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IBEEM-MSU / ibeem_variability

Code for Youngflesh et al. In Review
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BLIDs vs. BTIDs #6

Closed kellykapsar closed 6 months ago

kellykapsar commented 6 months ago

In script 6a, the bird data are loaded in by "BLIDsPiece-XX.rda" (https://github.com/IBEEM-MSU/ibeem_variability/blob/ef626b11aaea2a0e1320063bffd21774ac3f4841/Scripts/6-rasterize/6a-raster-compile.sh#L8)

However, when the pieces were created in 3a, we used "BTIDsPiece-XX.rda" (https://github.com/IBEEM-MSU/ibeem_variability/blob/ef626b11aaea2a0e1320063bffd21774ac3f4841/Scripts/3-extract-species-env/3a-split-sp-ids-birdtree.R#L24)

Given that birdtree is the master taxonomy, I'm assuming it should be BTIDs in script 6?

kellykapsar commented 6 months ago

Also, as I'm testing the loop for rasterizing breeding ranges in 6a, there are a couple of IDs that don't have associated shapefiles (Ex: 842, 897). Any idea why? I've added some code to just document that in the slurm output, but wasn't sure if it's an issue that they're missing or if they were just removed at some point.

caseyyoungflesh commented 6 months ago

In script 6a, the bird data are loaded in by "BLIDsPiece-XX.rda" (

https://github.com/IBEEM-MSU/ibeem_variability/blob/ef626b11aaea2a0e1320063bffd21774ac3f4841/Scripts/6-rasterize/6a-raster-compile.sh#L8 )

However, when the pieces were created in 3a, we used "BTIDsPiece-XX.rda" (

https://github.com/IBEEM-MSU/ibeem_variability/blob/ef626b11aaea2a0e1320063bffd21774ac3f4841/Scripts/3-extract-species-env/3a-split-sp-ids-birdtree.R#L24 )

Given that birdtree is the master taxonomy, I'm assuming it should be BTIDs in script 6?

Good catch. That's right! Should be BTID in script 6. That shouldn't change any results.

caseyyoungflesh commented 6 months ago

Also, as I'm testing the loop for rasterizing breeding ranges in 6a, there are a couple of IDs that don't have associated shapefiles (Ex: 842, 897). Any idea why? I've added some code to just document that in the slurm output, but wasn't sure if it's an issue that they're missing or if they were just removed at some point.

I think 6a L64 should actually be the below (which is from 3b L76). The issue is likely the name mismatch between Birdtree (what we ended up using) and the version of the taxonomy that we used initially. This shouldn't change anything about the results as this was just for the rasters (as above). 

  curr.range <- sf::st_read(paste0(dir, 'data/L1/range/bird-breeding/birdtree-', 
                                   curr.sp, '-breeding.shp'),
                            quiet = TRUE)

L144 at 1c creates the BirdLife (rather than Birdtree) taxonomy version which it was trying to read in.

kellykapsar commented 6 months ago

Fixed in 76f481c