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Article: A need for speed in Bayesian population models: a practical guide to marginalizing and recovering discrete latent states.

Yackulic, Charles B / Dodrill, Michael / Dzul, Maria / Sanderlin, Jamie S / Reid, Janice A

Ecological applications : a publication of the Ecological Society of America

2020 Volume 30, Issue 5, Page(s) e02112

Abstract: Bayesian population models can be exceedingly slow due, in part, to the choice to simulate discrete latent states. Here, we discuss an alternative approach to discrete latent states, marginalization, that forms the basis of maximum likelihood population ... ...

Abstract	Bayesian population models can be exceedingly slow due, in part, to the choice to simulate discrete latent states. Here, we discuss an alternative approach to discrete latent states, marginalization, that forms the basis of maximum likelihood population models and is much faster. Our manuscript has two goals: (1) to introduce readers unfamiliar with marginalization to the concept and provide worked examples and (2) to address topics associated with marginalization that have not been previously synthesized and are relevant to both Bayesian and maximum likelihood models. We begin by explaining marginalization using a Cormack-Jolly-Seber model. Next, we apply marginalization to multistate capture-recapture, community occupancy, and integrated population models and briefly discuss random effects, priors, and pseudo-R
MeSH term(s)	Bayes Theorem ; Computer Simulation ; Likelihood Functions ; Models, Statistical ; Population Density ; Population Dynamics
Language	English
Publishing date	2020-04-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1074505-1
ISSN	1939-5582 ; 1051-0761
ISSN (online)	1939-5582
ISSN	1051-0761
DOI	10.1002/eap.2112
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Article ; Online: Occupancy modeling and resampling overcomes low test sensitivity to produce accurate SARS-CoV-2 prevalence estimates.

Sanderlin, Jamie S / Golding, Jessie D / Wilcox, Taylor / Mason, Daniel H / McKelvey, Kevin S / Pearson, Dean E / Schwartz, Michael K

BMC public health

2021 Volume 21, Issue 1, Page(s) 577

Abstract: Background: We evaluated whether occupancy modeling, an approach developed for detecting rare wildlife species, could overcome inherent accuracy limitations associated with rapid disease tests to generate fast, accurate, and affordable SARS-CoV-2 ... ...

Abstract	Background: We evaluated whether occupancy modeling, an approach developed for detecting rare wildlife species, could overcome inherent accuracy limitations associated with rapid disease tests to generate fast, accurate, and affordable SARS-CoV-2 prevalence estimates. Occupancy modeling uses repeated sampling to estimate probability of false negative results, like those linked to rapid tests, for generating unbiased prevalence estimates. Methods: We developed a simulation study to estimate SARS-CoV-2 prevalence using rapid, low-sensitivity, low-cost tests and slower, high-sensitivity, higher cost tests across a range of disease prevalence and sampling strategies. Results: Occupancy modeling overcame the low sensitivity of rapid tests to generate prevalence estimates comparable to more accurate, slower tests. Moreover, minimal repeated sampling was required to offset low test sensitivity at low disease prevalence (0.1%), when rapid testing is most critical for informing disease management. Conclusions: Occupancy modeling enables the use of rapid tests to provide accurate, affordable, real-time estimates of the prevalence of emerging infectious diseases like SARS-CoV-2.
MeSH term(s)	Bayes Theorem ; COVID-19/diagnosis ; COVID-19/epidemiology ; Humans ; Mass Screening/methods ; Models, Theoretical ; Prevalence ; SARS-CoV-2 ; Sensitivity and Specificity
Language	English
Publishing date	2021-03-23
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1471-2458
ISSN (online)	1471-2458
DOI	10.1186/s12889-021-10609-y
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Article: Precision gain versus effort with joint models using detection/non-detection and banding data.

Sanderlin, Jamie S / Block, William M / Strohmeyer, Brenda E / Saab, Victoria A / Ganey, Joseph L

Ecology and evolution

2019 Volume 9, Issue 2, Page(s) 804–817

Abstract: Capture-recapture techniques provide valuable information, but are often more cost-prohibitive at large spatial and temporal scales than less-intensive sampling techniques. Model development combining multiple data sources to leverage data source ... ...

