Hierarchical Count Table Module

Usage

mod_hierarchical_count_table(
  module_id,
  table_dataset_name,
  pop_dataset_name,
  subjid_var = "USUBJID",
  show_pop_flag_selection = FALSE,
  show_event_group_by = FALSE,
  show_time_at_risk_options = FALSE,
  show_modal_on_click = TRUE,
  default_hierarchy = NULL,
  hierarchy_choices = NULL,
  default_group = NULL,
  group_choices = NULL,
  default_total = TRUE,
  default_min_percent = 0,
  default_remove_rows_under_min_percent = FALSE,
  default_pop_flags = NULL,
  pop_flag_choices = NULL,
  default_pop_flags_after_groups = FALSE,
  default_event_group = NULL,
  event_group_choices = NULL,
  default_event_date = NULL,
  event_date_choices = NULL,
  default_origin_date = NULL,
  origin_date_choices = NULL,
  default_censor_date = NULL,
  censor_date_choices = NULL,
  default_risk = FALSE,
  smq_name = "SMQ",
  smq_vars = NULL,
  smq_na_label = "Other",
  udaec_name = "UDAEC",
  udaec_list = NULL,
  udaec_na_label = "Other",
  any_event_text = "Participants with any event",
  intended_use_label =
    "Use only for internal review and monitoring during the conduct of clinical trials.",
  receiver_id = NULL
)

Arguments

module_id

[character(1)]

Module Shiny id.

table_dataset_name

[character(1)]

Name of the event dataset.

pop_dataset_name

[character(1)]

Name of the population dataset.

subjid_var

[character(1)]

A string representing the participant identifier column in both datasets.

show_pop_flag_selection

[logical(1)]

A flag to indicate whether to show the population flag selection. Other associated arguments are default_pop_flags and pop_flag_choices.

show_event_group_by

[logical(1)]

A flag to indicate whether to show the event by-group selection. This takes precedence over show_time_at_risk_options, both cannot be shown together.

show_time_at_risk_options

[logical(1)]

A flag to indicate whether to show the time at risk related user selections (event/origin/censor date selections, and time at risk checkbox). This is ignored when show_event_group_by is TRUE, both cannot be shown together.

show_modal_on_click

[logical(1)]

A flag to indicate whether clicking a table cell should display a modal dialog with the participant IDs.

default_hierarchy

[character(1:4)|NULL]

Optional character vector specifying the default hierarchy variables. Variables must be columns in table_dataset_name. Up to four variables can be selected, and their order determines the nesting order in the table.

hierarchy_choices

[character(1+)|NULL]

A character vector specifying the possible choices for the hierarchy variables selection (optional). If it is not specified then all factor and character variables from the event data will be used.

default_group

[character(1|2)|NULL]

A default value for the group variables selection (optional).

group_choices

[character(1+)|NULL]

A character vector specifying the possible choices for the group variables selection (optional). If it is not specified then all factor and character variables from the population data will be used.

default_total

[logical(1)]

A default value for checkbox determining whether to add a total group column.

default_min_percent

[numeric(1)]

Initial minimum percentage threshold, between 0 and 100. The threshold is applied separately to each displayed group cell. Cells below the threshold show a dash instead of their count and percentage. The default is 0.

default_remove_rows_under_min_percent

[logical(1)]

Initial setting controlling whether to remove hierarchy rows for which no displayed group cell meets default_min_percent. When FALSE, the rows remain visible and only cells below the threshold are replaced by a dash.

default_pop_flags

[character(1+) | NULL]

A vector of variable names from the population dataset, used as the default for selected population flag variables (optional).

Participants are identified as being within a population when the value of the flag variable is "Y".

Not applicable when show_pop_flag_selection is FALSE.

pop_flag_choices

[character(1+) | NULL]

A vector of variable names from the population dataset, specifying the possible choices for the population flag variables (optional). If it is not specified then all FL suffixed factor and character variables from the population dataset will be used.

Participants are identified as being within a population when the value of the flag variable is "Y".

Not applicable when show_pop_flag_selection is FALSE.

default_pop_flags_after_groups

[logical(1)]

A flag specifying the default value for the checkbox that determines whether to show the population flags after the group variables.

