---
title: "Definition of a gtsummary Object"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Definition of a gtsummary Object}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  warning = FALSE,
  comment = "#>"
)
```

This vignette is meant for those who wish to contribute to {gtsummary}, or users who wish to gain an understanding of the inner-workings of a {gtsummary} object so they may more easily modify them to suit your own needs.
If this does not describe you, please refer to the [{gtsummary} website](https://www.danieldsjoberg.com/gtsummary/) to an introduction on how to use the package's functions and tutorials on advanced use.

_This overview is for informational purposes. Documenting the internal structures does not mean the internal structures of the package won't be updated. If they are updated, this is not considered a breaking change._

## Introduction

Every {gtsummary} table has a few characteristics common among all tables created with the package.
Here, we review those characteristics, and provide instructions on how to construct a {gtsummary} object.

We begin by creating two common {gtsummary} tables to be used as illustrative examples.

```{r setup, message=FALSE}
library(gtsummary)

tbl_regression_ex <-
  lm(age ~ grade + marker, trial) |> 
  tbl_regression() |> 
  bold_p(t = 0.5)

tbl_summary_ex <-
  trial |> 
  tbl_summary(by = trt, include = c(trt, age, grade, response))
```

## Structure of a {gtsummary} object

Every {gtsummary} object is a list comprising of, at minimum, these elements:

```r
.$table_body    .$table_styling         
```

#### table_body

The `.$table_body` object is the data frame that will ultimately be printed as the output.
To utilize all functions that work with {gtsummary} tables (e.g. {gtsummary} selectors), the table must include columns `"label"`, `"row_type"`, and `"variable"`.
The `"label"` column is printed, and the other two are hidden from the final output.

```{r}
tbl_summary_ex$table_body
```

#### table_styling

The `.$table_styling` object is a list of data frames containing information about how `.$table_body` is printed, formatted, and styled.  
The list contains the following data frames `header`, `footnote_header`, `footnote_body`, `footnote_spanning_header`, `abbreviation`, `source_note`, `fmt_fun`, `text_format`, `fmt_missing`, `cols_merge` and the following objects `caption` and `horizontal_line_above`.

**`header`**

The `header` table has the following columns and is one row per column found in `.$table_body`.
The table contains styling information that applies to entire column or the columns headers.

```{r, echo=FALSE}
dplyr::tribble(
  ~Column, ~Description,
  "column", "Column name from `.$table_body`",
  "hide", "Logical indicating whether the column is hidden in the output. This column is also scoped in `modify_header()` (and friends) to be used in a selecting environment",
  "align", "Specifies the alignment/justification of the column, e.g. 'center' or 'left'",
  "label", "Label that will be displayed (if column is displayed in output)",
  "interpret_label", "the {gt} function that is used to interpret the column label, `gt::md()` or `gt::html()`",
  "modify_stat_{*}", "any column beginning with `modify_stat_` is a statistic available to report in `modify_header()` (and others)",
  "modify_selector_{*}", "any column beginning with `modify_selector_` is a column that is scoped in `modify_header()` (and friends) to be used in a selecting environment"
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = "small",
    data_row.padding = gt::px(1),
    summary_row.padding = gt::px(1),
    grand_summary_row.padding = gt::px(1),
    footnotes.padding = gt::px(1),
    source_notes.padding = gt::px(1),
    row_group.padding = gt::px(1)
  )
```

**`footnote_header`**

Each {gtsummary} table may contain footnotes in the column headers.
Updates/changes to footnote are appended to the bottom of the tibble.

```{r, echo=FALSE}
dplyr::tribble(
  ~Column, ~Description,
  "column", "Column name from `.$table_body`",
  "footnote", "string containing footnote to add to column/row",
  "text_interpret", "the {gt} function that is used to interpret the source note, `gt::md()` or `gt::html()`",
  "replace", "logical indicating whether this footnote should replace any existing footnote in that header (TRUE) or be added to any existing (FALSE)",
  "remove", "logical indicating whether to remove all footnotes in the column header"
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = "small",
    data_row.padding = gt::px(1),
    summary_row.padding = gt::px(1),
    grand_summary_row.padding = gt::px(1),
    footnotes.padding = gt::px(1),
    source_notes.padding = gt::px(1),
    row_group.padding = gt::px(1)
  )
``` 

**`footnote_body`**

Each {gtsummary} table may include footnotes in the body of the table.
Updates/changes to footnote are appended to the bottom of the tibble.

