26 research outputs found
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On the estimation and application of spatial and temporal autocorrelation in headwater streams
This collection of three manuscripts serves to improve methods for collecting, interpreting, and utilizing autocorrelated data from headwater stream networks. Each stream network is comprised of linear segments. These segments lie within a unique branching structure that connects the segments via flowing water, and the connectivity provided by water varies seasonally. These aspects separate stream networks from other landscapes, and provide unique challenges to the statistical analysis of stream-based phenomenon. Two chapters of this work relied on a unique and comprehensive set of data. These data constitute a complete census of habitat unit fish counts from 40 randomly selected headwater basins in western Oregon. The first objective of this work was to evaluate how different sampling designs captured spatial autocorrelation, given the samples were drawn from a population of spatially autocorrelated observations. Spatially distributed clusters of sampling locations were more apt to capture spatial autocorrelation than samples without clusters or small clusters located at tributary junctions. A similar investigation was made concerning sampling design performance in relation to estimating autocorrelation function values. All sampling designs lead generally to negatively biased estimates, and practical differences among the sampling designs were not observed. The second objective was to investigate spatial autocorrelation model range parameters as measures of patch sizes. It is common practice to use range parameters to infer the size of patches within spatially autocorrelated data, but this methodology lacks sufficient justification. The census data were used to compute range parameter values, and another proposed autocorrelative measure of patch size: the integral scale. The same data were used to compute patch sizes under several patch definitions, and the relationship of range parameters and integral scale values with patch sizes was explored. Range parameter values did not equal and were not strongly correlated with average patch sizes, though range parameter values were more correlated with maximum patch and gap sizes. Integral scale values matched the magnitude of, but were not strongly correlated with, average patch sizes. The third objective was to refine the analysis of temporally autocorrelated hydrology data from paired watershed studies. Paired watershed studies are used to evaluate forest harvesting effects on stream biota and hydrology (i.e. fish, amphibians, insects, stream flow, and sediment yield). Traditionally, treatment effects are discerned using prediction intervals. This work provided an improved method for constructing prediction intervals for use in change detection in paired watershed studies. The improved prediction intervals included variation associated with estimating linear and autocorrelation model parameters
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Using Cure Models for Analyzing the Influence of Pathogens on Salmon Survival
Parasites and pathogens influence the size and stability of wildlife populations, yet many population models ignore
the population-level effects of pathogens. Standard survival analysis methods (e.g., accelerated failure time models)
are used to assess how survival rates are influenced by disease. However, they assume that each individual is equally
susceptible and will eventually experience the event of interest; this assumption is not typically satisfied with regard to
pathogens of wildlife populations. In contrast, mixture cure models, which comprise logistic regression and survival
analysis components, allow for different covariates to be entered into each part of the model and provide better
predictions of survival when a fraction of the population is expected to survive a disease outbreak. We fitted mixture
cure models to the host–pathogen dynamics of Chinook Salmon Oncorhynchus tshawytscha and Coho Salmon O.
kisutch and the myxozoan parasite Ceratomyxa shasta. Total parasite concentration, water temperature, and discharge
were used as covariates to predict the observed parasite-induced mortality in juvenile salmonids collected as part of
a long-term monitoring program in the Klamath River, California. The mixture cure models predicted the observed
total mortality well, but some of the variability in observed mortality rates was not captured by the models. Parasite
concentration and water temperature were positively associated with total mortality and the mortality rate of both
Chinook Salmon and Coho Salmon. Discharge was positively associated with total mortality for both species but only
affected the mortality rate for Coho Salmon. The mixture cure models provide insights into how daily survival rates
change over time in Chinook Salmon and Coho Salmon after they become infected with C. shasta
SSNdesign -- an R package for pseudo-Bayesian optimal and adaptive sampling designs on stream networks
Streams and rivers are biodiverse and provide valuable ecosystem services.
Maintaining these ecosystems is an important task, so organisations often
monitor the status and trends in stream condition and biodiversity using field
sampling and, more recently, autonomous in-situ sensors. However, data
collection is often costly and so effective and efficient survey designs are
crucial to maximise information while minimising costs. Geostatistics and
optimal and adaptive design theory can be used to optimise the placement of
sampling sites in freshwater studies and aquatic monitoring programs.
