/
tm_t_events_patyear.R
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tm_t_events_patyear.R
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#' Template: Event Rates Adjusted for Patient-Years
#'
#' Creates a valid expression to generate a table of event rates adjusted for patient-years.
#'
#' @inheritParams template_arguments
#' @param events_var (`character`)\cr name of the variable for number of observed events.
#' @param label_paramcd (`character`)\cr `paramcd` variable text to use in the table title.
#'
#' @inherit template_arguments return
#'
#' @seealso [tm_t_events_patyear()]
#'
#' @keywords internal
template_events_patyear <- function(dataname,
parentname,
arm_var,
events_var,
label_paramcd,
aval_var = "AVAL",
add_total = TRUE,
total_label = default_total_label(),
na_level = default_na_str(),
control = control_incidence_rate(),
drop_arm_levels = TRUE,
basic_table_args = teal.widgets::basic_table_args()) {
# initialize
y <- list()
# data
data_list <- list()
data_list <- add_expr(
data_list,
substitute(
expr = anl <- df,
env = list(df = as.name(dataname))
)
)
data_list <- add_expr(
data_list,
prepare_arm_levels(
dataname = "anl",
parentname = parentname,
arm_var = arm_var,
drop_arm_levels = drop_arm_levels
)
)
data_list <- add_expr(
data_list,
substitute(
expr = dataname <- df_explicit_na(dataname, na_level = na_str),
env = list(dataname = as.name("anl"), na_str = na_level)
)
)
data_list <- add_expr(
data_list,
substitute(
expr = parentname <- df_explicit_na(parentname, na_level = na_str),
env = list(parentname = as.name(parentname), na_str = na_level)
)
)
y$data <- bracket_expr(data_list)
# layout
layout_list <- list()
basic_title <- tools::toTitleCase(paste("Event Rates Adjusted for Patient-Years by", label_paramcd))
basic_footer <- paste(
"CI Method:",
if (control$conf_type == "normal") {
"Normal (rate)"
} else if (control$conf_type == "normal_log") {
"Normal (log rate)"
} else if (control$conf_type == "exact") {
"Exact"
} else {
"Byar's method"
}
)
parsed_basic_table_args <- teal.widgets::parse_basic_table_args(
teal.widgets::resolve_basic_table_args(
user_table = basic_table_args,
module_table = teal.widgets::basic_table_args(
title = basic_title,
main_footer = basic_footer
)
)
)
layout_list <- add_expr(
layout_list,
substitute(
expr = expr_basic_table_args %>%
rtables::split_cols_by(var = arm_var) %>%
rtables::add_colcounts(),
env = list(arm_var = arm_var, expr_basic_table_args = parsed_basic_table_args)
)
)
if (add_total) {
layout_list <- add_expr(
layout_list,
substitute(
expr = rtables::add_overall_col(label = total_label),
env = list(total_label = total_label)
)
)
}
layout_list <- add_expr(
layout_list,
substitute(
expr = estimate_incidence_rate(
vars = aval_var,
n_events = events_var,
control = control_incidence_rate(
conf_level = conf_level,
conf_type = conf_type,
input_time_unit = input_time_unit,
num_pt_year = num_pt_year
)
),
env = list(
aval_var = aval_var,
events_var = events_var,
conf_level = control$conf_level,
conf_type = control$conf_type,
input_time_unit = control$input_time_unit,
num_pt_year = control$num_pt_year
)
)
)
y$layout <- substitute(
expr = lyt <- layout_pipe,
env = list(layout_pipe = pipe_expr(layout_list))
)
# table
y$table <- substitute(
expr = {
result <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = parent)
result
},
env = list(parent = as.name(parentname))
)
y
}
#' teal Module: Event Rates Adjusted for Patient-Years
#'
#' This module produces a table of event rates adjusted for patient-years.
#'
#' @inheritParams module_arguments
#' @inheritParams template_events_patyear
#' @param events_var ([teal.transform::choices_selected()])\cr object with
#' all available choices and preselected option for the variable with all event counts.
