build_from_derived {metatools}

Build a dataset from derived

Description

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)