Error while using `predict` on a tidymodels workflow

Machine Learning and Modeling
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1

I am following the tutorial here and applying that on my own data. I am building a recipe which has only one step, converting string to factor. The data I am working with dflog has three variables, Height, Weight and Gender and Gender is what I am trying to predict. Here's a sample of the data:

dflog <- structure(list(Gender = c("Male", "Male", "Female", "Male", "Male", 
"Male", "Male", "Female", "Female", "Female", "Female", "Male", 
"Male", "Female", "Female", "Male", "Female", "Female", "Female", 
"Male", "Male", "Male", "Male", "Female", "Male", "Male", "Female", 
"Female", "Female", "Female", "Male", "Male", "Male", "Male", 
"Male", "Male", "Male", "Female", "Male", "Male", "Female", "Female", 
"Female", "Female", "Female", "Male", "Female", "Female", "Female", 
"Female"), Height = c(69.6916891296127, 65.1884775622368, 58.2253970159585, 
70.8668694250787, 73.0719769487447, 67.3421407592253, 67.0405897586907, 
64.9250143571263, 67.8118152454112, 65.5325102349844, 63.1140543077552, 
67.1104474203962, 71.9384959492937, 64.7432660120597, 64.6784085432949, 
67.4242401728615, 65.1259560448078, 60.8782407546953, 65.6783060394966, 
70.0742964754103, 71.4713872338541, 73.298338885144, 70.144874073255, 
68.2595974675301, 70.8874866086991, 73.5692978094574, 61.3511138475123, 
60.5856377146781, 63.4931430001388, 67.1820800126776, 68.5613711736471, 
68.3141883278045, 69.9297057558467, 71.8725840567383, 63.0000474918155, 
66.7034796444077, 64.5987969022366, 61.2575726538818, 65.0054061792742, 
76.0270818630512, 61.7890437911651, 61.6830285758629, 62.5498457985719, 
62.1876806542036, 63.3198176682499, 74.5178760319385, 67.0449228375836, 
59.0455310013641, 64.5902856291067, 66.2874422639476), Weight = c(190.145864881414, 
151.886942249695, 114.961707275311, 199.657175172799, 206.79014203395, 
197.532280979268, 188.605099476104, 142.118166114949, 146.259558415089, 
120.847428543239, 145.26879625192, 160.050285251246, 217.55978401917, 
141.434997471028, 123.010507026547, 176.485090451344, 144.532731183071, 
128.031249745851, 146.51337666912, 205.387909895344, 192.929107075105, 
194.948577135866, 190.585376753341, 174.142421017912, 182.887947720361, 
216.61777777797, 121.966343592203, 116.430074671494, 160.554603918248, 
164.779375641609, 175.041945711247, 174.243488335751, 199.721623719246, 
193.13807676563, 165.555965906858, 189.430028578934, 173.992094268605, 
131.46928157665, 152.801310681396, 232.313470969478, 123.140730916332, 
116.423510279721, 118.90320396155, 124.606873604888, 119.315988261806, 
201.957971666922, 140.815517479934, 105.380905400503, 140.176081684439, 
168.905571923085)), class = c("spec_tbl_df", "tbl_df", "tbl", 
"data.frame"), row.names = c(NA, -50L), spec = structure(list(
    cols = list(Gender = structure(list(), class = c("collector_character", 
    "collector")), Height = structure(list(), class = c("collector_double", 
    "collector")), Weight = structure(list(), class = c("collector_double", 
    "collector"))), default = structure(list(), class = c("collector_guess", 
    "collector")), skip = 1), class = "col_spec"))

Here's the code for what I am trying to do:

library(tidyverse)
library(tidymodels)

#Split the data
set.seed(666)
dflog_split <- initial_split(dflog, prop = 3/4)
dflog_train <- training(dflog_split)
dflog_test <- testing(dflog_split)

#Model spec
dflog_mod <- logistic_reg() %>% 
  set_engine("glm") %>% 
  set_mode("classification")

#Build a recipe
dflog_rec <- recipe(Gender ~ ., data = dflog_train) %>% 
  step_string2factor(all_nominal())

#Build a workflow
dflog_workflow <- workflow() %>% 
  add_model(dflog_mod) %>% 
  add_recipe(dflog_rec)

#Fit
dflog_fit <- dflog_workflow %>% 
  fit(data = dflog_train)

dflog_fit %>% pull_workflow_fit() %>% tidy()

#Predict on test data
predict(dflog_fit, dflog_test)

Running the predict function gives me this error:

Error: Can't subset columns that don't exist.
x Column `Gender` doesn't exist.
Run `rlang::last_error()` to see where the error occurred.