#'
#' @inherit module_arguments return seealso
#'
#' @examples
#' library(dplyr)
#' ADSL <- tmc_ex_adsl
#' ADAETTE <- tmc_ex_adaette %>%
#' filter(PARAMCD %in% c("AETTE1", "AETTE2", "AETTE3")) %>%
#' mutate(is_event = CNSR == 0) %>%
#' mutate(n_events = as.integer(is_event))
#'
#' app <- init(
#' data = cdisc_data(
#' ADSL = ADSL,
#' ADAETTE = ADAETTE,
#' code = "
#' ADSL <- tmc_ex_adsl
#' ADAETTE <- tmc_ex_adaette %>%
#' filter(PARAMCD %in% c(\"AETTE1\", \"AETTE2\", \"AETTE3\")) %>%
#' mutate(is_event = CNSR == 0) %>%
#' mutate(n_events = as.integer(is_event))
#' "
#' ),
#' modules = modules(
#' tm_t_events_patyear(
#' label = "AE Rate Adjusted for Patient-Years At Risk Table",
#' dataname = "ADAETTE",
#' arm_var = choices_selected(
#' choices = variable_choices(ADSL, c("ARM", "ARMCD")),
#' selected = "ARMCD"
#' ),
#' add_total = TRUE,
#' events_var = choices_selected(
#' choices = variable_choices(ADAETTE, "n_events"),
#' selected = "n_events",
#' fixed = TRUE
#' ),
#' paramcd = choices_selected(
#' choices = value_choices(ADAETTE, "PARAMCD", "PARAM"),
#' selected = "AETTE1"
#' )
#' )
#' )
#' )
#' if (interactive()) {
#' shinyApp(app$ui, app$server)
#' }
#'
#' @export
tm_t_events_patyear <- function(label,
dataname,
parentname = ifelse(
inherits(arm_var, "data_extract_spec"),
teal.transform::datanames_input(arm_var),
"ADSL"
),
arm_var,
events_var,
paramcd,
aval_var = teal.transform::choices_selected(
teal.transform::variable_choices(dataname, "AVAL"), "AVAL",
fixed = TRUE
),
avalu_var = teal.transform::choices_selected(
teal.transform::variable_choices(dataname, "AVALU"), "AVALU",
fixed = TRUE
),
add_total = TRUE,
total_label = default_total_label(),
na_level = default_na_str(),
conf_level = teal.transform::choices_selected(
c(0.95, 0.9, 0.8), 0.95,
keep_order = TRUE
),
drop_arm_levels = TRUE,
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
message("Initializing tm_t_events_patyear")
checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
checkmate::assert_class(arm_var, "choices_selected")
checkmate::assert_class(events_var, "choices_selected")
checkmate::assert_class(paramcd, "choices_selected")
checkmate::assert_class(aval_var, "choices_selected")
checkmate::assert_class(avalu_var, "choices_selected")
checkmate::assert_class(conf_level, "choices_selected")
checkmate::assert_flag(add_total)
checkmate::assert_string(total_label)
checkmate::assert_string(na_level)
checkmate::assert_flag(drop_arm_levels)
checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE)
checkmate::assert_class(basic_table_args, "basic_table_args")
args <- c(as.list(environment()))
data_extract_list <- list(
arm_var = cs_to_des_select(arm_var, dataname = parentname),
paramcd = cs_to_des_filter(paramcd, dataname = dataname),
aval_var = cs_to_des_select(aval_var, dataname = dataname),
avalu_var = cs_to_des_select(avalu_var, dataname = dataname),
events_var = cs_to_des_select(events_var, dataname = dataname)
)
module(
label = label,
ui = ui_events_patyear,
ui_args = c(data_extract_list, args),
server = srv_events_patyear,
server_args = c(
data_extract_list,
list(
dataname = dataname,
parentname = parentname,
label = label,
total_label = total_label,
na_level = na_level,
basic_table_args = basic_table_args
)
),
datanames = teal.transform::get_extract_datanames(data_extract_list)
)
}
#' @keywords internal
ui_events_patyear <- function(id, ...) {
ns <- NS(id)
a <- list(...)
