Tag: MichiganUP

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Forest gap regeneration modelling

Last week the second of two papers describing our forest tree regeneration, growth, and harvest simulation model was published in Ecological Modelling. These two papers initially started out as a single manuscript, but on the recommendation of a reviewer and the editor at Ecological Modelling we split that manuscript into two. That history explains why this second paper to be published focuses on a component of the integrated model we presented a couple of months ago.

There’s a nice overview of the work these two papers contribute to on the MSU Center for System Integration and Sustainability (CSIS) website, and abstracts and citations for both papers are copied at the bottom of this blog post. Here I’ll go into a little bit more detail on the approach to our modelling:

“The model simulates the initial height of the tallest saplings 10 years following gap creation (potentially either advanced regeneration or gap colonizers), and grows them until they are at least 7 m in height when they are passed to FVS for continued simulation. Our approach does not aim to produce a thorough mechanistic model of regeneration dynamics, but rather is one that is sufficiently mechanistically-based to allow us to reliably predict regeneration for trees most likely to recruit to canopy positions from readily-collectable field data.”

In the model we assume that each forest gap contains space for a given number of 7m tall trees. For each of these spaces in a gap, we estimate the probability that it is in one of four states 10 years after harvest:

  1. occupied by a 2m or taller sugar maple tree (SM)
  2. occupied by a 2m or taller ironwood tree (IW)
  3. occupied by a 2m or taller tree of another species (OT)
  4. not occupied by a tree 2m or taller (i.e., empty, ET)

To estimate the probabilities of these states for each of the gap spaces, given different environmental conditions, we use regression modelling for composition data:

“The gap-level probability for each of the four gap-space states (i.e., composition probabilities) is estimated by a regression model for composition data (Aitchison, 1982 and Aitchison, 1986). Our raw composition data are a vector for each of our empirical gaps specifying the proportion of all saplings with height >2 m that were sugar maple, ironwood, or other species (i.e., SM, IW, and OT). If the total number of trees with height >2 m is denoted by t, the proportion of empty spaces (ET) equals zero if t > n, otherwise ET = (n − t)/n. These raw composition data provide information on the ratios of the components (i.e., gap-space states). The use of standard statistical methods with raw composition data can lead to spurious correlation effects, in part due to the absence of an interpretable covariance structure (Aitchison, 1986). However, transforming composition data, for example by taking logarithms of ratios (log-ratios), enables a mapping of the data onto the whole of real space and the use of standard unconstrained multivariate analyses (Aitchison and Egozcue, 2005). We transformed our composition data with a centred log-ratio transform using the ‘aComp’ scale in the ‘compositions’ package (van den Boogaart and Tolosana-Delgado, 2008) in R (R Development Core Team, 2009). These transformed data were then ready for use in a standard multivariate regression model. A centred log-ratio transform is appropriate in our case as our composition data are proportions (not amounts) and the difference between components is relative (not absolute). The ‘aComp’ transformation uses the centred log-ratio scalar product (Aitchison, 2001) and worked examples of the transformation computation can be found in Tolosana-Delgado et al. (2005).”

One of the things I’d like to highlight here is that the R script I wrote to do this modelling is available online as supplementary material to the paper. You can view the R script here and the data we ran it for here.

If you look at the R script you can see that for each gap, proportions of gap-spaces in the four states predicted by the regression model are interpreted as the probability that gap-space is in the corresponding state. With these probabilities we predict the state of each gap space by comparing a random value between 0 and 1 to the cumulative probabilities for each state estimated for the gap. Table 1 in the paper shows an example of this.

With this model setup we ran the model for scenarios of different soil conditions, deer densities, canopy openness and Ironwood basal area (the environmental factors in the model that influence regeneration). The results for these scenarios are shown in the figure below.


Hopefully this gives you an idea about how the model works. The paper has all the details of course, so check that out. If you’d like a copy of the paper(s) or have any questions just get in touch (email or @jamesmillington on twitter)

Millington, J.D.A., Walters, M.B., Matonis, M.S. and Liu, J. (2013) Filling the gap: A compositional gap regeneration model for managed northern hardwood forests Ecological Modelling 253 17–27
doi: 10.1016/j.ecolmodel.2012.12.033
Regeneration of trees in canopy gaps created by timber harvest is vital for the sustainability of many managed forests. In northern hardwood forests of the Great Lakes region of North America, regeneration density and composition are highly variable because of multiple drivers that include browsing by herbivores, seed availability, and physical characteristics of forest gaps and stands. The long-term consequences of variability in regeneration for economic productivity and wildlife habitat are uncertain. To better understand and evaluate drivers and long-term consequences of regeneration variability, simulation models that combine statistical models of regeneration with established forest growth and yield models are useful. We present the structure, parameterization, testing and use of a stochastic, regression-based compositional forest gap regeneration model developed with the express purpose of being integrated with the US Forest Service forest growth and yield model ‘Forest Vegetation Simulator’ (FVS) to form an integrated simulation model. The innovative structure of our regeneration model represents only those trees regenerating in gaps with the best chance of subsequently growing into the canopy (i.e., the tallest). Using a multi-model inference (MMI) approach and field data collected from the Upper Peninsula of Michigan we find that ‘habitat type’ (a proxy for soil moisture and nutrients), deer density, canopy openness and basal area of mature ironwood (Ostrya virginiana) in the vicinity of a gap drive regeneration abundance and composition. The best model from our MMI approach indicates that where deer densities are high, ironwood appears to gain a competitive advantage over sugar maple (Acer saccharum) and that habitat type is an important predictor of overall regeneration success. Using sensitivity analyses we show that this regeneration model is sufficiently robust for use with FVS to simulate forest dynamics over long time periods (i.e., 200 years).

