listings: Create a listing from a 'data.frame' or 'tibble'

In rlistings: Clinical Trial Style Data Readout Listings

Create a listing from a data.frame or tibble

Description

Create listings displaying key_cols and disp_cols to produce a compact and elegant representation of the input data.frame or tibble.

Usage

as_listing(
  df,
  key_cols = names(df)[1],
  disp_cols = NULL,
  non_disp_cols = NULL,
  unique_rows = FALSE,
  default_formatting = list(all = fmt_config()),
  col_formatting = NULL,
  main_title = NULL,
  subtitles = NULL,
  main_footer = NULL,
  prov_footer = NULL,
  split_into_pages_by_var = NULL
)

as_keycol(vec)

is_keycol(vec)

get_keycols(df)

listing_dispcols(df)

add_listing_dispcol(df, new)

listing_dispcols(df) <- value

add_listing_col(
  df,
  name,
  fun = NULL,
  format = NULL,
  na_str = "NA",
  align = "left"
)

Arguments

df	(data.frame or listing_df) the data.frame to be converted to a listing or listing_df to be modified.
key_cols	(character) vector of names of columns which should be treated as key columns when rendering the listing. Key columns allow you to group repeat occurrences.
disp_cols	(character or NULL) vector of names of non-key columns which should be displayed when the listing is rendered. Defaults to all columns of df not named in key_cols or non_disp_cols.
non_disp_cols	(character or NULL) vector of names of non-key columns to be excluded as display columns. All other non-key columns are treated as display columns. Ignored if disp_cols is non-NULL.
unique_rows	(flag) whether only unique rows should be included in the listing. Defaults to FALSE.
default_formatting	(list) a named list of default column format configurations to apply when rendering the listing. Each name-value pair consists of a name corresponding to a data class (or "numeric" for all unspecified numeric classes) and a value of type fmt_config with the format configuration that should be implemented for columns of that class. If named element "all" is included in the list, this configuration will be used for all data classes not specified. Objects of type fmt_config can take 3 arguments: format, na_str, and align.
col_formatting	(list) a named list of custom column formatting configurations to apply to specific columns when rendering the listing. Each name-value pair consists of a name corresponding to a column name and a value of type fmt_config with the formatting configuration that should be implemented for that column. Objects of type fmt_config can take 3 arguments: format, na_str, and align. Defaults to NULL.
main_title	(string or NULL) the main title for the listing, or NULL (the default).
subtitles	(character or NULL) a vector of subtitles for the listing, or NULL (the default).
main_footer	(character or NULL) a vector of main footer lines for the listing, or NULL (the default).
prov_footer	(character or NULL) a vector of provenance footer lines for the listing, or NULL (the default). Each string element is placed on a new line.
split_into_pages_by_var	(character or NULL) the name of a variable for on the listing should be split into pages, with each page corresponding to one unique value/level of the variable. See split_into_pages_by_var() for more details.
vec	(string) name of a column vector from a listing_df object to be annotated as a key column.
new	(character) vector of names of columns to be added to the set of display columns.
value	(string) new value.
name	(string) name of the existing or new column to be displayed when the listing is rendered.
fun	(function or NULL) a function which accepts df and returns the vector for a new column, which is added to df as name, or NULL if marking an existing column as a listing column.
format	(string or function) a format label (string) or formatter function.
na_str	(string) string that should be displayed in place of missing values.
align	(string) alignment values should be rendered with.

Details

At its core, a listing_df object is a tbl_df object with a customized print method and support for the formatting and pagination machinery provided by the formatters package.

listing_df objects have two 'special' types of columns: key columns and display columns.

Key columns act as indexes, which means a number of things in practice.

All key columns are also display columns.

listing_df objects are always sorted by their set of key columns at creation time. Any listing_df object which is not sorted by its full set of key columns (e.g., one whose rows have been reordered explicitly during creation) is invalid and the behavior when rendering or paginating that object is undefined.

Each value of a key column is printed only once per page and per unique combination of values for all higher-priority (i.e., to the left of it) key columns. Locations where a repeated value would have been printed within a key column for the same higher-priority-key combination on the same page are rendered as empty space. Note, determination of which elements to display within a key column at rendering is based on the underlying value; any non-default formatting applied to the column has no effect on this behavior.

Display columns are columns which should be rendered, but are not key columns. By default this is all non-key columns in the incoming data, but in need not be. Columns in the underlying data which are neither key nor display columns remain within the object available for computations but are not rendered during printing or export of the listing.

Value

A listing_df object, sorted by its key columns.

df with name created (if necessary) and marked for display during rendering.

Examples

dat <- ex_adae

# This example demonstrates the listing with key_cols (values are grouped by USUBJID) and
# multiple lines in prov_footer
lsting <- as_listing(dat[1:25, ],
  key_cols = c("USUBJID", "AESOC"),
  main_title = "Example Title for Listing",
  subtitles = "This is the subtitle for this Adverse Events Table",
  main_footer = "Main footer for the listing",
  prov_footer = c(
    "You can even add a subfooter", "Second element is place on a new line",
    "Third string"
  )
) %>%
  add_listing_col("AETOXGR") %>%
  add_listing_col("BMRKR1", format = "xx.x") %>%
  add_listing_col("AESER / AREL", fun = function(df) paste(df$AESER, df$AREL, sep = " / "))

mat <- matrix_form(lsting)

cat(toString(mat))

# This example demonstrates the listing table without key_cols
# and specifying the cols with disp_cols.
dat <- ex_adae
lsting <- as_listing(dat[1:25, ],
  disp_cols = c("USUBJID", "AESOC", "RACE", "AETOXGR", "BMRKR1")
)

mat <- matrix_form(lsting)

cat(toString(mat))

# This example demonstrates a listing with format configurations specified
# via the default_formatting and col_formatting arguments
dat <- ex_adae
dat$AENDY[3:6] <- NA
lsting <- as_listing(dat[1:25, ],
  key_cols = c("USUBJID", "AESOC"),
  disp_cols = c("STUDYID", "SEX", "ASEQ", "RANDDT", "ASTDY", "AENDY"),
  default_formatting = list(
    all = fmt_config(align = "left"),
    numeric = fmt_config(
      format = "xx.xx",
      na_str = "<No data>",
      align = "right"
    )
  )
) %>%
  add_listing_col("BMRKR1", format = "xx.x", align = "center")

mat <- matrix_form(lsting)

cat(toString(mat))

rlistings documentation built on June 22, 2024, 9:17 a.m.