A Lifetime of Research and Consulting in Environmental and Ecological Statistics Bryan F.J. Manly Western EcoSystems Technology, Laramie, Wyoming, USA Consulting in Environmental & Ecological Statistics Page 1 of 46 5 July 2013
Summary This talk describes how I first learned about statistics as a subject, met biologists and started working in the area of biological applications, and how this led to most of my work being to do with animals and fish in oceans and rivers. Consulting in Environmental & Ecological Statistics Page 2 of 46 5 July 2013
City University, London! After high school I went to the City University in London to do a degree in applied mathematics. There I saw statistics for the first time because it was an optional part of the applied mathematics syllabus in high school that our teacher said that he did not know anything about.! Later I realized that the teaching of statistics and operational research was not very good because the lecturers did really actually use the methods - one day I went with a group of other students to ask the lecturer in operational research for an example of when linear programming would be useful and he could not tell us one - which told us a lot. Consulting in Environmental & Ecological Statistics Page 3 of 46 5 July 2013
! Basically after getting my degree I had to teach myself statistics, although I knew quite a but about analysis of variance.! In the final university year everyone had to do a project. I chose one on the use of sequential testing for industrial quality control. When I submitted a paper on this to the Royal Statistical Society it was accepted for publication. Only later did I realize how lucky that was, and how it changed my life. This was lucky 1. Consulting in Environmental & Ecological Statistics Page 4 of 46 5 July 2013
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Fisons Limited, Felixstowe! My first job was with Fisons Limited, a company that was involved with the production of agricultural products, medical drugs, and lots of other things. I was in the technical assistance section that basically provided help to other staff with anything to do with computing and the analysis of data.! I soon became the main person doing statistical analyses and I gained my first experience of talking to scientists about their work and suggesting appropriate ways to deal with their data.! When I started work in 1966 Fisons did not have a computer so I often drove to London and ran my programs all night on a rented computer. Consulting in Environmental & Ecological Statistics Page 6 of 46 5 July 2013
The University of Salford! Although the work at Fisons was good, I wanted a job in a university. Because of my one published paper I got one as an Assistant Lecturer at the University of Salford. That is when I really had to start learning more statistics.! I was still working on sequential tests for quality control, with four more papers on that topic - not really very useful - to come. Consulting in Environmental & Ecological Statistics Page 7 of 46 5 July 2013
Meeting with a Biologist! My interest in applications of statistics in biology in general, and ecology in particular came about through a chance meeting in the tea room with Mike Parr from the Department of Biology who was collecting mark-recapture data on dragonflies as part of the PhD that he was working on. He had a question about using his data to estimate relative survival rates of dragonflies of different types. This was lucky 2.! I had no idea what mark-recapture data was about so Mike Parr explained, as follows. Consulting in Environmental & Ecological Statistics Page 8 of 46 5 July 2013
(a) Go to a pond where dragonflies are. (b) Catch as many as you can with nets. (c) Mark them on their wings with dots of paint to number them, and release them. (d) Repeat (a) and (b) for several days, recording when any marked dragonflies are recaptured. Consulting in Environmental & Ecological Statistics Page 9 of 46 5 July 2013
! Mike said that it is possible to estimate the size of a population when it is sampled, the survival rates between two sample times, and the number of new dragonflies joining the population between two sample times, using several old methods of analysis, including one developed by Ronald Fisher (Fisher and Ford, 1947), and the very new Jolly-Seber method (Jolly, 1965; Seber, 1965).! Mike had his data sheets on his desk to show how he recorded his results.! I asked him why people did not just estimate the probability of capture in a sample by the fraction of dragonflies captured out of those that were known to be alive because they were seen both in earlier and later samples (see below). Consulting in Environmental & Ecological Statistics Page 10 of 46 5 July 2013
! Having estimated this probability, the number of animals alive at the sample time can then be estimated by the total number of dragonflies collected divided by the probability of capture - very simple! Consulting in Environmental & Ecological Statistics Page 11 of 46 5 July 2013
