---
title: AET05_ALL
subtitle: Adverse Event Rate Adjusted for Patient-Years at Risk -- All Occurrences
---
------------------------------------------------------------------------
{{< include ../../_utils/envir_hook.qmd >}}
```{r setup, echo = FALSE, warning = FALSE, message = FALSE}
library(tern)
library(dplyr)
adsl <- random.cdisc.data::cadsl
adaette <- random.cdisc.data::cadaette
# Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
adsl <- df_explicit_na(adsl)
adaette <- df_explicit_na(adaette)
# Create analysis dataset anl from the 2 parameters AEREPTTE & AETOT1
anl_events <- adaette %>%
filter(PARAMCD == "AETOT1") %>%
select(USUBJID, ARM, ARMCD, n_events = AVAL) %>%
mutate(n_events = as.integer(n_events))
anl_tte <- adaette %>%
filter(PARAMCD == "AEREPTTE") %>%
select(USUBJID, ARM, ARMCD, AVAL)
anl <- full_join(anl_tte, anl_events, by = c("USUBJID", "ARM", "ARMCD"))
```
```{r include = FALSE}
webr_code_labels <- c("setup")
```
{{< include ../../_utils/webr_no_include.qmd >}}
## Output
::::: panel-tabset
## Standard Table
::: {.panel-tabset .nav-justified group="webr"}
## {{< fa regular file-lines sm fw >}} Preview
```{r variant1, test = list(result_v1 = "result")}
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ARM") %>%
estimate_incidence_rate(
vars = "AVAL",
n_events = "n_events",
control = control_incidence_rate(num_pt_year = 100)
)
result <- build_table(lyt, anl, alt_counts_df = adsl)
result
```
```{r include = FALSE}
webr_code_labels <- c("variant1")
```
{{< include ../../_utils/webr.qmd >}}
:::
## Table Setting Type of Confidence Interval
The type of confidence interval can be specified through the `conf_type` argument.
::: {.panel-tabset .nav-justified group="webr"}
## {{< fa regular file-lines sm fw >}} Preview
```{r variant2, test = list(result_v2 = "result")}
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ARM") %>%
estimate_incidence_rate(
vars = "AVAL",
n_events = "n_events",
control = control_incidence_rate(conf_type = "exact", num_pt_year = 100)
)
result <- build_table(lyt, anl, alt_counts_df = adsl)
result
```
```{r include = FALSE}
webr_code_labels <- c("variant2")
```
{{< include ../../_utils/webr.qmd >}}
:::
## Data Setup
```{r setup}
#| code-fold: show
```
:::::
{{< include ../../_utils/save_results.qmd >}}
## `teal` App
::: {.panel-tabset .nav-justified}
## {{< fa regular file-lines fa-sm fa-fw >}} Preview
```{r teal, opts.label = c("skip_if_testing", "app")}
library(teal.modules.clinical)
## Data reproducible code
data <- teal_data()
data <- within(data, {
library(dplyr)
ADSL <- random.cdisc.data::cadsl
ADAETTE <- random.cdisc.data::cadaette
# Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
ADSL <- df_explicit_na(ADSL)
ADAETTE <- df_explicit_na(ADAETTE)
# Create analysis dataset anl from the 2 parameters AEREPTTE & AETOT1
anl_events <- ADAETTE %>%
filter(PARAMCD %in% c("AETOT1", "AETOT2", "AETOT3")) %>%
select(USUBJID, STUDYID, PARAMCD, ARM, ARMCD, n_events = AVAL) %>%
mutate(n_events = as.integer(n_events))
anl_tte <- ADAETTE %>%
filter(PARAMCD == "AEREPTTE") %>%
select(USUBJID, STUDYID, ARM, ARMCD, AVAL, AVALU)
ADAETTE <- full_join(anl_tte, anl_events, by = c("USUBJID", "STUDYID", "ARM", "ARMCD"))
})
datanames <- c("ADSL", "ADAETTE")
names(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]
## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]
ADAETTE <- data[["ADAETTE"]]
## Setup App
app <- init(
data = data,
modules = modules(
tm_t_events_patyear(
label = "AE Rate Adjusted for Patient-Years at Risk - All Occurrences Table",
dataname = "ADAETTE",
arm_var = choices_selected(
choices = variable_choices(ADSL, c("ARM", "ARMCD")),
selected = "ARMCD"
),
paramcd = choices_selected(
choices = value_choices(ADAETTE, "PARAMCD"),
selected = "AETOT1"
),
events_var = choices_selected(
choices = variable_choices(ADAETTE, "n_events"),
selected = "n_events",
fixed = TRUE
)
)
)
)
shinyApp(app$ui, app$server)
```
{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
