Data Assimilation in the Snow

by Sarah Dance

Snowbird mountains

I’ve just got back from attending the Society of Industrial and Applied Mathematics (SIAM) Conference on Dynamical Systems in the beautiful mountains of Snowbird, Utah,USA.  I was invited to attend the meeting to give part of a Mini-Tutorial on Data Assimilation(available here) with Elaine Spiller and Eric Kostelich.

Even though my undergraduate degree and PhD were in Applied Mathematics, I don’t tend to go to many Mathematics conferences. I often meet with fellow data assimilation practitioners at Meteorology conferences instead.  So it was great to see people proving data assimilation related theorems, applying data assimilation in different applications like neuroscience and cancer treatment, and of course to get some new ideas from dynamical systems approaches that have potential to be applied in different ways.  I particularly enjoyed Mary Silber’s talk on using Landsat data to understand vegetation pattern formation in the drylands of Africa

A slow march through the desert

Gowda/Silber’s work on African drylands. This image shows shrublands in Somalia from high above. Two images – from 1952 (purple) and 2006 (green) – are overlaid here for comparison. The colors highlight the large communities of shrubs and grasses which grow in bands along this sloping landscape. Over the fifty years shown here, all the vegetation has moved uphill – the green bands of modern plant growth are further up the hillside than the purple bands from 1952.

Tales from the Alice Holt Forest: carbon fluxes, data assimilation and fieldwork

by Ewan Pinnington

Forests play an important role in the global carbon cycle, removing large amounts of CO2 from the atmosphere and thus helping to mitigate the effect of human-induced climate change. The state of the global carbon cycle in the IPCC AR5 suggests that the land surface is the most uncertain component of the global carbon cycle. The response of ecosystem carbon uptake to land use change and disturbance (e.g. fire, felling, insect outbreak) is a large component of this uncertainty. Additionally, there is much disagreement on whether forests and terrestrial ecosystems will continue to remove the same proportion of CO2 from the atmosphere under future climate regimes. It is therefore important to improve our understanding of ecosystem carbon cycle processes in the context of a changing climate.

Here we focus on the effect on ecosystem carbon dynamics of disturbance from selective felling (thinning) at the Alice Holt research forest in Hampshire, UK. Thinning is a management practice used to improve ecosystem services or the quality of a final tree crop and is globally widespread. At Alice Holt a program of thinning was carried out in 2014 where one side of the forest was thinned and the other side left unmanaged. During thinning approximately 46% of trees were removed from the area of interest.

Figure 1: At the top of Alice Holt flux tower.

 

Using the technique of eddy-covariance at flux tower sites we can produce direct measurements of the carbon fluxes in a forest ecosystem. T

he flux tower at Alice Holt has been producing measurements since 1999 (Wilkinson et al., 2012), a view from the flux tower is shown in Figure 1. These measurements represent the Net Ecosystem Exchange of CO2 (NEE). The NEE is composed of both photosynthesis and respiration fluxes. The total amount of carbon removed from the atmosphere through photosynthesis is termed the Gross Primary Productivity (GPP). The Total Ecosystem Respiration (TER) is made up of autotrophic respiration (Ra) from plants and heterotrophic respiration (Rh) from soil microbes and other organisms incapable of photosynthesis. We then have, NEE = -GPP + TER, so that a negative NEE value represents removal of carbon from the atmosphere and a positive NEE value represents an input of carbon to the atmosphere. A schematic of these fluxes is shown in Figure 2.                                                               

Figure 2: Fluxes of carbon around a forest ecosystem.

 

The flux tower at Alice Holt is on the boundary between the thinned and unthinned forest. This allows us to partition the NEE observations between the two areas of forest using a flux footprint model (Wilkinson et al., 2016). We also conducted an extensive fieldwork campaign in 2015 to estimate the difference in structure between the thinned and unthinned forest. However, these observations are not enough alone to understand the effect of disturbance. We therefore also use mathematical models describing the carbon balance of our ecosystem, here we use the DALEC2 model of ecosystem carbon balance (Bloom and Williams, 2015). In order to find the best estimate for our system we use the mathematical technique of data assimilation in order to combine all our available observations with our prior model predictions. More infomation on the novel data assimilation techniques developed can be found in Pinnington et al., 2016. These techniques allow us to find two distinct parameter sets for the DALEC2 model corresponding to the thinned and unthinned forest. We can then inspect the model output for both areas of forest and attempt to further understand the effect of selective felling on ecosystem carbon dynamics.

