---
title: ENTXX
subtitle: Enrollment Variants
---
------------------------------------------------------------------------
{{< include ../../_utils/envir_hook.qmd >}}
```{r setup, echo = FALSE, warning = FALSE, message = FALSE}
library(dplyr)
library(forcats)
library(tern)
adsl <- random.cdisc.data::cadsl
# Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
adsl <- df_explicit_na(adsl)
adsl <- adsl %>%
mutate(
REGION1 = droplevels(REGION1),
COUNTRY = droplevels(COUNTRY),
INVID_INVNAM = paste(INVID, INVNAM, sep = " / ")
) %>%
mutate(
INVID = factor(INVID),
SITEID = factor(SITEID),
INVNAM = factor(INVNAM),
INVID_INVNAM = factor(INVID_INVNAM)
) %>%
var_relabel(
INVID_INVNAM = "Investigator Number/Name",
REGION1 = "Geographic Region 1",
COUNTRY = "Country",
INVID = "Investigator Identifier"
) %>%
arrange(REGION1, COUNTRY, INVID)
```
```{r include = FALSE}
webr_code_labels <- c("setup")
```
{{< include ../../_utils/webr_no_include.qmd >}}
## Output
::::::: panel-tabset
## ENT01 -- Enrollment by Region, <br/> Country, and Investigator Number
::: {.panel-tabset .nav-justified group="webr"}
## {{< fa regular file-lines sm fw >}} Preview
```{r variant1, test = list(result_v1 = "result")}
# Define the split function
split_fun <- drop_split_levels
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ARM") %>%
add_overall_col(label = "All Patients") %>%
split_rows_by("REGION1", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adsl$REGION1)) %>%
summarize_row_groups() %>%
split_rows_by("COUNTRY", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adsl$COUNTRY)) %>%
summarize_row_groups() %>%
analyze_vars("INVID", .stats = "count_fraction") %>%
append_varlabels(adsl, "INVID", 2L)
result <- build_table(lyt, adsl) %>%
prune_table()
result
```
```{r include = FALSE}
webr_code_labels <- c("variant1")
```
{{< include ../../_utils/webr.qmd >}}
:::
## ENT01A -- Enrollment by Country <br/> and Investigator Number
::: {.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") %>%
add_overall_col(label = "All Patients") %>%
split_rows_by("COUNTRY", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adsl$COUNTRY)) %>%
summarize_row_groups() %>%
analyze_vars("INVID", .stats = "count_fraction") %>%
append_varlabels(adsl, "INVID", 1L)
result <- build_table(lyt, adsl) %>%
prune_table()
result
```
```{r include = FALSE}
webr_code_labels <- c("variant2")
```
{{< include ../../_utils/webr.qmd >}}
:::
## ENT02 -- Enrollment by Region, Country, <br/> and Investigator Number/Name
::: {.panel-tabset .nav-justified group="webr"}
## {{< fa regular file-lines sm fw >}} Preview
```{r variant3, test = list(result_v3 = "result")}
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ARM") %>%
add_overall_col(label = "All Patients") %>%
split_rows_by("REGION1", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adsl$REGION1)) %>%
summarize_row_groups() %>%
split_rows_by("COUNTRY", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adsl$COUNTRY)) %>%
summarize_row_groups() %>%
analyze_vars("INVID_INVNAM", .stats = "count_fraction") %>%
append_varlabels(adsl, "INVID_INVNAM", 2L)
result <- build_table(lyt, adsl) %>%
prune_table()
result
```
```{r include = FALSE}
webr_code_labels <- c("variant3")
```
{{< include ../../_utils/webr.qmd >}}
:::
## ENT02A -- Enrollment by Country <br/> and Investigator Number/Name
::: {.panel-tabset .nav-justified group="webr"}
## {{< fa regular file-lines sm fw >}} Preview
```{r variant4, test = list(result_v4 = "result")}
lyt <- basic_table(show_colcounts = TRUE) %>%
split_cols_by("ARM") %>%
add_overall_col(label = "All Patients") %>%
split_rows_by("COUNTRY", split_fun = split_fun, label_pos = "topleft", split_label = obj_label(adsl$COUNTRY)) %>%
summarize_row_groups() %>%
analyze_vars("INVID_INVNAM", .stats = "count_fraction") %>%
append_varlabels(adsl, "INVID_INVNAM", 1L)
result <- build_table(lyt, adsl) %>%
prune_table()
result
```
```{r include = FALSE}
webr_code_labels <- c("variant4")
```
{{< 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
Note that for this module application, only the variables passed into `by_vars` are used when `row_groups` is selected. Variables passed into `analyze_vars` are additionally used when `row_groups` is deselected.
```{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
# Ensure character variables are converted to factors and empty strings and NAs are explicit missing levels.
ADSL <- df_explicit_na(ADSL)
adsl_labels <- col_labels(ADSL)
ADSL <- ADSL %>%
mutate(
REGION1 = droplevels(REGION1),
COUNTRY = droplevels(COUNTRY),
INVID_INVNAM = paste(INVID, INVNAM, sep = " / ")
) %>%
arrange(REGION1, COUNTRY, INVID) %>%
mutate(
INVID = factor(INVID),
SITEID = factor(SITEID),
INVNAM = factor(INVNAM),
INVID_INVNAM = factor(INVID_INVNAM)
)
col_labels(ADSL) <- c(adsl_labels, c(INVID_INVNAM = "Investigator Number/Name"))
})
datanames <- "ADSL"
names(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]
## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]
## Setup App
app <- init(
data = data,
modules = modules(
tm_t_summary_by(
label = "Enrollment Table",
dataname = "ADSL",
arm_var = choices_selected(
choices = variable_choices(ADSL, c("ARM", "ARMCD")),
selected = "ARM"
),
by_vars = choices_selected(
choices = variable_choices(ADSL, c("REGION1", "COUNTRY", "SITEID", "INVID", "INVNAM", "INVID_INVNAM")),
selected = c("REGION1")
),
summarize_vars = choices_selected(
choices = variable_choices(ADSL, c("REGION1", "COUNTRY", "SITEID", "INVID", "INVNAM", "INVID_INVNAM")),
selected = c("SITEID")
),
denominator = choices_selected(
choices = c("n", "N", "omit"),
selected = "N",
fixed = TRUE
),
useNA = "ifany",
row_groups = TRUE
)
)
)
shinyApp(app$ui, app$server)
```
{{< include ../../_utils/shinylive.qmd >}}
:::
{{< include ../../repro.qmd >}}