is_single_dataset_value <- teal.transform::is_single_dataset(
a$arm_var, a$paramcd, a$aval_var, a$avalu_var, a$events_var
)
teal.widgets::standard_layout(
output = teal.widgets::white_small_well(teal.widgets::table_with_settings_ui(ns("patyear_table"))),
encoding = tags$div(
### Reporter
teal.reporter::simple_reporter_ui(ns("simple_reporter")),
###
tags$label("Encodings", class = "text-primary"),
teal.transform::datanames_input(a[c("arm_var", "paramcd", "aval_var", "avalu_var", "events_var")]),
teal.transform::data_extract_ui(
id = ns("arm_var"),
label = "Select Treatment Variable",
data_extract_spec = a$arm_var,
is_single_dataset = is_single_dataset_value
),
checkboxInput(ns("add_total"), "Add All Patients column", value = a$add_total),
teal.transform::data_extract_ui(
id = ns("paramcd"),
label = "Select an Event Type Parameter",
data_extract_spec = a$paramcd,
is_single_dataset = is_single_dataset_value
),
teal.transform::data_extract_ui(
id = ns("aval_var"),
label = "Analysis Variable",
data_extract_spec = a$aval_var,
is_single_dataset = is_single_dataset_value
),
teal.transform::data_extract_ui(
id = ns("events_var"),
label = "Event Variable",
data_extract_spec = a$events_var,
is_single_dataset = is_single_dataset_value
),
teal.transform::data_extract_ui(
id = ns("avalu_var"),
label = "Analysis Unit Variable",
data_extract_spec = a$avalu_var,
is_single_dataset = is_single_dataset_value
),
teal.widgets::optionalSelectInput(
inputId = ns("conf_level"),
label = "Confidence Level",
a$conf_level$choices,
a$conf_level$selected,
multiple = FALSE,
fixed = a$conf_level$fixed
),
teal.widgets::optionalSelectInput(
ns("conf_method"),
"CI Method",
choices = c("Normal (rate)", "Normal (log rate)", "Exact", "Byar's method"),
selected = "Normal (rate)",
multiple = FALSE,
fixed = FALSE
),
teal.widgets::panel_group(
teal.widgets::panel_item(
"Additional table settings",
checkboxInput(
ns("drop_arm_levels"),
label = "Drop columns not in filtered analysis dataset",
value = a$drop_arm_levels
),
teal.widgets::optionalSelectInput(
ns("num_pt_year"),
"Time Unit for AE Rate (in Patient-Years)",
choices = c(0.1, 1, 10, 100, 1000),
selected = 100,
multiple = FALSE,
fixed = FALSE
),
selectInput(
ns("input_time_unit"),
"Analysis Unit",
choices = NULL,
selected = NULL,
multiple = FALSE
)
)
)
),
forms = tagList(
teal.widgets::verbatim_popup_ui(ns("rcode"), button_label = "Show R code")
),
pre_output = a$pre_output,
post_output = a$post_output
)
}
#' @keywords internal
srv_events_patyear <- function(id,
data,
reporter,
filter_panel_api,
dataname,
parentname,
arm_var,
paramcd,
aval_var,
avalu_var,
events_var,
add_total,
total_label,
na_level,
drop_arm_levels,
label,
basic_table_args) {
with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
checkmate::assert_class(data, "reactive")
checkmate::assert_class(shiny::isolate(data()), "teal_data")
moduleServer(id, function(input, output, session) {
observeEvent(anl_q(), {
data_anl <- merged$anl_q()[["ANL"]]
aval_unit_var <- merged$anl_input_r()$columns_source$avalu_var
if (length(aval_unit_var) > 0) {
choices <- stats::na.omit(unique(data_anl[[aval_unit_var]]))
choices <- gsub("s$", "", tolower(choices))
updateSelectInput(
session,
"input_time_unit",
choices = choices,
selected = choices[1]
)
}
})
selector_list <- teal.transform::data_extract_multiple_srv(
data_extract = list(
arm_var = arm_var,
paramcd = paramcd,
aval_var = aval_var,
avalu_var = avalu_var,
events_var = events_var
),
datasets = data,
select_validation_rule = list(
arm_var = ~ if (length(.) != 1 && length(.) != 2) "Please select exactly 1 or 2 treatment variables",
aval_var = shinyvalidate::sv_required("Analysis Variable is required"),
events_var = shinyvalidate::sv_required("Events Variable is required")
),
filter_validation_rule = list(
paramcd = shinyvalidate::sv_required("A Event Type Parameter is required")
)
)
iv_r <- reactive({
iv <- shinyvalidate::InputValidator$new()
iv$add_rule("conf_level", shinyvalidate::sv_required("Please choose a confidence level"))
iv$add_rule(
"conf_level",
shinyvalidate::sv_between(
0, 1,
inclusive = c(FALSE, FALSE),
message_fmt = "Confidence level must be between 0 and 1"
)
)
iv$add_rule("conf_method", shinyvalidate::sv_required("A CI method is required"))
iv$add_rule("num_pt_year", shinyvalidate::sv_required("Time Unit for AE Rate is required"))
teal.transform::compose_and_enable_validators(iv, selector_list)
})
anl_inputs <- teal.transform::merge_expression_srv(
datasets = data,
selector_list = selector_list,
merge_function = "dplyr::inner_join"
)
adsl_inputs <- teal.transform::merge_expression_module(
datasets = data,
data_extract = list(arm_var = arm_var),
anl_name = "ANL_ADSL"
)
anl_q <- reactive({
data() %>%
teal.code::eval_code(as.expression(anl_inputs()$expr)) %>%
teal.code::eval_code(as.expression(adsl_inputs()$expr))
})
merged <- list(
anl_input_r = anl_inputs,
adsl_input_r = adsl_inputs,
anl_q = anl_q
)
