Distance sampling with a random scale detection function

Cornelia Oedekoven was supported by a studentship jointly funded by the University of St Andrews and EP-SRC, through the National Centre for Statistical Ecology (EP-SRC Grant EP/C522702/1). Hans Skaug thanks the Center for Stock Assessment Research for facilitating his visit to University of California, Santa Cruz.Distance sampling was developed to estimate wildlife abundance from observational surveys with uncertain detection in the search area. We present novel analysis methods for estimating detection probabilities that make use of random effects models to allow for unmodeled heterogeneity in detection. The scale parameter of the half-normal detection function is modeled by means of an intercept plus an error term varying with detections, normally distributed with zero mean and unknown variance. In contrast to conventional distance sampling methods, our approach can deal with long-tailed detection functions without truncation. Compared to a fixed effect covariate approach, we think of the random effect as a covariate with unknown values and integrate over the random effect. We expand the random scale to a mixed scale model by adding fixed effect covariates. We analyzed simulated data with large sample sizes to demonstrate that the code performs correctly for random and mixed effect models. We also generated replicate simulations with more practical sample sizes (∼100) and compared the random scale half-normal with the hazard rate detection function. As expected each estimation model was best for different simulation models. We illustrate the mixed effect modeling approach using harbor porpoise vessel survey data where the mixed effect model provided an improved model fit in comparison to a fixed effect model with the same covariates. We propose that a random or mixed effect model of the detection function scale be adopted as one of the standard approaches for fitting detection functions in distance sampling.PostprintPeer reviewe

Report on estimating the size of dolphin schools, based on data obtained during a charter cruise of the M/V Gina Anne, October 11 -November 25, 1979

Estimates of dolphin school sizes made by observers and crew members aboard tuna seiners or by observers on ship or aerial surveys are important components of population estimates of dolphins which are involved in the yellowfin tuna fishery in the eastern Pacific. Differences in past estimates made from tuna seiners and research ships and aircraft have been noted by Brazier (1978). To compare various methods of estimating dolphin school sizes a research cruise was undertaken with the following major objectives: 1) compare estimates made by observers aboard a tuna seiner and in the ship's helicopter, from aerial photographs, and from counts made at the backdown channel, 2) compare estimates of observers who are told the count of the school size after making their estimate to the observer who is not aware of the count to determine if observers can learn to estimate more accurately, and 3) obtain movie and still photographs of dolphin schools of known size at various stages of chase, capture and release to be used for observer training. The secondary objectives of the cruise were to: 1) obtain life history specimens and data from any dolphins that were killed incidental to purse seining. These specimens and data were to be analyzed by the U.S. National Marine Fisheries Service ( NMFS ) , 2) record evasion tactics of dolphin schools by observing them from the helicopter while the seiner approached the school, 3) examine alternative methods for estimating the distance and bearing of schools where they were first sighted, 4) collect the Commission's standard cetacean sighting, set log and daily activity data and expendable bathythermograph data. (PDF contains 31 pages.