Geostatistical modelling and experimental design on stream networks pose
statistical challenges due to the branching structure of the network, flow
connectivity and directionality, and differences in flow volume. Thus, unique
challenges of geostatistics and experimental design on stream networks
necessitates the development of new open-source software for implementing the
theory. We present SSNdesign, an R package for solving optimal and adaptive
design problems on stream networks that integrates with existing open-source
software. We demonstrate the mathematical foundations of our approach, and
illustrate the functionality of SSNdesign using two case studies involving real
data from Queensland, Australia. In both case studies we demonstrate that the
optimal or adaptive designs outperform random and spatially balanced survey
designs. The SSNdesign package has the potential to boost the efficiency of
freshwater monitoring efforts and provide much-needed information for
freshwater conservation and management.Comment: Main document: 18 pages, 7 figures Supp Info A: 11 pages, 0 figures
Supp Info B: 24 pages, 6 figures Supp Info C: 3 pages, 0 figure
Deconstructing dams and disease: predictions for salmon disease risk following Klamath River dam removals
The health of fish populations and the river systems they inhabit have broad ecological, cultural, recreational, and economic relevance. This is exemplified by the iconic anadromous salmonid fishes native to the West Coast of North America. Salmon populations have been constrained since the mid nineteenth century by dam construction and water reallocation. In the Klamath River (Oregon and California, USA), a series of dams built in the early-mid 20th century cut the basin in two and blocked anadromous fish access to more than 600 river kilometers. This dramatic loss of habitat, coupled with infectious diseases and resulting epizootics, have impacted the wellbeing of these salmonid populations. In 2023-2024, the Klamath River will undergo the largest river restoration project in US history. Removal of the four lowermost dams will cause profound physical changes to the river, including flow, water temperature, and channel geomorphology. The dam removals will reconnect the lower and upper portions of the basin, and provide fish passage after a century of segregation. Reestablishment of upstream and downstream fish movements will also alter the occupancy and abundance of the salmonid hosts and their pathogens. The increased habitat availability and longer migration routes will increase duration of pathogen exposure and potential impacts on juvenile survival and adult pre-spawn mortality. However, restoration of more natural flow and sediment regimes will decrease overall fish disease risk by disrupting complex parasite life cycles. To better understand these multifarious, competing factors, we review the salmonid species in the Klamath River, and provide an overview of their historical pathogen challenges and associated diseases and use this as a framework to predict the effects of dam removals on disease dynamics. Our review and predictions are a synthesis of expertise from tribal biologists, fish health specialists and fish biologists, many of whom have lived and worked on the Klamath River for decades. We conclude with recommendations for expansion of current pathogen monitoring and research efforts to measure changes in host-pathogen dynamics basin-wide
A Multi-Lab Test of the Facial Feedback Hypothesis by the Many Smiles Collaboration
Following theories of emotional embodiment, the facial feedback hypothesis suggests that individuals’ subjective experiences of emotion are influenced by their facial expressions. However, evidence for this hypothesis has been mixed. We thus formed a global adversarial collaboration and carried out a preregistered, multicentre study designed to specify and test the conditions that should most reliably produce facial feedback effects. Data from n = 3,878 participants spanning 19 countries indicated that a facial mimicry and voluntary facial action task could both amplify and initiate feelings of happiness. However, evidence of facial feedback effects was less conclusive when facial feedback was manipulated unobtrusively via a pen-in-mouth task
A multi-lab test of the facial feedback hypothesis by the Many Smiles Collaboration
Following theories of emotional embodiment, the facial feedback hypothesis suggests that individuals' subjective experiences of emotion are influenced by their facial expressions. However, evidence for this hypothesis has been mixed. We thus formed a global adversarial collaboration and carried out a preregistered, multicentre study designed to specify and test the conditions that should most reliably produce facial feedback effects. Data from n = 3,878 participants spanning 19 countries indicated that a facial mimicry and voluntary facial action task could both amplify and initiate feelings of happiness. However, evidence of facial feedback effects was less conclusive when facial feedback was manipulated unobtrusively via a pen-in-mouth task
The wide-field, multiplexed, spectroscopic facility WEAVE : survey design, overview, and simulated implementation