```{r, echo=FALSE}
dplyr::tribble(
  ~Column, ~Description,
  "column", "Column name from `.$table_body`",
  "rows", "expression selecting rows in `.$table_body`, `NA` indicates to add footnote to header",
  "footnote", "string containing footnote to add to column/row",
  "text_interpret", "the {gt} function that is used to interpret the source note, `gt::md()` or `gt::html()`",
  "replace", "logical indicating whether this footnote should replace any existing footnote in that header (TRUE) or be added to any existing (FALSE)",
  "remove", "logical indicating whether to remove all footnotes in the column header",
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = "small",
    data_row.padding = gt::px(1),
    summary_row.padding = gt::px(1),
    grand_summary_row.padding = gt::px(1),
    footnotes.padding = gt::px(1),
    source_notes.padding = gt::px(1),
    row_group.padding = gt::px(1)
  )
``` 

**`footnote_spanning_header`**

Each {gtsummary} table may include footnotes in the spanning headers of the table.
Updates/changes to footnote are appended to the bottom of the tibble.

```{r, echo=FALSE}
dplyr::tribble(
  ~Column, ~Description,
  "level", "Integer specifying the spanning header level, similar to `gt::tab_spanner(level)`",
  "column", "Column name from `.$table_body`",
  "footnote", "string containing footnote to add to column/row",
  "text_interpret", "the {gt} function that is used to interpret the source note, `gt::md()` or `gt::html()`",
  "replace", "logical indicating whether this footnote should replace any existing footnote in that header (TRUE) or be added to any existing (FALSE)",
  "remove", "logical indicating whether to remove all footnotes in the column header",
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = "small",
    data_row.padding = gt::px(1),
    summary_row.padding = gt::px(1),
    grand_summary_row.padding = gt::px(1),
    footnotes.padding = gt::px(1),
    source_notes.padding = gt::px(1),
    row_group.padding = gt::px(1)
  )
``` 

**`abbreviation`**

Abbreviations are added one at a time, and at the time of table rendering, they are coalesced into a single source note.

```{r, echo=FALSE}
dplyr::tribble(
  ~Column, ~Description,
  "column", "Optional column name from `.$table_body`. When present, the abbreviation is only printed when the column appears in the rendered table",
  "abbreviation", "string containing the abbreviation to add",
  "text_interpret", "the {gt} function that is used to interpret the source note, `gt::md()` or `gt::html()`",
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = "small",
    data_row.padding = gt::px(1),
    summary_row.padding = gt::px(1),
    grand_summary_row.padding = gt::px(1),
    footnotes.padding = gt::px(1),
    source_notes.padding = gt::px(1),
    row_group.padding = gt::px(1)
  )
``` 

**`source_note`**

A tibble with the source notes to include.
Each source note is assigned an ID based on the order it is added to the table.
Source notes are added one at a time and present much like footnotes, but are not linked to a header or cell in the table.

```{r, echo=FALSE}
dplyr::tribble(
  ~Column, ~Description,
  "id", "Integer idenitfying the source note",
  "source_note", "string containing the abbreviation to add",
  "text_interpret", "the {gt} function that is used to interpret the source note, `gt::md()` or `gt::html()`",
  "remove", "logical indicating whether the source note should be included or removed from final table"
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = "small",
    data_row.padding = gt::px(1),
    summary_row.padding = gt::px(1),
    grand_summary_row.padding = gt::px(1),
    footnotes.padding = gt::px(1),
    source_notes.padding = gt::px(1),
    row_group.padding = gt::px(1)
  )
``` 

**`fmt_fun`**

Numeric columns/rows are styled with the functions stored in `fmt_fun`.
Updates/changes to styling functions are appended to the bottom of the tibble.


```{r, echo=FALSE}
dplyr::tribble(
  ~Column, ~Description,
  "column", "Column name from `.$table_body`",
  "rows", "expression selecting rows in `.$table_body`",
  "fmt_fun", "list of formatting/styling functions"
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = "small",
    data_row.padding = gt::px(1),
    summary_row.padding = gt::px(1),
    grand_summary_row.padding = gt::px(1),
    footnotes.padding = gt::px(1),
    source_notes.padding = gt::px(1),
    row_group.padding = gt::px(1)
  )
``` 

**`text_format`**

Columns/rows are styled with bold, italic, or indenting stored in `text_format`.
Updates/changes to styling functions are appended to the bottom of the tibble.


```{r, echo=FALSE}
dplyr::tribble(
  ~Column, ~Description,
  "column", "Column name from `.$table_body`",
  "rows", "expression selecting rows in `.$table_body`",
  "format_type", "one of `c('bold', 'italic', 'indent')`",
  "undo_text_format", "logical indicating where the formatting indicated should be undone/removed."
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = "small",
    data_row.padding = gt::px(1),
    summary_row.padding = gt::px(1),
    grand_summary_row.padding = gt::px(1),
    footnotes.padding = gt::px(1),
    source_notes.padding = gt::px(1),
    row_group.padding = gt::px(1)
  )
``` 

**`fmt_missing`**

By default, all `NA` values are shown blanks.
Missing values in columns/rows are replaced with the `symbol`.
For example, reference rows in `tbl_regression()` are shown with an em-dash.
Updates/changes to styling functions are appended to the bottom of the tibble.