Abstract	Capture-recapture techniques provide valuable information, but are often more cost-prohibitive at large spatial and temporal scales than less-intensive sampling techniques. Model development combining multiple data sources to leverage data source strengths and for improved parameter precision has increased, but with limited discussion on precision gain versus effort. We present a general framework for evaluating trade-offs between precision gained and costs associated with acquiring multiple data sources, useful for designing future or new phases of current studies.We illustrated how Bayesian hierarchical joint models using detection/non-detection and banding data can improve abundance, survival, and recruitment inference, and quantified data source costs in a northern Arizona, USA, western bluebird (
Language	English
Publishing date	2019-02-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2635675-2
ISSN	2045-7758
ISSN	2045-7758
DOI	10.1002/ece3.4825
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Article ; Online: Factors affecting lifetime reproduction, long-term territory-specific reproduction, and estimation of habitat quality in northern goshawks.

Reynolds, Richard T / Lambert, Jeffrey S / Kay, Shannon L / Sanderlin, Jamie S / Bird, Benjamin J

PloS one

2019 Volume 14, Issue 5, Page(s) e0215841

Abstract: One measure of habitat quality is a species' demographic performance in a habitat and the gold standard metric of performance is reproduction. Such a measure, however, may be misleading if individual quality is a fitness determinant. We report on factors ...

Abstract	One measure of habitat quality is a species' demographic performance in a habitat and the gold standard metric of performance is reproduction. Such a measure, however, may be misleading if individual quality is a fitness determinant. We report on factors affecting lifetime reproduction (LR), the total number of lifetime fledglings produced by an individual, and long-term territory-specific reproduction in a multi-generational study of northern goshawks (Accipiter gentilis). LR increased with longer lifespans and more breeding attempts and was strongly correlated with the number of recruits in two filial generations indicating that LR was a good fitness predictor. Extensive differences in LR attested to heterogeneity in individual quality, a requisite for the ideal pre-emptive distribution model (IPD) of habitat settling wherein high quality individuals get the best habitats forcing lower quality individuals into poorer habitats with lower reproduction. In response to 7‒9-year prey abundance cycles, annual frequency of territory occupancy by breeders was highly variable and low overall with monotonic increases in vacancies through low prey years. Occupancy of territories by breeders differed from random; some appeared preferred while others were avoided, producing a right-skewed distribution of total territory-specific fledgling production. However, mean fledglings per nest attempt was only slightly lower in less versus more productive territories, and, contrary to IPD predictions of increases in annual territory-specific coefficients of variation (CV) in reproduction as breeder densities increase, the CV of production decreased as density increased. Rather than habitat quality per se, conspecific attraction elicited territory selection by prospecting goshawks as 70% of settlers comprised turnovers on territories, resulting in occupancy continuity and increased territory-specific reproduction. Top-producing territories had as few as 2 long-lived (high LR) and up to 6 short-lived (low LR) sequential breeders. While individual quality appeared to effect territory-specific heterogeneity in reproductive performance, our data suggests that differences in individual quality may be washed-out by a random settling of prospectors in response to conspecific attraction.
MeSH term(s)	Animals ; Birds/physiology ; Breeding ; Ecosystem ; Longevity ; Population Dynamics ; Predatory Behavior ; Reproduction
Language	English
Publishing date	2019-05-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0215841
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Article: A need for speed in Bayesian population models: a practical guide to marginalizing and recovering discrete latent states

Yackulic, Charles B / Dodrill, Michael / Dzul, Maria / Sanderlin, Jamie S / Reid, Janice A

