New Forestry Routine Features

[crollinson]

Description

Two main changes to the forestry routines:

1. New IANTH setting where 2 means f_vbh becomes the fraction area harvested rather than trying to achieve biomass harvest targets. (It's hard to set a biomass harvest target when you're not sure what the long-term productivity will be -- much easier to think about areas harvested.)
2. Add code to allow harvest to occur below DBH threshold to better facilitate selective harvesting regimes like understory thins or timber improvement thins.

This also begins to reconcile differences in the implementation of the plantation code, following what @mpaiao had done. "Secondary" forest is now references plantations in most parts of the LU code, although I have not reviewed/modified plantation behavior while "primary" forest is just natural forest.

Note: There are more changes coming eventually, including updates to the plantation schemes and potential to have multiple management schemes operating at once. Plantation updates probably within the next 6 months, multiple management is a long ways off.

Collaborators

Most of what I did is operationally or conceptually consistent with what Marcos Longo (@mpaiao) did a long time ago that never got pulled into the mainline.

Motivation and Context

These changes are to facilitate work of an NSF-funded project focused on interactions between forest management & climate change. These changes should help make ED behavior more compatible with how US forest managers think about harvesting routines by adding more control.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Other (fix or feature that would cause existing functionality to change)
  NOTE: Headers for land use drivers will need to be updated to add 2 lines for the harvest rates below the DBH threshold. See example. Based on what I could find, LU driver templates are not currently in any of the ED folders nor test cases, but I can provide one if necessary.

Checklist:

• My change requires a change to the documentation.
• I have updated the documentation accordingly.
• I have added tests to cover my changes.

Testing :

• All new and existing tests passed.
  None of the routine ED tests include land use change or forest harvesting. However, here are two files showing change in AGB and stem density in a short test of different selective harvests that I ran.

HarvestDifferences_AGB.pdf
HarvestDifferences_Density.pdf

Code for above tests at Willow Creek with ED2INs & LU drivers associated with above can be found here: https://github.com/MortonArb-ForestEcology/MANDIFORE_modeling/tree/master/WCr_Test_UnderstoryThin

[mpaiao]

@crollinson Just to give feedback on this merge. We discussed this merge at the ED2 workshop, and we will merge once the ED-2.2 merge is incorporated into the mainline.

[mdietze]

Just wanted to follow up on this PR. @crollinson there's now a lot of conflicts after we pulled in @mpaiao ED2.2 release code. Wanted to check in to see when you think you'll get to those.

[mpaiao]

I started to look into and work on this merge, but I will be quite busy in the next two weeks. I don't anticipate this being a difficult merge — the conflicts look big, but it's more that the code was restructured (especially ed_params.f90) and the changes are in different locations. It will require some manual merge, though, and I will likely need help from @crollinson to make sure we don't miss anything in the process.

[crollinson]

I'll try to do this Monday next week -- this week is not going to be a good week.

[mpaiao]

@crollinson I am going through the code merging but this part is a bit confusing to me, and I think this approach here may be saving too many trees. In my original implementation, harvprob is used to define the disturbance rate. In general, survivorship should reflect the survivorship in the immediate vicinity of disturbed area (in this case, where the tree was logged), which is why survivorship was set to zero. For the time being I kept your approach for the area-based option (ianth_disturb=2), but I am not sure how to reconcile this part with the original survivorship definition, especially with understory thinning.

[mpaiao]

The only idea I had so far is to create a new dist_type for thinned canopy. The upside is that it would be consistent with the ED idea that disturbances change the microenvironment (in the case of thinning, more in the water part than in the light). The one potential downside is that we would have more dist_types (tree felling, skid trails and roads, and artificially thinned canopy).

I don't see a problem to add a new dist_type if it is justified, but before I go ahead, I'd like to throw the idea and see what people think, or if anyone has other ideas.

[mpaiao]

@crollinson After a very long delay, I went through your pull request. I think it looks great, but over the years there were quite a few code conflicts. I made a pull request to your branch that merges the nearly-current mainline (except #424). Most of the conflicts were trivial, but I did suggest a somewhat different approach for canopy thinning.

Basically I made canopy thinning as a different disturbance type, so we can keep track of their post-treatment recovery, but by doing so, I changed the mortality/survivorship logic too. I know now it is an hectic time with AGU and holidays, but if you have time early next year, could you please take a look? Thanks!

The number of files that changed was rather horrifying (607!!), but there are far fewer with actual changes. You can basically ignore everything that is in R or in BRAMS, as I plan to drop these files from the ED2 distribution (as per issue #423) if others agree.

[mpaiao]

@crollinson Just checking if you would have time at some point to double check the proposed changes, so I can merge this PR to the main distribution of ED2. Thanks!

[crollinson]

@mpaiao I'll try to take a look at this next week.

[crollinson]

@mpaiao -- sorry it's taken me a while to get to this. I think I reviewed and approved all of the merge conflicts, but let me know if I messed it up. I think your skid trail stuff has similar logic as an understory harvest or at least close enough, but I can always make changes and submit a clean PR in the future if I need to tweak forestry routines again in the future.

[mpaiao]

Thanks for reviewing it @crollinson! Indeed I agree the skid trail disturbance is similar to the canopy thinning. The only reason why I kept them separate is that they may have different survivorships. That said, keeping them separate has the added cost of more patches and the different dist_type flags, which may prevent merging them.

I will go ahead and merge it, but I will try to get back to this in the upcoming weeks. We currently have a statement that allows merging non-managed patches of different dist_type once they are sufficiently old, but the age threshold is rather long for patches created with disturbances that mostly impact the under storey.

[mpaiao]

I am revising it more closely, and I think something is missing: I do not see the canopy thinning additions anymore. I am wondering if they somehow disappeared, or if this is what you meant by I think your skid trail stuff has similar logic as an understory harvest or at least close enough.

I actually had made a pull request to your branch that deconflicted the mainline with your branch, I wonder if this is somehow in there only. Sorry to ask again, would you mind double checking the code? I just want to make sure your changes are incorporated to the mainline. Thanks!

[crollinson]

Okay, I see what happened now -- I didn't realize there was a pull request on my branch and got confused with what was what and what needed to be done. Sorry about that! Yeah, that never got pulled in, so I think I ended up reverting most of my changes. 🤦‍♀️

Can I roll back my branch and then merge your pull request? I've never done a complicated pull request like this before.

The code I implemented allowed for 2 kinds of thinning: 1) Canopy thinning where you remove big trees (harvest rate above size threshold); 2) Understory thinning where you removed small trees (harvest rate below size threshold). Both are very common in US forestry. The understory thin logic was kinda similar to your skid trails, but with a couple differences and very different description. Both kinds were primarily applied on a per area basis since having a biomass threshold for forestry didn't make sense when you were designing schemes out for the future and didn't have biomass or basal area targets.

[mpaiao]

@crollinson No worries at all! Sure, please go ahead and roll back your branch and merge the pull request. If you have not attempted any rebasing, I think something like:

git reset --hard a04d89c should uncommit ba0b54b and roll back to the latest commit you had when you originally submitted this pull request (a04d89c). But please double check the command and the version, because git reset --hard is not reversible and well into the dangerous zone. Then you should be able to merge my PR onto your branch, and we can go from there.

As per the area based vs. mass based, I am 100% onboard, most future logging scenarios for the Amazon don't have biomass targets either. And the canopy thinning is something I had set aside, but is quite common in the tropics, so your PR will be very useful for tropical forestry too.