The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
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 to an introduction on how to use the package’s functions and tutorials on advanced use.
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.
Every {gtsummary} object is a list comprising of, at minimum, these elements:
The .$table_body object is the data frame that will
ultimately be printed as the output. The table must include columns
"label", "row_type", and
"variable". The "label" column is printed, and
the other two are hidden from the final output.
tbl_summary_ex$table_body
#> # A tibble: 8 × 7
#> variable var_type row_type var_label label stat_1 stat_2
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 age continuous label Age Age 46 (37, 60) 48 (3…
#> 2 age continuous missing Age Unknown 7 4
#> 3 grade categorical label Grade Grade <NA> <NA>
#> 4 grade categorical level Grade I 35 (36%) 33 (3…
#> 5 grade categorical level Grade II 32 (33%) 36 (3…
#> 6 grade categorical level Grade III 31 (32%) 33 (3…
#> 7 response dichotomous label Tumor Response Tumor Response 28 (29%) 33 (3…
#> 8 response dichotomous missing Tumor Response Unknown 3 4The .$table_styling object is a list of data frames
containing information about how .$table_body is printed,
formatted, and styled.
The list contains the following data frames header,
footnote, footnote_abbrev,
fmt_fun, text_format,
fmt_missing, cols_merge and the following
objects source_note, caption,
horizontal_line_above.
header
The header table has the following columns and is one
row per column found in .$table_body. The table contains
styling information that applies to entire column or the columns
headers.
| Column | Description |
|---|---|
| column | Column name from .$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() |
| spanning_header | Includes text printed above columns as spanning headers. |
| interpret_spanning_header | the {gt} function that is used to interpret the column spanning headers, 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 |
footnote &
footnote_abbrev
Each {gtsummary} table may contain a single footnote per header and
cell within the table. Footnotes and footnote abbreviations are handled
separately. Updates/changes to footnote are appended to the bottom of
the tibble. A footnote of NA_character_ deletes an existing
footnote.
| 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 |
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.
| Column | Description |
|---|---|
| column | Column name from .$table_body |
| rows | expression selecting rows in .$table_body |
| fmt_fun | list of formatting/styling functions |
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.
| 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. |
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.
| 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 |
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.
| 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’. |
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.
| Column | Description |
|---|---|
| id | ID of the source note |
| sounrce_note | string containing the source note |
| 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 removed from the table |
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()
tbl_regression_ex$table_styling
#> $header
#> # A tibble: 24 × 8
#> column hide align interpret_label label interpret_spanning_h…¹
#> <chr> <lgl> <chr> <chr> <chr> <chr>
#> 1 variable TRUE center gt::md varia… gt::md
#> 2 var_label TRUE center gt::md var_l… gt::md
#> 3 var_type TRUE center gt::md var_t… gt::md
#> 4 reference_row TRUE center gt::md refer… gt::md
#> 5 row_type TRUE center gt::md row_t… gt::md
#> 6 header_row TRUE center gt::md heade… gt::md
#> 7 N_obs TRUE center gt::md N_obs gt::md
#> 8 N TRUE center gt::md **N** gt::md
#> 9 coefficients_type TRUE center gt::md coeff… gt::md
#> 10 coefficients_label TRUE center gt::md coeff… gt::md
#> # ℹ 14 more rows
#> # ℹ abbreviated name: ¹interpret_spanning_header
#> # ℹ 2 more variables: spanning_header <chr>, modify_stat_N <int>
#>
#> $footnote
#> # A tibble: 0 × 4