Ecological applications. 2020 July, v. 30, no. 5

2020

Abstract	Bayesian population models can be exceedingly slow due, in part, to the choice to simulate discrete latent states. Here, we discuss an alternative approach to discrete latent states, marginalization, that forms the basis of maximum likelihood population models and is much faster. Our manuscript has two goals: (1) to introduce readers unfamiliar with marginalization to the concept and provide worked examples and (2) to address topics associated with marginalization that have not been previously synthesized and are relevant to both Bayesian and maximum likelihood models. We begin by explaining marginalization using a Cormack‐Jolly‐Seber model. Next, we apply marginalization to multistate capture–recapture, community occupancy, and integrated population models and briefly discuss random effects, priors, and pseudo‐R². Then, we focus on recovery of discrete latent states, defining different types of conditional probabilities and showing how quantities such as population abundance or species richness can be estimated in marginalized code. Last, we show that occupancy and site‐abundance models with auto‐covariates can be fit with marginalized code with minimal impact on parameter estimates. Marginalized code was anywhere from five to >1,000 times faster than discrete code and differences in inferences were minimal. Discrete latent states and fully conditional approaches provide the best estimates of conditional probabilities for a given site or individual. However, estimates for parameters and derived quantities such as species richness and abundance are minimally affected by marginalization. In the case of abundance, marginalized code is both quicker and has lower bias than an N‐augmentation approach. Understanding how marginalization works shrinks the divide between Bayesian and maximum likelihood approaches to population models. Some models that have only been presented in a Bayesian framework can easily be fit in maximum likelihood. On the other hand, factors such as informative priors, random effects, or pseudo‐R² values may motivate a Bayesian approach in some applications. An understanding of marginalization allows users to minimize the speed that is sacrificed when switching from a maximum likelihood approach. Widespread application of marginalization in Bayesian population models will facilitate more thorough simulation studies, comparisons of alternative model structures, and faster learning.
Keywords	Bayesian theory ; mark-recapture studies ; models ; species abundance ; species richness ; statistical analysis
Language	English
Dates of publication	2020-07
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; JOURNAL ARTICLE
ZDB-ID	1074505-1
ISSN	1939-5582 ; 1051-0761
ISSN (online)	1939-5582
ISSN	1051-0761
DOI	10.1002/eap.2112
Database	NAL-Catalogue (AGRICOLA)

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Article: Climate refugia for Pinus spp. in topographic and bioclimatic environments of the Madrean sky islands of México and the United States

Haire, Sandra L. / Villarreal, Miguel L. / Cortés-Montaño, Citlali / Flesch, Aaron D. / Iniguez, José M. / Romo-Leon, Jose Raul / Sanderlin, Jamie S.

Plant ecology. 2022 May, v. 223, no. 5

2022

Abstract: Climate refugia, or places where habitats are expected to remain relatively buffered from regional climate extremes, provide an important focus for science and conservation planning. Within high-priority, multi-jurisdictional landscapes like the Madrean ... ...

Abstract	Climate refugia, or places where habitats are expected to remain relatively buffered from regional climate extremes, provide an important focus for science and conservation planning. Within high-priority, multi-jurisdictional landscapes like the Madrean sky islands of the United States and México, efforts to identify and manage climate refugia are hindered by the lack of high-quality and consistent transboundary datasets. To fill these data gaps, we assembled a bi-national field dataset (n = 1416) for five pine species (Pinus spp.) and used generalized boosted regression to model pine habitats in relation to topographic variability as a basis for identifying potential microrefugia at local scales in the context of current species’ distribution patterns. We developed additional models to quantify climatic refugial attributes using coarse scale bioclimatic variables and finer scale seasonal remote sensing indices. Terrain metrics including ruggedness, slope position, and aspect defined microrefugia for pines within elevation ranges preferred by each species. Response to bioclimatic variables indicated that small shifts in climate were important to some species (e.g., P. chihuahuana, P. strobiformis), but others exhibited a broader tolerance (e.g., P. arizonica). Response to seasonal climate was particularly important in modeling microrefugia for species with open canopy structure and where regular fires occur (e.g., P. engelmannii and P. chihuahuana). Hotspots of microrefugia differed among species and were either limited to northern islands or occurred across central or southern latitudes. Mapping and validation of refugia and their ecological functions are necessary steps in developing regional conservation strategies that cross jurisdictional boundaries. A salient application will be incorporation of climate refugia in management of fire to restore and maintain pine ecology. Una versión en español de este artículo está disponible como descarga.
Keywords	canopy ; climate ; data collection ; landscapes ; refuge habitats ; topography ; Mexico
Language	English
Dates of publication	2022-05
Size	p. 577-598.
Publishing place	Springer Netherlands
Document type	Article
ZDB-ID	1364679-5
ISSN	1573-5052 ; 1385-0237
ISSN (online)	1573-5052
ISSN	1385-0237
DOI	10.1007/s11258-022-01233-w
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Occupancy modeling and resampling overcomes low test sensitivity to produce accurate SARS-CoV-2 prevalence estimates

Jamie S. Sanderlin / Jessie D. Golding / Taylor Wilcox / Daniel H. Mason / Kevin S. McKelvey / Dean E. Pearson / Michael K. Schwartz

BMC Public Health, Vol 21, Iss 1, Pp 1-

2021 Volume 10

Abstract: Abstract Background We evaluated whether occupancy modeling, an approach developed for detecting rare wildlife species, could overcome inherent accuracy limitations associated with rapid disease tests to generate fast, accurate, and affordable SARS-CoV-2 ...

