atable_compact: More compact formatting than atable() In atable: Create Tables for Reporting Clinical Trials

 atable_compact R Documentation

More compact formatting than atable()

Description

This is a wrapper for atable(), calculating the same statistics, but with different format.

Usage

atable_compact(x, ...)

## S3 method for class 'data.frame'
atable_compact(
x,
target_cols,
group_col = NULL,
indent_character = atable_options("indent_character_compact"),
blocks = NULL,
format_factor = atable_options("format_statistics_compact.statistics_factor"),
format_numeric = atable_options("format_statistics_compact.statistics_numeric"),
...
)


Arguments

 x object passed to atable. ... Passed to atable. target_cols character. Some of colnames(x). group_col character or NULL. If character then, one of colnames(x). indent_character character length 1. Default is defined in table_options("indent_character_compact"). For Latex-Format use e.g. indent_character="\quad". For Word-Format use e.g. indent_character=paste0(rep(intToUtf8(160), 5), collapse = "") and e.g. Package officer and its functions officer::read_docx(), officer::body_add_table and print-methods. blocks NULL or a list, passed to atable, see help there. format_factor a function that defines the format of factor variables. Default is defined in atable_options. See check_format_statistics for the return-value of this function. format_numeric a function that defines the format of numeric variables. Analog to format_factor.

Details

The compact formatting is:

Numeric target_cols get one line in the table; the line contains the mean and SD of the variable.

Factor target_cols also get one line in the table, when they have only two levels and only the first level is displayed in the table and the name of the variable is omitted. This is intended for item like "Sex at birth: Female/Male". Knowing the percentage of Female is sufficient in this case (when NAs are not counted). Be careful with items like "Pregnant: Yes/No". Here only the level "Yes" will be printed and the name of the item (Pregnant) is omitted, making the table uninformative. Factors with three or more levels get one line per level, the levels are intended and a header line containing the name of the variable is added.

Arguments in ... are passed to atable. See the help there. atable_compact is not designed for splitted atables, so argument split_cols must be omitted or NULL. Also argument format_to is ignored. Other features of atable (blocking, add_margins, alias) are available, see examples.

data.frame

Methods (by class)

• data.frame: a compact version of atable.

Examples

# For Console:
atable_compact(
atable::test_data,
target_cols = c("Numeric", "Numeric2", "Split2", "Factor", "Ordered"),
group_col = "Group2",
blocks = list("Primary Endpoint" = "Numeric",
"Secondary Endpoints" = c("Numeric2", "Split2", "Factor")),

# The target_cols are "Numeric", "Numeric2", "Split2", "Factor", "Ordered".
# The group_col is "Group2".
# The data.frame is grouped by group_col and the summary statistcs of the target_cols are
# calculated: mean, sd for numeric, counts and percentages for factors.
# Some target_cols are blocked: the first block 'Primary Endpoint' contains the variable Numeric.
# The second block 'Secondary  Endpoint' contains the variables "Numeric2", "Split2", "Factor".
# The blocks are intended.
# For variable Split2 only the first level is reported, as the variable has only two levels and
# the name 'Split2' does not appear in the table.
# The variable Factor has more than two levels, so all of them are
# reported and appropriately intended.
# The variable Ordered is not part of a block and thus not intended.

# For Latex:
# Same as for Console, but with different indent_character:

tab = atable_compact(atable::test_data,
target_cols = c("Numeric", "Numeric2", "Logical", "Factor", "Ordered"),
group_col = "Group2",

tab = atable::translate_to_LaTeX(tab)

# Then call e.g. Hmisc::latex(tab, ...)

# Example for Word format:
## Not run:
tab = atable_compact(
atable::test_data,
target_cols = c("Numeric", "Numeric2", "Split2", "Factor", "Ordered", "Character"),
group_col = "Group2",
blocks = list("Primary Endpoint" = "Numeric",
"Secondary Endpoints" = c("Numeric2", "Split2", "Factor")),
indent_character = paste0(rep(intToUtf8(160), 5), collapse = ""))

# The argument indent_character has the value intToUtf8(160) (non breakable space).
# This is the important part:
# Spaces at the beginning of a cell of a data.frame are somehow lost on the way to the docx.
# Other indent_characters may also do the job.