```{r, echo=FALSE}
dplyr::tribble(
  ~Column, ~Description,
  "column", "Column name from `.$table_body`",
  "rows", "expression selecting rows in `.$table_body`",
  "symbol", "string to replace missing values with, e.g. an em-dash"
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = "small",
    data_row.padding = gt::px(1),
    summary_row.padding = gt::px(1),
    grand_summary_row.padding = gt::px(1),
    footnotes.padding = gt::px(1),
    source_notes.padding = gt::px(1),
    row_group.padding = gt::px(1)
  )
``` 

**`cols_merge`**

This object is _experimental_ and may change in the future.
This tibble gives instructions for merging columns into a single column.
The implementation in `as_gt()` will be updated after `gt::cols_label()` gains a `rows=` argument.

```{r, echo=FALSE}
dplyr::tribble(
  ~Column, ~Description,
  "column", "Column name from `.$table_body`",
  "rows", "expression selecting rows in `.$table_body`",
  "pattern", "glue pattern directing how to combine/merge columns. The merged columns will replace the column indicated in 'column'."
) %>%
  gt::gt() %>%
  gt::fmt_markdown(columns = everything()) %>%
  gt::tab_options(
    table.font.size = "small",
    data_row.padding = gt::px(1),
    summary_row.padding = gt::px(1),
    grand_summary_row.padding = gt::px(1),
    footnotes.padding = gt::px(1),
    source_notes.padding = gt::px(1),
    row_group.padding = gt::px(1)
  )
``` 

**`caption`**

String that is made into the table caption.
The attribute `"text_interpret"` is either `c("md", "html")`.

**`horizontal_line_above`**

Expression identifying a row where a horizontal line is placed above in the table.

Example from `tbl_regression()`

```{r} 
tbl_regression_ex$table_styling
```

## Constructing a {gtsummary} object

#### table_body

When constructing a {gtsummary} object, the author will begin with the `.$table_body` object.
Recall the `.$table_body` data frame must include columns `"label"`, `"row_type"`, and `"variable"`.
Of these columns, only the `"label"` column will be printed with the final results.
The `"row_type"` column typically will control whether or not the label column is indented.
The `"variable"` column is often used in the `inline_text()` family of functions, and merging {gtsummary} tables with `tbl_merge()`.

```{r}
tbl_regression_ex %>%
  getElement("table_body") %>%
  select(variable, row_type, label)
```

The other columns in `.$table_body` are created by the user and are likely printed in the output.
Formatting and printing instructions for these columns is stored in `.$table_styling`.

### table_styling

There are a few internal {gtsummary} functions to assist in constructing and modifying a `.$table_header` data frame.

1. `as_gtsummary()` / `.create_gtsummary_object(table_body)` After a user creates a `table_body`, pass it to this function and the skeleton of a gtsummary object is created and returned (including the full `table_styling` list of tables).

1. `.update_table_styling()` After columns are added or removed from `table_body`, run this function to update `.$table_styling` to include or remove styling instructions for the columns. FYI the default styling for each new column is to hide it.

1. `modify_table_styling()` This exported function modifies the printing instructions for a single column or groups of columns.

1. `modify_table_body()` This exported function helps users make changes to `.$table_body`. The function runs `.update_table_styling()` internally to maintain internal validity with the printing instructions.

## Printing a {gtsummary} object

All {gtsummary} objects are printed with `print.gtsummary()`.
Before a {gtsummary} object is printed, it is converted to a {gt} object using `as_gt()`.
This function takes the {gtsummary} object as its input, and uses the information in `.$table_styling` to construct a list of {gt} calls that will be executed on `.$table_body`.
After the {gtsummary} object is converted to {gt}, it is then printed as any other {gt} object.

In some cases, the package defaults to printing with other engines, such as flextable (`as_flex_table()`), huxtable (`as_hux_table()`), kableExtra (`as_kable_extra()`),  and kable (`as_kable()`).
The default print engine is set with the theme element `"pkgwide-str:print_engine"`

While the actual print function is slightly more involved, it is basically this:

```{r, eval = FALSE}
print.gtsummary <- function(x) {
  get_theme_element("pkgwide-str:print_engine") %>%
    switch(
      "gt" = as_gt(x),
      "flextable" = as_flex_table(x),
      "huxtable" = as_hux_table(x),
      "kable_extra" = as_kable_extra(x),
      "kable" = as_kable(x)
    ) %>%
    print()
}
```

## The `.$cards` object

When a gtsummary function is called that requires new statistics, these new calculations are stored in a tibble.
These tibbles are often calculated with functions from the {cards} and {cardx} packages.

These structured tibbles store labels for statistics, functions to format them, and more.
See the {cards} package documentation for details.

```{r}
tbl_summary_ex$cards[["tbl_summary"]]
```
