Restructure of Merow analysis
timcdlucas opened this issue · comments
I can't remember if I explained this somewhere.
I decided it was easier to use LocalOccurrenceData and LocalRaster rather than defining new modules for these two data sets.
Part of that was that I couldn't get Bioclim from the Bioclim module to align with the occurrence data (see #7).
Furthermore we're going to be defining a few new modules for this analysis anyway.
MaxLike, PointBiserialCorr and Transform.
Perhaps MaxLike is the best one to include the code for in the paper.
Finally, with respect to the code, there the "plan" workflow in chunk merowworkflow.
This is no evaluated as it doesn't work.
Then I was trying to bring the workflow in merowWorkingCopy up to date with the plan.
This chunk is evaluated.
Hope that all makes sense!
Cool, thanks Tim.
I was avoiding doing the maxlike module in the paper because I actually had to rewrite the model from scratch (annoyingly the package only handles raster/coordinate data and does it all in one big function), so it's a pretty long module.
Will have a look at tjose data tomorrow and see what's up and what the best compromise is.
I also realise I never pushed the maxlike module to the repo. Will do that too.
After a lot of digging around, I managed to work out the coordinate reference system for these data.
The lat/longs are a red herring. They use those as covariates so they've been centred and scaled against something. The X and Y give projected coordinates (in metres). Through a lot of trial and error and googling possible coordinate systems, I stumbled upon this metadata for a derivative data version
which implies this proj4 code: +proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +datum=NAD83 +units=m +no_defs
(A version of the Albers Equal Area projection, with datum near the southernmost point of Texas)
Setting that as the initial CRS, and converting into lat/longs gives us something that lines up with the USA. Phew.
I'll work that into the module code for these data and upload - I'd rather have all modules for the paper, it's more zoony.
Thanks! I'm so glad I don't have to deal with this again.
fixed, as in #7