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tbl_stack.R
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tbl_stack.R
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#' Stack tables
#'
#' Assists in patching together more complex tables. `tbl_stack()` appends two
#' or more gtsummary tables.
#' Column attributes, including number formatting and column footnotes, are
#' retained from the first passed gtsummary object.
#'
#' @param tbls (`list`)\cr
#' List of gtsummary objects
#' @param group_header (`character`)\cr
#' Character vector with table headers where length matches the length of `tbls`
#' @param quiet (scalar `logical`)\cr
#' Logical indicating whether to suppress additional messaging. Default is `FALSE`.
#'
#' @author Daniel D. Sjoberg
#' @export
#' @return A `tbl_stack` object
#'
#' @examplesIf (identical(Sys.getenv("NOT_CRAN"), "true") || identical(Sys.getenv("IN_PKGDOWN"), "true")) && gtsummary:::is_pkg_installed("cardx", reference_pkg = "gtsummary") && gtsummary:::is_pkg_installed("survival", reference_pkg = "cardx")
#' # Example 1 ----------------------------------
#' # stacking two tbl_regression objects
#' t1 <-
#' glm(response ~ trt, trial, family = binomial) %>%
#' tbl_regression(
#' exponentiate = TRUE,
#' label = list(trt ~ "Treatment (unadjusted)")
#' )
#'
#' t2 <-
#' glm(response ~ trt + grade + stage + marker, trial, family = binomial) %>%
#' tbl_regression(
#' include = "trt",
#' exponentiate = TRUE,
#' label = list(trt ~ "Treatment (adjusted)")
#' )
#'
#' tbl_stack(list(t1, t2))
#'
#' # Example 2 ----------------------------------
#' # stacking two tbl_merge objects
#' library(survival)
#' t3 <-
#' coxph(Surv(ttdeath, death) ~ trt, trial) %>%
#' tbl_regression(
#' exponentiate = TRUE,
#' label = list(trt ~ "Treatment (unadjusted)")
#' )
#'
#' t4 <-
#' coxph(Surv(ttdeath, death) ~ trt + grade + stage + marker, trial) %>%
#' tbl_regression(
#' include = "trt",
#' exponentiate = TRUE,
#' label = list(trt ~ "Treatment (adjusted)")
#' )
#'
#' # first merging, then stacking
#' row1 <- tbl_merge(list(t1, t3), tab_spanner = c("Tumor Response", "Death"))
#' row2 <- tbl_merge(list(t2, t4))
#'
#' tbl_stack(list(row1, row2), group_header = c("Unadjusted Analysis", "Adjusted Analysis"))
tbl_stack <- function(tbls, group_header = NULL, quiet = FALSE) {
set_cli_abort_call()
# check inputs ---------------------------------------------------------------
check_class(tbls, "list")
walk(tbls, ~check_class(.x, "gtsummary", message = "Each element of the list {.arg tbls} must be class {.cls gtsummary}."))
check_scalar_logical(quiet)
check_class(group_header, cls = "character", allow_empty = TRUE)
check_length(group_header, length = length(tbls), allow_empty = TRUE)
# will return call, and all arguments passed to tbl_stack
func_inputs <- as.list(environment())
# stack tables ---------------------------------------------------------------
# first, save a string of the new tbl ID column
tbl_id_colname <- .tbl_id_varname(tbls)
# stack the `table_body` data frames
results <- list()
results$table_body <-
map2(
tbls, seq_along(tbls),
function(tbl, id) {
# adding a table ID and group header
table_body <- tbl[["table_body"]] |> dplyr::mutate("{tbl_id_colname}" := id)
if (!is.null(group_header)) {
table_body <-
table_body |>
dplyr::mutate(groupname_col = group_header[id])
}
table_body |> dplyr::select(any_of(c("groupname_col")), matches("^tbl_id\\d+$"), everything())
}
) %>%
dplyr::bind_rows()
# creating table styling -----------------------------------------------------
# print message if column headers, footnotes, etc. are different among tbls
if (identical(quiet, FALSE)) .print_stack_differences(tbls)
results$table_styling$header <-
map(tbls, ~ .x[["table_styling"]][["header"]]) |>
dplyr::bind_rows() |>
dplyr::filter(.by = "column", dplyr::row_number() == 1)
# cycle over each of the styling tibbles and stack them in reverse order -----
for (style_type in c("footnote", "footnote_abbrev", "fmt_fun", "text_format", "indent", "fmt_missing", "cols_merge")) {
results$table_styling[[style_type]] <-
map(
rev(seq_along(tbls)),
function(i) {
df <- tbls[[i]]$table_styling[[style_type]]
if ("rows" %in% names(df) && nrow(df) > 0) {
# adding tbl_id to the rows specifications,
# e.g. data$tbl_id == 1L & .data$row_type != "label"
df$rows <-
map(df$rows, ~ .add_tbl_id_to_quo(.x, tbls[[i]]$table_body, i, tbl_id_colname, style_type))
}
df |>
dplyr::mutate_at(vars(any_of(c(
"column", "text_interpret",
"footnote", "format_type", "symbol"
))), as.character)
}
) |>
dplyr::bind_rows()
}
# combining rows spec for same column
if (nrow(results$table_styling$cols_merge) > 0) {
results$table_styling$cols_merge <-
results$table_styling$cols_merge |>
tidyr::nest(rows = "rows") |>
dplyr::mutate(rows = map(.data$rows, ~ .x$rows |> unlist()))
results$table_styling$cols_merge$rows <-
map(
results$table_styling$cols_merge$rows,
~ .x |> reduce(function(.x1, .y1) expr(!!quo_squash(.x1) | !!quo_squash(.y1)))
)
