A Traceability Focused Grammar of Clinical Data Summary

Documentation for package ‘Tplyr’ version 1.2.1

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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