Millington, J.D.A., Walters, M.B., Matonis, M.S. and Liu, J. (2013) Modelling for forest management synergies and trade-offs: Northern hardwood tree regeneration, timber and deer Ecological Modelling 248 103–112
doi: 10.1016/j.ecolmodel.2012.09.019
In many managed forests, tree regeneration density and composition following timber harvest are highly variable. This variability is due to multiple environmental drivers – including browsing by herbivores such as deer, seed availability and physical characteristics of forest gaps and stands – many of which can be influenced by forest management. Identifying management actions that produce regeneration abundance and composition appropriate for the long-term sustainability of multiple forest values (e.g., timber, wildlife) is a difficult task. However, this task can be aided by simulation tools that improve understanding and enable evaluation of synergies and trade-offs between management actions for different resources. We present a forest tree regeneration, growth, and harvest simulation model developed with the express purpose of assisting managers to evaluate the impacts of timber and deer management on tree regeneration and forest dynamics in northern hardwood forests over long time periods under different scenarios. The model couples regeneration and deer density sub-models developed from empirical data with the Ontario variant of the US Forest Service individual-based forest growth model, Forest Vegetation Simulator. Our error analyses show that model output is robust given uncertainty in the sub-models. We investigate scenarios for timber and deer management actions in northern hardwood stands for 200 years. Results indicate that higher levels of mature ironwood (Ostrya virginiana) removal and lower deer densities significantly increase sugar maple (Acer saccharum) regeneration success rates. Furthermore, our results show that although deer densities have an immediate and consistent negative impact on forest regeneration and timber through time, the non-removal of mature ironwood trees has cumulative negative impacts due to feedbacks on competition between ironwood and sugar maple. These results demonstrate the utility of the simulation model to managers for examining long-term impacts, synergies and trade-offs of multiple forest management actions.

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Wrapping up 2012

Nearing the end of 2012 and the total number of posts on this blog has been even fewer this year than in 2011. At least I have been tweeting a bit more of late. Here’s a quick round-up of activities and publications since my last post with a look at some of what’s going on in 2013.

The Geoforum paper on narrative explanation of simulation modelling is now officially published, as is the first of two Ecological Modelling papers on the Michigan forest modelling work. Citations and abstract for both are below, and are included on my updated publications list. I’ll post more details and info on each in the New Year (promise!). I’ll likely wait to summarise the Michigan paper until the second paper of that couplet is published – hopefully that won’t be too long as it’s now going through the proofs stage.

The proceedings for the iEMSs conference I attended in Leipzig, Germany, this summer are now online. That means that the two papers I presented there are also available. One paper was on the use of social psychology theory for modelling farmer decision-making, and the model I discuss in that paper is available for you to examine. The other paper was a standpoint contribution to a workshop on the place of narrative for explaning decision-making in agent-based models. From that workshop we’re working on a paper to be published in Environmental Modelling and Software about model description methods for agent-based models. More on that next year too hopefully.

In one of my earlier posts this year I talked about agent-based modelling spatial patterns of school choice (I’ll get the images for that post online again soon… maybe). I’ve managed to write up the early stages of that work and have submitted it to JASSS. We’ll see how that goes down. I hope to continue on that work in the new year also, possibly while in New Zealand at the University of Auckland. I’ll be in Auckland visiting and working with George Perry and David O’Sullivan, with whom I published the recent Geoforum paper (highlighted above). On the way to New Zealand I’ll be stopping off in Los Angeles for the Association of American Geographers conference which I haven’t been to previously and which should be interesting.

So that’s it for 2012. A New Year’s resolution for 2013 – post at least once every month on this blog! Especially from Down Under.

Happy Holidays!

Abstracts
Millington, J.D.A., O’Sullivan, D., Perry, G.L.W. (2012) Model histories: Narrative explanation in generative simulation modelling Geoforum 43 1025–1034
The increasing use of computer simulation modelling brings with it epistemological questions about the possibilities and limits of its use for understanding spatio-temporal dynamics of social and environmental systems. These questions include how we learn from simulation models and how we most appropriately explain what we have learnt. Generative simulation modelling provides a framework to investigate how the interactions of individual heterogeneous entities across space and through time produce system-level patterns. This modelling approach includes individual- and agent-based models and is increasingly being applied to study environmental and social systems, and their interactions with one another. Much of the formally presented analysis and interpretation of this type of simulation resorts to statistical summaries of aggregated, system-level patterns. Here, we argue that generative simulation modelling can be recognised as being ‘event-driven’, retaining a history in the patterns produced via simulated events and interactions. Consequently, we explore how a narrative approach might use this simulated history to better explain how patterns are produced as a result of model structure, and we provide an example of this approach using variations of a simulation model of breeding synchrony in bird colonies. This example illustrates not only why observed patterns are produced in this particular case, but also how generative simulation models function more generally. Aggregated summaries of emergent system-level patterns will remain an important component of modellers’ toolkits, but narratives can act as an intermediary between formal descriptions of model structure and these summaries. Using a narrative approach should help generative simulation modellers to better communicate the process by which they learn so that their activities and results can be more widely interpreted. In turn, this will allow non-modellers to foster a fuller appreciation of the function and benefits of generative simulation modelling.