}
# take the first non-NULL element from tbls[[.]]
for (style_type in c("caption", "source_note", "horizontal_line_above")) {
results$table_styling[[style_type]] <-
map(seq_along(tbls), ~ tbls[[.x]][["table_styling"]][[style_type]]) |>
reduce(.f = \(.x, .y) .x %||% .y)
}
# adding label for grouping variable, if present -----------------------------
class(results) <- c("tbl_stack", "gtsummary")
results <-
modify_table_styling(
results,
any_of("groupname_col"),
label = get_theme_element("tbl_stack-str:group_header", default = "**Group**"),
align = "left",
hide = FALSE
)
# returning results ----------------------------------------------------------
results$call_list <- list(tbl_stack = match.call())
results$tbls <- tbls
results
}
# function prints changes to column labels and spanning headers
.print_stack_differences <- function(tbls) {
tbl_differences <-
map2(
tbls, seq_len(length(tbls)),
~ .x[["table_styling"]][["header"]] |>
dplyr::mutate(..tbl_id.. = .y)
) |>
dplyr::bind_rows() |>
dplyr::select("..tbl_id..", "column", "label", "spanning_header") |>
tidyr::pivot_longer(cols = c("label", "spanning_header")) |>
dplyr::group_by(.data$column, .data$name) |>
dplyr::mutate(
new_value = .data$value[1],
name_fmt = dplyr::case_when(
name == "label" ~ "Column header",
name == "spanning_header" ~ "Spanning column header"
)
) |>
dplyr::filter(.data$new_value != .data$value) |>
dplyr::ungroup() |>
dplyr::arrange(.data$name != "label", .data$name_fmt, .data$..tbl_id..)
if (nrow(tbl_differences) > 0) {
cli::cli_inform(
c("Column headers among stacked tables differ. Headers from the first table are used.",
i = "Use {.code quiet = TRUE} to suppress this message.")
)
}
return(invisible())
}
.add_tbl_id_to_quo <- function(x, table_body, tbl_id, tbl_id_colname, style_type) {
# if NULL AND style_type is a type that adds header changes (i.e. footnote in header),
# then just return the NULL
# the requires the stacking to pick one of the header footnotes and use it
# the others will be discarded when printed.
row_is_null <- eval_tidy(x, data = table_body) |> is.null()
if (row_is_null && style_type %in% c("footnote", "footnote_abbrev")) {
return(x)
}
# otherwise if NULL, add the tbl_id condition
if (row_is_null) {
return(expr(!!sym(tbl_id_colname) == !!tbl_id))
}
# if quosure, add tbl_id
if (inherits(x, "quosure")) {
return(
quo(!!sym(tbl_id_colname) == !!tbl_id & (!!rlang::f_rhs(x))) %>%
structure(.Environment = attr(x, ".Environment"))
)
}
# if expression, add tbl_id
expr(!!sym(tbl_id_colname) == !!tbl_id & (!!x))
}
.tbl_id_varname <- function(tbls) {
# get column names that begin with 'tbl_id##'
tbl_id_colnames <-
map(tbls, ~dplyr::select(.x$table_body, matches("^tbl_id\\d+$")) |> names()) |>
unlist() |>
unique() |>
discard(is.na)
# return 'tbl_id1' if no columns found
if (is_empty(tbl_id_colnames)) {
return("tbl_id1")
}
# if there are other tbl_id columns, return the next in the sequence
tbl_max_id <-
sub(pattern = "^tbl_id", replacement = "", x = tbl_id_colnames) |>
as.integer() |>
max()
return(paste0("tbl_id", tbl_max_id + 1L))
}