Package 'rlistings'

Title: Clinical Trial Style Data Readout Listings
Description: Listings are often part of the submission of clinical trial data in regulatory settings. We provide a framework for the specific formatting features often used when displaying large datasets in that context.
Authors: Gabriel Becker [aut] (original creator of the package), Adrian Waddell [aut], Joe Zhu [aut, cre], Davide Garolini [ctb], Emily de la Rua [ctb], Abinaya Yogasekaram [ctb], F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <[email protected]>
License: Apache License 2.0
Version: 0.2.9
Built: 2024-09-18 05:24:31 UTC
Source: https://github.com/insightsengineering/rlistings

Help Index

Create a listing from a data.frame or tibble

Description

[Experimental]

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))

Methods for listing_df objects

Description

See core documentation in formatters::formatters-package for descriptions of these functions.

Usage

## S3 method for class 'listing_df'
print(
  x,
  widths = NULL,
  tf_wrap = FALSE,
  max_width = NULL,
  fontspec = NULL,
  col_gap = 3L,
  ...
)

## S4 method for signature 'listing_df'
toString(x, widths = NULL, fontspec = NULL, col_gap = 3L, ...)

## S4 method for signature 'listing_df'
x[i, j, drop = FALSE]

## S4 method for signature 'listing_df'
main_title(obj)

## S4 method for signature 'listing_df'
subtitles(obj)

## S4 method for signature 'listing_df'
main_footer(obj)

## S4 method for signature 'listing_df'
prov_footer(obj)

## S4 replacement method for signature 'listing_df'
main_title(obj) <- value

## S4 replacement method for signature 'listing_df'
subtitles(obj) <- value

## S4 replacement method for signature 'listing_df'
main_footer(obj) <- value

## S4 replacement method for signature 'listing_df'
prov_footer(obj) <- value

## S4 method for signature 'listing_df'
num_rep_cols(obj)

Arguments

x

(listing_df)
the listing.
widths

(numeric or NULL)
Proposed widths for the columns of x. The expected length of this numeric vector can be retrieved with ncol(x) + 1 as the column of row names must also be considered.
tf_wrap

(flag)
whether the text for title, subtitles, and footnotes should be wrapped.
max_width

(integer(1), string or NULL)
width that title and footer (including footnotes) materials should be word-wrapped to. If NULL, it is set to the current print width of the session (getOption("width")). If set to "auto", the width of the table (plus any table inset) is used. Parameter is ignored if tf_wrap = FALSE.
fontspec

(font_spec)
a font_spec object specifying the font information to use for calculating string widths and heights, as returned by font_spec().
col_gap

(numeric(1))
space (in characters) between columns.
...

additional parameters passed to formatters::toString().
i

(any)
object passed to base [ methods.
j

(any)
object passed to base [ methods.
drop

relevant for matrices and arrays. If TRUE the result is coerced to the lowest possible dimension (see the examples). This only works for extracting elements, not for the replacement. See drop for further details.

obj

(listing_df)
the listing.
value

typically an array-like R object of a similar class as x.

Value

  • Accessor methods return the value of the aspect of obj.

  • Setter methods return obj with the relevant element of the listing updated.

Examples

lsting <- as_listing(mtcars)
main_title(lsting) <- "Hi there"

main_title(lsting)

Make pagination data frame for a listing

Description

Make pagination data frame for a listing

Usage

## S4 method for signature 'listing_df'
make_row_df(
  tt,
  colwidths = NULL,
  visible_only = TRUE,
  rownum = 0,
  indent = 0L,
  path = character(),
  incontent = FALSE,
  repr_ext = 0L,
  repr_inds = integer(),
  sibpos = NA_integer_,
  nsibs = NA_integer_,
  fontspec = dflt_courier
)

Arguments

tt

(listing_df)
the listing to be rendered.
colwidths

(numeric)
internal detail, do not set manually.
visible_only

(flag)
ignored, as listings do not have non-visible structural elements.
rownum

(numeric(1))
internal detail, do not set manually.
indent

(integer(1))
internal detail, do not set manually.
path

(character)
path to the (sub)table represented by tt. Defaults to character().
incontent

(flag)
internal detail, do not set manually.
repr_ext

(integer(1))
internal detail, do not set manually.
repr_inds

(integer)
internal detail, do not set manually.
sibpos

(integer(1))
internal detail, do not set manually.
nsibs

(integer(1))
internal detail, do not set manually.
fontspec

(font_spec)
a font_spec object specifying the font information to use for calculating string widths and heights, as returned by font_spec().

Value

a data.frame with pagination information.

See Also

formatters::make_row_df()

Examples

lsting <- as_listing(mtcars)
mf <- matrix_form(lsting)

Transform rtable to a list of matrices which can be used for outputting

Description

Although rtables are represented as a tree data structure when outputting the table to ASCII or HTML, it is useful to map the rtable to an in-between state with the formatted cells in a matrix form.