Figure 3: Model predicted cumulative fluxes for 2015 after data assimilatiom. Solid line: NEE, dotted line: TER, dashed line: GPP. Orange: model prediction for thinned forest, blue: model prediction for unthinned forest. Shaded region: model uncertainty after assimilation (± 1 standard deviation).

 

In Figure 3 we show the cumulative fluxes for both the thinned and unthinned forest after disturbance in 2015. We would probably assume that removing 46% of the trees from the thinned section would reduce the amount of carbon uptake in comparison to the unthinned section. However, we can see that both forests removed a total of approximately 425 g C m-2 in 2015, despite the thinned forest having 46% of its trees removed in the previous year. From our best modelled predictions this unchanged carbon uptake is possible due to significant reductions in TER. So, even though the thinned forest has lower GPP, its net carbon uptake is similar to the unthinned forest. Our model suggests that GPP is a main driver for TER, therefore removing a large amount of trees has significantly reduced ecosystem respiration. This result is supported by other ecological studies (Heinemeyer et al., 2012, Högberg et al., 2001, Janssens et al., 2001). This has implications for future predictions of land surface carbon uptake and whether forests will continue to sequester atmospheric CO2 at similar rates, or if they will be limited by increased GPP leading to increased respiration. For more information on this work please see Pinnington et al., 2017.

 

References

Wilkinson, M. et al., 2012: Inter-annual variation of carbon uptake by a plantation oak woodland in south-eastern England. Biogeosciences, 9 (12), 5373–5389.

 

Wilkinson, M., et al., 2016: Effects of management thinning on CO2 exchange by a plantation oak woodland in south-eastern England. Biogeosciences, 13 (8), 2367–2378, doi: 10.5194/bg-13-2367-2016.

 

Bloom, A. A. and M. Williams, 2015: Constraining ecosystem carbon dynamics in a data-limited world: integrating ecological “common sense” in a model data fusion framework. Biogeosciences, 12 (5), 1299–1315, doi: 10.5194/bg-12-1299-2015.

 

Pinnington, E. M., et al., 2016: Investigating the role of prior and observation error correlations in improving a model forecast of forest carbon balance using four-dimensional variational data assimilation. Agricultural and Forest Meteorology, 228229, 299 – 314, doi: http://dx.doi.org/10.1016/j.agrformet.2016.07.006.

 

Pinnington, E. M., et al., 2017: Understanding the effect of disturbance from selective felling on the carbon dynamics of a managed woodland by combining observations with model predictions, J. Geophys. Res. Biogeosci., 122, doi:10.1002/2017JG003760.

 

Heinemeyer, A., et al., 2012: Exploring the “overflow tap” theory: linking forest soil co2 fluxes and individual mycorrhizo- sphere components to photosynthesis. Biogeosciences, 9 (1), 79–95.

 

Högberg, P., et al., 2001: Large-scale forest girdling shows that current photosynthesis drives soil respiration. Nature, 411 (6839), 789–792.

 

Janssens, I. A., et al., 2001: Productivity overshadows temperature in determining soil and ecosystem respiration across european forests. Global Change Biology, 7 (3), 269–278, doi: 10.1046/j.1365-2486.2001.00412.x.

2017 Annual European Geosciences Union (EGU) Conference

    by Liz Cooper

The 2017 Annual European Geosciences Union (EGU) conference was held at the International Centre in Vienna from 23rd to 28th April.  During that time over 14,000 scientists from 107 countries shared ideas and results in the form of talks, posters and PICOs .The PICO (Presenting Interactive COntent) format is a relatively new idea for presenting work, where participants prepare an interactive presentation. In each PICO session the presenters first take turns to give a 2 minutes summary of their work for a large audience. The PICOS are then each displayed on an interactive touch screen and conference delegates can chat to the presenters and get further details on the research, with the PICO for illustration. This format has features of both traditional poster and oral presentations and provides a great scope for audience participation. I saw several which took advantage of this, including a very popular flood forecasting adventure game by a fellow Reading Phd student Louise Arnal.

