tidytableone: Tidy construction of "Table 1"

#
# #### Load the packages --------------------------------
#
# library(dplyr)
# library(tidytableone)
#
#
# #### Create some missing --------------------------------
#
# pbc_mayo2 <- pbc_mayo |>
#   mutate(dplyr::across(
#     .cols = all_of(c("time")),
#     .fns = ~ ifelse(row_number(.x) %in% sample(1:n(), size = (10 * n(
#     ) / 100)), NA, .x)
#   ))
#
#
# #### Tidy table ones --------------------------------
#
# ## Strata, Continous ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time"))
#
# ## Strata, categorical ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("stage"))
#
# ## Strata, both ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time",
#                                "stage"))
#
# ## Strata, both, more vars ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time",
#                                "stage",
#                                "bili",
#                                "status"))
#
# ## No strata, Continous ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time"))
#
#
# ## No strata, categorical ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("stage"))
#
# ## No strata, both ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time",
#                                "stage"))
#
# ## No strata, both, more vars ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time",
#                                "stage",
#                                "bili",
#                                "status"))
#
#
#
# #### Adorn tidy table ones --------------------------------
#
# ## Strata, Continous ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time")) |>
#   adorn_tidytableone()
#
# ## Strata, categorical ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("stage")) |>
#   adorn_tidytableone()
#
# pbc_mayo2 |>
#   mutate(trt = forcats::fct_na_value_to_level(trt,
#                                               level = "(Missing)")) %>%
# latable::create_table_one(data = .,
#                           strata = "trt",
#                           vars = c("stage"))
#
# pbc_mayo2 %>%
#   latable::create_table_one(data = .,
#                             strata = "trt",
#                             vars = c("stage"))
#
#
#
# ## Strata, both ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time",
#                                "stage")) |>
#   adorn_tidytableone()
#
# ## Strata, both, more vars ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time",
#                                "stage",
#                                "bili",
#                                "status")) |>
#   adorn_tidytableone()
#
# ## No strata, Continous ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time")) |>
#   adorn_tidytableone()
#
#
# ## No strata, categorical ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("stage")) |>
#   adorn_tidytableone()
#
# ## No strata, both ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time",
#                                "stage")) |>
#   adorn_tidytableone()
#
# ## No strata, both, more vars ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time",
#                                "stage",
#                                "bili",
#                                "status")) |>
#   adorn_tidytableone()
#
#
#
# #### Adorn tidy table ones --------------------------------
#
# ## Strata, Continous ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time")) |>
#   adorn_tidytableone(missing = "ifany",
#                      combine_level_col = FALSE)
#
# ## Strata, categorical ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("stage")) |>
#   adorn_tidytableone(missing = "ifany")
#
#
# pbc_mayo2 |>
#   mutate(trt = forcats::fct_na_value_to_level(trt,
#                                               level = "(Missing)")) %>%
#   latable::create_table_one(data = .,
#                             strata = "trt",
#                             vars = c("stage"))
#
# pbc_mayo2 %>%
#   latable::create_table_one(data = .,
#                             strata = "trt",
#                             vars = c("stage"))
#
#
#
# ## Strata, both ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time",
#                                "stage")) |>
#   adorn_tidytableone(missing = "ifany")
#
# ## Strata, both, more vars ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time",
#                                "stage",
#                                "bili",
#                                "status")) |>
#   adorn_tidytableone(missing = "ifany")
#
# ## No strata, Continous ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time")) |>
#   adorn_tidytableone(missing = "ifany")
#
#
# ## No strata, categorical ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("stage")) |>
#   adorn_tidytableone(missing = "ifany")
#
# ## No strata, both ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time",
#                                "stage")) |>
#   adorn_tidytableone(missing = "ifany")
#
# ## No strata, both, more vars ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time",
#                                "stage",
#                                "bili",
#                                "status")) |>
#   adorn_tidytableone(missing = "ifany")
#
#
#
#
#
# #### Adorn tidy table ones --------------------------------
#
