prediction for rank-deficient fit results in .pred_res outcome name

[EmilHvitfeldt]

As the title says, when you predict from a rank-deficient fit, in 4.3.0 or later, the output of predict.lm() comes with an attribute attr(*, "non-estim"), which messes up the prediction coming from {parsnip}, giving it an column name of .pred_res instead of .pred. Which THEN turns into errors for most of the {tune} functions. Should be a fairly easy fix.

I found it when working on tidymodels/workshops#105.

R 4.2.0

data <- data.frame(
  y = c(1,2,3,4), 
  x1 = c(1,1,2,3), 
  x2 = c(3,4,5,2), 
  x3 = c(4,2,6,0), 
  x4 = c(2,1,3,0)
)
data2 <- data.frame(
  x1 = c(3,2,1,3),
  x2 = c(3,2,1,4),
  x3 = c(3,4,5,1),
  x4 = c(0,0,2,3)
)

lm(y ~ ., data = data) |> 
  predict(data2)
#> Warning in predict.lm(lm(y ~ ., data = data), data2): prediction from a
#> rank-deficient fit may be misleading
#>          1          2          3          4 
#>  3.8888889  1.7777778 -0.3333333  4.8888889

library(parsnip)

linear_reg() |>
  fit(y ~ ., data = data) |>
  predict(new_data = data2)
#> Warning in predict.lm(object = object$fit, newdata = new_data, type =
#> "response"): prediction from a rank-deficient fit may be misleading
#> # A tibble: 4 × 1
#>    .pred
#>    <dbl>
#> 1  3.89 
#> 2  1.78 
#> 3 -0.333
#> 4  4.89

R 4.3.0

data <- data.frame(
  y = c(1,2,3,4), 
  x1 = c(1,1,2,3), 
  x2 = c(3,4,5,2), 
  x3 = c(4,2,6,0), 
  x4 = c(2,1,3,0)
)
data2 <- data.frame(
  x1 = c(3,2,1,3),
  x2 = c(3,2,1,4),
  x3 = c(3,4,5,1),
  x4 = c(0,0,2,3)
)

lm(y ~ ., data = data) |> 
  predict(data2)
#> Warning in predict.lm(lm(y ~ ., data = data), data2): prediction from
#> rank-deficient fit; attr(*, "non-estim") has doubtful cases
#>          1          2          3          4 
#>  3.8888889  1.7777778 -0.3333333  4.8888889 
#> attr(,"non-estim")
#> 1 2 3 4 
#> 1 2 3 4

library(parsnip)

linear_reg() |>
  fit(y ~ ., data = data) |>
  predict(new_data = data2)
#> Warning in predict.lm(object = object$fit, newdata = new_data, type =
#> "response"): prediction from rank-deficient fit; attr(*, "non-estim") has
#> doubtful cases
#> # A tibble: 4 × 1
#>   .pred_res
#>       <dbl>
#> 1     3.89 
#> 2     1.78 
#> 3    -0.333
#> 4     4.89

^{Created on 2023-07-02 with reprex v2.0.2}

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