Millington, J.D.A., Walters, M.B., Matonis, M.S. and Liu, J. (2013) Modelling for forest management synergies and trade-offs: Northern hardwood tree regeneration, timber and deer Ecological Modelling 248 103–112
In many managed forests, tree regeneration density and composition following timber harvest are highly variable. This variability is due to multiple environmental drivers – including browsing by herbivores such as deer, seed availability and physical characteristics of forest gaps and stands – many of which can be influenced by forest management. Identifying management actions that produce regeneration abundance and composition appropriate for the long-term sustainability of multiple forest values (e.g., timber, wildlife) is a difficult task. However, this task can be aided by simulation tools that improve understanding and enable evaluation of synergies and trade-offs between management actions for different resources. We present a forest tree regeneration, growth, and harvest simulation model developed with the express purpose of assisting managers to evaluate the impacts of timber and deer management on tree regeneration and forest dynamics in northern hardwood forests over long time periods under different scenarios. The model couples regeneration and deer density sub-models developed from empirical data with the Ontario variant of the US Forest Service individual-based forest growth model, Forest Vegetation Simulator. Our error analyses show that model output is robust given uncertainty in the sub-models. We investigate scenarios for timber and deer management actions in northern hardwood stands for 200 years. Results indicate that higher levels of mature ironwood (Ostrya virginiana) removal and lower deer densities significantly increase sugar maple (Acer saccharum) regeneration success rates. Furthermore, our results show that although deer densities have an immediate and consistent negative impact on forest regeneration and timber through time, the non-removal of mature ironwood trees has cumulative negative impacts due to feedbacks on competition between ironwood and sugar maple. These results demonstrate the utility of the simulation model to managers for examining long-term impacts, synergies and trade-offs of multiple forest management actions.

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Catching up on 2012

This blog has been seriously neglected over the last six months, so there’s a lot of catching up to do here.

There’s lots of conferences and papers to list, but first I should highlight the slight difference in look of this blog and the entire website. I recently decided I was going to switch to Google sites to host www.landscapemodelling.net and move this blog from WordPress to Blogger (for multiple reasons I won’t go into here). The website is lacking many of the pages from its previous guise and the NetLogo models have been moved to openABM.org. I’m continuing to add the old (and maybe some new) content to the website but that’s likely to be a slow process (particularly given how long it’s taken me to get to write this post!). The link structure of the blog pages has changed – I think I’ve managed to change most links but there may still be some that are broken (if you find any please let me know). Many of the images are also currently missing – I’ll get to re-inserting those sometime…

I’ve managed to get to quite a few conferences this year in the US, UK and Germany.A particular highlight was getting to see my old PhD advisor George Perry in the US. George was on sabbatical at Harvard Forest and he invited me to the forest to give a seminar. It was also great to attend the 4th USFS FVS conference in Fort Collins, CO and to be one of the only four or so international attendees. There’s a list below of all the conference presentations I gave with links to the conference websites.

I’ve also been working hard to get a few papers published. The paper I’ve been working on with George and David O’Sullivan on the narrative properties of generative simulation models (i.e., agent-based models and the like) has now been accepted and is in press at Geoforum. Two papers I have been working on related to my work in Michigan have also been accepted, subject to corrections, by Ecological Modelling. The papers are closely linked, with one describing the northern hardwood forest gap regeneration model we developed and the second showing how that model can be used in the integrated model to examine trade-offs and synergies in managing for both timber and deer in the forests. The current (provisional) citations for the three papers are below. When all are available online and in print I’ll post again here with the abstracts and links to the full text (and likely tweet the links before I blog!)

I’m still working on lots of other things, including a paper on the school choice modelling I have been doing, and another paper for a special issue in Ecology and Society on feedbacks in Coupled Human and Natural Systems. I’m also preparing some exciting (I hope) new classes for the students at King’s, including a field day at Heartwood Forest and a class on GPS and mapping. More details on that to come in the future too I’m sure!

Papers
Millington, J.D.A., O’Sullivan, D., Perry, G.L.W. (in press) Model histories: Narrative explanation in generative simulation modelling Geoforum
[Online] [Geoforum]

Millington, J.D.A., Walters, M.B., Matonis, M.S. and Liu, J. (accepted) Modelling for forest management synergies and trade-offs: Tree regeneration, timber and deer; research manuscript accepted, subject to corrections, by Ecological Modelling
[Ecological Modelling]

Millington, J.D.A., Walters, M.B., Matonis, M.S. and Liu, J. (accepted) Filling the gap: A compositional gap regeneration model for managed northern hardwood forests; research manuscript accepted, subject to corrections, by Ecological Modelling
[Ecological Modelling]

