The Ideas Boom goes bust

PM_vs_MicksHair

Prime Minister Malcolm Turnbull delivering his speech that received a standing ovation from (most of) the audience. Even my hair was getting right into it.

He had just about everyone on their feet. The mood at the Prime Minister’s Prizes for Science was upbeat. We’d been treated to a stellar array of talent – science that could clearly lead to economic windfalls, science to help manage the country and its natural environment better, and outstanding teachers to help foster a more scientifically-literate community.

Malcolm Turnbull, the newly appointed Prime Minister, received a standing ovation for his speech that emphasized science as underpinning both the current and future prosperity of Australia. Standing ovations are a rare accolade from a scientific audience; rarer still when directed toward a politician, especially one from a party that had disparaged and cut funding to science so very recently.

Jane_Mick_PMPrize_300B

The mood was buoyant, as we celebrated science and great scientists such as QAECO’s own Dr Jane Elith.

That was six months ago. And not everyone had stood to applaud. Some wanted more tangible proof that science really was going to be placed at the heart of Australia’s prosperity. But even as I stood, I wondered two things.

Could the Prime Minister sway his cabinet to follow his call?

And for all the talk about science and innovation, what would it mean for funding? Perhaps more importantly, what would it mean for planning and better integration of research and higher education?

Six months would be telling. In particular, what would the Turnbull government’s first budget reveal? I was prepared to wait.

For too long now, funding of universities and major research institutes such as CSIRO has been distributed without a coherent plan for research and researchers. We can’t simply turn funding on and off like a tap and see changes in research performance. The human capital employed by that funding doesn’t change that quickly. It takes months, even years, of lost productivity to shift one’s research environment. Training and establishing a research career can take a decade or more.

We can’t have a research fellowship scheme that sees 200 fellowships one year, but only 50 in another. Or a fellowship scheme that is an expendable hostage in a game of political brinkmanship. Perhaps more importantly than the number of fellowships, we need capacity within our research institutions to accommodate that talent in the longer term. There is little point investing in fellowships if those recipients have limited opportunities once their fellowships expire.

If we want people to continue on research careers, they need to be able to see pathways. The instability and lack of planning means pathways are obscure for many young researchers. At the moment, they are living on hope, on skepticism, or on disappointment.

And we’re living on a slogan. The Ideas Boom. Let me tell you – there won’t be an Ideas Boom in Australia without a properly funded plan. Up until now, the Ideas Boom was simply a $28M advertising campaign. It still is.

The Ideas Boom will happen elsewhere, and some of Australia’s most innovative scientists will move there. Why? Because the budget does very little to lay the foundation for any coherent plan for science and innovation in Australia. In fact, the budget entrenches the Abbott government’s 20% funding cut to universities without providing further capacity to increase income.

Government expenditure on research is going south. As  a proportion of each country’s GDP, Australia spends less than half of the research expenditure of Iceland, Finland and Denmark. If this were an Olympic medal tally, the public would demand an inquiry – we’re being beaten by New Zealand! If we want an Ideas Boom, we’ll need more and smarter investment.

government-spending-on-r26d2c-percentage-of-gdp2c-2013-data

Government spending on R&D for major advanced economies. Sourced from the ABC FactCheck.

University income has been increasingly derived from sources other than the Federal government for several years now. Below are the values reported by The University of Melbourne – the majority of its funding will soon be from private sources, it seems, given further cuts to university funding. Other Australian universities are likely on a similar trend.

UniMelbIncome

The University of Melbourne has increasingly sourced its income from private sources, particularly fees. With further funding cuts entrenched, that trend will continue.

The budget plugs some holes in research funding. Notably, various specialized pieces of infrastructure will be funded, supporting a small fraction of Australia’s research capacity. And extra funding for GeoSciences Australia will help us find more resources to mine. Antarctic science is set to benefit from an expanded Antarctic program, including a new boat just over the horizon. But the announced support is haphazard against a background of cuts.

This is not an Ideas Boom. It’s business as usual – reduced funding across the board, and sprinkles of funding in pockets.

The standing ovation is over. Everyone has resumed their seats, with arms folded. The Ideas Boom is busted. Well, to be honest it can’t really be busted because it was never built.

