> 10           50.9 Chinstrap
#> # … with 23 more rows
#> 
#> $outcomes
#> # A tibble: 33 x 1
#>    `log(body_mass_g)`
#>                 <dbl>
#>  1               8.27
#>  2               8.26
#>  3               8.48
#>  4               7.90
#>  5               8.41
#>  6               8.28
#>  7               8.20
#>  8               8.17
#>  9               8.16
#> 10               8.21
#> # … with 23 more rows
#> 
#> $extras
#> $extras$offset
#> NULL

Validation

One of the most useful things about forge() is its robustness against malformed new data. It isn’t unreasonable to enforce that the new data a user provides at prediction time should have the same type as the data used at fit time. Type is defined in the vctrs sense, and for our uses essentially means that a number of checks on the test data have to pass, including:

Almost all of this validation is possible through the use of vctrs::vec_cast(), and is called for you by forge().

Column existence

The easiest example to demonstrate is missing columns in the testing data. forge() won’t let you continue until all of the required predictors used at training are also present in the new data.

test_missing_column <- subset(penguin_test, select = -species)

forge(test_missing_column, formula_eng)
#> Error: The following required columns are missing: 'species'.

Column types

After an initial scan for the column names is done, a deeper scan of each column is performed, checking the type of that column. For instance, what happens if the new species column was a double, not a factor?

test_species_double <- penguin_test
test_species_double$species <- as.double(test_species_double$species)

forge(test_species_double, formula_eng)
#> Error: Can't convert `species` <double> to match type of `species` <factor<600db>>.

An error is thrown, indicating that a double can’t be cast to a factor.

Lossless conversion

The error message above suggests that in some cases you can automatically cast from one type to another, and in fact that is true! Rather than being a double, what if species was just a character?

test_species_character <- penguin_test
test_species_character$species <- as.character(test_species_character$species)

forged_char <- forge(test_species_character, formula_eng)

forged_char$predictors
#> # A tibble: 33 x 2
#>    bill_length_mm species  
#>             <dbl> <fct>    
#>  1           47.5 Chinstrap
#>  2           47.6 Chinstrap
#>  3           52   Chinstrap
#>  4           46.9 Chinstrap
#>  5           53.5 Chinstrap
#>  6           49   Chinstrap
#>  7           46.2 Chinstrap
#>  8           50.9 Chinstrap
#>  9           45.5 Chinstrap
#> 10           50.9 Chinstrap
#> # … with 23 more rows

class(forged_char$predictors$species)
#> [1] "factor"

levels(forged_char$predictors$species)
#> [1] "Adelie"    "Chinstrap" "Gentoo"

Interesting, so in this case we can actually convert to a factor, and the class and even the levels are all restored. The key here is that this was a lossless conversion. We lost no information when converting the character species to a factor because the unique character values were a subset of the original levels.

An example of a conversion that would be lossy is if the character species column had a value that was not a level in the training data.

test_species_lossy <- penguin_test
test_species_lossy$species <- as.character(test_species_lossy$species)
test_species_lossy$species[2] <- "im new!"

forged_lossy <- forge(test_species_lossy, formula_eng)
#> Warning: Novel levels found in column 'species': 'im new!'. The levels have been
#> removed, and values have been coerced to 'NA'.

forged_lossy$predictors
#> # A tibble: 33 x 2
#>    bill_length_mm species  
#>             <dbl> <fct>    
#>  1           47.5 Chinstrap
#>  2           47.6 <NA>     
#>  3           52   Chinstrap
#>  4           46.9 Chinstrap
#>  5           53.5 Chinstrap
#>  6           49   Chinstrap
#>  7           46.2 Chinstrap
#>  8           50.9 Chinstrap
#>  9           45.5 Chinstrap
#> 10           50.9 Chinstrap
#> # … with 23 more rows

In this case:

Recipes and forge()

Just like with the formula method, a recipe can be used as the preprocessor at fit and prediction time. hardhat handles calling prep(), juice(), and bake() for you at the right times. For instance, say we have a recipe that just creates dummy variables out of species.

library(recipes)

rec <- recipe(bill_length_mm ~ body_mass_g + species, penguin_train) %>%
  step_dummy(species)

penguin_recipe <- mold(rec, penguin_train)

penguin_recipe$predictors
#> # A tibble: 300 x 3
#>    body_mass_g species_Chinstrap species_Gentoo
#>          <int>             <dbl>          <dbl>
#>  1        3750                 0              0
#>  2        3800                 0              0
#>  3        3250                 0              0
#>  4        3450                 0              0
#>  5        3650                 0              0
#>  6        3625                 0              0
#>  7        4675                 0              0
#>  8        3200                 0              0
#>  9        3800                 0              0
#> 10        4400                 0              0
#> # … with 290 more rows

