Measuring abundance [book review]

This 2020 book, Measuring Abundance:  Methods for the Estimation of Population Size and Species Richness was written by Graham Upton, retired professor of applied statistics, for the Data in the Wild series published by Pelagic Publishing, a publishing company based in Exeter.

“Measuring the abundance of individuals and the diversity of species are core components of most ecological research projects and conservation monitoring. This book brings together in one place, for the first time, the methods used to estimate the abundance of individuals in nature.”

Its purpose is to provide a collection of statistical methods for measuring animal abundance or lack thereof. There are four parts: a primer on statistical methods, going no further than maximum likelihood estimation and bootstrap. The term Bayesian only occurs once, in connection with the (a-Bayesian) BIC. (I first spotted a second entry, until I realised this was not a typo and the example truly was about Bawean warty pigs!) The second part is about stationary (or static) individuals, such as trees, and it mostly exposes different recognised ways of sampling, with a focus on minimising the surveyor’s effort. Examples include forestry sampling (with a chainsaw method!) and underwater sampling. There is very little statistics involved in this part apart from the rare appearance of a MLE with an asymptotic confidence interval. There is also very little about misspecified models, except for the occasional warning that the estimates may prove completely wrong. The third part is about mobile individuals, with capture-recapture methods receiving the lion’s share (!). No lion was actually involved in the studies used as examples (but there were grizzly bears from Yellowstone and Banff National Parks). Given the huge variety of capture-recapture models, very little input is found within the book as the practical aspects are delegated to R software like the RMark and mra packages. Very little is written on using covariates or spatial features in such models, mostly dedicated to printed output from R packages with AIC as the sole standard for comparing models. I did not know of distance methods (Chapter 8), which are less invasive counting methods. They however seem to rely on a particular model of missing on individuals as the distance increases. The last section is about estimating the number of species. With again a model assumption that may prove wrong. With the inclusion of diversity measures,

The contents of the book are really down to earth and intended for field data gatherers. For instance, “drive slowly and steadily at 20 mph with headlights and hazard lights on ” (p.91) or “Before starting to record, allow fish time to acclimatize to the presence of divers” (p.91). It is unclear to me how useful the book would prove to be for general statisticians, apart from revealing the huge diversity of methods actually employed in the field. To either build upon these or expose students to their reassessment. More advanced books are McCrea and Morgan (2014), Buckland et al. (2016) and the most recent Seber and Schofield (2019).

[Disclaimer about potential self-plagiarism: this post or an edited version will eventually appear in my Book Review section in CHANCE.]

Cédric Villani on COVID-19 [and Zoom for the local COVID-19 seminar]

From the “start” of the COVID-19 crisis in France (or more accurately after lockdown on March 13), the math department at Paris-Dauphine has run an internal webinar around this crisis, not solely focusing on the math or stats aspects but also involving speakers from other domains, from epidemiology to sociology, to economics. The speaker today was [Field medalist then elected member of Parliament] Cédric Villani, as a member of the French Parliament sciences and technology committee, l’Office parlementaire d’évaluation des choix scientifiques et technologiques (OPECST), which adds its recommendations to those of the several committees advising the French government. The discussion was interesting as an insight on the political processing of the crisis and the difficulties caused by the heavy-handed French bureaucracy, which still required to fill form A-3-b6 in emergency situations. And the huge delays in launching a genuine survey of the range and diffusion of the epidemic. Which, as far as I understand, has not yet started….

Estudio nacional epidemiológico de la infección por SARS-CoV2 en España [a proper survey]

[A proper survey on the prevalence of the virus in the Spanish population has been launched, with 36,000 representative households chosen from census bases. Thanks to Victor for pointing out the survey!]

• Se desarrollará en las próximas semanas en colaboración con los servicios de salud de las CCAA.

• La Atención Primaria tendrá un papel relevante en la realización de un estudio que pretende estimar el porcentaje de la población española que ha desarrollado anticuerpos frente al nuevo coronavirus.

• En colaboración con el INE, se han seleccionado más de 36.000 hogares españoles, para que la muestra tenga participantes de todos los grupos de edad y localizaciones geográficas.

27 de abril de 2020.- Hoy comienza el Estudio Nacional Epidemiológico de la infección por SARS-CoV2 en España (ENE-COVID), diseñado por el Ministerio de Sanidad y el Instituto de Salud Carlos III (ISCIII) con la colaboración de las CCAA.

Las CCAA proporcionarán el personal sanitario para la realización del proyecto y serán las encargadas de adecuar la logística del estudio de la forma que se considere más adecuada en cada territorio, garantizando que se cumplen todos los requisitos metodológicos del estudio.