What Mike's Data Looked Like (1 = capture, 0 = no capture on a sample day) Day Dragonfly 1 2 5 6 8 12 15 1 1 1 0 0 0 0 1 2 1 0 0 1 1 0 0 3 1 1 1 0 0 1 1 4 1 1 1 0 0 1 0 5 0 1 0 1 1 0 1 6 0 1 1 0 1 1 0 7 0 0 1 0 0 0 1................ Total 4 5 7 6 10 8 14 B&A 0 4 6 10 12 15 0 B&A&C 0 3 3 6 9 8 0 p 0.75 0.50 0.60 0.75 0.53 Est N 6.7 14.0 10.0 13.3 15.1 B&A = seen before and after sample time. B&A&C = seen before and after sample time and captured in sample. p = estimated probability of capture. EstN = estimated population size (Total/p). Consulting in Environmental & Ecological Statistics Page 12 of 46 5 July 2013
How a Statistician Might Record the Data Not so helpful for knowing what to do! Consulting in Environmental & Ecological Statistics Page 13 of 46 5 July 2013
! Mike said that did not know why people did not do that, and we passed on to discussing his survival rate problem. We decided to meet to discuss the problem again in a few days.! At the next meeting Mike was very excited. The method of estimating population size that I had suggested had never been published, although it was much simpler than the alternatives.! He said that we needed to write a paper about it immediately and get it published before anyone else noticed the method. We wrote the paper (Manly and Parr, 1968), and the Manly-Parr method for estimating population size later became well-known. Consulting in Environmental & Ecological Statistics Page 14 of 46 5 July 2013
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! This is an example of something that may often occur - it would not occur to someone taught about the standard methods to analyse mark-recapture data at university that there might be some simpler method available that no one had noticed - sometimes ignorance is helpful!! This method is still being used. On 27 June I was at a meeting of the U.S. Army Corps of engineers to discuss the estimation of fish survival in dams in the Columbia River and this paper was mentioned several times for possible use. Consulting in Environmental & Ecological Statistics Page 16 of 46 5 July 2013
! Mike introduced me to his friends and it soon became obvious that my future as a statistician would be much brighter if I worked with biological applications instead of quality control because there were plenty of interesting problems that were not difficult to solve and really needed solutions.! For example, no one had ever simulated the properties of estimators of markrecapture data - an easy thing to do and also easy to get a long paper published about it in a good ecology journal (Manly, 1970), plus a follow up paper in a statistics journal (Manly, 1971). Consulting in Environmental & Ecological Statistics Page 17 of 46 5 July 2013
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! I continued research and consulting in ecology in a similar way for many years, leading to a combination of joint papers with biologists and papers on my own concerned with more technical aspects of the statistics. Consulting in Environmental & Ecological Statistics Page 20 of 46 5 July 2013
University of Papua and New Guinea! I moved to the University of Papua New Guinea in 1970. There I was the only statistician in the country and I continued to work with biologists there and overseas, particularly on mark-recapture data and the developing area of statistical methods for estimating the effect of natural selection on animal populations.! My contract with the University of Papua and New Guinea ended in 1973. Although I had never been to New Zealand I had contacts with New Zealanders, including having written a paper with George Seber, who was about to leave a position at the University of Otago. This enabled me to get a job at the University of Otago, where I worked from 1973 to 2000. This was lucky 3. Consulting in Environmental & Ecological Statistics Page 21 of 46 5 July 2013
University of Otago! Through work with biologists I knew many people in the government Department of Conservation. One day I got a telephone call from the head office in Wellington. The caller said that the Department needed someone to analyse data on fisheries bycatch of marine mammals and birds - someone that would not be considered biassed by the fishing industry or environmental groups. He asked whether I was interested. I said yes although I knew nothing much about fisheries or bycatch.! Strangely enough, from that time onwards most of the consulting that I have done has involved animals and fish in rivers or in the sea. Consulting in Environmental & Ecological Statistics Page 22 of 46 5 July 2013
! It turned out that it is usual for all types of fisheries to occasionally catch birds or marine mammals and this causes concern if the bycatch rate is anything other than minor.! In New Zealand the main problem was bycatch of the New Zealand sea lion, which only bred on islands off the coast of New Zealand and was considered threatened because of the small population (about 12,000 animals) and limited breeding sites. Consulting in Environmental & Ecological Statistics Page 23 of 46 5 July 2013
