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23 results for “Stochastic process”
HarmonEPS modified routines, post-processing scripts and example data used in Tsiringakis, A., Frogner, I.L., de Rooy, W., Andrae, U., Hally, A., Contreras Osorio, S., van der Veen, S. and Barkmeijer, J., An Update to the Stochastically Perturbed Parametrizations Scheme of HarmonEPS. Monthly Weather Review
<p>This dataset contains:</p> <p>- Modified code routines/configurations files used in the EPS of Harmonie-Arome (HarmonEPS) CY43H2.2 version of the model.</p> <p>- Verification scripts from the HARP verification tool, used to verify model output against SYNOP observations.</p> <p>- Post-processing and plotting scripts in python, used in the manuscript.</p> <p>- A subset of the data produced by this study as example input in the verification and post-processing/plotting scripts.</p> <p>This dataset is used in:</p> <p>~Tsiringakis, A., Frogner, I.L., de Rooy, W., Andrae, U., Hally, A., Contreras Osorio, S., van Der Veen, S. and Barkmeijer, J. An Update to the Stochastically Perturbed Parametrizations Scheme of HarmonEPS. Monthly Weather Review</p>
Inferring core processes using stochastic models of the geodynamo
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Learning stochastic process-based models of dynamical systems from knowledge and data - Libraries, incomplete models and data
<p>The archive contains all libraries of domain knowledge, the incomplete models and the data used in the experiments described in the manuscript titled "Learning stochastic process-based models of dynamical systems from knowledge and data" pubilshed in BMC Systems Biology</p>
Dataset of bank soil parameters and stochastic modelling of bank erosion processes in the Middle Yangtze River
<p><span>A probabilistic process-based model of bank erosion has proposed, </span><span>embedding the probability distributions of</span><span> different bank soil parameters. <span><span> The dataset includes the spatial distribution characteristics of critical shear stress, friction angle, and cohesion. The prediction results analyzed the effects of soil erosion resistance capacity and the variability of shear strength parameters in the simulation of bank erosion processes, obtaining the probability of mass failure and the distributions of bank erosion width. Additionally, the study investigated the effect of varying water content on bank erosion modeling and further analyzed how considering more influencing factors in the model affects prediction uncertainty and accuracy. Moreover, the relationship between the variability of these factors and river morphology was discussed. The dataset provides the aforementioned prediction results, and relevant plots were generated using MATLAB or Python, with the associated plotting code also uploaded.</span></span></span></p>
Simulation for "Asymptotic Behavior for a Time-Inhomogeneous Stochastic Differential Equation Driven by an α-Stable Lévy Process"
<p>The code and the video are related to the article G.Mihai, and E. Luirard. « Asymptotic Behavior for a Time-Inhomogeneous Stochastic Differential Equation Driven by an α-Stable Lévy Process », available on http://arxiv.org/abs/2112.07287.</p>
Data from: Process-based modelling of nonharmonic internal tides using adjoint, statistical, and stochastic approaches. Part II: adjoint frequency response analysis, stochastic models, and synthesis
<p>Meta data updated after publication.</p> <p> </p>
Data from: Process-based modelling of nonharmonic internal tides using adjoint, statistical, and stochastic approaches. Part I: statistical model and analysis of observational data
<p>Meta data updated after publication.</p> <p> </p>
A stochastic framework for predicting epidemiological risk areas using the Ornstein-Uhlenbeck process: Software and supplementary material
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Stochastic processes and ecological connectivity drive stream invertebrate community responses to short-term drought
1. Community responses to and recovery from disturbances depend on local (e.g. presence of refuges) and regional (connectivity to recolonization sources) factors. Droughts are becoming more frequent in boreal regions, and are likely to constitute a severe disturbance for boreal stream communities where organisms largely lack adaptations to such hydrological extremes. 2. We conducted an experiment in 24 seminatural stream flumes to assess the effects of local and regional factors on the responses of benthic invertebrate communities to a short-term drought. We manipulated flow (drought vs. constant-flow), spatial arrangement of leaf litter patches (aggregated vs. evenly distributed) and colonization from regional species pool (enhanced vs. ambient connectivity) to test the combined effects of disturbance, connectivity, and resource arrangement on the structural and functional responses of benthic invertebrate communities. 3. We found that a drought as short as one week reduced invertebrate richness and abundances, mainly through stochastic extinctions. Such changes in richness were not reflected in functional diversity. This suggests that communities were characterized by a high degree of functional redundancy, which allowed maintenance of functional diversity despite species losses. Feeding groups responded differently to drought, with organic matter decomposers responding more than scrapers and predators. 4. Three weeks was insufficient for a complete invertebrate community recovery from the drought. However, recovery was greater in channels subjected to enhanced connectivity, which increased taxonomic diversity and abundance of certain taxa. Spatial configuration of resources explained the least variation in our response variables, having a significant effect only on invertebrate abundance and evenness (both sampling occasions) and species richness (end of recovery period). 5. Even a short drought, if occurring late to the season, may not allow communities to recover before the onset of winter, thus having a potentially long-lasting effect on stream communities. For boreal headwaters, extreme dewatering poses a novel disturbance regime that may trigger substantial and potentially irreversible changes. An improved understanding of such changes is needed to underpin adaptive management strategies in these increasingly fragmented and disturbed ecosystems. 18-Dec-2020
Data from: Stochastic and deterministic processes drive wetland community assembly across a gradient of environmental filtering
The role of deterministic and stochastic processes in community assembly is a key question in community ecology. We evaluated the effect of an abiotic filter (hydroperiod) on the partitioned diversity of three taxonomic groups (birds, vegetation, macroinvertebrates) from prairie pothole wetlands in Alberta, Canada, which naturally vary in water permanence. We observed that alpha and gamma diversity were higher in permanent than temporary wetlands (16-25% and 34-47% respectively, depending on the taxon). This suggests an influence of deterministic constraints on the number of species a wetland can support. Taxa which cannot persist in shallow, temporary wetlands are excluded by the deterministic constraints that a shortened hydroperiod imposes. In contrast, we observed that beta diversity was significantly higher (2-12%) in temporary wetlands than permanent ones, and temporary wetlands supported more unique combinations of community composition than permanent wetlands, despite having a smaller regional species pool. This observation contradicts prior mesocosm studies that found beta diversity mirrored the pattern in gamma diversity along an environmental filtering gradient. We conclude that deterministic processes are more influential in more stable permanent wetlands, whereas stochastic processes play a more important role in assembly in dynamic temporary wetlands that must disassemble and re-establish annually. Considering three distinct taxonomic groups differing in their relative mobility, our large-scale field study demonstrates that both stochastic and deterministic processes act together to influence the assembly of multiple communities and that the relative importance of the two processes varies consistently along a gradient of environmental filtering.
