Array workflow

[schwarzmeyer]

Workflow to implement the exposure analyses using arrays

[carlosgjs]

instead of a boolean monthly, it could be useful to have a mode argument that can be set to "monthly" or "extreme", which allows for additional calculations to be added without changing the interface

[schwarzmeyer]

Agreed.

[schwarzmeyer]

Actually R/exposure_fast.R should be replaced by array_workflow/exposure.R. I’ve added the mode argument in the latter.

[carlosgjs]

Sounds good. Then this file will get removed?

[carlosgjs]

Is this a duplicate of R/array_to_tibble.R? can it be removed?

[schwarzmeyer]

Yes, R/array_to_tibble.R can be removed. Please keep the code from the array_workflow/code folder.

[carlosgjs]

Ok great. In that case please remove it from your branch so it doesn't get merged upon completion of your PR

[carlosgjs]

this could source R/array_to_tibble.R instead right? Using the common functions would shorten and simplify this script.

[carlosgjs]

Actually, how's is this different from scripts/array_workflow.R?

[schwarzmeyer]

scripts/array_workflow.R is an updated, cleaner version of the array_workflow/code/array_to_tibble_workflow.R. It basically shows how all the functions work together. That pdf document I shared on slack is based on the scripts/array_workflow.R. Is this script useful for you?

[carlosgjs]

Similar to the previous comment, please remove array_workflow/code/array_to_tibble_workflow.R from your branch so it doesn't get merged upon completion of your PR

Basically the aim is to not have duplicate code merged into the main branch.

[carlosgjs]

looks like tier_1 folder needs to be removed, it's already under data-raw

[carlosgjs]

@schwarzmeyer

[carlosgjs]

Also array_workflow/ needs to be removed

[carlosgjs]

@schwarzmeyer

[carlosgjs]

@schwarzmeyer you can test the yearly workflow with test data with:

Rscript scripts/main.R exposure --input_yml data-raw/shp_config.yml --workers 1

Currently this fails with:

ℹ Loading biodiversityhorizons
Error in `load_all()`:
! Failed to load R/species_threshold.R
Caused by error:
! object 'climate' not found
Backtrace:
     ▆
  1. ├─global run_exposure(args)
  2. │ └─global exposure_workflow(...)
  3. │   └─devtools::load_all()
  4. │     └─pkgload::load_all(...)
  5. │       └─pkgload::load_code(path, quiet = quiet)
  6. │         ├─withr (local) withr_with_dir(path, source_many(paths, encoding, env))
  7. │         │ └─base::force(code)
  8. │         └─pkgload:::source_many(paths, encoding, env)
  9. │           ├─rlang::try_fetch(...)
 10. │           │ ├─base::tryCatch(...)
 11. │           │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12. │           │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13. │           │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 14. │           │ └─base::withCallingHandlers(...)
 15. │           └─pkgload:::source_one(file, encoding, envir = envir)
 16. │             └─base::eval(expr, envir)
 17. │               └─base::eval(expr, envir)
 18. │                 └─base::array(...)
 19. └─base::.handleSimpleError(...)
 20.   └─rlang (local) h(simpleError(msg, call))
 21.     └─handlers[[1L]](cnd)
 22.       └─pkgload:::handle_source_error(cnd, file)
 23.         └─cli::cli_abort(msg, parent = cnd, call = quote(load_all()))
 24.           └─rlang::abort(...)
 25. ```