NEA's questions

O elemento de tema "tbl_summary-arg:type" no gtsummary não funciona, embora o argumento de tipo funcione bem com o mesmo código

library(gtsummary)
packageVersion("gtsummary")
#> [1] '2.1.0.9010'

# Reset theme to defaults first
reset_gtsummary_theme()
tbl_summary(trial) |> 
  # Converting to a flextable object because gtsummary 
  # objects aren't rendered properly on Stack Overflow
  as_flex_table()

# Apply my theme
set_gtsummary_theme(list("tbl_summary-arg:type" =
                           list(all_dichotomous() ~ "categorical")))
# check if it works
trial |>
  tbl_summary() |> 
  as_flex_table()

#Not working Patient Died   is still presented as dichotomous

#Checking type argument
reset_gtsummary_theme()
trial |>
  tbl_summary(type = all_dichotomous() ~ "categorical") |> 
  as_flex_table()

#works well

^{Criado em 2025-04-07 com reprex v2.1.1}

Estou esquecendo de algo que está fazendo com que não funcione?

Tenho uma variável xe quero dividi-la em três grupos com observações iguais. No entanto, usar quantis não resultou nos grupos mais iguais devido aos empates, pois os pontos de corte dos quantis podem resultar em empates sendo alocados em mais de um grupo. Estou procurando uma função ou algoritmo que possa encontrar os melhores pontos de corte, garantindo que os empates não sejam divididos entre vários grupos.

