Improve the Linkage Priority User Guide for Version 3.1 or later

[johngallo]

• [ ] Add a section after 10.3 on if we maximize for climate analogs, and for ifg we maximize for climate gradients.
• [ ] Mae the bibliography have a consistent format
• [ ] consider adding a screengrab of default parameters in section 4
• [ ] consider indicating which paramater values are changed from run to run for all steps of the tutorial, not just the ones with red boxes
• [ ] add more detail on how to include expert opinion
• [ ] screengrabs of parameters in section 10: shoudl it be lp_resistances.tif ? Most users will figure this out if they even notice...
• [ ] double check that there is an issue created for making a copy of the core input class and in the copy pasting in all the new fields, such as cav
• [ ] log an issue to make CF_Central lowercase to be more consistent with the rest
• [ ] clarify that cores with donut holes, especially lots of them, may cause Linkage Priority Tool to fail. (see 12/8 comment below)
• [ ] update the multicriteria diagram to include core area, see 10/24/23 comment below.

Figure is at https://app.diagrams.net/#G0B6x6qJKMGdJhczMxV1Z2dUhXUDA

[johngallo]

Also, put a trouble shooting "bomb" icon in (from Linkage Mapper user guide) in the section about making your core areas. Apparently, if your core area has lots of holes in it, (or possibly a very fine/smooth curved boundary too) then it fails. Ask for the the detailed dialog between Beta Tester Jon Cole and John Gallo in Dec 2021 for more details. In sum, from Jon: "Within the user set parameters of CoreMapper I had set the average habitat pixel value and the per-pixel value at 0.6 – which I thought would give the most realistic visualisation of fragmentation within the habitat patches. However, it also made them very complex and full of Swiss cheese holes and a very high edge to core ratio. When I reduced the per pixel value to 0 it created hole-less and smooth patches and allowed LinkageMapper to run all of the species in both time points. " ALSO, ideally we also fix this issue in the code, or at the very least add an error message along these lines if it fails at that point. I believe his cores worked for linkage pathways.

[johngallo]

Fix an error in the multicriteria diagram. Core area value is currently missing the "Area of Core" criteria.

For now, I'll add it into the folder of the beta version as a standalone diagram. See also v2Part4 https://drive.google.com/file/d/0B6x6qJKMGdJhczMxV1Z2dUhXUDA/view?usp=sharing&resourcekey=0-Q8opHRGxuwqzmVgv9VHwgg

[johngallo]

Also, put a trouble shooting "bomb" icon in (from Linkage Mapper user guide) in the section about making your core areas. Apparently, if your core area has lots of holes in it, (or possibly a very fine/smooth curved boundary too) then it fails. Ask for the the detailed dialog between Beta Tester Jon Cole and John Gallo in Dec 2021 for more details. In sum, from Jon: "Within the user set parameters of CoreMapper I had set the average habitat pixel value and the per-pixel value at 0.6 – which I thought would give the most realistic visualisation of fragmentation within the habitat patches. However, it also made them very complex and full of Swiss cheese holes and a very high edge to core ratio. When I reduced the per pixel value to 0 it created hole-less and smooth patches and allowed LinkageMapper to run all of the species in both time points. " ALSO, ideally we also fix this issue in the code, or at the very least add an error message along these lines if it fails at that point. I believe his cores worked for linkage pathways.

Jamie from CLT had a similar issue as above, but it was due to "simplify polygons" used in the cores and not the resistance, yielding areas of core overlapping null values. Solved this with an intersect. Could have been Jon's problem.