I was delighted to be able to present some of my own recent results at EGU, in a talk titled ‘The effect of domain length and parameter estimation on observation impact in data assimilation for inundation forecasting.’ (see photo)

Presenting at an international conference was a really valuable and enjoyable experience, if a little daunting beforehand. I found it a really useful opportunity to get feedback from experts in the field and find out more about work by people with related interests.

The EGU conference has many participants and covers a huge range of topics from atmospheric and space science to soil science and geomorphology. My research deals with data assimilation for inundation forecasting, so I was most interested in sessions within the Hydrological Sciences and Nonlinear Processes in Science programmes. Even within those disciplines there was a huge breadth of research on display and I saw some really interesting work on synchronization in data assimilation, approaches to detection of floods from satellite data and various methods for measuring and characterizing floods.

As well as subject-specific programmes, there was also a very good Early Career Scientist (ECS) programme at EGU, with networking events, discussion sessions and a dedicated ECS lounge with much appreciated free coffee!

EGU was a hugely enjoyable experience and Vienna is a beautiful city with excellent transport links. With so many parallel sessions it’s really essential to plan which talks and posters are a priority in advance but I would heartily recommend it to anyone involved in geosciences research.

Sewer network challenge at MathsForesees study group 2017

by Sanita Vetra-Carvalho

The second Maths Foresees study group was held on 3rd-6th April 2017, hosted by the Turing Gateway to Mathematics at the Isaac Newton Institute, Cambridge. The Maths Foresees network was established in May 2015 under the EPSRC Living with Environmental Change (LWEC) umbrella to forge strong links between researchers in the applied mathematics and environmental science communities and end-users of environmental research. The Maths Foresees events take a collaborative approach to industry problem solving where over the course of four days, mathematical and environmental scientists explored real challenges posed by companies operating in the environmental sector.

In this second event, there were five industry challenges presented to the participants (around 50 in total) from three companies: JBA, Sweco and Environmental Agency. All of the challenges this year were linked to flooding issues:

I joined the group interested solving sewer modelling challenge proposed by Sweco and presented by James Franklin. The urban flood model InfoWorks ICM (Integrated Catchment Modeling) by Innovyze that is used by Sweco, comprises a subsurface sewer network and a street-level road surface model. The two are coupled via manholes but smaller drains/gullies are not included since the exact locations of gullies and drains are not known (it would be very costly in manpower to locate them) and more importantly it would be computationally unfeasible to directly model gullies in InfoWorks model. As a consequence, the model does not represent floodwater drainage correctly. In a typical simulation, floodwater stays on the road surface and does not drain away as it should. This results in an inaccurate flood extents, particularly in urban environments (see an image below of a typical simulation of a storm).

A typical simulation using InfoWorks ICM: floodwater stays on the road surface and pools indefinitely rather than charging the network during the recession of a storm.

The challenge for the group was to see how we could improve the model representation of the collection network; that is how to represent gullies in the model to simulate a more realistic exchange (sinks and sources) of surface water between the sewer network and surface model.

Our group had two and half days to propose a solution. Our initial idea to couple a 2D surface shallow water model to a 1D sewer network model (also shallow water model) to model realistic fluid exchange between the two models turned out to be too difficult to accomplish in the limited time period. Hence, we concentrated our efforts on the main problem at hand, how to represent realistic sinks in the model without directly resolving gullies in the model. To this end, our group produced two 2D surface models: 2D shallow water model and 2D diffusive wave model. The second model was developed in parallel as in a future it would be easier to couple to a 1D drainage network. Our group run both models on an idealised road setting: 100m straight road with 3 manholes every 30m and 20 gullies every 10m, where directly resolved (see image below).