Abstract	Abstract Background We evaluated whether occupancy modeling, an approach developed for detecting rare wildlife species, could overcome inherent accuracy limitations associated with rapid disease tests to generate fast, accurate, and affordable SARS-CoV-2 prevalence estimates. Occupancy modeling uses repeated sampling to estimate probability of false negative results, like those linked to rapid tests, for generating unbiased prevalence estimates. Methods We developed a simulation study to estimate SARS-CoV-2 prevalence using rapid, low-sensitivity, low-cost tests and slower, high-sensitivity, higher cost tests across a range of disease prevalence and sampling strategies. Results Occupancy modeling overcame the low sensitivity of rapid tests to generate prevalence estimates comparable to more accurate, slower tests. Moreover, minimal repeated sampling was required to offset low test sensitivity at low disease prevalence (0.1%), when rapid testing is most critical for informing disease management. Conclusions Occupancy modeling enables the use of rapid tests to provide accurate, affordable, real-time estimates of the prevalence of emerging infectious diseases like SARS-CoV-2.
Keywords	Occupancy modeling ; Optimal sampling ; Repeated sampling ; Sampling strategies ; Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Factors affecting lifetime reproduction, long-term territory-specific reproduction, and estimation of habitat quality in northern goshawks.

Richard T Reynolds / Jeffrey S Lambert / Shannon L Kay / Jamie S Sanderlin / Benjamin J Bird

PLoS ONE, Vol 14, Iss 5, p e

2019 Volume 0215841

Abstract	One measure of habitat quality is a species' demographic performance in a habitat and the gold standard metric of performance is reproduction. Such a measure, however, may be misleading if individual quality is a fitness determinant. We report on factors affecting lifetime reproduction (LR), the total number of lifetime fledglings produced by an individual, and long-term territory-specific reproduction in a multi-generational study of northern goshawks (Accipiter gentilis). LR increased with longer lifespans and more breeding attempts and was strongly correlated with the number of recruits in two filial generations indicating that LR was a good fitness predictor. Extensive differences in LR attested to heterogeneity in individual quality, a requisite for the ideal pre-emptive distribution model (IPD) of habitat settling wherein high quality individuals get the best habitats forcing lower quality individuals into poorer habitats with lower reproduction. In response to 7‒9-year prey abundance cycles, annual frequency of territory occupancy by breeders was highly variable and low overall with monotonic increases in vacancies through low prey years. Occupancy of territories by breeders differed from random; some appeared preferred while others were avoided, producing a right-skewed distribution of total territory-specific fledgling production. However, mean fledglings per nest attempt was only slightly lower in less versus more productive territories, and, contrary to IPD predictions of increases in annual territory-specific coefficients of variation (CV) in reproduction as breeder densities increase, the CV of production decreased as density increased. Rather than habitat quality per se, conspecific attraction elicited territory selection by prospecting goshawks as 70% of settlers comprised turnovers on territories, resulting in occupancy continuity and increased territory-specific reproduction. Top-producing territories had as few as 2 long-lived (high LR) and up to 6 short-lived (low LR) sequential breeders. ...
Keywords	Medicine ; R ; Science ; Q
Subject code	590
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Spatial and temporal dynamics of Mexican spotted owl habitat in the southwestern US

Jones, Gavin M. / Shirk, Andrew J. / Yang, Zhiqiang / Davis, Raymond J. / Ganey, Joseph L. / Gutiérrez, Ralph J. / Healey, Sean P. / Hedwall, Shaula J. / Hoagland, Serra J. / Maes, Ron / Malcolm, Karl / McKelvey, Kevin S. / Sanderlin, Jamie S. / Schwartz, Michael K. / Seamans, Mark E. / Wan, Ho Yi / Cushman, Sam

Landsc Ecol. 2023 Jan., v. 38, no. 1 p.23-37

2023

Abstract: CONTEXT: Understanding habitat dynamics is essential for effective conservation as landscapes rapidly change. In a companion paper in this issue, Shirk et al. (2023) introduced an automated habitat monitoring system using Google Earth Engine and applied ... ...

