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Retrieve raw data

get_raw_data.Rd

[Stable]

Usage 

get_raw_data(x, dataname = NULL)

# S3 method for TealDataset
get_raw_data(x, dataname = NULL)

# S3 method for TealDatasetConnector
get_raw_data(x, dataname = NULL)

# S3 method for TealDataAbstract
get_raw_data(x, dataname = NULL)

Arguments

x

(TealDataset, TealDatasetConnector, TealDataAbstract)
object

dataname

(character)
Name of dataset to return raw data for.

Value

data.frame with the raw data inserted into the R6 objects. In case of TealDataAbstract, list of data.frame can be returned if user doesn't specify dataname - (get_raw_data from all datasets).

Examples 


# TealDataset ---------
ADSL <- teal.data::example_cdisc_data("ADSL")

x <- dataset(dataname = "ADSL", x = ADSL)
get_raw_data(x)
#> # A tibble: 400 × 55
#>    STUDYID USUBJID    SUBJID SITEID   AGE AGEU  SEX   RACE  ETHNIC COUNTRY DTHFL
#>    <chr>   <chr>      <chr>  <chr>  <int> <fct> <fct> <fct> <fct>  <fct>   <fct>
#>  1 AB12345 AB12345-C… id-128 CHN-3     32 YEARS M     ASIAN HISPA… CHN     Y    
#>  2 AB12345 AB12345-C… id-262 CHN-15    35 YEARS M     BLAC… NOT H… CHN     N    
#>  3 AB12345 AB12345-R… id-378 RUS-3     30 YEARS F     ASIAN NOT H… RUS     N    
#>  4 AB12345 AB12345-C… id-220 CHN-11    26 YEARS F     ASIAN NOT H… CHN     N    
#>  5 AB12345 AB12345-C… id-267 CHN-7     40 YEARS M     ASIAN NOT H… CHN     N    
#>  6 AB12345 AB12345-C… id-201 CHN-15    49 YEARS M     ASIAN NOT H… CHN     Y    
#>  7 AB12345 AB12345-U… id-45  USA-1     34 YEARS F     ASIAN NOT H… USA     N    
#>  8 AB12345 AB12345-U… id-261 USA-1     32 YEARS F     ASIAN NOT H… USA     N    
#>  9 AB12345 AB12345-N… id-173 NGA-11    24 YEARS F     BLAC… NOT H… NGA     N    
#> 10 AB12345 AB12345-C… id-307 CHN-1     24 YEARS M     ASIAN NOT H… CHN     Y    
#> # ℹ 390 more rows
#> # ℹ 44 more variables: INVID <chr>, INVNAM <chr>, ARM <fct>, ARMCD <fct>,
#> #   ACTARM <fct>, ACTARMCD <fct>, TRT01P <fct>, TRT01A <fct>, TRT02P <fct>,
#> #   TRT02A <fct>, REGION1 <fct>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>,
#> #   BMRKR2 <fct>, ITTFL <fct>, SAFFL <fct>, BMEASIFL <fct>, BEP01FL <fct>,
#> #   AEWITHFL <fct>, RANDDT <date>, TRTSDTM <dttm>, TRTEDTM <dttm>,
#> #   TRT01SDTM <dttm>, TRT01EDTM <dttm>, TRT02SDTM <dttm>, TRT02EDTM <dttm>, …