# ## Strata, Continous ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time")) |>
#   adorn_tidytableone(missing = "always",
#                      combine_level_col = FALSE)
#
# ## Strata, categorical ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("stage")) |>
#   adorn_tidytableone(missing = "always")
#
#
# ## Strata, both ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time",
#                                "stage")) |>
#   adorn_tidytableone(missing = "always")
#
# ## Strata, both, more vars ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time",
#                                "stage",
#                                "bili",
#                                "status")) |>
#   adorn_tidytableone(missing = "always")
#
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time",
#                                "stage",
#                                "bili",
#                                "status")) |>
#   adorn_tidytableone(missing = "always",
#                      combine_level_col = FALSE) |>
#   lamisc::flex_print()
#
#
# ## No strata, Continous ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time")) |>
#   adorn_tidytableone(missing = "always")
#
#
# ## No strata, categorical ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("stage")) |>
#   adorn_tidytableone(missing = "always")
#
# ## No strata, both ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time",
#                                "stage")) |>
#   adorn_tidytableone(missing = "always")
#
# ## No strata, both, more vars ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time",
#                                "stage",
#                                "bili",
#                                "status")) |>
#   adorn_tidytableone(missing = "always")
#
#
#
#
# #### Continous text --------------------------------
#
# ## Strata, Continous ----------------
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time")) |>
#   adorn_tidytableone(missing = "always",
#                      combine_level_col = TRUE,
#                      default_continuous = "{mean} ({sd})\n{median} [{iqr}]\n{median} [{range}]\n{range}",
#                      missing_text = "Unknown")
#
#
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time")) |>
#   adorn_tidytableone(missing = "always",
#                      combine_level_col = TRUE,
#                      default_continuous = "{mean} ({sd})\n{median} [{iqr}]\n{median} [{range}]\n{range}",
#                      missing_text = "Unknown")
#
#
# #### With labels --------------------------------
#
#
# # With labels
# library(labelled)
#
# # Tibble with labels
# var_labels <- tibble::tribble(
#   ~vars,                                      ~labels,
#   "id",                                "Case Number",
#   "time",          "Number of days since registration",
#   "status",                         "Status at endpoint",
#   "trt",                            "Treatment group",
#   "age",                              "Age, in years",
#   "sex",                                        "Sex",
#   "ascites",                        "Presence of ascites",
#   "hepato", "Presence of hepatomegaly or enlarged liver",
#   "spiders",     "Blood vessel malformations in the skin",
#   "edema",                          "Presence of edema",
#   "bili",                   "Serum bilirunbin (mg/dl)",
#   "chol",                  "Serum cholesterol (mg/dl)",
#   "albumin",                       "Serum albumin (g/dl)",
#   "copper",                      "Urine copper (ug/day)",
#   "alk_phos",             "Alkaline phosphotase (U/liter)",
#   "ast",          "Aspartate aminotransferase (U/ml)",
#   "trig",                      "Triglycerides (mg/dl)",
#   "platelet",                             "Platelet count",
#   "protime",           "Standardised blood clotting time",
#   "stage", "Histologic stage of disease (needs biopsy)"
# )
#
# labels_list <- setNames(as.list(var_labels$labels), var_labels$vars)
#
# # Apply labels
# labelled::var_label(pbc_mayo) <- labels_list
#
# pbc_mayo2 <- pbc_mayo |>
#   mutate(dplyr::across(
#     .cols = all_of(c("time")),
#     .fns = ~ ifelse(row_number(.x) %in% sample(1:n(), size = (10 * n(
#     ) / 100)), NA, .x)
#   ))
#
# labelled::var_label(pbc_mayo2) <- labels_list
#
# create_tidy_table_one(data = pbc_mayo2,
#                       strata = "trt",
#                       vars = c("time")) |>
#   adorn_tidytableone(missing = "always",
#                      combine_level_col = TRUE,
#                      default_continuous = "{mean} ({sd})\n{median} [{iqr}]\n{median} [{range}]\n{range}",
#                      missing_text = "Unknown")
#
#
#
# create_tidy_table_one(data = pbc_mayo2,
#                       # strata = "trt",
#                       vars = c("time",
#                                "stage")) |>
#   adorn_tidytableone(missing = "ifany",
#                      combine_level_col = TRUE,
#                      default_continuous = "{mean} ({sd})\n{median} [{iqr}]\n{median} [{range}]\n{range}",
#                      missing_text = "Unknown")
#
#
#
# # if (any(tidy_t1$var_type == "continuous") & any(tidy_t1$var_type == "categorical")) {
# #
# #
# # } else if (any(tidy_t1$var_type == "continuous")) {
# #
# #
# #
# # } else if (any(tidy_t1$var_type == "categorical")) {
# #
# #
# # }
#