Conferences
Millington, J.D.A., Walters, M.B., Matonis, M.S., Liu, J. Trade-offs in long-term forest ecosystem management: Timber, birds and deer Presented at: 19th ialeUK conference, Edinburgh, UK, September 2012
[ialeUK]

Millington, J.D.A. Using social psychology theory for modelling farmer decision-making Presented at: 6th International Congress on Environmental Modelling and Software, Leipzig, Germany, July 2012
[iEMSs 2012]

Millington, J.D.A., O’Sullivan, D., Perry, G.L.W. Narrative explanation of agent decision-making Presented at: 6th International Congress on Environmental Modelling and Software, Leipzig, Germany, July 2012
[iEMSs 2012]

Millington, J.D.A., Walters, M.B., Matonis, M.S., Liu, J. Investigating Combined Long-Term Effects of Variable Tree Regeneration and Timber Management on Forest Wildlife and Timber Production Using FVS Presented at: Fourth Forest Vegetation Simulator (FVS) Conference, Fort Collins, Colorado, April 2012
[FVS 2012]

Millington, J.D.A. Agricultural Landscape Change: Using social psychology theory in agent-based models of land-use change Presented at: US-IALE Symposium, Newport, Rhode Island, April 2012
[US-IALE 2012]

Millington, J.D.A., Walters, M.B., Matonis, M.S., Liu, J. Regeneration for Sustainability: Coordinating Long-term Forest Ecosystem Management for Timber Production and Wildlife Habitat Presented at: US-IALE Symposium, Newport, Rhode Island, April 2012
[US-IALE 2012]

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Answering forest management questions

Although I’ve been working on new ideas since leaving Michigan and returning to London about a year ago, there’s still lots to do to examining alternative forest management strategies.

Several years ago we set out to develop a simulation model that could be used to investigate the effects of interactions between timber harvest and deer browse disturbances on economic productivity and wildlife habitat. We’ve already published several papers on this work, but just before Christmas we submitted a manuscript to Ecological Modelling entitled ‘Modelling for forest management synergies and trade-offs: Tree regeneration, timber and wildlife’. In the manuscript we report error analyses of the full simulation model (which uses the USFS Forest Vegeation Simulator) and use the model to investigate scenarios of different timber and deer management actions. Our results indicate that greater harvest of commercially low-value ironwood and lower deer densities significantly increase sugar maple regeneration success over the long term.

I expect we’ll also report some of these results at the Fourth Forest Vegetation Simulator (FVS) Conference to be held in April this year in Fort Collins, CO. Our abstract, entitled ‘Investigating combined long-term effects of variable tree regeneration and timber management on forest wildlife and timber production using FVS’, has been accepted for oral presentation. It would be great to be there myself to present the paper and discuss things with other FVS experts, but I’m not sure if that will be possible. If it’s not, Megan Matonis will present as, handily, she’s currently doing her PhD in that neck of the woods at Colorado State University.

In the meantime, Megan and I are in the process of finishing off a different manuscript describing the mesic conifer planting experiment we did in Michigan. In that experiment we planted seedlings of white pine (Pinus strobus), hemlock (Tsuga canadensis), and white spruce (Picea glauca) in northern hardwood stands with variable deer densities and then monitored browse on the seedlings over two years. We found that damage to pine and hemlock seedlings was inversely related to increasing snow depth, and our data suggest a positive relationship between hemlock browse and deer density. These results suggest that hemlock restoration efforts will not be successful without protection from deer. Hopefully we’ll submit the manuscript, possibly to the Northern Journal of Applied Forestry, in the next month or so.

All of this work has been pursued with management in mind, so it was nice this week to receive a call from Bob Doepker, a manager at the Michigan Department of Natural Resources with whom we worked to co-ordinate data collection and establish key research questions. Bob had some questions about the details and implications of our previous findings for deer habitat, tree regeneration and how they should be managed. It was good to catch up, and no doubt our ongoing work will continue to contribute to contemporary management understanding and planning.

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Philosophy of Modelling and RGS 2011

I just updated the Philosophy of Modelling page on my website. It’s not anything too detailed but I was prompted to add something by my activities over the last few weeks. I’ve been working on both making progress with my ‘modelling narratives’ project and a paper I’ve started working on with John Wainwright exploring the epistemological roles agent-based simulation might play beyond mathematical and statistical modelling (expected to appear in the new-ish journal Dialogues in Human Geography).

It’s only a few weeks now until this year’s Royal Geographical Society annual meeting (31 Aug – 2 Sept). I’m making two presentations, unfortunately both in the same session! It seems my work sits squarely within ‘Environmental modelling and decision making’, as the both abstract I submitted were allocated to that session on the Friday afternoon (Skempton Building, Room 060b; last session of the week so people might be flagging!). The first presentation will deal with the ‘generative’ properties of agent-based modelling [.pdf] and what that implies for how we might study and use that modelling approach, and the second will summarise the Michigan forest modelling work we’ve completed so far. Both abstracts are below.

This also seems a good point to highlight that King’s Geography Department are hosting a drinks reception on the Thurdsay evening from 18:45 at Eastside Bar, Princes Garden, SW7 1AZ. Free drinks for the first 50 guests, so get there sharpish!

