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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. If the list is unnamed,then it will use the names of the objects.

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 TRUE, so only variables with the origin of 'Predecessor' will be used. If FALSE any derivation matching the dataset.variable will be used.

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>