We report a novel technique to model abundance patterns of wintering seaducks in relation to the ... more We report a novel technique to model abundance patterns of wintering seaducks in relation to the construction of an offshore wind farm (OWF) based on seven years of aerial survey transect data. Distance sampling was used to estimate seaduck densities adjusted for covariates affecting detection probabilities. A generalized additive model (GAM) generated seaduck densities in sampling units in relation to spatially explicit covariates, using bootstrapping to account for uncertainties in both processes. Generalized estimating equations generated precision measures for the GAM robust to spatial and temporal autocorrelation. Comparison of pre- and post- construction model generated surfaces showed significant reductions in long-tailed duck numbers only within the OWF (despite the fact that the model was uninformed about the OWF location), although the absolute numbers involved were trivial in a flyway population context. This method provides quantification of distributional effects on org...
Deciding how best to t regression splines to data is a dicult non-linear optimization problem. In... more Deciding how best to t regression splines to data is a dicult non-linear optimization problem. In this paper we present a method for determining good ts using a spacially adaptive local smoothing algorithm (SALSA). We present results that show our method generates models that t as well as those generated by techniques using smoothing splines, and discuss an application of our technique that enables the automatic landmarking of certain object boundaries.
For both developers and government licensing organisations it is important to have the ability to... more For both developers and government licensing organisations it is important to have the ability to quantify spatially explicit change in the density and/or distribution of animals in and around marine renewables sites and, in particular, to identify if change occurs near renewables devices [1]. The publicly available MRSea package (Marine Renewable Strategic environmental assessment) [2] has recently been developed for analysing data collected for assessing potential impacts of renewable developments on marine wildlife, although the methods contained in this package have wide applicability. As a part of work commissioned by Marine Scotland, a number of candidate modelling methods were critically compared and the Complex REgion Spatial Smoother (CReSS) [3] with spatially adaptive knot placement using SALSA [4] was the recommended approach due to its success at locating spatially explicit impact-related change. The CReSS/SALSA approach was coupled with Generalised Estimating Equations ...
Collisions between aircraft and birds and other animals occur frequently and are known in the avi... more Collisions between aircraft and birds and other animals occur frequently and are known in the aviation industry as wildlife strikes. They are considered to be one of the most serious safety and financial risks to the global aviation industry. The International Civil Aviation Organisation, a United Nations specialised Agency, requires that the appropriate authority shall take action to eliminate or to prevent the establishment of any source which may attract wildlife to the aerodrome, or its vicinity, unless an appropriate wildlife assessment indicates that they are unlikely to create conditions conducive to a wildlife hazard problem. Namibian airports reduce the wildlife strike risk by managing the airport habitat and actively chasing birds and other hazardous animals away. The bird strike risk in airspace between airports is not managed or assessed in Namibia. Following one White-Backed Vulture strike and several reports of near-misses with vultures by pilots of small aircraft, thi...
Background: Clinicopathological scores are used to predict the likelihood of recurrence-free surv... more Background: Clinicopathological scores are used to predict the likelihood of recurrence-free survival for patients with clear cell renal cell carcinoma (ccRCC) after surgery. These are fallible, particularly in the middle range. This inevitably means that a significant proportion of ccRCC patients who will not develop recurrent disease enroll into clinical trials. As an exemplar of using digital pathology, we sought to improve the predictive power of “recurrence free” designation in localized ccRCC patients, by precise measurement of ccRCC nuclear morphological features using computational image analysis, thereby replacing manual nuclear grade assessment. Materials and Methods: TNM 8 UICC pathological stage pT1-pT3 ccRCC cases were recruited in Scotland and in Singapore. A Leibovich score (LS) was calculated. Definiens Tissue studio® (Definiens GmbH, Munich) image analysis platform was used to measure tumor nuclear morphological features in digitized hematoxylin and eosin (H&E) images. Results: Replacing human-defined nuclear grade with computer-defined mean perimeter generated a modified Leibovich algorithm, improved overall specificity 0.86 from 0.76 in the training cohort. The greatest increase in specificity was seen in LS 5 and 6, which went from 0 to 0.57 and 0.40, respectively. The modified Leibovich algorithm increased the specificity from 0.84 to 0.94 in the validation cohort. Conclusions: CcRCC nuclear mean perimeter, measured by computational image analysis, together with tumor stage and size, node status and necrosis improved the accuracy of predicting recurrence-free in the localized ccRCC patients. This finding was validated in an ethnically different Singaporean cohort, despite the different H and E staining protocol and scanner used. This may be a useful patient selection tool for recruitment to multicenter studies, preventing some patients from receiving unnecessary additional treatment while reducing the number of patients required to achieve adequate power within neoadjuvant and adjuvant clinical studies.