! Catches of the sea lion occurred during squid fishing close to the breeding sites and government observers were put on some of the fishing vessels to record any bycatch.! The sampled bycatch is used to estimate the total bycatch from the whole fishing fleet, and if the estimate exceeds a critical number then the fishery is closed down, upsetting a lot of people who lose their jobs, etc.! I went to many meetings that were concerned with the New Zealand sea lion and other bycatch, and discovered that the staff from the Ministry of Fisheries and the Department of Conservation seemed to be suspicious of each other and sometimes seemed to disagree about policy. Consulting in Environmental & Ecological Statistics Page 24 of 46 5 July 2013
! Staff from both of the government departments seemed suspicious of the fishing industry representatives, and the fishing industry representatives seemed to be suspicious of everyone.! This was the first time that I had been involved in situations where the results from statistical analyses may have a big impact on government policies and there financial impact. That is when I realized that statisticians should not take sides. Instead they should just present the results of unbiased analyses of the data, and leave others to make the decisions about what to do. Consulting in Environmental & Ecological Statistics Page 25 of 46 5 July 2013
! I also realized that sometimes interested parties do not want to end the general confusion surrounding environmental issues because this may result in nothing much being done by whoever is in charge. Consulting in Environmental & Ecological Statistics Page 26 of 46 5 July 2013
CCAMLR! While in New Zealand I was also asked to be a representative for New Zealand on the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) - an international organization involving many countries around the world, but with a limited budget for research.! It relies mainly on individual governments supplying scientists to do whatever work is required. I was asked to join the Statistics Subcommittee of the Committee on Environmental Monitoring. Consulting in Environmental & Ecological Statistics Page 27 of 46 5 July 2013
! At the first meeting that I attended there were about 10 people present. Only the UK and New Zealand had thought that it would be useful to have a statistician on a Statistics Subcommittee!! The composition of the committee said a lot about the extent to which statisticians in general are thought of as being useful. I wondered what people think of a Biology Subcommittee with eight statisticians and two biologists.! The work of the committee really was all about statistics. It seemed that there may have been no statisticians on the subcommittee in the past because it soon became apparent that some of the statistics being done was wrong. Consulting in Environmental & Ecological Statistics Page 28 of 46 5 July 2013
! One example was that the method for detecting anomalous years had confused the standard error of the mean with the standard deviation of individual observations.! It is rather surprising that an international organization was publishing its annual report with some simple mistakes in the statistics, but it just highlights the need for statisticians to get involved with organizations like this, and realize the extremely important contributions that they can make, even if it is just getting the numbers right. Consulting in Environmental & Ecological Statistics Page 29 of 46 5 July 2013
Western EcoSystems Technology Inc.! I left New Zealand in 2000 to go to work for Western EcoSystems Technology Inc., a company that was started in 1990 by Lyman McDonald that I had worked with on research projects for quite a few years. I met him during a sabbatical leave at Louisiana State University in 1981 and visited him that year where he worked at the University of Wyoming.! Lyman came to New Zealand several times and I had a sabbatical year at the University of Wyoming in 1988. It was Lyman who noticed that some of my methods developed for analysing data on natural selection could be used to model resource selection by animals. This was lucky 4 because that developed later into a big field of interest for biologists. Consulting in Environmental & Ecological Statistics Page 30 of 46 5 July 2013
AMMOP! In Wyoming I soon got involved in the planning and analysis of data from the Alaska Marine Mammal Observer Program (AMMOP), which is concerned with the salmon driftnet and setnet fisheries in that state. It was my experience with work on New Zealand sea lions that got me the job.! Bycatch of marine mammals and birds does not seem to be much of an issue in Alaska, but this has to be demonstrated from data because of the Marine Mammal Protection Act. Consulting in Environmental & Ecological Statistics Page 31 of 46 5 July 2013
