Base scale not working with tibble

[TiberiusGracchus2020]

Applying base scale to multiple columns in a tibble results in an incorrectly scaled output and breaks the tibble on sort. Fresh windows, fresh and latest R/RStudio, latest tidyverse.

library(tibble)
iris <- as_tibble(iris)
iris[1:3] <- scale(iris[1:3])
head(iris)
#> # A tibble: 6 x 5
#>   Sepal.Length[,"~ [,"Sepal.Width"] [,"Petal.Length~ Sepal.Width[,"S~
#>              <dbl>            <dbl>            <dbl>            <dbl>
#> 1           -0.898           1.02              -1.34           -0.898
#> 2           -1.14           -0.132             -1.34           -1.14 
#> 3           -1.38            0.327             -1.39           -1.38 
#> 4           -1.50            0.0979            -1.28           -1.50 
#> 5           -1.02            1.25              -1.34           -1.02 
#> 6           -0.535           1.93              -1.17           -0.535
#> # ... with 7 more variables: [,"Sepal.Width"] <dbl>, [,"Petal.Length"] <dbl>,
#> #   Petal.Length[,"Sepal.Length"] <dbl>, [,"Sepal.Width"] <dbl>,
#> #   [,"Petal.Length"] <dbl>, Petal.Width <dbl>, Species <fct>

[krlmlr]

scale() is a matrix, it must be a list or data frame to be distributed across columns when assigning.

library(tibble)
iris <- as_tibble(iris)
scale <- scale(iris[1:3])
class(scale)
#> [1] "matrix"
iris[1:3] <- as.data.frame(scale)
head(iris)
#> # A tibble: 6 x 5
#>   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
#>          <dbl>       <dbl>        <dbl>       <dbl> <fct>  
#> 1       -0.898      1.02          -1.34         0.2 setosa 
#> 2       -1.14      -0.132         -1.34         0.2 setosa 
#> 3       -1.38       0.327         -1.39         0.2 setosa 
#> 4       -1.50       0.0979        -1.28         0.2 setosa 
#> 5       -1.02       1.25          -1.34         0.2 setosa 
#> 6       -0.535      1.93          -1.17         0.4 setosa

^{Created on 2020-04-15 by the reprex package (v0.3.0)}

[TiberiusGracchus2020]

Fixed by rolling Tibble package version back to 2.1.3

[krlmlr]

See https://tibble.tidyverse.org/dev/articles/invariants.html for details. What is your use case?

[TiberiusGracchus2020]

Standardizing (mean 0, sd =1) multiple columns at once before aggregating to create an index measure. Data science/ analytics

[krlmlr]

Are you calling scale() in a script of yours, or is a package failing now?

[TiberiusGracchus2020]

calling from a script

[krlmlr]

I wonder if this is common enough to warrant a compatibility fix that will be converted to an error later on.

We would disallow assignment of columns if the right-hand side is a matrix, and issue a deprecation warning. To get rid of the warning, users would need to use as.data.frame() or list() to specify the intended behavior.

Would that help your use case?

[krlmlr]

Alternatively, we could also revert to previous behavior and ask users to wrap in a list if they really want a matrix column.

[TiberiusGracchus2020]

I'm no expert, but for my case, the previous behavior is desirable. The tibble is "broken" after I execute the same command in the latest version, sorting returns an error:
Error in xj[i, , drop = FALSE] : subscript out of bounds
Scale with tibble has been a rather serious component of my toolset for data wrangling, but I'm not an expert in R.

[krlmlr]

Thanks. Now:

library(tibble)
iris <- as_tibble(iris)
iris[1:3] <- as.data.frame(scale(iris[1:3]))
head(iris)
#> # A tibble: 6 x 5
#>   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
#>          <dbl>       <dbl>        <dbl>       <dbl> <fct>  
#> 1       -0.898      1.02          -1.34         0.2 setosa 
#> 2       -1.14      -0.132         -1.34         0.2 setosa 
#> 3       -1.38       0.327         -1.39         0.2 setosa 
#> 4       -1.50       0.0979        -1.28         0.2 setosa 
#> 5       -1.02       1.25          -1.34         0.2 setosa 
#> 6       -0.535      1.93          -1.17         0.4 setosa

^{Created on 2020-04-16 by the reprex package (v0.3.0)}

Added a section to https://tibble.tidyverse.org/dev/articles/invariants.html#column-subassignment-x-j-a.

[TiberiusGracchus2020]

Thanks!

[mlane3]

oh my gosh thanks so much!

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