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Build a dataset from derived

Source: R/build.R
build_from_derived.Rd

This function builds a dataset out of the columns that just need to be pulled through. So any variable that has a derivation in the format of 'dataset.variable' will be pulled through to create the new dataset. When there are multiple datasets present, they will be joined by the shared `key_seq` variables. These columns are often called 'Predecessors' in ADaM, but this is not universal so that is optional to specify.

Usage

build_from_derived(
  metacore,
  ds_list,
  dataset_name = NULL,
  predecessor_only = TRUE,
  keep = FALSE
)

Arguments

metacore

metacore object that contains the specifications for the dataset of interest.

ds_list

Named list of datasets that are needed to build the from

dataset_name

Optional string to specify the dataset that is being built. This is only needed if the metacore object provided hasn't already been subsetted.

predecessor_only

By default `FALSE`, but if `TRUE` will only use derivations with the origin of 'Predecessor'

keep

Boolean to determine if the original columns should be kept. By default `FALSE`, so only the ADaM columns are kept. If `TRUE` the resulting dataset will have all the ADaM columns as well as any SDTM column that were renamed in the ADaM (i.e `ARM` and `TRT01P` will be in the resulting dataset)

Value

dataset

Examples

library(metacore)
library(haven)
library(magrittr)
load(metacore_example("pilot_ADaM.rda"))
spec <- metacore %>% select_dataset("ADSL")
ds_list <- list(DM = read_xpt(metatools_example("dm.xpt")))
build_from_derived(spec, ds_list, predecessor_only = FALSE)
#> # A tibble: 306 × 13
#>    STUDYID     USUBJID SUBJID SITEID TRT01P   AGE AGEU  RACE  SEX   ETHNIC DTHFL
#>    <chr>       <chr>   <chr>  <chr>  <chr>  <dbl> <chr> <chr> <chr> <chr>  <chr>
#>  1 CDISCPILOT… 01-701… 1015   701    Place…    63 YEARS WHITE F     HISPA… ""   
#>  2 CDISCPILOT… 01-701… 1023   701    Place…    64 YEARS WHITE M     HISPA… ""   
#>  3 CDISCPILOT… 01-701… 1028   701    Xanom…    71 YEARS WHITE M     NOT H… ""   
#>  4 CDISCPILOT… 01-701… 1033   701    Xanom…    74 YEARS WHITE M     NOT H… ""   
#>  5 CDISCPILOT… 01-701… 1034   701    Xanom…    77 YEARS WHITE F     NOT H… ""   
#>  6 CDISCPILOT… 01-701… 1047   701    Place…    85 YEARS WHITE F     NOT H… ""   
#>  7 CDISCPILOT… 01-701… 1057   701    Scree…    59 YEARS WHITE F     HISPA… ""   
#>  8 CDISCPILOT… 01-701… 1097   701    Xanom…    68 YEARS WHITE M     NOT H… ""   
#>  9 CDISCPILOT… 01-701… 1111   701    Xanom…    81 YEARS WHITE F     NOT H… ""   
#> 10 CDISCPILOT… 01-701… 1115   701    Xanom…    84 YEARS WHITE M     NOT H… ""   
#> # ℹ 296 more rows
#> # ℹ 2 more variables: RFSTDTC <chr>, RFENDTC <chr>