Aerial Surveys for Cetaceans in the Former Akutan, Alaska, Whaling Grounds

Randomized aerial surveys were flown between 26 July and 26 August 1984 to search for cetaceans in two areas of southwestern Alaska: one on both Bering Sea and Pacific Ocean sides of the Aleutian Islands near the defunct Akutan shore-whaling station, which operated from 1912 through 1938, the other overlapping continental slope and shallow continental shelf waters between the Aleutians and the Pribilof Islands. ... Searches covered about 3940 nautical miles (nm), including some 2403 nm of random transects. Sightings were made of gray whales (10 sightings, 14 individuals), fin whales (3, 11), minke whales (1, 1), unidentified beaked whales (1, 6), Dall's porpoises (47, 131), killer whales (8, 26), and harbor porpoises (4, 7). A Fourier series model was used to estimate density of Dall's porpoises as 115 individuals (CV=0.263) per 1000 sq nm on the whaling grounds and 16.6 individuals (CV=0.0) per sq nm in the Bering Sea north of the whaling grounds. These estimates are comparable to those previously reported for the same general areas (97.2 animals per 1000 sq nm, SD=49.5). There were too few sightings of other cetaceans to permit calculation of meaningful density estimates. At least four species of great whales (blue, fin, humpback and sperm) were sufficiently abundant during the first four decades of this century to support significant whaling activities within about 100 sq nm of Akutan (more than 5300 whales were caught during 23 years of whaling, 1912-39). Although previous studies of the fisheries showed a downward trend in catch per unit of effort and an increase in distance traveled to take whales, whales were still being taken at relatively high rates (0.28-0.51 whales per gross catcher day) at the end of the fishery in 1939. Populations of fin, humpback, blue and sperm whales were probably significantly reduced by shore and pelagic whaling conducted widely in the North Pacific since 1939. ...Key words: aerial surveys, cetaceans, Bering Sea, North Pacific Ocean, historical whaling Des relevés aériens ont été effectués au hasard entre le 26 juillet et le 26 août 1984, afin de déterminer la présence de cétacés dans deux régions du Sud-Ouest de l'Alaska : l'une située des deux côtés des îles Aléoutiennes (du côté de la mer de Béring et du côté de l'océan Pacifique), près de ce qui fut jadis le port baleinier d'Akukan qui resta en opération de 1912 à 1939; l'autre couvrant à la fois les eaux du talus continental et celles, peu profondes, de la plate-forme continentale, entre les îles Aléoutiennes et les îles Pribilof. Les relevés furent effectuées à des altitudes comprises entre 150 et 245 m, d'un appareil d'observation Partenavia P68, muni d'un nez de plexiglas, permettant de voir dans l'axe de déplacement. Les recherches ont été effectuées sur environ 3940 milles nautiques (mn), y compris 2403 mn de recoupements au hasard. One a relevé la présence de baleines grises (10 relevés, 14 individus), de rorquals communs (3, 11), de petits rorquals (1, 1), de baleines à bec non identifiées (1, 6), de marsouins de Dall (47, 131), d'épaulards (8, 26) et de marsouins communs. On a utilisé un modèle en séries de Fourier pour déterminer approximativement la densité de marsouins de Dall à 115 individus (CV = 0.263) aux 1000 mn² dans les zones de pêche à la baleine, et à 16.6 individus (CV = 0.0) aux 1000 mn² dans la mer de Béring au nord des zones de pêche. Ces évaluations sont comparables à celles rapportées précédemment pour ces mêmes zones en général (97.2 animaux aux 1000 mn², DS = 49.5). Trop peu d'autres cétacés ont été aperçus pour justifier le calcul des densités approximatives. Durant les quarante premières années de ce siècle, il y avait au moins quatre espèces de grandes baleines (rorquals bleus, rorquals communs, rorquals à bosse et cachalots) en quantité suffisante pour alimenter une industrie baleinière dans un rayon d'environ 100 mn d'Akutan. (Plus de 5300 baleines furent pêchées durant les 23 années que dura la pêche à la baleine, de 1912 à 1939). Bien que des études précédentes sur la pêche aient montré une tendance à la baisse du nombre de prises par rapport au nombre d'unités d'effort et une augmentation de la distance à parcourir pour capturer les baleines, celles-ci étaient capturées à un taux relativement élevé (de 0.28 à 0.51 baleine par unité d'effort brute par jour) à la fin de la pêche en 1939. Les populations de rorquals communs, de rorquals à bosse, de rorquals bleus et de cachalots ont probablement été réduites de façon significative par le pêche côtière et la pêche pélagique, qui ont été pratiquées à grande échelle dans le Pacifique Nord depuis 1939. Le petit nombre de cétacés aperçus durant les présents relevés porte à croire que les populations dans les zones de pêche et dans leur vicinité, restent peu élevées en raison de ces activités. Mots clés : relevé aérien, cétacés, mer de Béring, Pacifique Nord, ancienne pêche à la balein

Baffin Bay Narwhal Population Distribution and Numbers: Aerial Surveys in the Canadian High Arctic, 2002–04