# Prepare the analysis environment (filter data, check data, populate envir).
validate_checks <- reactive({
teal::validate_inputs(iv_r())
adsl_filtered <- merged$anl_q()[[parentname]]
anl_filtered <- merged$anl_q()[[dataname]]
input_arm_var <- as.vector(merged$anl_input_r()$columns_source$arm_var)
input_aval_var <- as.vector(merged$anl_input_r()$columns_source$aval_var)
input_avalu_var <- as.vector(merged$anl_input_r()$columns_source$avalu_var)
input_events_var <- as.vector(merged$anl_input_r()$columns_source$events_var)
input_paramcd <- unlist(paramcd$filter)["vars_selected"]
# validate inputs
validate_standard_inputs(
adsl = adsl_filtered,
adslvars = c("USUBJID", "STUDYID", input_arm_var),
anl = anl_filtered,
anlvars = c("USUBJID", "STUDYID", input_paramcd, input_events_var, input_aval_var, input_avalu_var),
arm_var = input_arm_var
)
validate(
need(
!any(is.na(merged$anl_q()[["ANL"]][[input_events_var]])),
"`Event Variable` for selected parameter includes NA values."
)
)
NULL
})
# The R-code corresponding to the analysis.
table_q <- reactive({
validate_checks()
ANL <- merged$anl_q()[["ANL"]]
label_paramcd <- get_paramcd_label(ANL, paramcd)
my_calls <- template_events_patyear(
dataname = "ANL",
parentname = "ANL_ADSL",
arm_var = as.vector(merged$anl_input_r()$columns_source$arm_var),
aval_var = as.vector(merged$anl_input_r()$columns_source$aval_var),
events_var = as.vector(merged$anl_input_r()$columns_source$events_var),
label_paramcd = label_paramcd,
add_total = input$add_total,
total_label = total_label,
na_level = na_level,
control = control_incidence_rate(
conf_level = as.numeric(input$conf_level),
conf_type = if (input$conf_method == "Normal (rate)") {
"normal"
} else if (input$conf_method == "Normal (log rate)") {
"normal_log"
} else if (input$conf_method == "Exact") {
"exact"
} else {
"byar"
},
input_time_unit = if (input$input_time_unit %in% c("day", "week", "month", "year")) {
input$input_time_unit
} else {
"year"
},
num_pt_year = as.numeric(input$num_pt_year)
),
drop_arm_levels = input$drop_arm_levels,
basic_table_args = basic_table_args
)
teal.code::eval_code(merged$anl_q(), as.expression(my_calls))
})
# Outputs to render.
table_r <- reactive({
table_q()[["result"]]
})
teal.widgets::table_with_settings_srv(
id = "patyear_table",
table_r = table_r
)
# Render R code.
teal.widgets::verbatim_popup_srv(
id = "rcode",
verbatim_content = reactive(teal.code::get_code(table_q())),
title = label
)
### REPORTER
if (with_reporter) {
card_fun <- function(comment, label) {
card <- teal::report_card_template(
title = "Event Rates Adjusted For Patient-Years Table",
label = label,
with_filter = with_filter,
filter_panel_api = filter_panel_api
)
card$append_text("Table", "header3")
card$append_table(table_r())
if (!comment == "") {
card$append_text("Comment", "header3")
card$append_text(comment)
}
card$append_src(teal.code::get_code(table_q()))
card
}
teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)
}
###
})
}