Creating custom source extension • shinyCohortBuilder

If you want to use shinyCohortBuilder with a custom source type, a set of methods needs to be defined.

Currently there exists one official extension cohortBuilder.db package that allows you to use shinyCohortBuilder (and cohortBuilder) with database connections.

The goal of this document is to explain how to create custom extensions to shinyCohortBuilder.

In general to create the custom layer you need to create an R package where:

The custom Source extension for cohortBuilder methods is implemented (see. vignettes("custom-extensions", package = "cohortBuilder")).
A set of integration S3 methods for shinyCohortBuilder are implemented.
Extra filters (added in the extension) GUI layers are implemented (see custom GUI filters).

If you have cohortBuilder integration ready for the selected source type (a new package named cohortBuilder.<type>), the next step is to add shinyCohortBuilder integration.

Below we describe all the required and optional methods you need to define within the created package.

.render_filters - method used to define structure for filters rendering in a selected step

Required parameters:

source - Source object.
cohort - Cohort object.
step_id - Id of the filtering step.
ns - Namespace function.
... - Unused, added for S3 integration only.

Details:

The method should return HTML structure including statistics output placeholder and a list of filter renderings.
In order to get all the filters included in the selected step use cohort$get_step(step_id)$filters.
Data statistics outputs should be consistent with .update_data_stats method described below.
Each filter should be rendered with usage of .render_filter method.
List of filters rendering should be wrapped into shiny::div(class = "cb_filters", `data-step_id` = step_id).

Examples:

shinyCohortBuilder - default method

.render_filters.default <- function(source, cohort, step_id, ns, ...) {
  step <- cohort$get_step(step_id)
  shiny::tagList(
    shiny::htmlOutput(ns(paste0(step_id, "-stats")), class = "scb_data_stats"),
    step$filters %>%
      purrr::map(~ .render_filter(.x, step_id, cohort, ns = ns)) %>%
      shiny::div(class = "cb_filters", `data-step_id` = step_id)
  )
}

shinyCohortBuilder - tblist data class

.render_filters.tblist <- function(source, cohort, step_id, ns, ...) {
  step <- cohort$get_step(step_id)

  group_filters(cohort$get_source(), step$filters) %>%
    purrr::imap(~ dataset_filters(.x, .y, step_id, cohort, ns = ns)) %>%
    shiny::div(class = "cb_filters", `data-step_id` = step_id)
}

In this example we group all the defined filters by related datasets from source (group_filters), and attach a separate statistics placeholder for each dataset (dataset_filters).

cohortBuilder.db - db data class

render_filters.db <- function(source, cohort, step_id, ns) {
  step <- cohort$get_step(step_id)

  group_filters_db(cohort$get_source(), step$filters) %>%
    purrr::imap(~ dataset_filters_db(.x, .y, step_id, cohort, ns = ns)) %>%
    div(class = "cb_filters", `data-step_id` = step_id)
}

.update_data_stats - logic for updating data statistics

Required parameters:

source - Source object.
step_id - Id of the filtering step.
cohort - Cohort object.
session - Shiny session object.
... - Unused, added for S3 integration only.

Details:

The function should define rendering output for consistent with the output placeholder stated within .render_filters.
It’s recommended the statistics are taken from the Cohort cache cohort$get_cache(step_id, state = "pre").
It’s recommended the output performs previous step data validation (in terms of data existence) and returns descriptive message to the user.
Use cohort$attributes$stats to get displayed statistics state chosen by the user (“pre”, “post”, both or NULL).
For printing the statistics use .pre_post_stats (or .pre_post_stats_text)` which returns formatted statistics output.
You may directly assign the rendering to the output or use .sendOutput method (useful when sending output in loop see “tblist” source example below).

Examples:

shinyCohortBuilder - default method

.update_data_stats.default <- function(source, step_id, cohort, session, ...) {
  ns <- session$ns
  stats <- cohort$attributes$stats

  session$output[[paste0(step_id, "-stats")]] <- shiny::renderUI({
    previous <- cohort$get_cache(step_id, state = "pre")$n_rows
    if (!previous > 0) {
      return("No data selected in previous step.")
    }
    current <- cohort$get_cache(step_id, state = "post")$n_rows
    .pre_post_stats(current, previous, percent = TRUE, stats = stats)
  })
}

shinyCohortBuilder - tblist data class

.update_data_stats.tblist <- function(source, step_id, cohort, session, ...) {
  stats <- cohort$attributes$stats
  step <- cohort$get_step(step_id)

  dataset_names <- names(cohort$get_source()$attributes$datasets)
  data_filters <- purrr::map_chr(step$filters, get_filter_dataset)
  dataset_names <- intersect(dataset_names, data_filters)

