Array workflow #113
Array workflow #113
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…e using monthly climate data
feat: function to summarize results added
…_range.R, but faster
| #' @export | ||
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| exposure_fast <- function(species.names, species.data, climate.data, niche.data, monthly = TRUE){ |
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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
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Actually R/exposure_fast.R should be replaced by array_workflow/exposure.R. I’ve added the mode argument in the latter.
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Sounds good. Then this file will get removed?
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| #' Transform climate data in array format to tibble format | |||
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Is this a duplicate of R/array_to_tibble.R? can it be removed?
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Yes, R/array_to_tibble.R can be removed. Please keep the code from the array_workflow/code folder.
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Ok great. In that case please remove it from your branch so it doesn't get merged upon completion of your PR
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| # here I will convert the array into a tibble | ||
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| lons <- climate$lon + 0.5 |
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this could source R/array_to_tibble.R instead right? Using the common functions would shorten and simplify this script.
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Actually, how's is this different from scripts/array_workflow.R?
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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?
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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.
Remove duplicated version of array_to_tibble.R
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| # pixi environments | |||
| .pixi | |||
| *.egg-info | |||
| .Rproj.user | |||
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This has a conflict with the main branch because additional lines were also added there. Looks like what you want is to keep both sets of changes. Here are general instructions on resolving conflicts. But basically you want to keep both changes, i.e.
From this:
.pixi
*.egg-info
<<<<<<< array_workflow
.Rproj.user
# tier_1 file that exceedes 25Mb
tier_1/data/climate/historical_array.rds
=======
outputs/
*.DS_Store
# Ignore processed species files
data-raw/bien_ranges/processed/
>>>>>>> main
Just remove the conflict markers to get to this:
.pixi
*.egg-info
.Rproj.user
# tier_1 file that exceedes 25Mb
tier_1/data/climate/historical_array.rds
outputs/
*.DS_Store
# Ignore processed species files
data-raw/bien_ranges/processed/
Workflow to implement the exposure analyses using arrays