# TealDatasetConnector ---------
library(magrittr)
pull_fun_adsl <- callable_function(teal.data::example_cdisc_data) %>%
  set_args(list(dataname = "ADSL"))
dc <- dataset_connector("ADSL", pull_fun_adsl)
load_dataset(dc)
get_raw_data(dc)
#> # A tibble: 400 × 55
#>    STUDYID USUBJID    SUBJID SITEID   AGE AGEU  SEX   RACE  ETHNIC COUNTRY DTHFL
#>    <chr>   <chr>      <chr>  <chr>  <int> <fct> <fct> <fct> <fct>  <fct>   <fct>
#>  1 AB12345 AB12345-C… id-128 CHN-3     32 YEARS M     ASIAN HISPA… CHN     Y    
#>  2 AB12345 AB12345-C… id-262 CHN-15    35 YEARS M     BLAC… NOT H… CHN     N    
#>  3 AB12345 AB12345-R… id-378 RUS-3     30 YEARS F     ASIAN NOT H… RUS     N    
#>  4 AB12345 AB12345-C… id-220 CHN-11    26 YEARS F     ASIAN NOT H… CHN     N    
#>  5 AB12345 AB12345-C… id-267 CHN-7     40 YEARS M     ASIAN NOT H… CHN     N    
#>  6 AB12345 AB12345-C… id-201 CHN-15    49 YEARS M     ASIAN NOT H… CHN     Y    
#>  7 AB12345 AB12345-U… id-45  USA-1     34 YEARS F     ASIAN NOT H… USA     N    
#>  8 AB12345 AB12345-U… id-261 USA-1     32 YEARS F     ASIAN NOT H… USA     N    
#>  9 AB12345 AB12345-N… id-173 NGA-11    24 YEARS F     BLAC… NOT H… NGA     N    
#> 10 AB12345 AB12345-C… id-307 CHN-1     24 YEARS M     ASIAN NOT H… CHN     Y    
#> # ℹ 390 more rows
#> # ℹ 44 more variables: INVID <chr>, INVNAM <chr>, ARM <fct>, ARMCD <fct>,
#> #   ACTARM <fct>, ACTARMCD <fct>, TRT01P <fct>, TRT01A <fct>, TRT02P <fct>,
#> #   TRT02A <fct>, REGION1 <fct>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>,
#> #   BMRKR2 <fct>, ITTFL <fct>, SAFFL <fct>, BMEASIFL <fct>, BEP01FL <fct>,
#> #   AEWITHFL <fct>, RANDDT <date>, TRTSDTM <dttm>, TRTEDTM <dttm>,
#> #   TRT01SDTM <dttm>, TRT01EDTM <dttm>, TRT02SDTM <dttm>, TRT02EDTM <dttm>, …

# TealData ----------------
adsl <- cdisc_dataset(
  dataname = "ADSL",
  x = teal.data::example_cdisc_data("ADSL"),
  code = "library(teal.data)\nADSL <- teal.data::example_cdisc_data(\"ADSL\")"
)

adtte <- cdisc_dataset(
  dataname = "ADTTE",
  x = teal.data::example_cdisc_data("ADTTE"),
  code = "library(teal.data)\nADTTE <- teal.data::example_cdisc_data(\"ADTTE\")"
)

rd <- teal.data:::TealData$new(adsl, adtte)
get_raw_data(rd)
#> $ADSL
#> # A tibble: 400 × 55
#>    STUDYID USUBJID    SUBJID SITEID   AGE AGEU  SEX   RACE  ETHNIC COUNTRY DTHFL
#>    <chr>   <chr>      <chr>  <chr>  <int> <fct> <fct> <fct> <fct>  <fct>   <fct>
#>  1 AB12345 AB12345-C… id-128 CHN-3     32 YEARS M     ASIAN HISPA… CHN     Y    
#>  2 AB12345 AB12345-C… id-262 CHN-15    35 YEARS M     BLAC… NOT H… CHN     N    
#>  3 AB12345 AB12345-R… id-378 RUS-3     30 YEARS F     ASIAN NOT H… RUS     N    
#>  4 AB12345 AB12345-C… id-220 CHN-11    26 YEARS F     ASIAN NOT H… CHN     N    
#>  5 AB12345 AB12345-C… id-267 CHN-7     40 YEARS M     ASIAN NOT H… CHN     N    
#>  6 AB12345 AB12345-C… id-201 CHN-15    49 YEARS M     ASIAN NOT H… CHN     Y    
#>  7 AB12345 AB12345-U… id-45  USA-1     34 YEARS F     ASIAN NOT H… USA     N    
#>  8 AB12345 AB12345-U… id-261 USA-1     32 YEARS F     ASIAN NOT H… USA     N    
#>  9 AB12345 AB12345-N… id-173 NGA-11    24 YEARS F     BLAC… NOT H… NGA     N    
#> 10 AB12345 AB12345-C… id-307 CHN-1     24 YEARS M     ASIAN NOT H… CHN     Y    
#> # ℹ 390 more rows
#> # ℹ 44 more variables: INVID <chr>, INVNAM <chr>, ARM <fct>, ARMCD <fct>,
#> #   ACTARM <fct>, ACTARMCD <fct>, TRT01P <fct>, TRT01A <fct>, TRT02P <fct>,
#> #   TRT02A <fct>, REGION1 <fct>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>,
#> #   BMRKR2 <fct>, ITTFL <fct>, SAFFL <fct>, BMEASIFL <fct>, BEP01FL <fct>,
#> #   AEWITHFL <fct>, RANDDT <date>, TRTSDTM <dttm>, TRTEDTM <dttm>,
#> #   TRT01SDTM <dttm>, TRT01EDTM <dttm>, TRT02SDTM <dttm>, TRT02EDTM <dttm>, …
#> 
#> $ADTTE
#> # A tibble: 2,000 × 67
#>    STUDYID USUBJID    SUBJID SITEID   AGE AGEU  SEX   RACE  ETHNIC COUNTRY DTHFL
#>    <chr>   <chr>      <chr>  <chr>  <int> <fct> <fct> <fct> <fct>  <fct>   <fct>
#>  1 AB12345 AB12345-B… id-105 BRA-1     38 YEARS M     BLAC… HISPA… BRA     N    
#>  2 AB12345 AB12345-B… id-105 BRA-1     38 YEARS M     BLAC… HISPA… BRA     N    
#>  3 AB12345 AB12345-B… id-105 BRA-1     38 YEARS M     BLAC… HISPA… BRA     N    
#>  4 AB12345 AB12345-B… id-105 BRA-1     38 YEARS M     BLAC… HISPA… BRA     N    
#>  5 AB12345 AB12345-B… id-105 BRA-1     38 YEARS M     BLAC… HISPA… BRA     N    
#>  6 AB12345 AB12345-B… id-134 BRA-1     47 YEARS M     WHITE NOT H… BRA     Y    
#>  7 AB12345 AB12345-B… id-134 BRA-1     47 YEARS M     WHITE NOT H… BRA     Y    
#>  8 AB12345 AB12345-B… id-134 BRA-1     47 YEARS M     WHITE NOT H… BRA     Y    
#>  9 AB12345 AB12345-B… id-134 BRA-1     47 YEARS M     WHITE NOT H… BRA     Y    
#> 10 AB12345 AB12345-B… id-134 BRA-1     47 YEARS M     WHITE NOT H… BRA     Y    
#> # ℹ 1,990 more rows
#> # ℹ 56 more variables: INVID <chr>, INVNAM <chr>, ARM <fct>, ARMCD <fct>,
#> #   ACTARM <fct>, ACTARMCD <fct>, TRT01P <fct>, TRT01A <fct>, TRT02P <fct>,
#> #   TRT02A <fct>, REGION1 <fct>, STRATA1 <fct>, STRATA2 <fct>, BMRKR1 <dbl>,
#> #   BMRKR2 <fct>, ITTFL <fct>, SAFFL <fct>, BMEASIFL <fct>, BEP01FL <fct>,
#> #   AEWITHFL <fct>, RANDDT <date>, TRTSDTM <dttm>, TRTEDTM <dttm>,
#> #   TRT01SDTM <dttm>, TRT01EDTM <dttm>, TRT02SDTM <dttm>, TRT02EDTM <dttm>, …
#> 

