Retrieve raw data
get_raw_data.Rd![[Stable]](figures/lifecycle-stable.svg)
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 ---------
library(scda)
ADSL <- synthetic_cdisc_data("latest")$adsl
x <- dataset(dataname = "ADSL", x = ADSL)
get_raw_data(x)
#> # A tibble: 400 × 56
#> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL
#> <chr> <chr> <chr> <chr> <int> <fct> <fct> <fct> <fct> <fct> <fct>
#> 1 AB12345 AB12345-C… id-128 CHN-3 32 YEARS M ASIAN HISPA… CHN Y
#> 2 AB12345 AB12345-C… id-262 CHN-15 35 YEARS M BLAC… NOT H… CHN N
#> 3 AB12345 AB12345-R… id-378 RUS-3 30 YEARS F ASIAN NOT H… RUS N
#> 4 AB12345 AB12345-C… id-220 CHN-11 26 YEARS F ASIAN NOT H… CHN N
#> 5 AB12345 AB12345-C… id-267 CHN-7 40 YEARS M ASIAN NOT H… CHN N
#> 6 AB12345 AB12345-C… id-201 CHN-15 49 YEARS M ASIAN NOT H… CHN Y
#> 7 AB12345 AB12345-U… id-45 USA-1 34 YEARS F ASIAN NOT H… USA N
#> 8 AB12345 AB12345-U… id-261 USA-1 32 YEARS F ASIAN NOT H… USA N
#> 9 AB12345 AB12345-N… id-173 NGA-11 24 YEARS F BLAC… NOT H… NGA N
#> 10 AB12345 AB12345-C… id-307 CHN-1 24 YEARS M ASIAN NOT H… CHN Y
#> # … with 390 more rows, and 45 more variables: INVID <chr>, INVNAM <chr>,
#> # ARM <fct>, ARMCD <fct>, ACTARM <fct>, ACTARMCD <fct>, TRT01P <fct>,
#> # TRT01A <fct>, TRT02P <fct>, TRT02A <fct>, REGION1 <fct>, STRATA1 <fct>,
#> # STRATA2 <fct>, BMRKR1 <dbl>, BMRKR2 <fct>, ITTFL <fct>, SAFFL <fct>,
#> # BMEASIFL <fct>, BEP01FL <fct>, AEWITHFL <fct>, RANDDT <date>,
#> # TRTSDTM <dttm>, TRTEDTM <dttm>, TRT01SDTM <dttm>, TRT01EDTM <dttm>,
#> # TRT02SDTM <dttm>, TRT02EDTM <dttm>, AP01SDTM <dttm>, AP01EDTM <dttm>, …
# TealDatasetConnector ---------
library(scda)
pull_fun_adsl <- callable_function(
function() {
synthetic_cdisc_data("latest")$adsl
}
)
dc <- dataset_connector("ADSL", pull_fun_adsl)
load_dataset(dc)
get_raw_data(dc)
#> # A tibble: 400 × 56
#> 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
#> # … with 390 more rows, and 45 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>, AP01SDTM <dttm>, AP01EDTM <dttm>, …
# TealData ----------------
library(scda)
latest_data <- synthetic_cdisc_data("latest")
adsl <- cdisc_dataset(
dataname = "ADSL",
x = latest_data$adsl,
code = "library(scda)\nADSL <- synthetic_cdisc_data(\"latest\")$adsl"
)
adtte <- cdisc_dataset(
dataname = "ADTTE",
x = latest_data$adtte,
code = "library(scda)\nADTTE <- synthetic_cdisc_data(\"latest\")$adtte"
)
rd <- teal.data:::TealData$new(adsl, adtte)
get_raw_data(rd)
#> $ADSL
#> # A tibble: 400 × 56
#> 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
#> # … with 390 more rows, and 45 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>, AP01SDTM <dttm>, AP01EDTM <dttm>, …
#>
#> $ADTTE
#> # A tibble: 2,000 × 68
#> STUDYID USUBJID SUBJID SITEID AGE AGEU SEX RACE ETHNIC COUNTRY DTHFL
#> <chr> <chr> <chr> <chr> <int> <fct> <fct> <fct> <fct> <fct> <fct>
#> 1 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N
#> 2 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N
#> 3 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N
#> 4 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N
#> 5 AB12345 AB12345-B… id-105 BRA-1 38 YEARS M BLAC… HISPA… BRA N
#> 6 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y
#> 7 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y
#> 8 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y
#> 9 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y
#> 10 AB12345 AB12345-B… id-134 BRA-1 47 YEARS M WHITE NOT H… BRA Y
#> # … with 1,990 more rows, and 57 more variables: INVID <chr>, INVNAM <chr>,
#> # ARM <fct>, ARMCD <fct>, ACTARM <fct>, ACTARMCD <fct>, TRT01P <fct>,
#> # TRT01A <fct>, TRT02P <fct>, TRT02A <fct>, REGION1 <fct>, STRATA1 <fct>,
#> # STRATA2 <fct>, BMRKR1 <dbl>, BMRKR2 <fct>, ITTFL <fct>, SAFFL <fct>,
#> # BMEASIFL <fct>, BEP01FL <fct>, AEWITHFL <fct>, RANDDT <date>,
#> # TRTSDTM <dttm>, TRTEDTM <dttm>, TRT01SDTM <dttm>, TRT01EDTM <dttm>,
#> # TRT02SDTM <dttm>, TRT02EDTM <dttm>, AP01SDTM <dttm>, AP01EDTM <dttm>, …
#>
# TealDataConnector --------
library(scda)
adsl <- scda_cdisc_dataset_connector(dataname = "ADSL", "adsl")
adlb <- scda_cdisc_dataset_connector(dataname = "ADLB", "adlb")
open_fun <- callable_function(library)
open_fun$set_args(list(package = "scda"))
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(adsl, adlb))
rdc$set_ui(
function(id, connection, connectors) {
ns <- NS(id)
tagList(
connection$get_open_ui(ns("open_connection")),
textInput(ns("name"), p("Choose", code("scda data version")), value = "latest"),
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$is_opened()) {
for (connector in connectors) {
set_args(connector, args = list(name = input$name))
# 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)
}