row binding data frames with Surv objects

[topepo]

validation_set() uses rbind() to concatenate the training and validation sets.

This fails for Surv objects (but dplyr::bind_rows() does the right thing):

library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(survival)

lung$suv_obj <- Surv(lung$time, lung$status)
lung_1 <- head(lung)
lung_2 <- tail(lung)


r_bound <- rbind(lung_1, lung_2)
inherits(r_bound$suv_obj, "Surv")
#> [1] FALSE
class(r_bound$suv_obj)
#> [1] "matrix" "array"

dplyr_bound <- bind_rows(lung_1, lung_2)
inherits(dplyr_bound$suv_obj, "Surv")
#> [1] TRUE
class(dplyr_bound$suv_obj)
#> [1] "Surv"

^{Created on 2023-08-03 with reprex v2.0.2}

[topepo]

There are a lot of other places that this will occur when the Surv object is in a basic R data frame.

For example, the partitioning functions use base R subscripting:

x$data[sort(x$train_id), , drop = FALSE]

and that drops the class. These can be changed to:

  ind <- sort(x$train_id)
  dplyr::slice(x$data, ind)

and it solves the issue.

We would have to do this change in a lot of places:

• {training,testing,validation}.initial_validation_split
• as.data.frame.rsplit

so it would be a system-wide change. For some methods, the latter uses column subscripting at the same time so I would also use dplyr::select() to keep the Surv objects intact.

[topepo]

I think I know what to do about these lines but will hold off before making changes there.

permuted_col <-
   x$data[as.integer(x, data = data, ...), x$col_id, drop = FALSE]
x$data[, x$col_id] <- permuted_col

[topepo]

The fix also changes the row names of the resulting object (restarting the numbers):

── Failure ('test-rsplit.R:31:3'): as.data.frame ───────────────────────────────
as.data.frame(rs4) (`actual`) not equal to dat1[c(1, 1, 1, 2, 2, 2), ] (`expected`).

`attr(actual, 'row.names')` is an integer vector (1, 2, 3, 4, 5, ...)
`attr(expected, 'row.names')` is a character vector ('1', '1.1', '1.2', '2', '2.1', ...)

[hfrick]

@topepo I'm trying to understand why the subsetting via [ is a problem with Surv objects. It isn't in the reprex below so I'm wondering what I'm missing?

library(dplyr)
library(survival)

lung2 <- lung %>% mutate(surv_obj = Surv(time, status))
class(lung2)
#> [1] "data.frame"

lung2[1:3, , drop = FALSE] %>% 
  pull(surv_obj) %>% 
  class()
#> [1] "Surv"

lung2[1:3, "surv_obj" , drop = FALSE] %>% 
  pull(surv_obj) %>% 
  class()
#> [1] "Surv"

^{Created on 2023-08-10 by the reprex package (v2.0.1)}

[EmilHvitfeldt]

As far as I understand, the problem arrises when you don't load the survival package.

[hfrick]

Ah, thank you! I think that situation might not be that common but still totally worth guarding against. That's just different from the initial example because rbind() drops the class even with the survival package loaded.

srv <-
  list(
    age = c(74, 68, 56, 57, 60, 74, 76, 77, 39, 75, 66, 58),
    sex = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 2),
    surv_obj = structure(
      c(306, 455, 1010, 210, 883, 1022, 1, 1, 0, 1, 1, 0,
        116, 188,  191, 105, 174,  177, 1, 0, 0, 0, 0, 0),
      dim = c(12L, 2L),
      dimnames = list(NULL, c("time", "status")),
      type = "right",
      class = "Surv"))
surv_df <-
  structure(
    srv,
    row.names = paste(1:12),
    class = "data.frame")

surv_df
#>    age sex surv_obj.time surv_obj.status
#> 1   74   1           306             116
#> 2   68   1           455             188
#> 3   56   1          1010             191
#> 4   57   1           210             105
#> 5   60   1           883             174
#> 6   74   1          1022             177
#> 7   76   1             1               1
#> 8   77   1             1               0
#> 9   39   1             0               0
#> 10  75   2             1               0
#> 11  66   1             1               0
#> 12  58   2             0               0
surv_df$surv_obj |> class()
#> [1] "Surv"

surv_df[1:3, , drop = FALSE]$surv_obj |> class()
#> [1] "matrix" "array"

^{Created on 2023-08-10 by the reprex package (v2.0.1)}

[hfrick]

closed in #444

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