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Messages - Jonathan S. Clough

#61
Using SLAMM / Re: category error
September 21, 2016, 06:46:32 AM
Mary-- thanks so much for the follow-up.  We have been chasing deadlines here in Vermont so I just had a chance to come in today to answer and was happy to see that it had been resolved.

One of the tests that we performed for SLAMM 6.7 was to reproduce results from previous versions after a fairly major rewrite to the core procedures (to allow categories to be flexible and add a new California category set).   While there may still be some glitches, I am hopeful that the new version is fairly stable at this point.  The code re-write should allow us to bring the capability to edit category types and the "succession flow chart" in the near future.

Please let us know if you have further questions and my apologies about the delay in responding.
#62
Written by Warren Pinnacle Consulting, Inc. scientists.  The paper is open access:

http://www.sciencedirect.com/science/article/pii/S1364815216302705

Highlights
• Marsh fate modeling was applied to coastal NY State at a 5 m horizontal resolution.
• Simulation results predict extensive marsh losses in microtidal regimes.
• Results also indicate changes in the composition of marsh types.
• An uncertainty estimation of model results was also reported on.
• Uncertainty results suggest output variability is primarily due to SLR signal.

Abstract

The Sea-Level Affecting Marshes Model was applied to coastal New York State at a 5 m horizontal resolution to investigate marsh conservation and potential migration under multiple sea-level rise scenarios. Feedbacks between sea-level rise and marsh accretion rates based on mechanistic modeling were included. Simulation results predict extensive marsh losses in microtidal regimes behind the barrier islands of Long Island, vulnerable dry lands on barrier islands, and opportunities for upland migration of coastal marshes. Results also indicate changes in the composition of marsh types. Confidence of predictions due to model parameter variabilities and spatial data error were estimated with the uncertainty estimation module. Likelihood maps of land cover changes were produced. Uncertainty results suggest that variability in land cover projections is mostly due to the wide range in potential sea-level rise signals by 2100 while impact from uncertainties in model parameters, spatial data errors and linked models is less significant.
#63
Dear Colleague,

We are pleased to announce a webinar to present the results of our updated Sea Level Affecting Marshes Model (SLAMM) to work more effectively in California Estuaries.

This webinar is open to the public so we encourage you to share the link to thee webinar (below) widely with any interested colleagues.

Project Overview

The Nature Conservancy (TNC) funded Warren Pinnacle Consulting Inc. (WPC) and Environmental Science Associates (ESA) to collaborate with us on an initial phase to revise SLAMM for California estuaries by updating the habitat classifications, conceptual models, and decision tree pathways for multiple types of California estuaries including seasonally closed.

The Sea Level Affecting Marshes Model (SLAMM) (http://warrenpinnacle.com/prof/SLAMM/ ) has proven useful in other geographies to assess the vulnerability of coastal habitats to sea level rise and to identify marsh migration pathways. Its relative simplicity and modest data requirements allow application at a reasonable cost. SLAMM uses topography and parameterized physical conditions to predict the evolution of marsh habitats in response to sea level rise. The model does this by traversing a decision tree simulating changes in tidal marsh area and habitat type in response to long-term sea-level rise by accounting for five dominant processes involved in wetland conversion: inundation, erosion, overwash, saturation, and accretion. The model uses a complex decision tree that incorporates both geometric and qualitative relationships to model habitat conversions in coastal habitats through spatial relationships (e.g. adjacency, elevation). The decision tree was developed for the Georgia and South Carolina coasts and therefore works well for East and Gulf Coast estuaries.

However, until now SLAMM has not had the correct habitat types, physical processes, or decision tree pathways to properly model marsh transitions in response to sea level rise for many West Coast estuaries.