Posted in Uncategorized | 2 Comments

An election looms, and the temperature continues to rise…

In one of my subjects, I used data on the relationship between the global temperature and CO2 concentrations to teach how variability can mask relationships, making inference uncertain. The example was based on an Australian political debate in 2009 about whether the temperature of the Earth had stopped increasing despite an increase in atmospheric CO2.

With an Australian election looming in 2016, it seems timely to return to that debate, and evaluate the positions of the different protagonists now that we have some more data. It is nice to hold our politicians to account.

Let’s first look at the data. I will use the latest HadCRUT4 data for global surface temperature, and the average annual CO2 concentration data measured at Mauna Loa (both downloaded on 20 April 2016). We have the CO2 data from 1959 to 2015, so I will use that period. You can see that the CO2 concentration has continued to increase since 2008, largely unabated it would seem.

CO2_To2015

Atmospheric CO2 concentration as measured at Mauna Loa by NOAA. Data from 2009 onwards, available after the Senator’s debate, are shown in blue.

Temperature increases have been noticeably more variable, although that variation is consistent with annual variations of the past.

Temp_To2015

The HadCRUT4 measures of the global annual surface temperature anomaly, as measured by the Hadley Centre and the Climatic Research Unit.

Now, back to the debate.

SenatorWongSenator Wong believed that the Earth’s temperature would continue to increase in line with increases in CO2 concentrations. We can characterize that by a regression model that has a linear relationship with atmospheric CO2 over the entire time period. Of course, Senator Wong’s position was not just influenced by the data, but also by the overwhelming majority of climate scientists who agreed with her position given their understanding the Earth’s climate system. Nevertheless, we will ignore that extra information here.

We can estimate the best fitting line for such a relationship, and predict the uncertainty around it – this uncertainty represents the range of predicted variation given that the recorded temperature at the Earth’s surface only approximates the heat content of the world. In the graphs I show here, the uncertainty bounds are 95% prediction intervals – we expect 95% of the observations to fall within the bound represented by the dashed lines.

Subsequently, we can determine how well that relationship fits the data that have been collected from 2009 onwards. With the CO2 concentration increasing, the Earth’s temperature has continued to increase. However, that increase has been somewhat below the average trend, with the notable exception of the data in 2015, which has exhibited a large spike.

Temp_To2015_Linear

Relationship between the global temperature anomaly and CO2 concentration measured at Mauna Loa. The solid line is a linear regression, and the dashed lines are the 95% prediction interval. The regression was estimated on data up until 2008 (black dots), and the predictions are compared to data for 2009-2015 (blue dots).

However, we can say that Senator Wong’s position is largely consistent with the data collected after 2009; her predictions fall within the uncertainty bounds. Also, it is worth noting that the large spike in temperature in 2015 might well have been larger given the magnitude of increase in the CO2 concentration.

SenatorFieldingSenator Fielding believed that the Earth’s temperature had stopped increasing after 1998. We can characterize that by a regression model that has a linear relationship with atmospheric CO2 up until 1998, and then a flat line after that period. Again, we can estimate the best fitting model for such a relationship, characterize the uncertainty around the predictions, and compare those predictions to the data collected from 2009 onwards.

 

Temp_To2015_Bent

Relationship between the global temperature anomaly and CO2 concentrations measured at Mauna Loa. The solid line is a piecewise linear regression that fits a sloped line to data up until 1998, and then a flat line from 1999 to 2008. Data for 1998 were removed to reduce the influence of cherry picking. The regression was estimated for data up until 2008 (black dots), and the predictions are compared to data for 2009-2015 (blue dots).

Senator Fielding’s position was also largely in line with the data up until 2014. While the model characterizing Senator Wong’s position was a touch on the high side of the data, the model characterizing Senator Fielding’s position notably under-predicted the temperature.

And Senator Fielding’s model severally under-predicts the temperature of 2015 – the temperature spike of 2015 is well outside the expected bounds, even when considering the variation in the data.

So, here we are 7 years and several governments after this political debate. The data  support Senator Wong’s position, and are now contradicting Senator Fielding’s position; the temperature continues to increase.

