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In some cases, warnings during `add_p()` are printed twice

Open ddsjoberg opened this issue 5 months ago • 0 comments

library(gtsummary)
packageVersion("gtsummary")
#> [1] '2.0.1.9011'

tmax <- data.frame(Subject = c(1, 1, 1, 1, 2, 2, 2, 2, 4, 4, 4, 4, 5, 5, 5, 5), 
                   Treatment = c("T", "R", "T", "R", "R", "T", "R", "T", "T", "R", "T", "R", "R", "T", "R", "T"), 
                   TMAX = c(1.333, 1.667, 0.667, 1.667, 2, 0.667, 2, 2, 1, 1, 2, 1, 0.667, 1, 2, 1))

tmax |> 
  tbl_summary(
    by = Treatment,
    include = -Subject,
    missing = 'no', 
    type = list(TMAX ~ "continuous")
  ) |> 
  add_p(
    test = list(all_continuous() ~ "paired.wilcox.test"),
    group = Subject
  ) |> 
  as_kable()
#> The following warning was returned in `add_p()` for variable "TMAX"
#> ! Values from `TMAX` are not uniquely identified; output will contain
#>   list-cols. • Use `values_fn = list` to suppress this warning. • Use
#>   `values_fn = {summary_fun}` to summarise duplicates. • Use the following
#>   dplyr code to identify duplicates.  {data} |> dplyr::summarise(n =
#>   dplyr::n(), .by = c(Subject, Treatment)) |> dplyr::filter(n > 1L)
#> The following errors were returned during `as_kable()`:
#> ✖ For variable `TMAX` (`Treatment`) and "statistic" and "p.value" statistics:
#>   'x' must be numeric
#> The following warnings were returned during `as_kable()`:
#> ! For variable `TMAX` (`Treatment`) and "statistic" and "p.value" statistics:
#>   Values from `TMAX` are not uniquely identified; output will contain
#>   list-cols. • Use `values_fn = list` to suppress this warning. • Use
#>   `values_fn = {summary_fun}` to summarise duplicates. • Use the following
#>   dplyr code to identify duplicates.  {data} |> dplyr::summarise(n =
#>   dplyr::n(), .by = c(Subject, Treatment)) |> dplyr::filter(n > 1L)
Characteristic R N = 8 T N = 8 p-value
TMAX 1.67 (1.00, 2.00) 1.00 (0.83, 1.67)

Created on 2024-08-31 with reprex v2.1.1

ddsjoberg avatar Sep 01 '24 00:09 ddsjoberg