merge_expression_module: Merge expression module

In teal.transform: Functions for Extracting and Merging Data in the 'teal' Framework

Merge expression module

Description

Convenient wrapper to combine data_extract_multiple_srv() and merge_expression_srv() when no additional processing is required. Compare the example below with that found in merge_expression_srv().

Usage

merge_expression_module(
  datasets,
  join_keys = NULL,
  data_extract,
  merge_function = "dplyr::full_join",
  anl_name = "ANL",
  id = "merge_id"
)

## S3 method for class 'reactive'
merge_expression_module(
  datasets,
  join_keys = NULL,
  data_extract,
  merge_function = "dplyr::full_join",
  anl_name = "ANL",
  id = "merge_id"
)

## S3 method for class 'list'
merge_expression_module(
  datasets,
  join_keys = NULL,
  data_extract,
  merge_function = "dplyr::full_join",
  anl_name = "ANL",
  id = "merge_id"
)

Arguments

datasets	(named list of reactive or non-reactive data.frame) object containing data as a list of data.frame. When passing a list of non-reactive data.frame objects, they are converted to reactive data.frame objects internally.
join_keys	(join_keys) of variables used as join keys for each of the datasets in datasets. This will be used to extract the keys of every dataset.
data_extract	(named list of data_extract_spec).
merge_function	(character(1)) A character string of a function that accepts the arguments x, y and by to perform the merging of datasets.
anl_name	(character(1)) Name of the analysis dataset.
id	An ID string that corresponds with the ID used to call the module's UI function.

Value

Reactive expression with output from merge_expression_srv().

See Also

merge_expression_srv()

Examples

library(shiny)
library(teal.data)
library(teal.widgets)

ADSL <- data.frame(
  STUDYID = "A",
  USUBJID = LETTERS[1:10],
  SEX = rep(c("F", "M"), 5),
  AGE = rpois(10, 30),
  BMRKR1 = rlnorm(10)
)
ADLB <- expand.grid(
  STUDYID = "A",
  USUBJID = LETTERS[1:10],
  PARAMCD = c("ALT", "CRP", "IGA"),
  AVISIT = c("SCREENING", "BASELINE", "WEEK 1 DAY 8", "WEEK 2 DAY 15")
)
ADLB$AVAL <- rlnorm(120)
ADLB$CHG <- rnorm(120)

data_list <- list(
  ADSL = reactive(ADSL),
  ADLB = reactive(ADLB)
)

join_keys <- join_keys(
  join_key("ADSL", "ADSL", c("STUDYID", "USUBJID")),
  join_key("ADSL", "ADLB", c("STUDYID", "USUBJID")),
  join_key("ADLB", "ADLB", c("STUDYID", "USUBJID", "PARAMCD", "AVISIT"))
)

adsl_extract <- data_extract_spec(
  dataname = "ADSL",
  select = select_spec(
    label = "Select variable:",
    choices = c("AGE", "BMRKR1"),
    selected = "AGE",
    multiple = TRUE,
    fixed = FALSE
  )
)
adlb_extract <- data_extract_spec(
  dataname = "ADLB",
  filter = filter_spec(vars = "PARAMCD", choices = c("ALT", "CRP", "IGA"), selected = "ALT"),
  select = select_spec(
    label = "Select variable:",
    choices = c("AVAL", "CHG"),
    selected = "AVAL",
    multiple = TRUE,
    fixed = FALSE
  )
)

ui <- fluidPage(
  standard_layout(
    output = div(
      verbatimTextOutput("expr"),
      dataTableOutput("data")
    ),
    encoding = tagList(
      data_extract_ui("adsl_var", label = "ADSL selection", adsl_extract),
      data_extract_ui("adlb_var", label = "ADLB selection", adlb_extract)
    )
  )
)

server <- function(input, output, session) {
  data_q <- qenv()

  data_q <- eval_code(
    data_q,
    "ADSL <- data.frame(
        STUDYID = 'A',
        USUBJID = LETTERS[1:10],
        SEX = rep(c('F', 'M'), 5),
        AGE = rpois(10, 30),
        BMRKR1 = rlnorm(10)
      )"
  )

  data_q <- eval_code(
    data_q,
    "ADLB <- expand.grid(
        STUDYID = 'A',
        USUBJID = LETTERS[1:10],
        PARAMCD = c('ALT', 'CRP', 'IGA'),
        AVISIT = c('SCREENING', 'BASELINE', 'WEEK 1 DAY 8', 'WEEK 2 DAY 15'),
        AVAL = rlnorm(120),
        CHG = rlnorm(120)
       )"
  )

  merged_data <- merge_expression_module(
    data_extract = list(adsl_var = adsl_extract, adlb_var = adlb_extract),
    datasets = data_list,
    join_keys = join_keys,
    merge_function = "dplyr::left_join"
  )

  code_merge <- reactive({
    for (exp in merged_data()$expr) data_q <- eval_code(data_q, exp)
    data_q
  })

  output$expr <- renderText(paste(merged_data()$expr, collapse = "\n"))
  output$data <- renderDataTable(code_merge()[["ANL"]])
}

if (interactive()) {
  shinyApp(ui, server)
}

teal.transform documentation built on May 29, 2024, 5:06 a.m.