Note, the average temperature anomaly for 2016 so far is 0.979 C (based only on 2 months of HadCRUT4 data, so this is an uncertain estimate of the entirety of 2016). If that anomaly holds, we can conclude that Senator Fielding was sorely wrong, and even the model characterizing Senator Wong’s position might under-predict the temperate increase.

Seeing how atmospheric CO2 concentrations continue to increase, with concomitant increases in the heat content of the Earth, I can only conclude that the global community really should be acting much more rapidly. And I would hope that Australia would take the lead with this. I wonder the extent to which this will feature in the election campaign.

Posted in Communication, Probability and Bayesian analysis | Tagged , , , , , , , ,

While I was sleeping: optimising ecological surveys over space and time

With the recent online publication of a new paper, here’s a blog post about how the research arose – a fun confluence of mathematical and cognitive collaboration across two sides of the world. And some of it was achieved while I was sleeping…

Moore, A.L., and McCarthy, M.A. (in press). Optimising ecological survey effort over space and time. Methods in Ecology and Evolution. DOI: 10.1111/2041-210X.12564. An open access (author-submitted) version is via here.

I’ve been interested in imperfect detection during ecological surveys for a while now. It began in earnest when I worked with Brendan Wintle on the topic during his PhD. He was considering the question of required survey effort, and was building occupancy-detection models around the same time that Darryl MacKenzie, Drew Tyre, and Howard Stauffer were also working on this same model. Prior to that, my interest had been pique by Kirsten Parris’ work on imperfect detection of frogs.

bundaroo2

If searching this site for the cascade treefrog (Litoria pearsoniana), how many times should you go, realizing that activity varies from night to night so multiple visits would be useful, but we don’t want to incur multiple travel costs unnecessarily?

Since then, one branch of my research has considered the question of maximizing detections of species given a search budget. A key paper here is my work with Cindy Hauser on optimizing detections of species across landscapes. It is central to my new research, so if you want some background, see here. One of the key features of that paper is that the probability of failed detection at a site is modelled by the function:

q = exp(-bx),

with search effort x, and detection rate b.

Now, the model Cindy and I developed has two clear limitations. First, it ignores the cost of travelling to sites. Secondly, it assumes that the detection rate of species when present at a site is known precisely, and doesn’t vary from visit to visit (although it can vary from site to site).

However, we know that these assumptions are not likely to be met. Travel costs can be substantial in at least some surveys – if driving to a site that is far away, we might spend as much time in the car as actually searching for a species in the field. And the detection rate of species can vary from visit to visit at a site depending on the activity level of the animal, the flowering intensity of the plant, etc.

The combination of travel costs and variation in detection raises an interesting trade-off. If we want to maximize the chance of detecting a species at least once when it is present at a site, then we would want to visit the site once when the detection rate is highest if the detection rate varies. But if the variation in the detection rate is unpredictable (i.e., the rate is stochastic), then we would want to visit the site as many times as possible to increase the chance of visiting the site at least once when the detection rate was high.

However, travel costs impose a competing constraint; multiple visits to a site will impose a travel costs for each visit. Travel costs will eat into our budget of time for actually surveying the site, and we will want to visit a site as few times as possible, and spend more time at the site during each visit.

So, Alana Moore and I set out to investigate this issue. We first tackled question: “If we had a budget of time to spend surveying one site, how should we split that time over multiple visits?” We assumed that detection rates varied according to a log-normal distribution (with a particular mean and standard deviation), and then found the number of visits that optimized the expected probability of detecting the species at least once at the site.

The solution to this optimization was not particularly simple. We needed to find the number of visits (n) that minimized this lovely integral:

LovelyEquation.jpg

This integral is the expected probability of failed detection when detection rate varies according to a log-normal distribution with a given mean (μ) and standard deviation (σ). The model assumes a search budget of x, a per-visit cost of travel of c, and n surveys. We then find the number of surveys (the value of n) that minimizes this function.