Background’Gold-standard’ data to evaluate linkage algorithms are rare. Synthetic data have the a... more Background’Gold-standard’ data to evaluate linkage algorithms are rare. Synthetic data have the advantage that all the true links are known. In the domain of population reconstruction, the ability to synthesize populations on demand, with varying characteristics, allows a linkage approach to be evaluated across a wide range of data. We have implemented ValiPop, a microsimulation model, for this purpose. ApproachValiPop can create many varied populations based upon sets of desired population statistics, thus allowing linkage algorithms to be evaluated across many populations, rather than across a limited number of real world ’gold-standard’ data sets. Given the potential interactions between different desired population statistics, the creation of a population does not necessarily imply that all desired population statistics have been met. To address this we have developed a statistical approach to validate the adherence of created populations to the desired statistics, using a gener...
Page 216. Predictive Modeling of Dominant Macroalgae Abundance on Temperate Island Shelves (Azore... more Page 216. Predictive Modeling of Dominant Macroalgae Abundance on Temperate Island Shelves (Azores, Northeast Atlantic) 8 Fernando Tempera1, 2, Monique MacKenzie3, Igor Bashmachnikov1, 4, Marji Puotinen5, Ricardo ...
... Andrews, St. Andrews, Fife KY16 9LZ, UK. c Forest Research, Northern Research Station, Roslin... more ... Andrews, St. Andrews, Fife KY16 9LZ, UK. c Forest Research, Northern Research Station, Roslin, Midlothian EH25 9SY, UK. ... Andrews, St. Andrews, Fife KY16 9LZ, UK. e Centre for Ecology and Hydrology Banchory, Hill of Brathens, Banchory, Kincardineshire AB31 4BW, UK. ...
One of the needs of the Pelagos Sanctuary for the Conservation of Mediterranean Marine Mammals is... more One of the needs of the Pelagos Sanctuary for the Conservation of Mediterranean Marine Mammals is information on critical habitats for cetaceans. This study modelled habitat use and preferences of fin whales and striped dolphins (the two most abundant species in the ...
ABSTRACT Investigation of activity budgets in relation to seasonal, intrinsic (age, sex) and extr... more ABSTRACT Investigation of activity budgets in relation to seasonal, intrinsic (age, sex) and extrinsic (time of day, spatial) covariates enables an understanding of how such covariates shape behavioural strategies. However, conducting such investigations in the wild is challenging, because of the required large sample size of individuals across the annual cycle, and difficulties in categorising behavioural states and analysing the resulting individual-referenced and serially correlated data. In this study, from telemetry tags deployed on 63 grey seals Halichoerus grypus and 126 harbour seals Phoca vitulina we used behavioural data, and movement data within a Bayesian state–space model (SSM), to define population-level activity budgets around Britain. Using generalised estimating equations (GEEs) we then examined how time spent in four states (resting on land (hauled out), resting at sea, foraging and travelling) was influenced by seasonal, intrinsic and extrinsic covariates. We present and discuss the following key findings. 1) We found no evidence that regional variation in foraging effort was linked to regional population trajectories in harbour seals. 2) Grey seals demonstrated sex-specific seasonal differences in their activity budgets, independent from those related to reproductive costs. 3) In these sympatric species there was evidence of temporal separation in time hauled out, but not in time foraging. 4) In both species, time spent resting at sea was separated into inshore (associated with tidal haul out availability) and offshore areas. Time spent resting at sea and on land was interchangeable to some extent, suggesting a degree of overlap in their functionality. This may result in a relaxation of the constraints associated with a central place foraging strategy. More generally, we demonstrate how a large dataset, incorporating differing tag parameters, can be analysed to define activity budgets and subsequently address important ecological questions.
Large-scale experimental studies are often needed to assess the effects of some intervention on n... more Large-scale experimental studies are often needed to assess the effects of some intervention on numbers of species of conservation interest. Buckland et al. 2009 developed a two-stage approach for analysing count data from such studies. In a first step, a ...