Millington RGS 2011 Abstracts

Model Histories: The generative properties of agent-based modelling
Fri 2 Sept, Session 4, Skempton Building, Room 060b
James Millington (King’s College London)
David O’Sullivan (University of Auckland, New Zealand)
George Perry (University of Auckland, New Zealand)
Novels, Kundera has suggested, are a means to explore unrealised possibilities and potential futures, to ask questions and investigate scenarios, starting from the present state of the world as we observe it – the “trap the world has become”. In this paper, we argue that agent-based simulation models (ABMs) are much like Kundera’s view of novels, having generative properties that provide a means to explore alternative possible futures (or pasts) by allowing the user to investigate the likely results of causal mechanisms given pre-existing structures and in different conditions. Despite the great uptake in the application of ABMs, many have not taken full advantage of the representational and explanatory opportunities inherent in ABMs. Many applications have relied too much on ‘statistical portraits’ of aggregated system properties at the expense of more detailed stories about individual agent context and particular pathways from initial to final conditions (via heterogeneous agent interactions). We suggest that this generative modelling approach allows the production of narratives that can be used to i) demonstrate and illustrate the significance of the mechanisms underlying emergent patterns, ii) inspire users to reflect more deeply on modelled system properties and potential futures, and iii) provide a means to reveal the model building process and the routes to discovery that lie therein. We discuss these issues in the context of, and using examples from, the increasing number of studies using ABMs to investigate human-environment interactions in geography and the environmental sciences.

Trees, Birds and Timber: Coordinating Long-term Forest Management
Fri 2 Sept, Session 4, Skempton Building, Room 060b
James Millington (King’s College London)
Megan Matonis (Colorado State University, United States)
Michael Walters (Michigan State University, United States)
Kimberly Hall (The Nature Conservancy, United States)
Edward Laurent (American Bird Conservancy, United States)
Jianguo Liu (Michigan State University, United States)
Forest structure is an important determinant of habitat use by songbirds, including species of conservation concern. In this paper, we investigate the combined long-term impacts of variable tree regeneration and timber management on stand structure, bird occupancy probabilities, and timber production in the northern hardwood forests of Michigan’s Upper Peninsula. We develop species-specific relationships between bird occupancy and forest stand structure from field data. We integrate these bird-forest structure relationships with a forest model that couples a forest-gap tree regeneration submodel developed from our field data with the US Forest Service Forest Vegetation Simulator (Ontario variant). When simulated over a century, we find that higher tree regeneration densities ensure conditions allowing larger harvests of merchantable timber, and reducing the impacts of timber harvest on bird forest-stand occupancy probability. When regeneration is poor (e.g., 25% or less of trees succeed in regenerating), timber harvest prescriptions have a greater relative influence on bird species occupancy probabilities than on the volume of merchantable timber harvested. Our results imply that forest and wildlife managers need to work together to ensure tree regeneration and prevent detrimental impacts on timber output and habitat for avian species over the long-term. Where tree regeneration is currently poor (e.g., due to deer herbivory), forest and wildlife managers should pay particularly close attention to the long-term impacts of timber harvest prescriptions on bird species.

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Summer 2011 Papers

Since I last posted, THREE of the papers I’ve mentioned here previously have become available online! Here are their details, abstracts are below. Email me if you can’t get hold of them yourself.

Millington, J.D.A., Walters, M.B., Matonis, M.S., Laurent, E.J., Hall, K.R. and Liu, J. (2011) Combined long-term effects of variable tree regeneration and timber management on forest songbirds and timber production Forest Ecology and Management 262 718-729 doi: 10.1016/j.foreco.2011.05.002

Millington, J.D.A. and Perry, G.L.W. (2011) Multi-model inference in biogeography Geography Compass 5(7) 448-530 doi: 10.1111/j.1749-8198.2011.00433.x

Millington, J.D.A., Demeritt, D. and Romero-Calcerrada, R. (2011) Participatory evaluation of agent-based land use models Journal of Land Use Science 6(2-3) 195-210 doi:10.1080/1747423X.2011.558595

Millington, J.D.A. et al. (2011) Combined long-term effects of variable tree regeneration and timber management on forest songbirds and timber production Forest Ecology and Management 262 718-729
Abstract
The structure of forest stands is an important determinant of habitat use by songbirds, including species of conservation concern. In this paper, we investigate the combined long-term impacts of variable tree regeneration and timber management on stand structure, songbird occupancy probabilities, and timber production in northern hardwood forests. We develop species-specific relationships between bird species occupancy and forest stand structure for canopy-dependent black-throated green warbler (Dendroica virens), eastern wood-pewee (Contopus virens), least flycatcher (Empidonax minimus) and rose-breasted grosbeak (Pheucticus ludovicianus) from field data collected in northern hardwood forests of Michigan’s Upper Peninsula. We integrate these bird-forest structure relationships with a forest simulation model that couples a forest-gap tree regeneration submodel developed from our field data with the US Forest Service Forest Vegetation Simulator (Ontario variant). Our bird occupancy models are better than null models for all species, and indicate species-specific responses to management-related forest structure variables. When simulated over a century, higher overall tree regeneration densities and greater proportions of commercially high value, deer browse-preferred, canopy tree Acer saccharum (sugar maple) than low-value, browse-avoided subcanopy tree Ostrya virginiana (ironwood) ensure conditions allowing larger harvests of merchantable timber and had greater impacts on bird occupancy probability change. Compared to full regeneration, no regeneration over 100 years reduces merchantable timber volumes by up to 25% and drives differences in bird occupancy probability change of up to 30%. We also find that harvest prescriptions can be tailored to affect both timber removal volumes and bird occupancy probability simultaneously, but only when regeneration is adequate. When regeneration is poor (e.g., 25% or less of trees succeed in regenerating), timber harvest prescriptions have a greater relative influence on bird species occupancy probabilities than on the volume of merchantable timber harvested. However, regeneration density and composition, particularly the density of Acer saccharum regenerating, have the greatest long-term effects on canopy bird occupancy probability. Our results imply that forest and wildlife managers need to work together to ensure tree regeneration density and composition are adequate for both timber production and the maintenance of habitat for avian species over the long-term. Where tree regeneration is currently poor (e.g., due to deer herbivory), forest and wildlife managers should pay particularly close attention to the long-term impacts of timber harvest prescriptions on bird species.