Usage

## S4 method for signature 'listing_df'
matrix_form(
  obj,
  indent_rownames = FALSE,
  expand_newlines = TRUE,
  fontspec = font_spec,
  col_gap = 3L
)

Arguments

obj

(ANY)
object to be transformed into a ready-to-render form (a MatrixPrintForm object).
indent_rownames

(flag)
silently ignored, as listings do not have row names nor indenting structure.
expand_newlines

(flag)
this should always be TRUE for listings. We keep it for debugging reasons.
fontspec

(font_spec)
a font_spec object specifying the font information to use for calculating string widths and heights, as returned by font_spec().
col_gap

(numeric(1))
the gap to be assumed between columns, in number of spaces with font specified by fontspec.

Value

a formatters::MatrixPrintForm object.

See Also

formatters::matrix_form()

Examples

lsting <- as_listing(mtcars)
mf <- matrix_form(lsting)

Paginate listings

Description

[Experimental]

Pagination of a listing. This can be vertical for long listings with many rows and/or horizontal if there are many columns. This function is a wrapper of formatters::paginate_to_mpfs() and it is mainly meant for exploration and testing.

Usage

paginate_listing(
  lsting,
  page_type = "letter",
  font_family = "Courier",
  font_size = 8,
  lineheight = 1,
  landscape = FALSE,
  pg_width = NULL,
  pg_height = NULL,
  margins = c(top = 0.5, bottom = 0.5, left = 0.75, right = 0.75),
  lpp = NA_integer_,
  cpp = NA_integer_,
  colwidths = NULL,
  tf_wrap = !is.null(max_width),
  rep_cols = NULL,
  max_width = NULL,
  col_gap = 3,
  fontspec = font_spec(font_family, font_size, lineheight),
  verbose = FALSE,
  print_pages = TRUE
)

Arguments

lsting

(listing_df or list)
the listing or list of listings to paginate.
page_type

(string)
name of a page type. See page_types. Ignored when pg_width and pg_height are set directly.
font_family

(string)
name of a font family. An error will be thrown if the family named is not monospaced. Defaults to "Courier".
font_size

(numeric(1))
font size. Defaults to 12.
lineheight

(numeric(1))
line height. Defaults to 1.
landscape

(flag)
whether the dimensions of page_type should be inverted for landscape orientation. Defaults to FALSE, ignored when pg_width and pg_height are set directly.
pg_width

(numeric(1))
page width in inches.
pg_height

(numeric(1))
page height in inches.
margins

(numeric(4))
named numeric vector containing "bottom", "left", "top", and "right" margins in inches. Defaults to .5 inches for both vertical margins and .75 for both horizontal margins.
lpp

(numeric(1) or NULL)
number of rows/lines (excluding titles and footers) to include per page. Standard is 70 while NULL disables vertical pagination.
cpp

(numeric(1) or NULL)
width (in characters) of the pages for horizontal pagination. NULL (the default) indicates no horizontal pagination should be done.
colwidths

(numeric)
vector of column widths (in characters) for use in vertical pagination.
tf_wrap

(flag)
whether the text for title, subtitles, and footnotes should be wrapped.
rep_cols

(numeric(1))
number of columns (not including row labels) to be repeated on every page. Defaults to 0.
max_width

(integer(1), string or NULL)
width that title and footer (including footnotes) materials should be word-wrapped to. If NULL, it is set to the current print width of the session (getOption("width")). If set to "auto", the width of the table (plus any table inset) is used. Parameter is ignored if tf_wrap = FALSE.
col_gap

(numeric(1))
width of gap between columns, in same units as extent in pagdf (spaces under a particular font specification).
fontspec

(font_spec)
a font_spec object specifying the font information to use for calculating string widths and heights, as returned by font_spec().
verbose

(flag)
whether additional informative messages about the search for pagination breaks should be shown. Defaults to FALSE.
print_pages

(flag)
whether the paginated listing should be printed to the console (cat(toString(x))).

Value

A list of listing_df objects where each list element corresponds to a separate page.

Examples

dat <- ex_adae
lsting <- as_listing(dat[1:25, ], disp_cols = c("USUBJID", "AESOC", "RACE", "AETOXGR", "BMRKR1"))
mat <- matrix_form(lsting)
cat(toString(mat))

paginate_listing(lsting, lpp = 10)

paginate_listing(lsting, cpp = 100, lpp = 40)

paginate_listing(lsting, cpp = 80, lpp = 40, verbose = TRUE)

Split Listing by Values of a Variable

Description

[Experimental]

Split is performed based on unique values of the given parameter present in the listing. Each listing can only be split by variable once. If this function is applied prior to pagination, parameter values will be separated by page.

Usage

split_into_pages_by_var(lsting, var, page_prefix = var)

Arguments

lsting

listing_df. The listing to split.
var

character. Name of the variable to split on.
page_prefix

character. Prefix to be appended with the split value (var level), at the end of the subtitles, corresponding to each resulting list element (listing).

Value

A list of lsting_df objects each corresponding to a unique value of var.

Note

This function should only be used after the complete listing has been created. The listing cannot be modified further after applying this function.

Examples

dat <- ex_adae[1:20, ]

lsting <- as_listing(
  dat,
  key_cols = c("USUBJID", "AGE"),
  disp_cols = "SEX",
  main_title = "title",
  main_footer = "footer"
) %>%
  add_listing_col("BMRKR1", format = "xx.x") %>%
  split_into_pages_by_var("SEX")

lsting