Aerial surveys of narwhals (Monodon monoceros) were conducted in the Canadian High Arctic during the month of August from 2002 to 2004. The surveys covered the waters of Barrow Strait, Prince Regent Inlet, the Gulf of Boothia, Admiralty Inlet, Eclipse Sound, and the eastern coast of Baffin Island, using systematic sampling methods. Fiords were flown along a single transect down the middle. Near-surface population estimates increased by 1.9 %– 8.7% when corrected for perception bias. The estimates were further increased by a factor of approximately 3, to account for individuals not seen because they were diving when the survey plane flew over (availability bias). These corrections resulted in estimates of 27 656 (SE = 14 939) for the Prince Regent and Gulf of Boothia area, 20 225 (SE = 7285) for the Eclipse Sound area, and 10 073 (SE = 3123) for the East Baffin Island fiord area. The estimate for the Admiralty Inlet area was 5362 (SE = 2681) but is thought to be biased. Surveys could not be done in other known areas of occupation, such as the waters of the Cumberland Peninsula of East Baffin, and channels farther west of the areas surveyed (Peel Sound, Viscount Melville Sound, Smith Sound and Jones Sound, and other channels of the Canadian Arctic archipelago). Despite these probable biases and the incomplete coverage, results of these surveys show that the summering range of narwhals in the Canadian High Arctic is vast. If narwhals are philopatri to their summering areas, as they appear to be, the total population of that range could number more than 60 000 animals. The largest numbers are in the western portion of their summer range, around Somerset Island, and also in the Eclipse Sound area. However, these survey estimates have large variances due to narwhal aggregation in some parts of the surveyed areas.Des levés aériens ont été effectués dans l’Extrême arctique canadien dans le but de répertorier les populations de narvals (Monodon monoceros) et ce, du mois d’août 2002 à août 2004. Les levés, réalisés à l’aide de méthodes d’échantillonnage systémiques, visaient les eaux du détroit de Barrow, de l’inlet Prince-Régent, du golfe de Boothia, de l’inlet de l’Amirauté, du détroit d’Éclipse et de la côte est de l’île de Baffin. Les fiords ont été survolés le long d’un simple transect situé dans le milieu. Les estimations de population près de la surface augmentaient de 1,9 % à 8,7 % une fois redressées pour tenir compte du biais de perception. Par ailleurs, les estimations ont été de nouveau révisées à la hausse moyennant un facteur d’environ 3 afin de tenir compte des individus qui n’ont pas été vus parce qu’ils se mettaient à plonger en présence de l’avion effectuant les levés (biais de disponibilité). Ces redressements ont donné lieu à des estimations de 27 656 (SE = 14 939) pour la région de l’inlet Prince-Régent et du golfe de Boothia, de 20 225 (SE = 7 285) pour la région du détroit d’Éclipse et de 10 073 (SE = 3 123) pour la région du fiord de l’est de l’île de Baffin. Quand à l’inlet de l’Amirauté, l’estimation s’est chiffrée à 5 362 (SE = 2 681), mais l’on croit que cette estimation pourrait être biaisée. Des levés n’ont pas pu être effectués dans d’autres zones d’occupation connues, comme dans les eaux de la péninsule Cumberland dans l’est de Baffin de même que dans les chenaux plus à l’ouest des régions examinées (détroit de Peel, détroit du Vicomte de Melville, détroit de Smith, détroit de Jones et d’autres chenaux de l’archipel Arctique canadien). Malgré la possibilité que les données soient biaisées et que certaines zones n’aient pas été examinées, les résultats de ces levés montrent que la répartition d’été des narvals dans l’Extrême arctique canadien est vaste. Si les narvals sont philopatriques à leurs aires d’été, comme il semblerait être le cas, la population totale de ce parcours pourrait dépasser les 60 000 individus. Les plus grands nombres se trouvent dans la partie ouest de cette répartition, soit près de l’île Somerset et dans la région du détroit d’Éclipse. Cependant, les estimations découlant de ces levés ont de grandes variances en raison du regroupement des narvals dans certaines parties des régions visées par les levés