x = c(26, 34, 27, 26, 38, 40, 34, 28, 27, 36, 29, 30, 29, 44, 30, 
      34, 32, 30, 26, 29, 34, 32, 38, 27, 35, 29, 28, 34, 26, 27, 27, 
      30, 27, 28, 27, 28, 28, 27, 29, 29, 28, 29, 29, 28, 29, 29, 28, 
      27, 29, 27, 36, 34, 34, 39, 34, 31, 31, 33, 35, 31, 31, 32, 37, 
      38, 32, 31, 28, 33, 33, 28, 27, 27, 30, 31, 32, 28, 27, 31, 36, 
      27, 33, 31, 34, 31, 35, 38, 37, 36, 39, 33, 33, 28, 41, 34, 35, 
      37, 37, 41, 32, 37, 30, 34, 38, 30, 40, 35, 31, 30, 30, 29, 29, 
      30, 29, 35, 28, 27, 27, 27, 29, 27, 28, 27, 27, 27, 26, 28, 28, 
      27, 29, 29, 27, 27, 27, 27, 29, 27, 28, 27, 28, 34, 29, 28, 28, 
      28, 29, 38, 33, 39, 28, 27, 28, 27, 29, 34, 29, 32, 70, 26, 29, 
      43, 48, 30, 30, 27, 26, 29, 27, 27, 27, 27, 28, 28, 27, 28, 28, 
      27, 28, 28, 38, 52, 26, 31, 56, 29, 29, 36, 28, 35, 32, 34, 35, 
      28, 27, 37, 26, 26, 32, 26, 27, 30, 28, 28, 30, 29, 30, 29, 29, 
      28, 26, 33, 39, 26, 31, 27, 28, 30, 30, 28, 28, 29, 26, 27, 26, 
      29, 28, 28, 27, 27, 27, 28, 27, 28, 28, 28, 28, 28, 27, 27, 29, 
      27, 26, 28, 28, 27, 27, 28, 27, 28, 28, 30, 27, 30, 28, 32, 34, 
      28, 27, 28, 28, 27, 28, 27, 27, 27, 28, 27, 28, 27, 27, 28, 27, 
      27, 27, 27, 27, 28, 27, 27, 27, 26, 27, 27, 30, 28, 27, 30, 30, 
      42, 26, 27, 40, 33, 29, 29, 29, 52, 58, 44, 32, 43, 30, 27, 38, 
      30, 27, 30, 27, 31, 39, 35, 32, 32, 34, 45, 31, 44, 42, 29, 29, 
      30, 30, 50, 30, 33, 31, 35, 27, 28, 27, 28, 55, 28, 28, 28, 27, 
      27, 28, 29, 27, 28, 27, 28, 28, 28, 28, 27, 28, 29, 34, 45, 27, 
      29, 61, 38, 62, 29, 36, 36, 30, 31, 45, 27, 30, 28, 29, 44, 45, 
      42, 52, 50, 52, 42, 38, 42, 32, 27, 37, 40, 52, 27, 36, 38, 39, 
      34, 30, 29, 34, 29, 26, 35, 43, 33, 40, 35, 33, 41, 61, 45, 35, 
      52, 50, 38, 43, 29, 35, 38, 39, 31, 28, 28, 29, 34, 27, 30, 32, 
      28, 26, 28, 27, 26, 29, 27, 26, 29, 29, 27, 29, 27, 27, 29, 27, 
      30, 29, 25, 30, 27, 29, 29, 30, 30, 27, 30, 28, 28, 27, 29, 29, 
      30, 29, 27, 28, 28, 28, 29, 28, 28, 27, 28, 29, 28, 29, 27, 28, 
      28, 28, 30, 27, 27, 28, 26, 28, 27, 27, 28, 28, 28, 28, 27, 27, 
      28, 27, 28, 27, 35, 27, 27, 28, 29, 27, 27, 28, 26, 27, 28, 28, 
      28, 27, 27, 27, 28, 32, 27, 28, 28, 29, 28, 28, 27, 28, 28, 30, 
      29, 28, 25, 27, 28, 30, 28, 30, 30, 28, 30, 30, 28, 29, 30, 28, 
      28, 26, 27, 28, 45, 36, 40, 28, 50, 45, 30, 45, 40, 30, 45, 45, 
      29, 45, 35, 40, 40, 30, 30, 30, 45, 40, 40, 40, 40, 40, 40, 35, 
      34, 49, 40, 30, 61, 35, 40, 30, 36, 35, 29, 27, 48, 28, 27, 27, 
      26, 27, 29, 27, 26, 27, 31, 27, 27, 28, 29, 28, 27, 28, 29, 38, 
      30, 26, 36, 40, 58, 57, 30, 33, 56, 35, 39, 37, 38, 46, 37, 39, 
      39, 45, 35, 46, 58, 65, 60, 45, 32, 36, 43, 32, 68, 39, 28, 31, 
      27, 28, 27, 37, 38, 30, 30, 28, 36, 45, 28, 26, 28, 28, 28, 27, 
      26, 28, 27, 26, 26, 27, 28, 31, 32, 37, 35, 29, 33, 35, 29, 41, 
      32, 36, 29, 28, 28, 28, 37, 36, 37, 35, 31, 32, 30, 27, 31, 32, 
      31, 33, 28, 33, 29, 27, 28, 31, 28, 31, 28, 34, 27, 27, 28, 27, 
      27, 27, 27, 26, 26, 26, 27, 27, 28, 26, 31, 26, 29, 31, 29, 29, 
      30, 29, 30, 31, 32, 29, 30, 27, 32, 27, 26, 31, 31, 31, 27, 27, 
      33, 27, 28, 28, 28, 26, 27, 27, 28, 30, 27, 27, 30, 29, 26, 27, 
      28, 27, 26, 26, 28, 27, 26, 28, 28, 26, 28, 27, 29, 27, 28, 28, 
      26, 26, 29, 28, 27, 27, 27, 28, 26, 25, 27, 29, 30, 36, 40, 28, 
      38, 26, 27, 27, 50, 27, 45, 27, 28, 26, 25, 35, 35, 44, 30, 27, 
      31, 27, 28, 27, 27, 28, 28, 28, 35, 33, 30, 28, 28, 29, 29, 36, 
      32, 36, 34, 32, 28, 28, 29, 28, 28, 32, 30, 35, 33, 36, 32, 30, 
      32, 36, 34)

quantile(x, probs = c(0.333, 0.666))
#> 33.3% 66.6% 
#>    28    31

l = cut(x, breaks = c(-Inf, 28, 31, Inf))
table(l)
#> l
#> (-Inf,28]   (28,31] (31, Inf] 
#>       387       185       246

#using different cut-off points yielded more equal groups
l = cut(x, breaks = c(-Inf, 28, 32, Inf))
table(l)
#> l
#> (-Inf,28]   (28,32] (32, Inf] 
#>       387       214       217

#again using different cut-off points which yielded more equal groups
l = cut(x, breaks = c(-Inf, 27, 32, Inf))
table(l)
#> l
#> (-Inf,27]   (27,32] (32, Inf] 
#>       222       379       217

^{Criado em 2024-10-07 com reprex v2.1.1}

Editar: Acho que a palavra "igual" não está clara, então acho que posso dizer que busco a alocação mais adequada que forneça a menor diferença entre os números de observação do grupo mais alto e mais baixo, agrupando apenas números consecutivos sem empates em mais de um grupo

Eu estava fazendo um novo tema no gtsummarypacote, mas parece que ele afeta a tbl_continuousfunção, embora eu não tenha feito nenhum argumento sobre isso tbl_continuousno meu tema. Além disso, não consigo encontrar na documentação nenhum elemento de tema específico para tbl_continuous.