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! Since getting involved with AMMOP the Kodiak Island setnet fishery has been sampled (2002 and 2005) and the Yakutat fishery (2007 and 2008). Last year part of the Southeast Alaska driftnet fishery was sampled, and that is currently being sampled for a second year.! The design and analysis of the AMMOP studies are not very complicated, with the main issues being practical ones like how to know where and when fishing is taking place. Consulting in Environmental & Ecological Statistics Page 35 of 46 5 July 2013
A Conference in Dunedin on This Topic Consulting in Environmental & Ecological Statistics Page 36 of 46 5 July 2013
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The Sacramento-San Joaquin Delta! An ongoing example of conflict and cooperation with environmental problems concerns the decline in numbers of several species of fish in the Sacramento- San Joaquin Delta of California, and, in particular, the decline of the delta smelt, which been declared a threatened species under the U.S. Endangered Species Act.! A particular question here is whether the decline in fish numbers is caused to any appreciable extent by the export of water from the Delta for agricultural and town use, through the Tracy and Banks pumping stations. Consulting in Environmental & Ecological Statistics Page 38 of 46 5 July 2013
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! There are a large number of stakeholders involved in discussions surrounding the decline in fish numbers and the effect, if any, of water exports. These include private environmental organizations who say on their websites that exports are destroying the delta smelt and other fish populations, and various water users groups who believe that the effects of exports are minimal.! Representatives from many federal and Californian government departments are involved in the issue (Fish and Wildlife Service, Bureau of Reclamation, California Department of Water Resources, etc.). The opinions of these individuals apparently varies from a conviction that exports are the culprit to a belief that this is unlikely. Consulting in Environmental & Ecological Statistics Page 40 of 46 5 July 2013
! I have been involved in various issues related to the Sacramento-San Joaquin Delta, including the analysis of markrecapture experiments on salmon smelt to estimate survival rates, population modelling of delta smelt, and models for predicting salvage numbers from river flow variables.! It seems that work in this area will go on for ever. Consulting in Environmental & Ecological Statistics Page 41 of 46 5 July 2013
The Army Corps of Engineers! Since last year I have been a consultant for the U.S. Army Corps of Engineers (USACE) that is responsible for managing the many dams that have been built on the Columbia River. When the dams were built no one seems to have been worried about any adverse effects on the fish in the river. Now these adverse effects are very important.! One question concerns why the number of times that fish go through a dam bypass when going downstream is related to the probability that they will return to the river to breed two or more years later. In particular, the bypasses are supposed to increase survival but more bypasses seems to mean a lower probability of returning. Consulting in Environmental & Ecological Statistics Page 42 of 46 5 July 2013
! The Manly and Parr (1968) methods has been proposed for answering this question. This says that if fish are released upstream of a dam then the probability p i of being detected going through the bypass system of the ith dam further down river can be estimated by the proportion of fish released and seen below the ith dam that are detected at the ith dam, with the situation shown below.! Although this seems reasonable, it does not allow for the possibility that going through the bypass reduces the survival probability either immediately or later. Consulting in Environmental & Ecological Statistics Page 43 of 46 5 July 2013
! For example, if going through a bypass kills a fish immediately then the estimated probability of going through the bypass would be zero, which is not correct.! The big question for the USACE is now how to estimate the effects of going through a bypass if the probabilities of capture and survival are related. The answer does not seem to be obvious but an answer may exist. Consulting in Environmental & Ecological Statistics Page 44 of 46 5 July 2013
Conclusion My career in statistics has been affected by a number of lucky events:! Getting a job as an Assistant Lecturer with only a 2nd class honours degree because of a published paper.! Meeting a biologist and noticing a simple way to analyse mark-recapture data.! Writing a paper with George Seber that enabled me to get a job at the University of Otago.! Meeting Lyman McDonald that led to the initial development of statistical methods for resource selection by animals. Consulting in Environmental & Ecological Statistics Page 45 of 46 5 July 2013
! Other lucky coincidences are to do with why I went to Papua New Guinea rather than Africa in 1970, and why I went to Dunedin rather than Melbourne in 1973. Consulting in Environmental & Ecological Statistics Page 46 of 46 5 July 2013