Millington, J.D.A. and Perry, G.L.W. (2011) Multi-model inference in biogeography Geography Compass 5(7) 448-530
Abstract
Multi-model inference (MMI) aims to contribute to the production of scientific knowledge by simultaneously comparing the evidence data provide for multiple hypotheses, each represented as a model. With roots in the method of ‘multiple working hypotheses’, MMI techniques have been advocated as an alternative to null-hypothesis significance testing. In this paper, we review two complementary MMI techniques – model selection and model averaging – and highlight examples of their use by biogeographers. Model selection provides a means to simultaneously compare multiple models to evaluate how well each is supported by data, and potentially to identify the best supported model(s). When model selection indicates no clear ‘best’ model, model averaging is useful to account for parameter uncertainty. Both techniques can be implemented in information-theoretic and Bayesian frameworks and we outline the debate about interpretations of the different approaches. We summarise recommendations for avoiding philosophical and methodological pitfalls, and suggest when each technique is best used. We advocate a pragmatic approach to MMI, one that emphasises the ‘thoughtful, science-based, a priori’ modelling that others have argued is vital to ensure valid scientific inference.

Millington et al. (2011) Participatory evaluation of agent-based land use models Journal of Land Use Science 6(2-3) 195-210
Abstract
A key issue facing contemporary agent-based land-use models (ABLUMs) is model evaluation. In this article, we outline some of the epistemological problems facing the evaluation of ABLUMs, including the definition of boundaries for modelling open systems. In light of these issues and given the characteristics of ABLUMs, participatory model evaluation by local stakeholders may be a preferable avenue to pursue. We present a case study of participatory model evaluation for an agent-based model designed to examine the impacts of land-use/cover change on wildfire regimes for a region of Spain. Although model output was endorsed by interviewees as credible, several alterations to model structure were suggested. Of broader interest, we found that some interviewees conflated model structure with scenario boundary conditions. If an interactive participatory modelling approach is not possible, an emphasis on ensuring that stakeholders understand the distinction between model structure and scenario boundary conditions will be particularly important.

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Changing the ‘Targets and Timetables’ Climate Change Narrative

Earlier this week I was in Leipzig, Germany, to meet the Ecological Modelling research group at the Helmholz Centre for Environmental Research (UFZ) and one of my PhD supervisors, Dr. George Perry. While there I was lucky to meet and talk with some renowned ecological modellers: Thorsten Wiegand, who’s work includes spatial point process modelling (although some of his discussion with George about that was a bit technical for me!); Volker Grimm, proponent the ‘Pattern-Oriented Modelling’ approach (look out for a new review of this in Phil Trans. of the Royal Society in the near future), and Andreas Huth, notable forest dynamics modeller.

At UFZ I gave a presentation I entitled “Future Forests: Managing and Creating Forests for Biodiversity, Recreation, Timber and Carbon” in which I talked about some of the work I did in Michigan and the new project I’m working on now in the UK. The talk seemed to go down well and the research group had some very good questions, both about technical aspects of the modelling and the issues it is applied to (i.e. forest ecosystem management and woodland creation, including the Woodland Carbon Code). Thanks to Juergen Groeneveld for organising this (and his hospitality at UFZ).

Much of the data I presented regarding the Michigan work was collected by Megan Matonis. Her analyses of that data, on which I helped and supervised, are now available to read in a paper that is currently in press with Forest Ecology and Management (email me if you can’t access the online version).

Another interesting activity at UFZ was hearing Roger Pielke Jr. talk about the need to ‘change the climate change narrative’. In his talk he suggested that understanding all carbon policy can be boiled down to a single sentence;

‘people engage in economic activity that uses energy from carbon emitting generation’.

He emphasised that he thinks the “Targets and Timetables” approach to reducing anthropogenic carbon emissions is flawed. As an example, he used the case of the UK and the Climate Change Act of 2008 which set the aim of an 80% cut in the country’s carbon emissions by 2050 compared to 1990 levels, with an intermediate target of 34% by 2020. However, Pielke argues that given the ‘iron’ law of climate policy (that we cannot mitigate emissions by reducing GDP, both because people will pay only so much to mitigation now, and because increasing GDP is seen as a virtue by way of its effects on povety reduction) we cannot hit these types of targets.