Funding for the WEAVE facility has been provided by UKRI STFC, the University of Oxford, NOVA, NWO, Instituto de Astrofísica de Canarias (IAC), the Isaac Newton Group partners (STFC, NWO, and Spain, led by the IAC), INAF, CNRS-INSU, the Observatoire de Paris, Région Île-de-France, CONCYT through INAOE, Konkoly Observatory (CSFK), Max-Planck-Institut für Astronomie (MPIA Heidelberg), Lund University, the Leibniz Institute for Astrophysics Potsdam (AIP), the Swedish Research Council, the European Commission, and the University of Pennsylvania.WEAVE, the new wide-field, massively multiplexed spectroscopic survey facility for the William Herschel Telescope, will see first light in late 2022. WEAVE comprises a new 2-degree field-of-view prime-focus corrector system, a nearly 1000-multiplex fibre positioner, 20 individually deployable 'mini' integral field units (IFUs), and a single large IFU. These fibre systems feed a dual-beam spectrograph covering the wavelength range 366-959 nm at R ∼ 5000, or two shorter ranges at R ∼ 20,000. After summarising the design and implementation of WEAVE and its data systems, we present the organisation, science drivers and design of a five- to seven-year programme of eight individual surveys to: (i) study our Galaxy's origins by completing Gaia's phase-space information, providing metallicities to its limiting magnitude for ∼ 3 million stars and detailed abundances for ∼ 1.5 million brighter field and open-cluster stars; (ii) survey ∼ 0.4 million Galactic-plane OBA stars, young stellar objects and nearby gas to understand the evolution of young stars and their environments; (iii) perform an extensive spectral survey of white dwarfs; (iv) survey ∼ 400 neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and kinematics of stellar populations and ionised gas in z 1 million spectra of LOFAR-selected radio sources; (viii) trace structures using intergalactic/circumgalactic gas at z > 2. Finally, we describe the WEAVE Operational Rehearsals using the WEAVE Simulator.PostprintPeer reviewe
The wide-field, multiplexed, spectroscopic facility WEAVE: Survey design, overview, and simulated implementation
WEAVE, the new wide-field, massively multiplexed spectroscopic survey
facility for the William Herschel Telescope, will see first light in late 2022.
WEAVE comprises a new 2-degree field-of-view prime-focus corrector system, a
nearly 1000-multiplex fibre positioner, 20 individually deployable 'mini'
integral field units (IFUs), and a single large IFU. These fibre systems feed a
dual-beam spectrograph covering the wavelength range 366959\,nm at
, or two shorter ranges at . After summarising the
design and implementation of WEAVE and its data systems, we present the
organisation, science drivers and design of a five- to seven-year programme of
eight individual surveys to: (i) study our Galaxy's origins by completing
Gaia's phase-space information, providing metallicities to its limiting
magnitude for 3 million stars and detailed abundances for
million brighter field and open-cluster stars; (ii) survey million
Galactic-plane OBA stars, young stellar objects and nearby gas to understand
the evolution of young stars and their environments; (iii) perform an extensive
spectral survey of white dwarfs; (iv) survey
neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and
kinematics of stellar populations and ionised gas in cluster galaxies;
(vi) survey stellar populations and kinematics in field galaxies
at ; (vii) study the cosmic evolution of accretion
and star formation using million spectra of LOFAR-selected radio sources;
(viii) trace structures using intergalactic/circumgalactic gas at .
Finally, we describe the WEAVE Operational Rehearsals using the WEAVE
Simulator.Comment: 41 pages, 27 figures, accepted for publication by MNRA
The wide-field, multiplexed, spectroscopic facility WEAVE: Survey design, overview, and simulated implementation
WEAVE, the new wide-field, massively multiplexed spectroscopic survey facility for the William Herschel Telescope, will see first light in late 2022. WEAVE comprises a new 2-degree field-of-view prime-focus corrector system, a nearly 1000-multiplex fibre positioner, 20 individually deployable 'mini' integral field units (IFUs), and a single large IFU. These fibre systems feed a dual-beam spectrograph covering the wavelength range 366−959\,nm at R∼5000, or two shorter ranges at R∼20000. After summarising the design and implementation of WEAVE and its data systems, we present the organisation, science drivers and design of a five- to seven-year programme of eight individual surveys to: (i) study our Galaxy's origins by completing Gaia's phase-space information, providing metallicities to its limiting magnitude for ∼3 million stars and detailed abundances for ∼1.5 million brighter field and open-cluster stars; (ii) survey ∼0.4 million Galactic-plane OBA stars, young stellar objects and nearby gas to understand the evolution of young stars and their environments; (iii) perform an extensive spectral survey of white dwarfs; (iv) survey ∼400 neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and kinematics of stellar populations and ionised gas in z1 million spectra of LOFAR-selected radio sources; (viii) trace structures using intergalactic/circumgalactic gas at z>2. Finally, we describe the WEAVE Operational Rehearsals using the WEAVE Simulator