Abstract	CONTEXT: Understanding habitat dynamics is essential for effective conservation as landscapes rapidly change. In a companion paper in this issue, Shirk et al. (2023) introduced an automated habitat monitoring system using Google Earth Engine and applied this framework to develop a dynamic model of Mexican spotted owl (Strix occidentalis lucida) habitat across the southwestern US from 1986 to 2020. OBJECTIVES: We explored the application of this dynamic model of Mexican spotted owl habitat in the context of the species’ ecology. METHODS: We evaluated environmental correlates of Mexican spotted owl habitat, assessed potential spatial non-stationarity in habitat selection, estimated long-term trends in habitat by quantifying changes in habitat amount and quality between 1986 and 2020, and evaluated the extent to which habitat changes over the past 35 years have been driven by wildfire. RESULTS: Topography and climate appeared to outweigh reflectance-based (vegetation) metrics in describing Mexican spotted owl habitat and habitat selection was non-stationary across modeling sub-regions. Total habitat area for Mexican spotted owls declined by ~ 21% since 1986 (0.6% annually), but trends varied spatially and some even reversed over the past decade. Wildfire was responsible for between 8 and 35% of total habitat loss, depending on the sub-region considered. CONCLUSIONS: The automated habitat monitoring system allowed trend estimation and accurate assessment of current habitat status for Mexican spotted owls; maps were accurate, spatially detailed, and current. The ability to continually produce accurate maps for large land areas for threatened species such as the Mexican spotted owl facilitates science-based land management on public lands in the southwestern US.
Keywords	Internet ; Strix occidentalis lucida ; automation ; climate ; dynamic models ; habitat destruction ; habitat preferences ; habitats ; land management ; temporal variation ; threatened species ; topography ; vegetation ; wildfires ; Southwestern United States
Language	English
Dates of publication	2023-01
Size	p. 23-37.
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	1027798-5
ISSN	1572-9761 ; 0921-2973
ISSN (online)	1572-9761
ISSN	0921-2973
DOI	10.1007/s10980-022-01418-8
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Automated habitat monitoring systems linked to adaptive management: a new paradigm for species conservation in an era of rapid environmental change

Shirk, Andrew J. / Jones, Gavin M. / Yang, Zhiqiang / Davis, Raymond J. / Ganey, Joseph L. / Gutiérrez, Ralph J. / Healey, Sean P. / Hedwall, Shaula J. / Hoagland, Serra J. / Maes, Ron / Malcolm, Karl / McKelvey, Kevin S. / Vynne, Carly / Sanderlin, Jamie S. / Schwartz, Michael K. / Seamans, Mark E. / Wan, Ho Yi / Cushman, Sam

Landsc Ecol. 2023 Jan., v. 38, no. 1 p.7-22

2023

Abstract: CONTEXT: Recent increases in ecological disturbances driven by climate change and our expanding human footprint make it challenging for natural resource managers to keep apprised of current conditions and adjust management plans accordingly. To ... ...

Abstract	CONTEXT: Recent increases in ecological disturbances driven by climate change and our expanding human footprint make it challenging for natural resource managers to keep apprised of current conditions and adjust management plans accordingly. To effectively conserve species in highly dynamic landscapes requires more timely habitat monitoring and a more responsive adaptive management cycle. OBJECTIVES: We introduce a framework to automatically monitor and assess species habitats over a range of spatial and temporal scales. We then apply this framework by developing an automated habitat monitoring system for the Mexican spotted owl (MSO) in Arizona and New Mexico, USA, that will be linked to federal agency adaptive management plans. METHODS: We automated the process of monitoring and assessing trends in MSO habitat on an annual schedule using the Google Earth Engine cloud-based spatial analysis platform and dynamic data repository. We ran this system retrospectively on historical data to monitor MSO habitat from 1986 to 2020. RESULTS: The automated habitat monitoring system provided a 35-year MSO habitat time series with high accuracy. Widespread habitat gains and losses occurred every year, underscoring the need for continuous monitoring and the benefits of an automated workflow. CONCLUSIONS: Automated habitat monitoring linked to adaptive management holds great promise in helping managers track the impacts of recent disturbances and adjust plans to meet goals even in increasingly dynamic landscapes. In a companion paper, Jones et al. (2023) demonstrate the utility of this approach by analyzing our MSO habitat time series to assess trends, drivers of change, and management implications.
Keywords	Internet ; Strix occidentalis lucida ; adaptive management ; automation ; climate change ; habitats ; humans ; time series analysis ; Arizona ; New Mexico
Language	English
Dates of publication	2023-01
Size	p. 7-22.
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	1027798-5
ISSN	1572-9761 ; 0921-2973
ISSN (online)	1572-9761
ISSN	0921-2973
DOI	10.1007/s10980-022-01457-1
Database	NAL-Catalogue (AGRICOLA)

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