The blueprint is a recipe blueprint.

recipe_eng <- penguin_recipe$blueprint

recipe_eng
#> Recipe blueprint: 
#>  
#> # Predictors: 2 
#>   # Outcomes: 1 
#>    Intercept: FALSE 
#> Novel Levels: FALSE 
#>  Composition: tibble

When we forge(), we can request outcomes to have the predictors and outcomes separated like with the formula method.

forge(penguin_test, recipe_eng, outcomes = TRUE)
#> $predictors
#> # A tibble: 33 x 3
#>    body_mass_g species_Chinstrap species_Gentoo
#>          <int>             <dbl>          <dbl>
#>  1        3900                 1              0
#>  2        3850                 1              0
#>  3        4800                 1              0
#>  4        2700                 1              0
#>  5        4500                 1              0
#>  6        3950                 1              0
#>  7        3650                 1              0
#>  8        3550                 1              0
#>  9        3500                 1              0
#> 10        3675                 1              0
#> # … with 23 more rows
#> 
#> $outcomes
#> # A tibble: 33 x 1
#>    bill_length_mm
#>             <dbl>
#>  1           47.5
#>  2           47.6
#>  3           52  
#>  4           46.9
#>  5           53.5
#>  6           49  
#>  7           46.2
#>  8           50.9
#>  9           45.5
#> 10           50.9
#> # … with 23 more rows
#> 
#> $extras
#> $extras$roles
#> NULL

A note on recipes

One complication with recipes is that, in the bake() step, the processing happens to the predictors and the outcomes all together. This means that you might run into the situation where the outcomes seem to be required to forge(), even if you aren’t requesting them.

rec2 <- recipe(bill_length_mm ~ body_mass_g + species, penguin_train) %>%
  step_dummy(species) %>%
  step_center(bill_length_mm) # Here we modify the outcome

penguin_recipe2 <- mold(rec2, penguin_train)

recipe_eng_log_outcome <- penguin_recipe2$blueprint

If our new_data doesn’t have the outcome, baking this recipe will fail even if we don’t request that the outcomes are returned by forge().

penguin_test_no_outcome <- subset(penguin_test, select = -bill_length_mm)

forge(penguin_test_no_outcome, recipe_eng_log_outcome)
#> Error: Can't subset columns that don't exist.
#> x Column `bill_length_mm` doesn't exist.

The way around this is to use the built-in recipe argument, skip, on the step containing the outcome. This skips the processing of that step at bake() time.

rec3 <- recipe(bill_length_mm ~ body_mass_g + species, penguin_train) %>%
  step_dummy(species) %>%
  step_center(bill_length_mm, skip = TRUE)

penguin_recipe3 <- mold(rec3, penguin_train)

recipe_eng_skip_outcome <- penguin_recipe3$blueprint

forge(penguin_test_no_outcome, recipe_eng_skip_outcome)
#> $predictors
#> # A tibble: 33 x 3
#>    body_mass_g species_Chinstrap species_Gentoo
#>          <int>             <dbl>          <dbl>
#>  1        3900                 1              0
#>  2        3850                 1              0
#>  3        4800                 1              0
#>  4        2700                 1              0
#>  5        4500                 1              0
#>  6        3950                 1              0
#>  7        3650                 1              0
#>  8        3550                 1              0
#>  9        3500                 1              0
#> 10        3675                 1              0
#> # … with 23 more rows
#> 
#> $outcomes
#> NULL
#> 
#> $extras
#> $extras$roles
#> NULL

There is a tradeoff here that you need to be aware of.

For example, if we used penguin_test with the above recipe (which has the outcome), bill_length_mm wouldn’t get centered when forge() is called. But we probably would not have skipped that step if we knew that our test data would have the outcome.

forge(penguin_test, recipe_eng_skip_outcome, outcomes = TRUE)$outcomes
#> # A tibble: 33 x 1
#>    bill_length_mm
#>             <dbl>
#>  1           47.5
#>  2           47.6
#>  3           52  
#>  4           46.9
#>  5           53.5
#>  6           49  
#>  7           46.2
#>  8           50.9
#>  9           45.5
#> 10           50.9
#> # … with 23 more rows

# Notice that the `outcome` values haven't been centered
# and are the same as before
head(penguin_test$bill_length_mm)
#> [1] 47.5 47.6 52.0 46.9 53.5 49.0