Previous decarbonisation of the UK economy has been achieved by replacing the contribution to GDP from high-emitting manufacturing with low-emitting financial services. He wonders how long can this go and presented his estimate that for the UK to actually hit its 2020 target it will have to build more than 40 nuclear power stations in the next 10 years. In this context, he suggested that the building of a third runway at Heathrow was an insignificant concern (in terms of the new emissions it would generate) when there are still 1.5 billion people globally who do not have access to electricity. His argument is that we do not know how to achieve the targets and the timetables we have set ourselves.

Pielke argues that we must change the climate change narrative from

“We need to use less energy and fossil fuels are cheap“

to

“We need more energy and fossil fuels are too expensive“.

This would allow these 1.5 billion people to access the electricity they aspire to whilst driving the growth of alternative, cleaner, sources of energy. I like this argument – and his one about making small steps towards these change to reach bigger changes – but it seems to run counter to his point about the insignificance of another runway at Heathrow (which by increasing capacity for flights would continue the narrative of cheap fossil-fuelled energy). Opening a third runway but only allowing non-fossil-fuelled aeroplanes to use it is ultimately most consistent with the change in narrative he argues for.

And of course, while at UFZ, George Perry and I took the opportunity to discuss past, current and ongoing work over beers and dinner. Mainly we discussed the idea surrounding the narrative properties of generative simulation models and on which I plan to submit a manuscript to a journal for publication soon. But we also thought about other areas of research including land use modelling (continuing our work in Spain) and landscape disturbance-succession modeling (including the use of the LFSM I’ve developed with paleo-estimates of wildfire regimes).

All-in-all a very interesting and productive trip!

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Long-Term Bird-Timber Trade-offs

Not surprisingly, during my time at Michigan State University many of my posts on this blog focused on the work I was doing there on forest ecosystem management. I’ll continue to write papers and use and develop the simulation model I initiated at MSU, but now I’m back in London I’m sure the emphasis on this blog will switch to the primary work I’ll be doing here. Before it does, here’s a post on the work I’ve done recently related to the Michigan study and which I’m about to submit for review.

I’ve written here previously about how I’ve been working on modelling the long-term impacts of poor tree regeneration on forest structure and estimating bird presence in forests given their structural characteristics. In my last few months in Michigan, I integrated these two issues as part of the development of the integrated ecological-economic simulation model. The aim was to assess trade-offs between between protecting bird species of conservation concern and ensuring the productivity of industrial forests given the variable tree regeneration densities we have seen across our study area and given the timber harvest options available. I was particularly interested in how the variations in tree regeneration we have seen across our study area [we have a paper on these currently under review – more details soon] might influence long-term forest sustainability. Simulation modelling is an excellent way to look at these types of issues over long time periods.

To examine the trade-offs I integrated bird occupancy models I had developed for four bird species (black-throated green warbler, eastern wood pewee, least flycatcher and rose-breasted grosbeak) with our our model of forest gap regeneration and FVS. I then used the model to simulate various scenarios of regeneration and timber harvest prescriptions. For example, I simulated different densities of trees regenerating in the forest gaps created by timber harvest and different proportions of these trees as either sugar maple or ironwood. These are the sorts of variables that Megan Matonis found to vary across our study area and that are most likely driven by white-tailed deer herbivory. With the simulation model we could then look at how these different scenarios influence forest structure and, in turn, bird occupancy probability. We also looked at how different timber harvest prescriptions interact with these different densities and compositions of regenerating trees.

Using our model for a simulated century we found that the four bird species we examined responded uniquely to changes in forest structure (in turn due to the variation in regeneration composition and density and timber harvest prescriptions). We also found that 100-year average timber volume removals, which varied with harvest prescriptions and regeneration, were related to bird occupancy for three of the four species, positively for two and negatively for one. These results suggest that timber harvest prescriptions can be tailored to influence both timber removal volumes and bird occupancy probability, but only when regeneration is adequate. This is illustrated by the figure below for one of the bird species.

Plot illustrating tradeoffs

Mean annual timber removed is plotted on the horizontal axis and mean bird occupancy probability on the vertical axis. The different colours of points are the different densities of regeneration (darker is higher) and the different shapes are the different timber harvest prescriptions. When regeneration is poorer (lighter colours), differences in the volume of timber removed are smaller between prescriptions (horizontal axis) than differences in bird occupancy probability (vertical axis, relative to the uncertainty bars).

These results imply that management actions that promote high tree regeneration rates (for example, by reducing deer herbivory) will benefit both bird populations and timber production in the long-term. Consequently, we suggest that where tree regeneration is currently poor, forest managers should pay closer attention to the long-term impacts of timber harvest prescriptions on bird species.

As I highlighted above, this work is very near being submitted for publication. I’ll post here as the review and publication process progresses (and maybe try to use fewer hyphens in the title).

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Changing Forest Structure

It’s been a while since I posted here about the forest modelling I’ve been working on here at MSU. Over the last couple of months I’ve been working on finalizing the regeneration modelling component, refining the timber harvest rules, linking simulations to the bird occupancy modelling I started this spring, and writing it all up for manuscripts.