Representation of an idealised 100m road with gullies and manholes

We compared runs where we resolved gullies directly on the mesh every 10m on both sides of the road (the case which is computationally unfeasible for Sweco to run but is the most realistic) to line sink runs where we averaged the effect of the number gullies on the road and removed the surface liquid from the model at each gridpoint that is adjacent to the pavement. Both of our 2D surface models showed that the line sink representation of the gullies removed approximately the same volume of surface water in the model as directly resolving each gully in the model thus making line sink solution a realistic and computationally affordable to represent the effect of gullies in the model. While our solution lacked the two-way flow exchange between the surface model and sewer network we proposed that if implemented in the InfoWorks model the volume of water sunk through line sinks would become a source in the sewer network through the nearest manhole in the model. Our findings and the proposed solution to the Sweco challenge was positively received by James Franklin. A full report of our solution will be published on Turing Gateway to Mathematics site over next two months.

I very much enjoyed being part of the Maths Foresees study group 2017 and am very thankful to all the organisers at MathsForesees network and Turing Gateway of Mathematics for organising this event as well as Isaac Newton Institute for hosting it. It was very refreshing to be ‘locked’ into the Isaac Newton Institute alongside other participants to solve these challenges in a mentally very rich and inspiring environment. The event naturally offered a very fruitful ground for networking too. I would encourage any mathematician interested in solving environmental problems to take a part in any future MathsForesees events!

Our boards of brainstorming @MathsForesees event

7th Japanese Data Assimilation Workshop

By Joanne A. Waller

For decades data assimilation (DA) has played a crucial role in numerical weather prediction (NWP) where it is used to provide initial conditions for weather forecasts. These ‘initial conditions’ describe the current atmospheric state and are estimated using data assimilation by blending previous forecasts with atmospheric observations, weighted by their respected uncertainties. However data assimilation is not only applicable to NWP and in recent years it has been applied widely to different applications where numerical simulations and observations are available.

At the end of February 2017 over 100 scientists from around the globe arrived at the Japanese RIKEN Advanced Institute for Computational Science (AICS)  for the 7th Japanese Data Assimilation Workshop. The aim of the symposium was to bring together scientist from from numerous different disciplines, such as neuroscience, cardiology, molecular dynamics, cosmology, nanoscale materials science, terrestrial magnetism, paleoclimate, oceanography, atmospheric chemistry and of course NWP, to discuss the data assimilation issues shared  across these broad applications.

Presentations and posters covered a wide variety of topics including: how data assimilation combined with advanced intelligence can help improve numerical models; how high performance computing can be used to deal with the new era of ‘Big Data’; how non-Gaussianity and non-linearity can be handled in data assimilation; ideas on how assimilate data into multi component models (i.e. systems that connect multiple models such as atmospheric, land and ocean models) and many more.

The conference provided a perfect platform for many cross-disciplinary discussions and this highlighted that much can be learnt in general about data assimilation by considering the issues that arise across different scientific areas.

(Photo from http://www.data-assimilation.riken.jp/risda2017/)

Mathematics of Planet Earth Jamboree

 by Jemima Tabeart

On 20th-22nd March the Mathematics of Planet Earth Centre for Doctoral Training (MPE CDT) held its third annual Jamboree event. This is a celebration of the work of the staff and students of the CDT and includes seminars from industrial and academic speakers, as well as the opportunity for students to present their research. For the first time this year, the first two days of the Jamboree were used to host an Industrial study group. Representatives from EDF Energy and AIR Worldwide (catastrophe modelling for the insurance and re-insurance industry) posed real-world problems to cross-cohort groups of students, who then attempted to provide some new mathematical insight into possible solutions.

 

Our group was given a task by EDF Energy to investigate the interaction of extreme wind and rain events in the UK. EDF Energy’s assets in the UK include nuclear and other types of power plants, so understanding of extreme events is important in order to they can take appropriate safety measures. Currently extreme rain and wind events are considered separately, and we were asked to consider ways of determining how to define and deal with extreme wind-rain events. We were given hourly reanalysis data from the last 40 years, on a coarse 1 degree grid over the UK. The group split into two parts: one looking at more conceptual ideas about how extreme events can be caused by an interaction of factors, and the other considering the data provided.

