---
title: "Combining Data Extract with Data Merge"
author: "NEST CoreDev"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Combining Data Extract with Data Merge}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
editor_options:
chunk_output_type: console
---
```{r setup, include = FALSE, echo=FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
`teal.transform` allows the app user to oversee transforming a relational set of data objects into the final dataset for analysis.
User actions create a R expression that subsets and merges the input data.
In the following example we will create an analysis dataset `ANL` by:
1. Selecting the column `AGE` from `ADSL`
2. Selecting the column `AVAL` and filtering the rows where `PARAMCD` is `OS` from `ADTTE`
3. Merging the results from the above datasets using the primary keys.
Note that primary key columns are maintained when selecting columns from datasets.
Let's see how to achieve this dynamic `select`, `filter`, and `merge` operations in a `shiny` app using `teal.transform`.
#### Step 1/5 - Preparing the Data
```{r}
library(teal.transform)
library(teal.data)
library(shiny)
# Define data.frame objects
ADSL <- teal.transform::rADSL
ADTTE <- teal.transform::rADTTE
# create a list of reactive data.frame objects
datasets <- list(
ADSL = reactive(ADSL),
ADTTE = reactive(ADTTE)
)
# create join_keys
join_keys <- join_keys(
join_key("ADSL", "ADSL", c("STUDYID", "USUBJID")),
join_key("ADSL", "ADTTE", c("STUDYID", "USUBJID")),
join_key("ADTTE", "ADTTE", c("STUDYID", "USUBJID", "PARAMCD"))
)
```
#### Step 2/5 - Creating data extract specifications
In the following code block, we create a `data_extract_spec` object for each dataset, as illustrated above.
It is created by the `data_extract_spec()` function which takes in four arguments:
1. `dataname` is the name of the dataset to be extracted.
2. `select` helps specify the columns from which we wish to allow the app user to select. It can be generated using the function `select_spec()`. In the case of `ADSL`, we restrict the selection to `AGE`, `SEX`, and `BMRKR1`, with `AGE` being the default selection.
3. `filter` helps specify the values of a variable we wish to filter during extraction. It can be generated using the function `filter_spec()`. In the case of `ADTTE`, we filter the variable `PARAMCD` by allowing users to choose from `CRSD`, `EFS`, `OS`, and `PFS`, with `OS` being the default filter.
4. `reshape` is a boolean which helps to specify if the data needs to be reshaped from long to wide format. By default it is set to `FALSE`.
```{r}
adsl_extract <- data_extract_spec(
dataname = "ADSL",
select = select_spec(
label = "Select variable:",
choices = c("AGE", "SEX", "BMRKR1"),
selected = "AGE",
multiple = TRUE,
fixed = FALSE
)
)
adtte_extract <- data_extract_spec(
dataname = "ADTTE",
select = select_spec(
choices = c("AVAL", "AVALC", "ASEQ"),
selected = "AVAL",
multiple = TRUE,
fixed = FALSE
),
filter = filter_spec(
vars = "PARAMCD",
choices = c("CRSD", "EFS", "OS", "PFS"),
selected = "OS"
)
)
data_extracts <- list(adsl_extract = adsl_extract, adtte_extract = adtte_extract)
```
#### Step 3/5 - Creating the UI
Here, we define the `merge_ui` function, which will be used to create the UI components for the `shiny` app.
Note that we take in the list of `data_extract` objects as input, and make use of the `data_extract_ui` function to create our UI.
```{r}
merge_ui <- function(id, data_extracts) {
ns <- NS(id)
sidebarLayout(
sidebarPanel(
h3("Encoding"),
div(
data_extract_ui(
ns("adsl_extract"), # must correspond with data_extracts list names
label = "ADSL extract",
data_extracts[[1]]
),
data_extract_ui(
ns("adtte_extract"), # must correspond with data_extracts list names
label = "ADTTE extract",
data_extracts[[2]]
)
)
),
mainPanel(
h3("Output"),
verbatimTextOutput(ns("expr")),
dataTableOutput(ns("data"))
)
)
}
```
#### Step 4/5 - Creating the Server Logic
Here, we define the `merge_srv` function, which will be used to create the server logic for the `shiny` app.
This function takes as arguments the datasets (as a list of reactive `data.frame`), the data extract specifications created above (the `data_extract` list), and the `join_keys` object (read more about the `join_keys` in the [Join Keys vignette of `teal.data`](https://insightsengineering.github.io/teal.data/latest-tag/articles/join-keys.html)).
We make use of the `merge_expression_srv` function to get a reactive list containing merge expression and information needed to perform the transformation - see more in `merge_expression_srv` documentation.
We print this expression in the UI and also evaluate it to get the final `ANL` dataset which is also displayed as a table in the UI.
```{r}
merge_srv <- function(id, datasets, data_extracts, join_keys) {
moduleServer(id, function(input, output, session) {
selector_list <- data_extract_multiple_srv(data_extracts, datasets, join_keys)
merged_data <- merge_expression_srv(
selector_list = selector_list,
datasets = datasets,
join_keys = join_keys,
merge_function = "dplyr::left_join"
)
ANL <- reactive({
data_list <- lapply(datasets, function(ds) ds())
eval(envir = list2env(data_list), expr = as.expression(merged_data()$expr))
})
output$expr <- renderText(paste(merged_data()$expr, collapse = "\n"))
output$data <- renderDataTable(ANL())
})
}
```
#### Step 5/5 - Creating the `shiny` App
Finally, we include `merge_ui` and `merge_srv` in the UI and server components of the `shinyApp`, respectively,
using the `data_extract`s defined in the first code block and the `datasets` object:
```{r eval=FALSE}
shinyApp(
ui = fluidPage(merge_ui("data_merge", data_extracts)),
server = function(input, output, session) {
merge_srv("data_merge", datasets, data_extracts, join_keys)
}
)
```