We drew from the Inventory and Classification of West Coast Estuaries to develop this SLAMM update for the three different Coastal and Marine Ecological Classification Standard (CMECS) estuarine classes: Embayment, Riverine, and Lagoonal. For this, "Phase I," we developed physical conceptual models, ecological conceptual models and decision tree pathways to be incorporated into SLAMM to model marsh response to sea level rise for each of these classes of California estuaries. We used best available data from representative California estuaries to explore relationships between GIS data inputs into SLAMM to help develop our physical and ecological conceptual models and decision tree pathways. We worked closely with NWI and other experts to crosswalk NWI categorization into SLAMM habitats. We also received great peer-review across expertise to improve our update to SLAMM to work for California estuaries. As a result, SLAMM 6.7 works for the great diversity in estuary type and morphology found along California's diverse coast. Other updates included in the new versions of SLAMM include: editable sea level rise curves, "Run-record" file, improved modeling of marsh erosion, and quantification of carbon sequestration for different scenarios.

We look forward to presenting these and other updates to SLAMM to you in the webinar 9:30-11:00 a.m. PST, Thursday July 28, 2016.

Webinar info is below please allow time to download any software plug-ins necessary.

...

Join Skype Meeting      

https://meet.lync.com/thenatureconservancy462/wheady/5K81KRN7


#64
I will look into this question.  If you have a chance please email me some screen captures highlighting the problem as that will speed debugging.  Thanks!  -- Jonathan
#65
Using SLAMM / Re: Time zero crash
March 23, 2016, 06:34:53 AM
1. This is a known bug.  Actually, rather than fixing it in the current version we've removed that check box given that Time-Zero runs are an important step that should not be jumped over in model setup or application.

2. It will save a bit of computational time, but that doesn't seem a good excuse to skip a step that can be used either to a.) test the model setup with regards to tide ranges, wetland maps, and wetland elevation maps, or b.) adjust the model so that all predictions after time zero are a function of SLR, not a function of data error at setup.

3. The time-zero step forms the bases for subsequent steps.  Because there is no SLR at time-zero, any changes here are due to horizontal or vertical data error, or some fringe of wetlands extending outside of their expected range.  Therefore if the model is to determine the effects from SLR, model results should be run from time zero and results should be interpreted from time-zero forward rather than from initial condition forward.

Hope this is useful -- J
#66
Using SLAMM / Re: problem in running simulation
March 05, 2016, 12:07:56 PM
Hi Patricia: 

Welcome.

First of all, all of your input files must be ESRI ASCII Rasters (format specified at the end of the tech doc) and they must all have the same cell size, number of rows and columns and lower-left corner statistics.  In other words, the spatial aspect of all cells in all inputs must be identical.

If this is not your problem, feel free to zip up your SLAMM6 file and Rasters and send them to us and we'll be able to quickly pinpoint the problem.

You should always go through the set map attributes button and QA/QC your maps and spatial-data setup before running a simulation.  All parameters must be specified (i.e. you cannot leave anything as zero as a default, especially not dates).  You must have a valid relationship between wetland maps, elevation maps, and tide ranges to get anything useful out of your simulation.  This is a very important step and once you have your files properly specified I can provide more details about how you test the model setup.

Best regards -- Jonathan
#67
Using SLAMM / Re: SLAMM in Linux
January 12, 2016, 10:50:19 AM
We have run large jobs using a parallel-processing version that we execute on a 32-processor Windows server.  The software is not currently cross-platform compiled, however.  All compiled versions that I know of require Windows. 

If you don't output maps to Microsoft Word, though, there's not much interface with the OS other than binary and text file reading and writing.  Therefore it should be compilable on an alternative platform without too much difficulty. 

You'd have to do that yourself with the open-source code for now.  To create a Linux-native version would likely require compiling with Lazarus for Free Pascal.   We originally tried to create a 64-bit version on that software but found the compiler to be quite buggy and we lost a lot of time going down that dead end.  However, that was 6 years ago and the open-source compiler has likely improved in the interim.

Oh, I'm remembering now that we did have some researchers run it in Linux using the "wine" software but we haven't done that yet ourselves.  They had success, though and wrote a paper about their work.  (http://ascelibrary.org/doi/abs/10.1061/41114(371)477)
#68
We are pleased to announce a symposium on  SLAMM: "the maturation of a landscape-ecologic model," part of the International Society for Ecological Modelling Global Conference 2016 in Baltimore MD, on May 8-12 of 2016.

http://www.isemconference.com/symposia-slamm.asp

The deadline to submit an abstract for the symposium on is Oct 16.  http://www.isemconference.com/submit-abstract.asp

Early registration deadline is Dec. 18 and the early registration fee is $520; after that date the standard fee will be $620; the standard student fee is $300. We anticipate fruitful interactions among participants as part of the symposium. Unfortunately, the field trip to Blackwater Wildlife Refuge has fallen through, but if there is interest, we may be able to prepare a guide for a self-guided tour.

