Adds taxonomic level of interest in the Recipe.
Usage
add_tax(rec, tax_info)
# S4 method for class 'Recipe'
add_tax(rec, tax_info)
# S4 method for class 'PrepRecipe'
add_tax(rec, tax_info)Examples
data(metaHIV_phy)
## Define recipe
rec <-
recipe(metaHIV_phy)
## add var info
rec <- add_tax(rec, tax_info = "Species")
rec
#> ── DAR Recipe ──────────────────────────────────────────────────────────────────
#> Inputs:
#>
#> ℹ phyloseq object with 451 taxa and 156 samples
#> ✖ undefined variable of interest. Use add_var() to add it to Recipe!
#> ℹ taxonomic level Species
#>
#>
## add tax info to a prep-Recipe returns an error
data(test_prep_rec)
err <- testthat::expect_error(
add_tax(test_prep_rec, tax_info = "Species")
)
err
#> <error/rlang_error>
#> Error in `add_tax()`:
#> ! tax_info can only be added to a non-PrepRecipe
#> ---
#> Backtrace:
#> ▆
#> 1. └─pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
#> 2. └─pkgdown::build_site(...)
#> 3. └─pkgdown:::build_site_local(...)
#> 4. └─pkgdown::build_reference(...)
#> 5. ├─pkgdown:::unwrap_purrr_error(...)
#> 6. │ └─base::withCallingHandlers(...)
#> 7. └─purrr::map(...)
#> 8. └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
#> 9. ├─purrr:::with_indexed_errors(...)
#> 10. │ └─base::withCallingHandlers(...)
#> 11. ├─purrr:::call_with_cleanup(...)
#> 12. └─pkgdown (local) .f(.x[[i]], ...)
#> 13. ├─base::withCallingHandlers(...)
#> 14. └─pkgdown:::data_reference_topic(...)
#> 15. └─pkgdown:::run_examples(...)
#> 16. └─pkgdown:::highlight_examples(code, topic, env = env)
#> 17. └─downlit::evaluate_and_highlight(...)
#> 18. └─evaluate::evaluate(code, child_env(env), new_device = TRUE, output_handler = output_handler)
#> 19. ├─base::withRestarts(...)
#> 20. │ └─base (local) withRestartList(expr, restarts)
#> 21. │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#> 22. │ │ └─base (local) doWithOneRestart(return(expr), restart)
#> 23. │ └─base (local) withRestartList(expr, restarts[-nr])
#> 24. │ ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#> 25. │ │ └─base (local) doWithOneRestart(return(expr), restart)
#> 26. │ └─base (local) withRestartList(expr, restarts[-nr])
#> 27. │ └─base (local) withOneRestart(expr, restarts[[1L]])
#> 28. │ └─base (local) doWithOneRestart(return(expr), restart)
#> 29. ├─evaluate:::with_handlers(...)
#> 30. │ ├─base::eval(call)
#> 31. │ │ └─base::eval(call)
#> 32. │ └─base::withCallingHandlers(...)
#> 33. ├─base::withVisible(eval(expr, envir))
#> 34. └─base::eval(expr, envir)
#> 35. └─base::eval(expr, envir)
#> 36. ├─testthat::expect_error(add_tax(test_prep_rec, tax_info = "Species"))
#> 37. │ └─testthat:::expect_condition_matching(...)
#> 38. │ └─testthat:::quasi_capture(...)
#> 39. │ ├─testthat (local) .capture(...)
#> 40. │ │ └─base::withCallingHandlers(...)
#> 41. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
#> 42. ├─dar::add_tax(test_prep_rec, tax_info = "Species")
#> 43. └─dar::add_tax(test_prep_rec, tax_info = "Species")