Aqui está meu código:

    > my_theme = list(
    +   "pkgwide-str:theme_name" = "JO JO",
    +   "pkgwide-fn:pvalue_fun" = function(x) style_pvalue(x, digits = 2),
    +   "pkgwide-fun:pre_conversion" = function(x) bold_labels(x),
    +   "pkgwide-str:ci.sep" = "-",
    +   #$ tbl_regression $#
    +   "tbl_regression-str:ref_row_text" = "1(r)",
    +   #$ tbl_summary $#
    +   "tbl_summary-fn:percent_fun" = function(x) style_percent(x, symbol = T, digits = 1),
    +   "tbl_summary-arg:statistic" = list(all_continuous() ~"{mean} ({sd})",
    +                                      all_categorical() ~ "{n} ({p})"))
    > check_gtsummary_theme(my_theme)
    ✔ Looks good!
    > set_gtsummary_theme(my_theme)
    Setting theme "JO JO"
    > tbl_continuous(
    +   data = trial,
    +   variable = age,
    +   by = trt,
    +   include = grade
    + )
    Error in `tbl_continuous()`:
    ! Problem with the `statistic` argument.
    Error converting string "p" to a function.
    ℹ Is the name spelled correctly and available?
    Run `rlang::last_trace()` to see where the error occurred.
    > rlang::last_trace()
    <error/rlang_error>
    Error in `tbl_continuous()`:
    ! Problem with the `statistic` argument.
    Error converting string "p" to a function.
    ℹ Is the name spelled correctly and available?
    ---
    Backtrace:
        ▆
     1. └─gtsummary::tbl_continuous(data = trial, variable = age, by = trt, include = grade)
    Run rlang::last_trace(drop = FALSE) to see 27 hidden frames.
    > rlang::last_trace(drop = FALSE)
    <error/rlang_error>
    Error in `tbl_continuous()`:
    ! Problem with the `statistic` argument.
    Error converting string "p" to a function.
    ℹ Is the name spelled correctly and available?
    ---
    Backtrace:
         ▆
      1. └─gtsummary::tbl_continuous(data = trial, variable = age, by = trt, include = grade)
      2.   ├─dplyr::bind_rows(...)
      3.   │ └─rlang::list2(...)
      4.   └─gtsummary:::map(...)
      5.     └─base::lapply(.x, .f, ...)
      6.       └─gtsummary (local) FUN(X[[i]], ...)
      7.         ├─cards::bind_ard(...)
      8.         │ └─dplyr::bind_rows(...)
      9.         │   └─rlang::list2(...)
     10.         ├─cards::ard_continuous(...)
     11.         ├─cards:::ard_continuous.data.frame(...)
     12.         │ ├─cards::process_formula_selectors(...)
     13.         │ └─cards:::process_formula_selectors.data.frame(...)
     14.         │   └─rlang::dots_list(...)
     15.         ├─rlang::set_names(...)
     16.         └─gtsummary:::.continuous_statistics_chr_to_fun(statistic)
     17.           └─base::lapply(...)
     18.             └─gtsummary (local) FUN(X[[i]], ...)
     19.               ├─rlang::set_names(...)
     20.               └─gtsummary:::map2(...)
     21.                 └─base::mapply(.f, .x, .y, MoreArgs = list(...), SIMPLIFY = FALSE)
     22.                   └─gtsummary (local) `<fn>`(dots[[1L]][[2L]], dots[[2L]][[2L]])
     23.                     └─base::tryCatch(...)
     24.                       └─base (local) tryCatchList(expr, classes, parentenv, handlers)
     25.                         └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
     26.                           └─value[[3L]](cond)
     27.                             └─cli::cli_abort(...)
     28.                               └─rlang::abort(...)
    > reset_gtsummary_theme()
    > tbl_continuous(
    +   data = trial,
    +   variable = age,
    +   by = trt,
    +   include = grade
    + )

Quando eu reseto o tema, ele emite a tabela sem problemas. Quero saber onde está o problema e também por que não há elementos de tema específicos para tbl_continuous.

Editar: Também tentei usar theme_gtsummary_mean_sd()o built-in gtsummarye o mesmo erro persiste.

    > theme_gtsummary_mean_sd()
    > trial |> 
    +   tbl_continuous(age)
    Error in `tbl_continuous()`:
    ! Problem with the `statistic` argument.
    Error converting string "p" to a function.
    ℹ Is the name spelled correctly and available?
    Run `rlang::last_trace()` to see where the error occurred.