We hope to see and meet many SLAMM users there.
#69
Using SLAMM / Re: Cell definition
May 22, 2015, 06:49:01 AM
We have never seen what you refer to in observation (1).  In my experience, SLAMM does not lose or gain grid cells.  Can you show us an example of this symptom?

With respect to (2), which decimal place?  Is this machine accuracy?  To save memory space, SLAMM utilizes single-precision mathematics.

Best regards -- Jonathan
#70
Model Formulation & Parameters / Re: Uplift
April 29, 2015, 07:11:56 AM
The local historic trend is compared to the global trend and global SLR scenarios are adjusted into the future ("localized") based on the difference between the local historic trend and the global trend.  Therefore, any eustatic SLR projection may be used.   
#71
Model Formulation & Parameters / Re: Tidal Creek
April 29, 2015, 07:04:50 AM
Yes.  Tidal Creek is not converted.
#72
Model Formulation & Parameters / Re: Uplift
April 23, 2015, 02:03:10 PM
The advantage to the uplift raster is the capability to model spatially variable uplift on a cell-by-cell basis, if you have that type of data.  Otherwise using the historical trend parameter (that can be varied by "sub-sites" that are polygons drawn within the study area) will give you the same results.  Best -- Jonathan
#73
Model Formulation & Parameters / Re: Tidal Creek
April 23, 2015, 09:53:25 AM
For the most part in interpreting SLAMM results we have lumped all saline open water together, despite the three classes included therein --

Estuarine Open Water, Open Ocean, Tidal Creeks,

The definition between Estuarine open water and Open Ocean is largely one of surrounding land masses:  From USFWS "The Estuarine System describes deepwater tidal habitats and adjacent tidal wetlands that are influenced by water runoff from and often semi-enclosed by land. They are located along low-energy coastlines and they have variable salinity."

Certainly some estuarine open water could be converted to open ocean through SLR, but there are some judgement calls required in terms of how much barrier island loss would be required before that occurs.  So we do not convert water in this manner.

In terms of tidal creeks, this is a very rare category and there is no attempt in the model to determine whether it is converted.  There are only 4 NWI categories in our crosswalk that result in tidal creek and they all seem to be obsolete based on the wetland code interpreter:  https://www.fws.gov/wetlands/Data/Wetland-Codes.html   We therefore make no attempt to determine when a tidal creek may then convert to estuarine open water (or riverine tidal?).

The model does predict when inland open water will be breached with salinity, but in terms of other open water categories it's best to assume that the model is not very precise in determining which type of open water category will occur into the future.
#74
Model Formulation & Parameters / Re: Uplift
April 23, 2015, 09:39:15 AM
Hello and welcome to the SLAMM Forum.

This would be a misinterpretation of the historical trend parameter, though you are correct that it can be related to local subsidence.

The historical trend parameter was designed to accept data from local NOAA gauges measuring long term SLR trends.  This input would then be compared to eustatic long term SLR trends.  If you assume a global (eustatic) historic trend of 1.7 mm/yr global historic trend based on IPCC (2007), then a site with no local subsidence or uplift or other local factors affecting SLR (water temperatures or regional weather patterns) would be expected to have a historical trend that is also 1.7.    Please see equation (2) in the Technical Documentation..

In other words, in SLAMM 6.2, if you add a historic trend parameter of 1.7 mm/year then local and global SLR would be assumed to be equal in projections.

If you have uplift of 0.5 mm/year in your location then you would expect a local gauge to have registered a long-term SLR of closer to 1.2 mm/year.  Therefore, if you want to reflect uplift of this extent you should use that value in the parameter.

I hope this is useful.  -- Jonathan
#75
My coworkers also point out that tide ranges need to be properly parameterized!  -- Jonathan