We report a novel technique to model abundance patterns of wintering seaducks in relation to the ... more We report a novel technique to model abundance patterns of wintering seaducks in relation to the construction of an offshore wind farm (OWF) based on seven years of aerial survey transect data. Distance sampling was used to estimate seaduck densities adjusted for covariates affecting detection probabilities. A generalized additive model (GAM) generated seaduck densities in sampling units in relation to spatially explicit covariates, using bootstrapping to account for uncertainties in both processes. Generalized estimating equations generated precision measures for the GAM robust to spatial and temporal autocorrelation. Comparison of pre- and post- construction model generated surfaces showed significant reductions in long-tailed duck numbers only within the OWF (despite the fact that the model was uninformed about the OWF location), although the absolute numbers involved were trivial in a flyway population context. This method provides quantification of distributional effects on org...
Deciding how best to t regression splines to data is a dicult non-linear optimization problem. In... more Deciding how best to t regression splines to data is a dicult non-linear optimization problem. In this paper we present a method for determining good ts using a spacially adaptive local smoothing algorithm (SALSA). We present results that show our method generates models that t as well as those generated by techniques using smoothing splines, and discuss an application of our technique that enables the automatic landmarking of certain object boundaries.
For both developers and government licensing organisations it is important to have the ability to... more For both developers and government licensing organisations it is important to have the ability to quantify spatially explicit change in the density and/or distribution of animals in and around marine renewables sites and, in particular, to identify if change occurs near renewables devices [1]. The publicly available MRSea package (Marine Renewable Strategic environmental assessment) [2] has recently been developed for analysing data collected for assessing potential impacts of renewable developments on marine wildlife, although the methods contained in this package have wide applicability. As a part of work commissioned by Marine Scotland, a number of candidate modelling methods were critically compared and the Complex REgion Spatial Smoother (CReSS) [3] with spatially adaptive knot placement using SALSA [4] was the recommended approach due to its success at locating spatially explicit impact-related change. The CReSS/SALSA approach was coupled with Generalised Estimating Equations ...
Collisions between aircraft and birds and other animals occur frequently and are known in the avi... more Collisions between aircraft and birds and other animals occur frequently and are known in the aviation industry as wildlife strikes. They are considered to be one of the most serious safety and financial risks to the global aviation industry. The International Civil Aviation Organisation, a United Nations specialised Agency, requires that the appropriate authority shall take action to eliminate or to prevent the establishment of any source which may attract wildlife to the aerodrome, or its vicinity, unless an appropriate wildlife assessment indicates that they are unlikely to create conditions conducive to a wildlife hazard problem. Namibian airports reduce the wildlife strike risk by managing the airport habitat and actively chasing birds and other hazardous animals away. The bird strike risk in airspace between airports is not managed or assessed in Namibia. Following one White-Backed Vulture strike and several reports of near-misses with vultures by pilots of small aircraft, thi...
Background: Clinicopathological scores are used to predict the likelihood of recurrence-free surv... more Background: Clinicopathological scores are used to predict the likelihood of recurrence-free survival for patients with clear cell renal cell carcinoma (ccRCC) after surgery. These are fallible, particularly in the middle range. This inevitably means that a significant proportion of ccRCC patients who will not develop recurrent disease enroll into clinical trials. As an exemplar of using digital pathology, we sought to improve the predictive power of “recurrence free” designation in localized ccRCC patients, by precise measurement of ccRCC nuclear morphological features using computational image analysis, thereby replacing manual nuclear grade assessment. Materials and Methods: TNM 8 UICC pathological stage pT1-pT3 ccRCC cases were recruited in Scotland and in Singapore. A Leibovich score (LS) was calculated. Definiens Tissue studio® (Definiens GmbH, Munich) image analysis platform was used to measure tumor nuclear morphological features in digitized hematoxylin and eosin (H&E) images. Results: Replacing human-defined nuclear grade with computer-defined mean perimeter generated a modified Leibovich algorithm, improved overall specificity 0.86 from 0.76 in the training cohort. The greatest increase in specificity was seen in LS 5 and 6, which went from 0 to 0.57 and 0.40, respectively. The modified Leibovich algorithm increased the specificity from 0.84 to 0.94 in the validation cohort. Conclusions: CcRCC nuclear mean perimeter, measured by computational image analysis, together with tumor stage and size, node status and necrosis improved the accuracy of predicting recurrence-free in the localized ccRCC patients. This finding was validated in an ethnically different Singaporean cohort, despite the different H and E staining protocol and scanner used. This may be a useful patient selection tool for recruitment to multicenter studies, preventing some patients from receiving unnecessary additional treatment while reducing the number of patients required to achieve adequate power within neoadjuvant and adjuvant clinical studies.