#> # ℹ 4 variables: column <chr>, rows <list>, text_interpret <chr>,
#> # footnote <chr>
#>
#> $footnote_abbrev
#> # A tibble: 2 × 4
#> column rows text_interpret footnote
#> <chr> <list> <chr> <chr>
#> 1 conf.low <quosure> gt::md CI = Confidence Interval
#> 2 std.error <quosure> gt::md SE = Standard Error
#>
#> $source_note
#> # A tibble: 0 × 4
#> # ℹ 4 variables: id <int>, source_note <chr>, text_interpret <chr>,
#> # remove <lgl>
#>
#> $text_format
#> # A tibble: 1 × 4
#> column rows format_type undo_text_format
#> <chr> <list> <chr> <lgl>
#> 1 p.value <quosure> bold FALSE
#>
#> $indent
#> # A tibble: 2 × 3
#> column rows n_spaces
#> <chr> <list> <int>
#> 1 label <lgl [1]> 0
#> 2 label <quosure> 4
#>
#> $fmt_missing
#> # A tibble: 4 × 3
#> column rows symbol
#> <chr> <list> <chr>
#> 1 estimate <quosure> —
#> 2 conf.low <quosure> —
#> 3 std.error <quosure> —
#> 4 statistic <quosure> —
#>
#> $fmt_fun
#> # A tibble: 10 × 3
#> column rows fmt_fun
#> <chr> <list> <list>
#> 1 estimate <quosure> <fn>
#> 2 N <quosure> <fn>
#> 3 N_obs <quosure> <fn>
#> 4 n_obs <quosure> <fn>
#> 5 conf.low <quosure> <fn>
#> 6 conf.high <quosure> <fn>
#> 7 p.value <quosure> <fn>
#> 8 std.error <quosure> <fn>
#> 9 statistic <quosure> <fn>
#> 10 var_nlevels <quosure> <fn>
#>
#> $cols_merge
#> # A tibble: 1 × 3
#> column rows pattern
#> <chr> <list> <chr>
#> 1 conf.low <quosure> {conf.low}, {conf.high}When constructing a {gtsummary} object, the author will begin with
the .$table_body object. Recall the
.$table_body data frame must include columns
"label", "row_type", and
"variable". Of these columns, only the "label"
column will be printed with the final results. The
"row_type" column typically will control whether or not the
label column is indented. The "variable" column is often
used in the inline_text() family of functions, and merging
{gtsummary} tables with tbl_merge().
tbl_regression_ex %>%
getElement("table_body") %>%
select(variable, row_type, label)
#> # A tibble: 5 × 3
#> variable row_type label
#> <chr> <chr> <chr>
#> 1 grade label Grade
#> 2 grade level I
#> 3 grade level II
#> 4 grade level III
#> 5 marker label Marker Level (ng/mL)The other columns in .$table_body are created by the
user and are likely printed in the output. Formatting and printing
instructions for these columns is stored in
.$table_styling.
There are a few internal {gtsummary} functions to assist in
constructing and modifying a .$table_header data frame.
.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).
.update_table_styling() After columns are added or
removed from table_body, run this function to update
.$table_styling to include or remove styling instructions
for the columns. FYI the default styling for each new column is to hide
it.
modify_table_styling() This exported function
modifies the printing instructions for a single column or groups of
columns.
modify_table_body() This exported function helps
users make changes to .$table_body. The function runs
.update_table_styling() internally to maintain internal
validity with the printing instructions.
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:
.$cards objectWhen a gtsummary function is called that requires new statistics, these new calculations are stored in a tibble. These tibbles are often calculated with functions from the {cards} and {cardx} packages.
These structured tibbles store labels for statistics, functions to format them, and more. See the {cards} package documentation for details.
tbl_summary_ex$cards[["tbl_summary"]]
#> {cards} data frame: 76 x 12
#> group1 group1_level variable variable_level stat_name stat_label stat
#> 1 trt Drug A grade I n n 35
#> 2 trt Drug A grade I N N 98
#> 3 trt Drug A grade I p % 0.357
#> 4 trt Drug B grade I n n 33
#> 5 trt Drug B grade I N N 102
#> 6 trt Drug B grade I p % 0.324
#> 7 trt Drug A grade II n n 32
#> 8 trt Drug A grade II N N 98
#> 9 trt Drug A grade II p % 0.327
#> 10 trt Drug B grade II n n 36
#> ℹ 66 more rows
#> ℹ Use `print(n = ...)` to see more rows
#> ℹ 5 more variables: context, fmt_fn, warning, error, gts_columnThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.