While it is not possible to find the optimal value of n analytically, one can find an analytical approximation. This is achieved by approximating the integral using Laplace’s method, and then optimizing that approximation. (As an aside, I like the idea of 18th century mathematics coming to play with 21st century ecology.) We found that the coefficient of variation in the detection rate (σ/μ), the search budget scaled by the mean detection rate (x/μ), and the scaled travel cost (c/μ) drove the optimal number of visits, with the coefficient of variation (σ/μ) and the ratio of the budget to the travel cost (x/c) being most influential. You can get the details of the model here (free – open access). We even tested how well our optimization worked using data from a field experiment – it seemed to work quite well.

Now, I really liked that paper. In fact, the idea that we can find a simple solution that approximately optimizes a rather complicated integral is appealing. However, it doesn’t get us on the path to optimize effort over space and time; it is only restricted to finding the optimal solution when surveying one site with a given budget. For the multiple site case, we need to determine the optimal budget for each site, and determine for which sites that optimal budget is zero – the sites we shouldn’t bother visiting. The solution above results in equations that seem much too complicated for that task if we want to find analytical solutions.

However, a much simpler equation arises when the detection rate follows a gamma distribution, another distribution that is commonly used to model variables that are constrained to be positive, and which is somewhat substitutable for a log-normal.

At this point, Alana Moore and I started working on the following solution in unison. I was in Melbourne, and as I worked on it, Alana was sleeping in Toulouse. I emailed Alana about my progress before bed, and then Alana tackled the problem as I slept. It was incredibly efficient, and we cracked the solution in a matter of days. Here’s how it works…

Now, if detection rates follow a gamma distribution, that rather complicated integral that we see above is replaced by an integral that can be simplified to a hyperbolic function.

E[q] = (1+θ(x/nc))nk.

Here, θ and k are parameters of the gamma distribution that depend on the mean and standard deviation of the detection rate (θ = σ2/μ; and k = σ2/μ2), while the search budget (x), travel cost (c) and number of visits (n) are the same as defined previously.

With that expression, we can derive the number of visits that minimizes the probability of failed detection, given a particular search budget x. I won’t give that function here – it isn’t really needed, but you can see it in the paper.

But if we substitute that optimal number of visits back into the hyperbolic function, we can derive the smallest possible probability of failed detection. That is equal to:

E[q]min = exp(-x),

where h is a scaling factor. This is interesting in two ways. Firstly, the probability of failed detection, when optimized for the number of surveys, essentially has the same functional form as the model in Hauser and McCarthy (2009).

Secondly, the functional form of the scaling factor h is also interesting. It is simply a declining function of the product of c and the variance:mean ratio of the detection rate (θ).

ScalingCoefficient

If searching this site for the cascade treefrog (Litoria pearsoniana), how many times should you go, realizing that activity varies from night to night so multiple visits would be useful, but we don’t want to incur multiple travel costs unnecessarily?

Therefore, we can see that the combination of travel costs and variation in detection rate acts to reduce the average rate of detection (μ) and that this influence is simply a function of the product of two terms (c and θ).

This outcome was particularly exciting – look at the equation again for the expected number of failed detections:

E[q]min = exp(-x).

Alana noticed this functional form first – it is exciting because this is the same functional form as the model in Hauser and McCarthy (2009). Given that, it seemed that we might simply plug the modified function into the optimization machinery of Hauser and McCarthy (2009), and we could optimize searches over both space and time.

At this point, I felt like this:

JackieHappy2

However, we had a couple of snags to overcome first. The first one – a relatively minor issue – was that some solutions for the optimal number of searches led to results that were less than one; these results are untenable, so we needed to add a constraint that the smallest number of searches was zero or one.

The next issue was more important. The optimization of Hauser and McCarthy (2009) relies on a simple ranking scheme to choose which sites were surveyed. This ranking is possible, in part, because any search effort to a site is spent immediately on searching, and not travelling; the optimal solution is either to not search the site or to spend some positive amount of effort on searching. However, in the case of travel costs, the initial part of search effort allocated to a site will be spent on travelling to a site, so we shouldn’t bother searching a site unless the search effort is greater than the travel cost.

This consideration introduces a discontinuity into the solution – we either don’t search a site (x*=0), or we spend effort such that we allocate more than the travel cost on the site (x*>c). That discontinuity means that we cannot use the ranking approach of Hauser and McCarthy (2009) to determine which sites to survey.

