R: A Traceability Focused Grammar of Clinical Data Summary

# A Traceability Focused Grammar of Clinical Data Summary

## Documentation for package ‘Tplyr’ version 1.3.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C F G H K N P R S T U

Tplyr-package | A grammar of summary data for clinical reports

## -- A --

add_anti_join | Add an anti-join onto a tplyr_meta object
add_column_headers | Attach column headers to a Tplyr output
add_filters | Add variables to a tplyr_meta object
add_layer | Attach a layer to a 'tplyr_table' object
add_layers | Attach a layer to a 'tplyr_table' object
add_missing_subjects_row | Add a missing subject row into a count summary.
add_risk_diff | Add risk difference to a count layer
add_total_group | Combine existing treatment groups for summary
add_total_row | Add a Total row into a count summary.
add_treat_grps | Combine existing treatment groups for summary
add_variables | Add variables to a tplyr_meta object
append_metadata | Append the Tplyr table metadata dataframe
apply_conditional_format | Conditional reformatting of a pre-populated string of numbers
apply_formats | Apply Format Strings outside of a Tplyr table
apply_row_masks | Replace repeating row label variables with blanks in preparation for display.

## -- B --

build | Trigger the execution of the 'tplyr_table'

## -- C --

collapse_row_labels | Collapse row labels into a single column

## -- F --

f_str | Create a 'f_str' object

## -- G --

get_by | Set or return by layer binding
get_count_layer_formats | Get or set the default format strings for descriptive statistics layers
get_data_labels | Get Data Labels
get_desc_layer_formats | Get or set the default format strings for descriptive statistics layers
get_layer_template | Create, view, extract, remove, and use Tplyr layer templates
get_layer_templates | Create, view, extract, remove, and use Tplyr layer templates
get_metadata | Get the metadata dataframe from a tplyr_table
get_meta_result | Extract the result metadata of a Tplyr table
get_meta_subset | Extract the subset of data based on result metadata
get_meta_subset.data.frame | Extract the subset of data based on result metadata
get_meta_subset.tplyr_table | Extract the subset of data based on result metadata
get_numeric_data | Retrieve the numeric data from a tplyr objects
get_pop_where | Set or return where binding for layer or table
get_precision_by | Set or return precision_by layer binding
get_precision_on | Set or return precision_on layer binding
get_shift_layer_formats | Get or set the default format strings for descriptive statistics layers
get_stats_data | Get statistics data
get_target_var | Set or return treat_var binding
get_tplyr_regex | Retrieve one of Tplyr's regular expressions
get_where | Set or return where binding for layer or table
get_where.tplyr_layer | Set or return where binding for layer or table
get_where.tplyr_table | Set or return where binding for layer or table
group_count | Create a 'count', 'desc', or 'shift' layer for discrete count based summaries, descriptive statistics summaries, or shift count summaries
group_desc | Create a 'count', 'desc', or 'shift' layer for discrete count based summaries, descriptive statistics summaries, or shift count summaries
group_shift | Create a 'count', 'desc', or 'shift' layer for discrete count based summaries, descriptive statistics summaries, or shift count summaries

## -- H --

header_n | Return or set header_n binding
header_n<- | Return or set header_n binding

## -- K --

keep_levels | Select levels to keep in a count layer

## -- N --

new_layer_template | Create, view, extract, remove, and use Tplyr layer templates

## -- P --

pop_data | Return or set population data bindings
pop_data<- | Return or set population data bindings
pop_treat_var | Return or set pop_treat_var binding

## -- R --

remove_layer_template | Create, view, extract, remove, and use Tplyr layer templates
replace_leading_whitespace | Reformat strings with leading whitespace for HTML

## -- S --

set_by | Set or return by layer binding
set_count_layer_formats | Get or set the default format strings for descriptive statistics layers
set_custom_summaries | Set custom summaries to be performed within a descriptive statistics layer
set_denoms_by | Set variables used in pct denominator calculation
set_denom_ignore | Set values the denominator calculation will ignore
set_denom_where | Set Logic for denominator subsetting
set_desc_layer_formats | Get or set the default format strings for descriptive statistics layers
set_distinct_by | Set counts to be distinct by some grouping variable.
set_format_strings | Set the format strings and associated summaries to be performed in a layer
set_format_strings.count_layer | Set the format strings and associated summaries to be performed in a layer
set_format_strings.desc_layer | Set the format strings and associated summaries to be performed in a layer
set_header_n | Return or set header_n binding
set_indentation | Set the option to prefix the row_labels in the inner count_layer
set_limit_data_by | Set variables to limit reported data values only to those that exist rather than fully completing all possible levels
set_missing_count | Set the display for missing strings
set_missing_subjects_row_label | Set the label for the missing subjects row
set_nest_count | Set the option to nest count layers
set_numeric_threshold | Set a numeric cutoff
set_ordering_cols | Set the ordering logic for the count layer
set_order_count_method | Set the ordering logic for the count layer
set_outer_sort_position | Set the value of a outer nested count layer to Inf or -Inf
set_pop_data | Return or set population data bindings
set_pop_treat_var | Return or set pop_treat_var binding
set_pop_where | Set or return where binding for layer or table
set_precision_by | Set or return precision_by layer binding
set_precision_data | Set precision data
set_precision_on | Set or return precision_on layer binding
set_result_order_var | Set the ordering logic for the count layer
set_shift_layer_formats | Get or set the default format strings for descriptive statistics layers
set_stats_as_columns | Set descriptive statistics as columns
set_target_var | Set or return treat_var binding
set_total_row_label | Set the label for the total row
set_treat_var | Return or set the treatment variable binding
set_where | Set or return where binding for layer or table
set_where.tplyr_layer | Set or return where binding for layer or table
set_where.tplyr_table | Set or return where binding for layer or table
str_extract_fmt_group | Extract format group strings or numbers
str_extract_num | Extract format group strings or numbers
str_indent_wrap | Wrap strings to a specific width with hyphenation while preserving indentation

## -- T --

Tplyr | A grammar of summary data for clinical reports
tplyr_adae | ADAE Data
tplyr_adas | ADAS Data
tplyr_adlb | ADLB Data
tplyr_adpe | ADPE Data
tplyr_adsl | ADSL Data
tplyr_layer | Create a 'tplyr_layer' object
tplyr_meta | Tplyr Metadata Object
tplyr_table | Create a Tplyr table object
treat_grps | Combine existing treatment groups for summary
treat_var | Return or set the treatment variable binding

## -- U --

use_template | Create, view, extract, remove, and use Tplyr layer templates