# TealDataConnector --------
library(magrittr)

slice_cdisc_data <- function(dataname, n) {
  head(example_cdisc_data(dataname), n)
}

random_data_connector <- function(dataname) {
  fun_dataset_connector(
    dataname = dataname,
    fun = slice_cdisc_data,
    fun_args = list(dataname = dataname),
  )
}

open_fun <- callable_function(library)
open_fun$set_args(list(package = "teal.data"))

con <- data_connection(open_fun = open_fun)
con$set_open_server(
  function(id, connection) {
    moduleServer(
      id = id,
      module = function(input, output, session) {
        connection$open(try = TRUE)
        return(invisible(connection))
      }
    )
  }
)

rdc <- relational_data_connector(
  connection = con,
  connectors = list(random_data_connector("ADSL"), random_data_connector("ADLB"))
)

rdc$set_ui(
  function(id, connection, connectors) {
    ns <- NS(id)
    tagList(
      connection$get_open_ui(ns("open_connection")),
      numericInput(inputId = ns("n"), label = "Choose number of records", min = 0, value = 1),
      do.call(
        what = "tagList",
        args = lapply(
          connectors,
          function(connector) {
            div(
              connector$get_ui(
                id = ns(connector$get_dataname())
              ),
              br()
            )
          }
        )
      )
    )
  }
)

rdc$set_server(
  function(id, connection, connectors) {
    moduleServer(
      id = id,
      module = function(input, output, session) {
        # opens connection
        connection$get_open_server()(id = "open_connection", connection = connection)
        if (connection$is_opened()) {
          for (connector in connectors) {
            set_args(connector, args = list(n = input$n))
            # pull each dataset
            connector$get_server()(id = connector$get_dataname())
            if (connector$is_failed()) {
              break
            }
          }
        }
      }
    )
  }
)

if (FALSE) {
load_datasets(rdc)
get_raw_data(rdc)
}

# TealData (with connectors) --------
drc <- cdisc_data(rdc)
if (FALSE) {
get_raw_data(drc)
}