Determining which sites to survey, in the absence of a simplifying algorithm, is a somewhat daunting task. Consider the case where we need to decide which of 300 sites to survey. In that case, there are 2300 different combinations of sites that can be surveyed.

Now 2 to the power of 300 is a very large number. In fact, it is approximately 2× 1090. To give you an idea of how large 2× 1090 is, we can compare it to the number of protons in the observable universe, which is approximately 1080 (apparently).

That is, searching through the combination of possible search strategies is approximately 20 billion times more involved than counting every proton in the observable universe. That is more difficult than I would have hoped.

At this point, I was feeling more like this:

JackieSad

Surely there had to be a better way. It seemed unlikely that this problem hadn’t been tackled before. Indeed, it turns out that the original solution that Cindy and I obtained is mathematically identical to the problem of searching for submarines, something that was solved by Bernard Koopman during World War II, and declassified in the 1950s. Surely the issue of fixed costs had been added already.

So, we started searching the Operations Research literature. The key was finding this paper by Vaibhav Srivastava and Francesco Bullo. I’ll admit that I didn’t understand it on first reading. In fact, I thought I didn’t understand it at all. But after a restless night in which I mulled over the problem in semi-sleep, I developed an algorithm that is essentially the same as in the Srivastava and Bullo paper. Brains sometimes work in strange ways (or at least mine does sometimes) – I must have gleaned enough from the Srivastava and Bullo paper on first reading to essentially replicate the idea, but I still don’t quite know how (the cases are a little differ, because we have a functional form that is not quite the same shape as imagined by Srivastava and Bullo).

The algorithm works by realising that the optimal solution occurs such that the marginal benefit of searching is the same across all sites that are searched. If we chose a particular marginal benefit, then we can select sites on the basis of the search efficiency; search efficiency can be measured by the reduction in the probability of failed detection divided by the total search effort for that site. Using a knapsack optimization approach, we rank sites according to this criterion, and then find the set of sites that fills the search budget (fills the knapsack). This ranking of sites will not find the optimal solution perfectly (because the items in the knapsack are discrete), but it works well.

Then, it is simply a matter of searching over the range of possible marginal benefits to find the optimal solution – we find the marginal benefit that leads to the largest reduction in missed detections when summed across all sites.This reduces the mind-bogglingly-large m-dimensional optimization problem (m being the number of sites that might be surveyed) to a one-dimensional problem – much more tractable.

In our new paper, we compared the solution from this algorithm to the true optimal case for a wide range of different parameter values, and show that the algorithm works well – it finds solutions for which the outcomes are very close to optimal.

So, that means we can determine the optimal allocation of search effort in space and time that finds the most occurrences of species in a landscape where sites vary in:

the probabilities of presence (or abundance) of the species;

the mean and standard deviation of the rate of detection; and

the cost of travel to the sites.

We are currently working on a few more tweaks where we relax another assumption or two of the Hauser and McCarthy model. But that is for further research…

If you want to read the paper that describes our new approach, see here for the journal website (requires subscription), or you can get a copy of the author-submitted version for free here.

 

 

 

Posted in CEED, Detectability, Ecological models, New research, Probability and Bayesian analysis | Tagged , , , , , , , , , , , ,

Postdoctoral Opportunities with the NESP Clean Air and Urban Landscapes Hub (CAUL)

The University of Melbourne node of the NESP Clean Air and Urban Landscapes Hub is advertising four Research Fellow (Level A) positions.  They are seeking candidates with expertise in amphibian ecology, urban ecology, urban greening and environmental psychology to contribute to research within the hub.  The amphibian ecology position forms part of a collaboration with the NESP Threatened Species Recovery Hub, and will be jointly based in the School of Ecosystem and Forest Sciences and the School of BioSciences.  The other three positions will be based in the School of Ecosystem and Forest Sciences.  The positions are fixed term until December 2017, and applications close on January 6th 2016.  More information and full position descriptions can be found at:

http://jobs.unimelb.edu.au/caw/en/job/887050/research-fellow-amphibian-ecology

http://jobs.unimelb.edu.au/caw/en/job/887051/research-fellow-urban-ecology

http://jobs.unimelb.edu.au/caw/en/job/887054/research-fellow-urban-greening

http://jobs.unimelb.edu.au/caw/en/job/887073/research-fellow-environmental-psychology

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Ecology and Environmental Sciences star in ERA15

The results of the latest assessment of research excellence in Australia have been released. Now, every university will spin the results to suit their own purpose*. While we can leave universities to report their results so they appear to shine in the best possible light, it would be interesting to see how different research fields performed.