Not applicable when show_pop_flag_selection is FALSE.

default_event_group

[character(1)|NULL]

A default value for the event group variable selection.

event_group_choices

[character(1+)|NULL]

A character vector specifying the possible choices for the event group variable selection (optional). If it is not specified then all factor and character variables from the event data will be used.

default_event_date

[character(1)|NULL]

A default value for the event date variable selection (optional). Not applicable when show_time_at_risk_options is FALSE.

event_date_choices

[character(1+)|NULL]

A character vector specifying the possible choices for the event date variable selection (optional). If it is not specified then all variables of class "Date" from the event data will be used. Not applicable when show_time_at_risk_options is FALSE.

default_origin_date

[character(1)|NULL]

A default value for the origin date variable selection (optional). Not applicable when show_time_at_risk_options is FALSE.

origin_date_choices

[character(1+)|NULL]

A character vector specifying the possible choices for the origin date variable selection (optional). If it is not specified then all variables of class "Date" from the population data will be used. Not applicable when show_time_at_risk_options is FALSE.

default_censor_date

[character(1)|NULL]

A default value for the censor date variable selection (optional). Not applicable when show_time_at_risk_options is FALSE.

censor_date_choices

[character(1+)|NULL]

A character vector specifying the possible choices for the censor date variable selection (optional). If it is not specified then all variables of class "Date" from the population data will be used. Not applicable when show_time_at_risk_options is FALSE.

default_risk

[logical(1)]

A default value for the checkbox determining whether to calculate time at risk. Not applicable when show_time_at_risk_options is FALSE.

smq_name

[character(1)]

Name of the derived SMQ hierarchy variable. The variable is created from the columns listed in smq_vars. Defaults to "SMQ".

smq_vars

[character(1+)|NULL]

Optional character vector of columns in table_dataset_name containing SMQ indicators or categories. When supplied together with smq_name, an additional SMQ hierarchy variable is available for selection. If NULL, no SMQ hierarchy is created.

smq_na_label

[character(1)]

Label used for the derived SMQ hierarchy variable (smq_name) when the source values in smq_vars are missing/NA for a participant. Defaults to "Other".

udaec_name

[character(1)]

Name of the derived UDAEC hierarchy variable. Defaults to "UDAEC". This argument is used together with udaec_list.

udaec_list

[list|NULL]

Optional named list defining UDAEC categories. The names of the list are the UDAEC category labels, and must be unique and non-empty. Each element must be a list containing at least one of the following definitions: No other entries are allowed.

smq_vars: A character vector of SMQ source column names. These columns must also be included in the top-level smq_vars argument.
pt_var and pt_values: The event-data column containing preferred terms and an atomic vector of values identifying the preferred terms for the category. pt_var must be a column in table_dataset_name, and both fields must be supplied together.

A category may contain either definition or both definitions. The udaec_list argument requires a non-NULL top-level smq_vars argument, and udaec_name defines the name of the derived UDAEC hierarchy variable. For example:


udaec_list <- list(
  "Cardiac disorders" = list(
    smq_vars = "SMQ01NAM",
    pt_var = "AEDECOD",
    pt_values = c("Atrial fibrillation", "Myocardial infarction")
  ),
  "Renal disorders" = list(
    pt_var = "AEDECOD",
    pt_values = c("Acute kidney injury")
  )
)

When supplied, the derived UDAEC variable is available as a hierarchy selection and its categories can be filtered in the module UI.

udaec_na_label

[character(1)]

Label used for the derived UDAEC hierarchy variable (udaec_name) for participants that do not match any of the categories defined in udaec_list. Defaults to "Other".

any_event_text

[character(1)]

A string specifying the text to be displayed in the table row for participants with any event. Defaults to "Participants with any event".

intended_use_label

[character(1)|NULL]

Either a string indicating the intended use for export, or NULL. The provided label will be displayed prior to the download and will also be included in the exported file.

receiver_id

[character(1)|NULL]

Unique identifier for the module receiving the selected participant ID in the data listing. This ID must be present in the app or be NULL.