Introduction
In addition of the embedded run() method to create a
tlg, chevron offers a script-based approach that allows the
user to quickly edit a chevron workflow without the need for modifying a
chevron_tlg object. The script is generated from
script_funs method which by default only output the script
corresponding to the preprocessing function in the generated script.
Using a chevron-defined object
The object returned by the script methods are vectors of
character with one element per line of the script, that can be easily
rendered.
res <- script_funs(aet01, adam_db = "syn_data", args = "args_list")
writeLines(res)
#> # Edit Preprocessing Function.
#> preprocess(aet01) <-
#> function (adam_db, ...)
#> {
#> adam_db$adae <- adam_db$adae %>% filter(.data$ANL01FL ==
#> "Y") %>% mutate(FATAL = with_label(.data$AESDTH == "Y",
#> "AE with fatal outcome"), SER = with_label(.data$AESER ==
#> "Y", "Serious AE"), SEV = with_label(.data$ASEV == "SEVERE",
#> "Severe AE (at greatest intensity)"), REL = with_label(.data$AREL ==
#> "Y", "Related AE"), WD = with_label(.data$AEACN == "DRUG WITHDRAWN",
#> "AE leading to withdrawal from treatment"), DSM = with_label(.data$AEACN %in%
#> c("DRUG INTERRUPTED", "DOSE INCREASED", "DOSE REDUCED"),
#> "AE leading to dose modification/interruption"), SERWD = with_label(.data$SER &
#> .data$WD, "Serious AE leading to withdrawal from treatment"),
#> SERDSM = with_label(.data$SER & .data$DSM, "Serious AE leading to dose modification/interruption"),
#> RELSER = with_label(.data$SER & .data$REL, "Related Serious AE"),
#> RELWD = with_label(.data$REL & .data$WD, "Related AE leading to withdrawal from treatment"),
#> RELDSM = with_label(.data$REL & .data$DSM, "Related AE leading to dose modification/interruption"),
#> CTC35 = with_label(.data$ATOXGR %in% c("3", "4", "5"),
#> "Grade 3-5 AE"), CTC45 = with_label(.data$ATOXGR %in%
#> c("4", "5"), "Grade 4/5 AE"))
#> adam_db$adsl <- adam_db$adsl %>% mutate(DCSREAS = reformat(.data$DCSREAS,
#> missing_rule))
#> adam_db
#> }
#>
#> # Create TLG
#> tlg_output <- run(object = aet01, adam_db = syn_data, verbose = TRUE, user_args = args_list)With a modified chevron object
The script generator depends on the functions actually stored in the
object. Modifying the chevron_tlg object can lead to a
different script.
aet01_custom <- aet01
preprocess(aet01_custom) <- function(adam_db, new_format, ...) {
reformat(adam_db, new_format)
}
res_funs <- script_funs(aet01_custom, adam_db = "syn_data", args = "args_list")Print the generated scripts. Note that a new argument
new_format has been added and the pre processing function
has been modified.
writeLines(res_funs)
#> # Edit Preprocessing Function.
#> preprocess(aet01_custom) <-
#> function (adam_db, new_format, ...)
#> {
#> reformat(adam_db, new_format)
#> }
#>
#> # Create TLG
#> tlg_output <- run(object = aet01_custom, adam_db = syn_data, verbose = TRUE, user_args = args_list)