 

Our part of the group identified some known extreme weather events, and focused on the data for these time periods. We looked at which events had both extreme wind and extreme rain, and mapped these to geographical locations to see where extreme wind-rain occurs most frequently. We also tried to see if there was a time lag between rain and wind events in the same location. Initial plots indicated that the most likely lag time was 0 hours, although this might be due to the relatively coarse resolutions. Other members of the group also suggested a method for combining the threshold values for extreme wind and rain to create a combined parameter. As well as a presentation of the main ideas that took place on the day to industry representatives, written reports will be sent to the respective companies so that they can take the suggestions further.

 

The study group was a great opportunity for cross-cohort work that brought together students with contrasting research interests. The challenge of producing something in a short amount of time is very different to what we normally expect as PhD students, and the ideas of getting stuck in straight away and not spending hours agonising over every decision is something that will be useful going forward. I really enjoyed working with real-world data and on problems outside my usual subject area – applying techniques I’ve learned during my PhD to other applications is very satisfying, and gives me the confidence that I am developing my transferable skills through my research!

DARE Board Meeting

On 22 February 2017 we held  our first advisory board meeting with stakeholders.

The presentations from the meeting may be downloaded here:

Flood Crowdsourcing and CCTV sites

by Sanita Vetra-Carvalho

Urban areas nowadays contain many observation networks such as CCTV cameras looking at buildings, streets, parking lots, rivers and traffic. Also, where there are people there are smartphone images,  which are another potential source of information that can be assimilated in urban flooding models to get more accurate flooding forecasts.

Increasing number of research teams and organisations are using this abundance of data and while much CCTV data is available as open data, smartphone images need to be collected from the community. Below we list the networks of CCTV data and crowdsourcing sites known to us for the areas we are interested in: London and the Thames Valley, Exeter, Newcastle, Leeds, Glasgow, and Tewkesbury. This list is not in any way extensive; if you know of further sites or webcams we would love to hear from you (email to: s.vetra-carvalho@reading.ac.uk)!

 

Traffic Webcams

London Traffic Cameras

Highway Traffic Cameras (England)

Leeds Traffic Cameras

Newcastle Traffic Cameras

M5 Southbound (inc. Exeter)

SouthWest Cameras (inc. Exeter)

Sctoland Traffic Cameras (inc. Glasgow)

Reading Town Traffic Cameras

 

River Watercams

Upper Thames Sailing Club (Cookham, Berkshire)

Farson Digital Watercams (UK wide)

Canal and Waterway list of watercams

Avon National Trust live river cameras (Tewkesbury)

 

Live CCTV Cameras

Exeter IP Cameras

 

Crowdsourcing sites

Met Office WoW site (UK wide)

FloodCrowd (UK wide)

Cobweb (EU wide)

 

Other useful flooding websites

Flood Map from Environmental Agency

National River Flow Archive

Loddon Valley Flood Action Group

River levels

 

 

 

Welcome

by Sarah Dance

Data Assimilation for the REsilient City (DARE) is a research project and network funded by an EPSRC Senior Fellowship in Digital Technology for Living with Environmental Change.

Data assimilation is an emerging mathematical technique for improving predictions from large and complex forecasting models, by combining uncertain model predictions with a diverse set of observational data in a dynamic feedback loop. The project will use advanced data assimilation to combine a range of advanced sensors with state-of-the-art computational models and produce a step-change in the skill of forecasts of urban natural hazards such as floods, snow, ice and heat stress. For more information about the research programme click here.

The Fellowship is held by Dr Sarah L. Dance at the University of Reading and she is working together with a team of other researchers and stakeholders. The Fellowship will influence the future research agenda for how digital technologies can be applied in new and transformative ways to help the human and natural environment be more resilient and adaptable to climate change. In addition to an innovative research programme,  Dr Dance is acting as a Champion for this area, developing outreach activities to other researchers, policy makers and industry through workshops, networks and other mechanisms.