Background’Gold-standard’ data to evaluate linkage algorithms are rare. Synthetic data have the a... more Background’Gold-standard’ data to evaluate linkage algorithms are rare. Synthetic data have the advantage that all the true links are known. In the domain of population reconstruction, the ability to synthesize populations on demand, with varying characteristics, allows a linkage approach to be evaluated across a wide range of data. We have implemented ValiPop, a microsimulation model, for this purpose. ApproachValiPop can create many varied populations based upon sets of desired population statistics, thus allowing linkage algorithms to be evaluated across many populations, rather than across a limited number of real world ’gold-standard’ data sets. Given the potential interactions between different desired population statistics, the creation of a population does not necessarily imply that all desired population statistics have been met. To address this we have developed a statistical approach to validate the adherence of created populations to the desired statistics, using a gener...
Page 216. Predictive Modeling of Dominant Macroalgae Abundance on Temperate Island Shelves (Azore... more Page 216. Predictive Modeling of Dominant Macroalgae Abundance on Temperate Island Shelves (Azores, Northeast Atlantic) 8 Fernando Tempera1, 2, Monique MacKenzie3, Igor Bashmachnikov1, 4, Marji Puotinen5, Ricardo ...
... Andrews, St. Andrews, Fife KY16 9LZ, UK. c Forest Research, Northern Research Station, Roslin... more ... Andrews, St. Andrews, Fife KY16 9LZ, UK. c Forest Research, Northern Research Station, Roslin, Midlothian EH25 9SY, UK. ... Andrews, St. Andrews, Fife KY16 9LZ, UK. e Centre for Ecology and Hydrology Banchory, Hill of Brathens, Banchory, Kincardineshire AB31 4BW, UK. ...
One of the needs of the Pelagos Sanctuary for the Conservation of Mediterranean Marine Mammals is... more One of the needs of the Pelagos Sanctuary for the Conservation of Mediterranean Marine Mammals is information on critical habitats for cetaceans. This study modelled habitat use and preferences of fin whales and striped dolphins (the two most abundant species in the ...
ABSTRACT Investigation of activity budgets in relation to seasonal, intrinsic (age, sex) and extr... more ABSTRACT Investigation of activity budgets in relation to seasonal, intrinsic (age, sex) and extrinsic (time of day, spatial) covariates enables an understanding of how such covariates shape behavioural strategies. However, conducting such investigations in the wild is challenging, because of the required large sample size of individuals across the annual cycle, and difficulties in categorising behavioural states and analysing the resulting individual-referenced and serially correlated data. In this study, from telemetry tags deployed on 63 grey seals Halichoerus grypus and 126 harbour seals Phoca vitulina we used behavioural data, and movement data within a Bayesian state–space model (SSM), to define population-level activity budgets around Britain. Using generalised estimating equations (GEEs) we then examined how time spent in four states (resting on land (hauled out), resting at sea, foraging and travelling) was influenced by seasonal, intrinsic and extrinsic covariates. We present and discuss the following key findings. 1) We found no evidence that regional variation in foraging effort was linked to regional population trajectories in harbour seals. 2) Grey seals demonstrated sex-specific seasonal differences in their activity budgets, independent from those related to reproductive costs. 3) In these sympatric species there was evidence of temporal separation in time hauled out, but not in time foraging. 4) In both species, time spent resting at sea was separated into inshore (associated with tidal haul out availability) and offshore areas. Time spent resting at sea and on land was interchangeable to some extent, suggesting a degree of overlap in their functionality. This may result in a relaxation of the constraints associated with a central place foraging strategy. More generally, we demonstrate how a large dataset, incorporating differing tag parameters, can be analysed to define activity budgets and subsequently address important ecological questions.
Large-scale experimental studies are often needed to assess the effects of some intervention on n... more Large-scale experimental studies are often needed to assess the effects of some intervention on numbers of species of conservation interest. Buckland et al. 2009 developed a two-stage approach for analysing count data from such studies. In a first step, a ...
Uploads
Papers by Monique Mackenzie