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)
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>