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How the generated programs name folders and packages

Source: R/code_options.R
tflspec_code_options.Rd

Two options make the code tflspec writes fit a study's setup file (such as tflplanner's programs/study_setup.R), which defines the study's folders as variables and attaches the packages every program uses.

Details

  • tflspec.paths: a named character vector, a variable for a folder, relative to the study folder – c(path_adam = "data/adam", path_ard = "output/ard"). A file under one of them is written through the variable: readRDS(file.path(path_adam, "adsl.rds")) instead of readRDS("data/adam/adsl.rds"). The folder that holds it most closely is the one used.

  • tflspec.attached: the packages the setup attaches with library() – c("cards", "dplyr"). Their functions are called without pkg:: in the program, the code of the spec it carries included (only the code: a string or a comment keeps what it says), and an ARD program does not write library(cards) itself. A package not listed keeps its prefix (cardx::).

Unset (the default), the code is as it has always been: literal paths and pkg:: on every call. The functions that write code read them: tfl_ard_code(), tfl_build_ard(), tfl_table_code(), tfl_report_code(), tfl_report_setup_code(), tfl_listing_code(), tfl_read_data_code(), tfl_fig_design_code() and tfl_fig_setup_code().

Examples

sp <- tfl_ard_spec(list(
  study = data.frame(key = "id", value = "USUBJID"),
  datasets = data.frame(dataset = "ADSL", path = "data/adam/adsl.rds"),
  populations = data.frame(population_id = "SAF", dataset = "ADSL",
                           where = "SAFFL == \"Y\""),
  analyses = data.frame(output_id = "T1", analysis_id = "AGE",
                        method = "continuous", population_id = "SAF",
                        by = "TRT01A", variables = "AGE")))
old <- options(tflspec.paths = c(path_adam = "data/adam"),
               tflspec.attached = "cards")
cat(tfl_ard_code(sp, part = "body"), sep = "\n")
#> report_id <- "T1"
#> 
#> # ---- data ----
#> adsl <- readRDS(file.path(path_adam, "adsl.rds"))
#> 
#> # ---- populations ----
#> pop_saf <- filter(adsl, SAFFL == "Y")
#> 
#> # ---- analyses ----
#> # AGE
#> ard_age <- pop_saf |>
#>   ard_summary(
#>     by = TRT01A,
#>     variables = AGE,
#>     fmt_fun = everything() ~ fmt_default
#>   ) |>
#>   apply_fmt_fun() |>
#>   tag_ard(report_id, "AGE", population = "SAF")
#> 
#> # the report's rows of the study ARD, with the fingerprint of its
#> # definition (tfl_ard_spec_hash())
#> ard_age |>
#>   save_ard(report_id, definition = "fe7f76871951d115ec0b5d0336afaeec")
options(old)