A través de las Consejerías de Sanidad o de los propios centros de salud, se irá citando a los participantes para la obtención de muestras. Las llamadas comenzarán este mismo lunes. “La participación es totalmente voluntaria”, ha destacado el ministro de Sanidad, Salvador Illa, “pero aprovecho para animar a todas las personas que sean contactadas a participar en el estudio. Los resultados serán de enorme utilidad para toda la sociedad española.

Con este estudio, el Ministerio de Sanidad y el ISCIII, dependiente del Ministerio de Ciencia e Innovación, en estrecha colaboración con las Comunidades Autónomas, pretenden estimar el porcentaje de la población española que ha desarrollado anticuerpos frente al nuevo coronavirus SARSCoV-2 (concepto conocido como seroprevalencia). La información obtenida será de enorme relevancia para la toma de decisiones de salud pública en el conjunto del Estado.

El papel de los servicios de Atención Primaria de Salud será especialmente relevante a lo largo de todo el proceso.

another surmortality graph

Another graph showing the recent peak in daily deaths throughout France as recorded by INSEE and plotted by Baptiste Coulmont from Paris 8 Sociology Department. And further discussed by Arthur Charpentier on Freakonometrics. With a few days off due to reporting, this brings an objective perspective on the impact of the epidemics (and of the quarantine) compared with the other years since 2001, without requiring tests or even surveys. (The huge peak in August 2003 was an heat wave that decimated elderly citizens throughout France.)

Monsieur le Président [reposted]

Let us carry out screening campaigns on representative samples of population!

Mr President of the Republic, as you rightly indicated, we are at war and everything must be done to combat the spread of CODIV-19. You had the wisdom to surround yourself with a Scientific Council and an Analysis, Research and Expertise Committee, both competent, and, as you know, applied mathematicians, statisticians have a role to play in this battle. Yes, to predict the evolution of the epidemic, mathematical models are used at different scales. This allows us estimate the number of people infected in the coming weeks and months. We are at war and these predictions are essential to the development of the best control strategy. They inform political decisions. This is especially with the help of these items of information that the confinement of the French population has been decided and renewed.

Mr President we are at war and these predictions must be the most robust possible. The more precise they are, the better the decisions they will guide. Mathematical models include a number of unknown parameters whose values ​​should be set based on expert advice or data. These include the transmission rate, incubation time, contagion time, and, of course, to initialize dynamic mathematical models, the number of covered individuals. To enjoy more reliable predictions, it is necessary to better estimate such crucial quantities. The proportion of healthy carriers appears to be a particularly critical parameter.

Mr President, we are at war and we must assess the proportions of healthy carriers by geographic areas. We do not currently have the means to implement massive screenings, but we can carry out surveys. This means, for a well-defined geographic area, to run biological tests on samples of individuals that are drawn at random and are representative of the total population of the area. Such data would come to supplement those already available and would considerably reduce the uncertainty in model predictions.

Mr. President, we are at war, let us give ourselves the means to fight effectively against this scourge. Thanks to a significant effort, the number of individuals that can be tested daily increases significantly, let’s devote some of these available tests to samples representative. For each individual drawn at random, we will perform a nasal swab, a blood test, let us collect clinical data and other items of information on its follow-up barriers. This would provide important information on the percentage of immunized French people. This data would open the possibility to feed mathematical models wisely, and hence to make informed decisions about the different strategies of deconfinement.

Mr. President, we are at war. This strategy, which could at first be deployed only in the most affected sectors, is, we believe, essential. It is doable: designing the survey and determining a representative sample is not an issue, going to the homes of the people in the sample, towards taking samples and having them fill out a questionnaire is also perfectly achievable if we give ourselves the means to do so. You only have to decide that a few of the available PCR tests and serological tests will be devoted to these statistical studies. In Paris and in the Grand Est, for instance, a mere few thousand tests on a representative population of individuals properly selected could better assess the situation and help in taking informed decisions.

Mr. President, a proposal to this effect has been presented to the Scientific Council and to the Analysis, Research and Expertise Committee that you have set up by a group of mathematicians at École Polytechnique with Professor Josselin Garnier at their head. You will realise by reading this tribune that the statistician that I am does support very strongly. I am in no way disputing the competence of the councils which support you but you have to act quickly and, I repeat, only dedicate a few thousand tests to statistics studies. Emergency is everywhere, assistance to the patients, to people in intensive care, must of course be the priority, but let us attempt to anticipate as well . We do not have the means to massively test the entire population, let us run polls.

Jean-Michel Marin
Professeur à l’Université de Montpellier
Président de la Société Française de Statistique
Directeur de l’Institut Montpelliérain Alexander Grothendieck
Vice-Doyen de la Faculté des Sciences de Montpellier