Death in hospital following ICU discharge : insights from the LUNG SAFE study

Background: To determine the frequency of, and factors associated with, death in hospital following ICU discharge to the ward. Methods: The Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE study was an international, multicenter, prospective cohort study of patients with severe respiratory failure, conducted across 459 ICUs from 50 countries globally. This study aimed to understand the frequency and factors associated with death in hospital in patients who survived their ICU stay. We examined outcomes in the subpopulation discharged with no limitations of life sustaining treatments (‘treatment limitations’), and the subpopulations with treatment limitations. Results: 2186 (94%) patients with no treatment limitations discharged from ICU survived, while 142 (6%) died in hospital. 118 (61%) of patients with treatment limitations survived while 77 (39%) patients died in hospital. Patients without treatment limitations that died in hospital after ICU discharge were older, more likely to have COPD, immunocompromise or chronic renal failure, less likely to have trauma as a risk factor for ARDS. Patients that died post ICU discharge were less likely to receive neuromuscular blockade, or to receive any adjunctive measure, and had a higher pre- ICU discharge non-pulmonary SOFA score. A similar pattern was seen in patients with treatment limitations that died in hospital following ICU discharge. Conclusions: A significant proportion of patients die in hospital following discharge from ICU, with higher mortality in patients with limitations of life-sustaining treatments in place. Non-survivors had higher systemic illness severity scores at ICU discharge than survivors. Trial Registration: ClinicalTrials.gov NCT02010073

Identifying associations between diabetes and acute respiratory distress syndrome in patients with acute hypoxemic respiratory failure : an analysis of the LUNG SAFE database

Background: Diabetes mellitus is a common co-existing disease in the critically ill. Diabetes mellitus may reduce the risk of acute respiratory distress syndrome (ARDS), but data from previous studies are conflicting. The objective of this study was to evaluate associations between pre-existing diabetes mellitus and ARDS in critically ill patients with acute hypoxemic respiratory failure (AHRF). Methods: An ancillary analysis of a global, multi-centre prospective observational study (LUNG SAFE) was undertaken. LUNG SAFE evaluated all patients admitted to an intensive care unit (ICU) over a 4-week period, that required mechanical ventilation and met AHRF criteria. Patients who had their AHRF fully explained by cardiac failure were excluded. Important clinical characteristics were included in a stepwise selection approach (forward and backward selection combined with a significance level of 0.05) to identify a set of independent variables associated with having ARDS at any time, developing ARDS (defined as ARDS occurring after day 2 from meeting AHRF criteria) and with hospital mortality. Furthermore, propensity score analysis was undertaken to account for the differences in baseline characteristics between patients with and without diabetes mellitus, and the association between diabetes mellitus and outcomes of interest was assessed on matched samples. Results: Of the 4107 patients with AHRF included in this study, 3022 (73.6%) patients fulfilled ARDS criteria at admission or developed ARDS during their ICU stay. Diabetes mellitus was a pre-existing co-morbidity in 913 patients (22.2% of patients with AHRF). In multivariable analysis, there was no association between diabetes mellitus and having ARDS (OR 0.93 (0.78-1.11); p = 0.39), developing ARDS late (OR 0.79 (0.54-1.15); p = 0.22), or hospital mortality in patients with ARDS (1.15 (0.93-1.42); p = 0.19). In a matched sample of patients, there was no association between diabetes mellitus and outcomes of interest. Conclusions: In a large, global observational study of patients with AHRF, no association was found between diabetes mellitus and having ARDS, developing ARDS, or outcomes from ARDS. Trial registration: NCT02010073. Registered on 12 December 2013

Antarctic pack-ice seal research, February and March 1995

As upper trophic level predators with a circumpolar distribution, the antarctic pack ice seals (crabeater, Lobodon carcinophagus; leopard, Hydrurga leptonyx; Ross, Ommatophoca rossii; and Weddell, Leptonychotes weddelli) provide a potential source of information about ecosystem interactions and environmental variability integrated over a wide range of spatial and temporal scales. In recent years, increasing attention has been focused on the need to conduct antarctic pack-ice seal research, and a multifaceted international research initiative to address priority pack-ice seal research topics is being developed: the Antarctic Pack Ice Seals (APIS) Program