A Traceability Focused Grammar of Clinical Data Summary

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Documentation for package ‘Tplyr’ version 1.2.1

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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