This is the last_error():

Can't subset columns that don't exist.
x Column `Gender` doesn't exist.
Backtrace:
  1. stats::predict(dflog_fit, dflog_test)
 24. vctrs:::stop_subscript_oob(...)
 25. vctrs:::stop_subscript(...)
Run `rlang::last_trace()` to see the full context.

And this is the last_trace():

<error/vctrs_error_subscript_oob>
Can't subset columns that don't exist.
x Column `Gender` doesn't exist.
Backtrace:
     █
  1. ├─stats::predict(dflog_fit, dflog_test)
  2. ├─workflows:::predict.workflow(dflog_fit, dflog_test)
  3. │ ├─hardhat::forge(new_data, blueprint)
  4. │ └─hardhat:::forge.data.frame(new_data, blueprint)
  5. │   └─blueprint$forge$process(...)
  6. │     ├─recipes::bake(object = rec, new_data = new_data)
  7. │     └─recipes:::bake.recipe(object = rec, new_data = new_data)
  8. │       ├─recipes::bake(object$steps[[i]], new_data = new_data)
  9. │       └─recipes:::bake.step_string2factor(object$steps[[i]], new_data = new_data)
 10. │         ├─purrr::map2_df(...)
 11. │         │ └─purrr::map2(.x, .y, .f, ...)
 12. │         ├─new_data[, col_names]
 13. │         └─tibble:::`[.tbl_df`(new_data, , col_names)
 14. │           └─tibble:::tbl_subset_col(x, j = j, j_arg)
 15. │             └─tibble:::vectbl_as_col_index(j, x, j_arg = j_arg)
 16. │               └─tibble:::vectbl_as_col_location(...)
 17. │                 ├─tibble:::subclass_col_index_errors(...)
 18. │                 │ ├─base::tryCatch(...)
 19. │                 │ │ └─base:::tryCatchList(expr, classes, parentenv, handlers)
 20. │                 │ │   └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 21. │                 │ │     └─base:::doTryCatch(return(expr), name, parentenv, handler)
 22. │                 │ └─base::force(expr)
 23. │                 └─vctrs::vec_as_location(j, n, names, arg = as_label(j_arg))
 24. └─vctrs:::stop_subscript_oob(...)
 25.   └─vctrs:::stop_subscript(...)

Not sure why this doesn't work.

1 Like
2

In the recipe, the outcome is affected by the first step. The issue is that, when making predictions, we can't assume that there is an outcome results that is available (a prediction of the outcome shouldn't require the observed outcome).

When predict tries to apply the recipe to the new data, the outcome (Gender captured by all_nominal()) isn't there.

The solution is to use the skip option. This means that the step is applied when making the training set but is skipped when data are being predicted:

> #Build a recipe
> dflog_rec <- recipe(Gender ~ ., data = dflog_train) %>% 
+   step_string2factor(all_nominal(), skip = TRUE)
> 
> #Build a workflow
> dflog_workflow <- workflow() %>% 
+   add_model(dflog_mod) %>% 
+   add_recipe(dflog_rec)
> 
> #Fit
> dflog_fit <- dflog_workflow %>% 
+   fit(data = dflog_train)
> 
> dflog_fit %>% pull_workflow_fit() %>% tidy()
# A tibble: 3 x 5
  term        estimate std.error statistic p.value
  <chr>          <dbl>     <dbl>     <dbl>   <dbl>
1 (Intercept)  -10.8     17.1       -0.634  0.526 
2 Height        -0.183    0.344     -0.534  0.593 
3 Weight         0.140    0.0572     2.45   0.0143
> 
> #Predict on test data
> predict(dflog_fit, dflog_test)
# A tibble: 12 x 1
   .pred_class
   <fct>      
 1 Female     
 2 Male       
 3 Female     
 4 Female     
 5 Male       
 6 Female     
 7 Female     
 8 Male       
 9 Male       
10 Male       
11 Female     
12 Female
1 Like
3

@Max thank you for the explanation, clear now. And thank you for the great job you are doing on parsnip and tidymodels!

4

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