  dataset_names %>% purrr::walk(
    ~ .sendOutput(
      paste0(step_id, "-stats_", .x),
      shiny::renderUI({
        previous <- cohort$get_cache(step_id, state = "pre")[[.x]]$n_rows
        if (!previous > 0) {
          return("No data selected in previous step.")
        }
        current <- cohort$get_cache(step_id, state = "post")[[.x]]$n_rows
        .pre_post_stats(current, previous, percent = TRUE, stats = stats)
      }),
      session
    )
  )
}

cohortBuilder.db

update_data_stats.db <- function(source, step_id, cohort, session) {
  stats <- cohort$attributes$stats

  dataset_names <- source$attributes$tables
  dataset_names %>% purrr::walk(
    ~ shinyCohortBuilder::sendOutput(
      paste0(step_id, "-stats_", .x),
      shiny::renderUI({
        previous <- cohort$get_cache(step_id, state = "pre")[[.x]]$n_rows
        if (!previous > 0) {
          return("No data selected in previous step.")
        }
        current <- cohort$get_cache(step_id, state = "post")[[.x]]$n_rows
        shinyCohortBuilder::pre_post_stats(current, previous, percent = TRUE, stats = stats)
      })
    )
  )
}

autofilter (optional) - automatically generate filters configuration based on Source data

Required parameters:

source - Source object,
attach_as - Should filters be added as the first step ("step") or as available filters for configuration panel ("meta"),
... - Unused, added for S3 integration only.

Details:

Generate filters based on Source data (i.e. column types) using cohortBuilder::filter.
When attach_as = "step" wrap them with cohortBuilder::step and attach to the Source using add_step method.
When attach_as = "meta" attach filters to the available_filters Source attribute (source$attributes$available_filters).
The method should return Source object.

Examples:

shinyCohortBuilder - tblist data class

autofilter.tblist <- function(source, attach_as = c("step", "meta"), ...) {
  attach_as <- rlang::arg_match(attach_as)
  step_rule <- source$dtconn %>%
    purrr::imap(~filter_rules(.x, .y)) %>%
    unlist(recursive = FALSE) %>%
    purrr::map(~do.call(cohortBuilder::filter, .)) %>%
    unname()

  if (identical(attach_as, "meta")) {
    source$attributes$available_filters <- step_rule
  } else {
    source %>%
      cohortBuilder::add_step(do.call(cohortBuilder::step, step_rule))
  }

  return(source)
}

.available_filters_choices - define choices for new step configuration panel

Required parameters:

source - Source object,
cohort - Cohort object,
... - Unused, added for S3 integration only.

Details:

The function should return shinyWidgets::prepare_choices output.
The argument value of prepare_choices should point to filter ids.

Examples:

shinyCohortBuilder - tblist data class

.available_filters_choices.tblist <- function(source, cohort, ...) {

  available_filters <- cohort$attributes$available_filters

  choices <- purrr::map(available_filters, function(x) {
    tibble::tibble(
      name = as.character(
        shiny::div(
          `data-tooltip-z-index` = 9999,
          `data-tooltip` = x$get_params("description"),
          `data-tooltip-position` = "top right",
          `data-tooltip-allow-html` = "true",
          x$name
        )
      ),
      id = x$id,
      dataset = x$get_params("dataset")
    )
  }) %>% dplyr::bind_rows()

  shinyWidgets::prepare_choices(choices, name, id, dataset)
}

.step_attrition - define how step attrition plot should be rendered

Required parameters:

source - Source object.
id - Id of the attrition plot output.
cohort - Cohort object.
session - Shiny session object.
... - Unused, added for S3 integration only.

Details:

The method should return list of two objects, output - returning UI output placeholder (having optional user input controllers affecting the output, see “tblist” example below) and render - rendering function defining the plot generating expression.
Within rendering function use cohort$show_attrition method to generate the plot (and pass required parameters to it when needed, see “tblist” class example where dataset is needed).
Use provided id parameter to as an id of plot output placeholder.

Examples:

shinyCohortBuilder - default method

.step_attrition.default <- function(source, id, cohort, session, ...) {
  ns <- session$ns

  list(
    render = shiny::renderPlot({
      cohort$show_attrition()
    }),
    output = shiny::plotOutput(id)
  )
}

shinyCohortBuilder - tblist data class

.step_attrition.tblist <- function(source, id, cohort, session, ...) {
  ns <- session$ns
  choices <- names(source$attributes$datasets)

  list(
    render = shiny::renderPlot({
      cohort$show_attrition(dataset = session$input$attrition_input)
    }),
    output = shiny::tagList(
      shiny::selectInput(ns("attrition_input"), "Choose dataset", choices),
      shiny::plotOutput(id)
    )
  )
}

.custom_attrition - (optional) a custom method used for your own version of attrition plot

The parameters and output structure is the same as for .step_attrition. The main difference is that you should put your custom logic for generating attrition (i.e. using a specific package meant for this).

When the method is defined, the attrition will be printed inside an extra tab of attrition modal.