Across our study area we’ve found that regeneration of juvenile trees following timber harvest varies greatly. For example, from our empirical data we find that sugar maple saplings were present in over 70% of northern forest gaps but were completely absent from 96% of gaps in southern areas. Megan Matonis suggested in her thesis that this variation is related to snow depth, deer density and soil nutrient conditions. To examine the potential long-term effects of these differences in regeneration on forest structure I’ve been running our simulation model with pre-set levels of regeneration that reflect our observations, ranging from the maximum possible (given the space available in a post-harvest gap) to a complete absence of regenerating juvenile trees.

These ‘gaps’ I’m talking about are created in northern hardwood forests when individual or small groups of trees are removed in an uneven-aged timber management approach. The removal of these trees creates openings (‘gaps’) in the forest canopy allowing light into lower levels for younger trees [gaps may also be created naturally but we’re focusing on those created by human activity which is the dominant driver in our study area]. When harvesting trees in this approach foresters aim to produce a forest structure with a ‘reverse-J’ distribution of tree sizes; high densities of small, young trees and low densities of larger, older trees (approximating a gamma-distribution like I found in our data previously). The idea is that through time an abundant supply of competing smaller trees will replace larger trees trees that are removed.

Representing this approach in our model (using FVS keywords [.pdf]) requires quite a bit of code, but working through the example provided by Don Vandendriesche [.pdf] helped. This approach requires the model user to specify a residual basal area (the area occupied by trees) and the ratio between the number of trees in successive size classes (the q-factor).

To examine my initial results (and to help debugging during the whole modelling process) I used R to plot size-class distributions for tree densities and basal area. As is the norm I used size-classes defined by the diameter-at-breast-height of the trees (5 cm or about 2 inches). Then I combined plots for simulated years into animated .gif files to see how the distributions changed through time for different regeneration levels. Here are a couple of examples (click for larger versions):


By the end of these 200-year simulations the same stand has a very different forest structure. In the top example regeneration is sufficient to replace trees removed during harvest, growing into larger size-classes as more resources (light and space) become available. But in the bottom example we see the consequences of when no new trees grow to replace the the removed trees – by the mid-21st century there are no trees in the smaller size-classes and timber harvesting has to become less frequent to meet timber removal goals (and remain viable).

I’m continuing to analyse the model output in a more quantitative manner and assessing the impacts of these potential changes in forest structure on bird habitat (specifically the probability that different species will be present in a forest stand). All together this should make a nice manuscript and provide some interesting information for the foresters working in these northern hardwood forests.

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US-IALE 2010 Preparation

Next week is the Twenty-fifth Anniversary Symposium of the US chapter of the International Association of Landscape Ecology (US-IALE). I’ll be in attendance in Athens, Georgia and am currently working on my presentation, entitled Ecological-economic modeling for sustainable forest management (scheduled for Thursday 8th, 2.20pm in room T/U). In the context of our larger modelling project I’ll present work we’ve published, stuff we’re still working on, and the initial results from putting it all together.

Several symposia have been organised and I plan to be at those that consider landscape ecology and wildfires, bioenergy and land-use change, and climate change and landscape connectivity. Particularly interesting should be Don McKenzie’s presentations on ecosystem energetics and scaling laws in the wildfire symposium and Paul Opdam’s presentations on Natura 2000 and the role of landscape ecology in the climate change symposium. Two of the plenary addresses I’d like to catch are Collapse and Sustainability: Lessons from History (Joseph A Tainter) and Linking Renaissance Ecologists with Citizen Scientists to Advanced Scientific Research and Literacy (Carol Brewer).

As usual CSIS has a strong presence at US-IALE this year with seven presentations, including the insights of Jack Liu and Wu Yang into the challenges and opportunities for landscape ecology and conservation in coupled human natural research, the analysis by Andres Vina and Xiaodong Chen of the potential conservation benefits that might be offset by natural disasters, Mao-Ning Tuanmu’s work on Giant Panda habitat and the work by Pete Esselman and Dana Infante on the National Assessment of the Status of Fish Habitat. The full list of CSIS presentations is below.

It’s shaping up to be a good couple of days! I’ll try to tweet and blog some thoughts as they arise during the conference and maybe reflect on things afterwards also.

CSIS Presentations at US-IALE 2010
6th April
Are conservation benefits offset by natural disasters? — The case of the May 12, 2008 Wenchuan Earthquake. Andrés Viña, Xiaodong Chen, Wei Liu, et al.

Coupling human and natural systems: Challenges and opportunities for landscape ecologists. Jianguo Liu

The spatial framework and results of the initial National Assessment of the Status of Fish Habitat. Peter C Esselman, Dana M Infante, et al.

7th April
Effects of human-environment relationships on the spatiotemporal dynamics of giant panda habitat. Mao-Ning Tuanmu, Wei Liu, Andrés Viña, et al.

8th April
Ecological-economic modeling for sustainable forest management. James D A Millington, Michael B Walters, Megan S Matonis, et al.

Mechanisms for effective conservation in coupled human-natural systems. Wu Yang, Wei Liu, Mao-Ning Tuanmu, et al.

Patterns and drivers of reforestation: A case study in the Qinling Mountains, China. Yu Li, Andrés Viña, Jianguo Liu