Which are Australia’s strongest research fields? The broad research fields with the most universities rated above world standard are “Medical and Health Sciences” and “Environmental Science”.

ERA15_2Digit

The number of Australian universities “above” or “well above” world standard as rated by the Excellence in Research for Australia process in 2015 for each of the 22 broad research fields.

Following them are “Chemical Sciences”, “Biological Sciences”, and “Engineering”, with “Mathematical Sciences”, “Agricultural and Veterinary Sciences”, and “History and Archaeology” not far behind.

Within the two strong fields in which I am involved (Environmental Sciences and Biological Sciences), the strongest areas are “Environmental Science and Management” and “Ecology”. Somewhat perversely, “Ecological Applications” is separated from “Ecology” – many of the publications assigned to one during the ERA process could just have easily be assigned to the other.  However, it is clear that Environmental Sciences and Ecology are two of Australia’s strongest research fields.

ERA15_4Digit

The number of Australian universities “above” or “well above” world standard as assessed by the Excellence in Research for Australia process in 2015 for the disciplines within the Environmental Sciences and Biological Sciences fields.

This strength of Environmental Sciences and Ecology in Australia is also reflected in Australia’s representation in the list of the most highly-cited authors in the Thomson-Reuters list, something I’ve noted previously.

highlycited1

The proportion of the world’s most highly-cited scientists within each of Thomson-Reuters’ 21 research categories who have their primary affiliation in Australia. The field of Environment/Ecology tops the list for Australia – approximately 1 in 12 of the world’s most highly-cited ecologists/environmental scientists are Australian.

Some other interesting data exist in ERA15, such as total research funding (see below). With that much research funding, you’d hope medical research in Australia would perform well!

But in terms of bang for buck, it is hard to go past some other fields, such as mathematics, environmental sciences and history.

ERA15_Funding

Research funding to different fields for the three years 2011-2013 as reported for ERA15. Ecology makes up about 15% of the research income in Biological Sciences – a touch under $50 million annually.

So, while the Environmental Sciences and Ecology are not the most heavily funded, they are two of Australia’s strongest research fields. Not only that, this research, conducted across many of Australia’s universities, has a large impact, helping manage Australia’s and the world’s environment more efficiently.

So people, let’s recognize the excellence of environmental and ecological research that occurs across Australia!

* Footnote: ANU even devised their own method for ranking institutions, and you won’t be surprised to know that (judged by their own criteria) ANU won. That outcome was parroted by Campus Review, which failed to note that at least one other university out-performed ANU on at least one of their criteria (the proportion of broad research fields rated above word standard). Universities love playing the ranking game, but I’m surprised a news outlet would publish claims without checking them.

 

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Lecturer in Ecological Modelling

Come and work with us!We’re looking for an outstanding academic to join the School of BioSciences within QAECO. We are particularly interested in applicants with expertise in modelling the distributions of species or biodiversity, or more generally in spatial modelling, working with Dr Jane Elith and others within QAECO.

The closing date for applications is 25 August. Information about the position and how to apply is available at:
http://jobs.unimelb.edu.au/caw/en/job/886115/lecturer-in-ecological-modelling

Please consider applying. Also, please spread the word by drawing this opportunity to the attention of potential applicants.

Posted in Communication, Jobs | Tagged , ,

Alpine Grazing Update

My blog has been a little quiet lately. But I’ve written a few things elsewhere. The latest is an update on the issue of cattle grazing in the Alpine National Park. You can read that over at The Conversation – an article I wrote with Libby Rumpff and Georgia Garrard.

Posted in Cattle grazing in the Alpine National Park | Tagged , , , ,