Data merge module server

Usage

merge_expression_srv(
  id = "merge_id",
  selector_list,
  datasets,
  join_keys,
  merge_function = "dplyr::full_join",
  anl_name = "ANL"
)

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

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

Arguments

id

An ID string that corresponds with the ID used to call the module's UI function.

selector_list

(reactive) output from data_extract_multiple_srv() or a reactive named list of outputs from data_extract_srv(). When using a reactive named list, the names must be identical to the shiny ids of the respective data_extract_ui().

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.

merge_function

(character(1) or reactive) 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.

Value

Reactive expression with output from merge_expression_srv().

Details

When additional processing of the data_extract list input is required, merge_expression_srv() can be combined with data_extract_multiple_srv() or data_extract_srv() to influence the selector_list input. Compare the example below with that found in merge_expression_module().

See also

merge_expression_module()

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 <- rlnorm(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 = tags$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)
    )
  )
)
#> `shiny::dataTableOutput()` is deprecated as of shiny 1.8.1.
#> Please use `DT::DTOutput()` instead.
#> Since you have a suitable version of DT (>= v0.32.1), shiny::dataTableOutput() will automatically use DT::DTOutput() under-the-hood.
#> If this happens to break your app, set `options(shiny.legacy.datatable = TRUE)` to get the legacy datatable implementation (or `FALSE` to squelch this message).
#> See <https://rstudio.github.io/DT/shiny.html> for more information.

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)
      )"
  )

  selector_list <- data_extract_multiple_srv(
    list(adsl_var = adsl_extract, adlb_var = adlb_extract),
    datasets = data_list
  )
  merged_data <- merge_expression_srv(
    selector_list = selector_list,
    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)
}