Scale-dependent species-area relationship: niche-based versus stochastic processes in a typical subtropical forest
<p><span>Determining the patterns and drivers of the small-scale species-area relationship (SAR) is crucial for improving our understanding of community assembly and biodiversity patterns. Niche-based and stochastic processes are two principal categories of mechanisms potentially driving SARs. However, their relative importance has rarely been quantified rigorously owing to scale-dependence and the simplified niche volumes often used. </span></p> <p><span>In a fully mapped, 24-ha plot of a typical subtropical forest, we built the SARs and well-defined niche-hyper-volumes of a broad range of environmental variables at scales of 10 - 70 m (cell sizes). We then simulated passive sampling and partitioned the variances of the SAR slopes to disentangle the two contrasting mechanisms.</span></p> <p><span>We found that the small-scale SAR best followed a power-law relationship, consistent with large-scale SARs. The SAR slope declined with increasing scale; it was lower than expected under passive sampling at scales below 30 m and higher at larger scales. Environmental niches explained more (39%-64%) of the slope at larger scales, exceeding 50% at scales > 30 m, and these niches always captured the majority of the structured slopes. Environmental position (environmental mean values) effects were steady in absolute strength across scales and explained most (98%-68%) of the niche effect, but this proportion decreased with increasing scale. The effect of environmental heterogeneity increased with spatial scales, starting to rise at the 30 m scale after controlling for environmental position. Excluding soil properties from analyses strongly reduced these niche effects, highlighting the importance of soils for structuring the small-scale SAR. There was also substantial stochasticity in the SAR slopes, which was only partially explained by passive sampling.</span></p> <p><span>Synthesis: Our results show that the small-scale SAR in the studied subtropical forest follows a power-law, exhibits a scale shift in slope at 30 m, and is strongly shaped by niche effects that are dominated by environmental position relative to heterogeneity. However, soil heterogeneity controls the increase of niche effect and shift in the SAR slope with increasing spatial scales. Hence, edaphic factors can be responsible for scale-dependence in small-scale SARs, thereby linking small-scale and large-scale SARs. </span></p>
A basic community dynamics experiment: Disentangling deterministic and stochastic processes in structuring ecological communities
<p>Community dynamics are governed by two opposed processes: species sorting, which produces deterministic dynamics leading to an equilibrium state, and ecological drift, which produces stochastic dynamics. Despite a great deal of theoretical and empirical work aiming to demonstrate the predominance of one or the other of these processes, the importance of drift in structuring communities and maintaining species diversity remains contested. Here we present the results of a basic community dynamics experiment using floating aquatic plants, designed to measure the relative contributions of species sorting and ecological drift to community change over about a dozen generations. We found that species sorting became overwhelmingly dominant as the experiment progressed, and directed communities towards a stable equilibrium state maintained by negative frequency-dependent selection. The dynamics of any particular species depended on how far its initial frequency was from its equilibrium frequency, however, and consequently the balance of sorting and drift varied among species.</p>
A basic community dynamics experiment: Disentangling deterministic and stochastic processes in structuring ecological communities
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Data from: Stochastic and deterministic processes drive wetland community assembly across a gradient of environmental filtering
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Stochastic processes and ecological connectivity drive stream invertebrate community responses to short-term drought
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Scale-dependent species-area relationship: niche-based versus stochastic processes in a typical subtropical forest
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Data from: Deterministic and stochastic processes lead to divergence in plant communities 25 years after the 1988 Yellowstone fires
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Data from: Individual variation, population-specific behaviours, and stochastic processes shape marine migration phenologies
1. The phenology of long distance migrations can influence individual fitness, moderate population dynamics, and regulate the availability of ecosystem services to other trophic levels. Phenology varies within and among populations, and can be influenced by conditions individuals experience both prior to departure and encounter en route. 2. Assessing how intrinsic and extrinsic factors (e.g. individual physical condition vs. environmental conditions) interact to influence variation in migratory phenologies across ecological scales is often limited due to logistical constraints associated with tracking large numbers of individuals from multiple populations simultaneously. 3. We used two natural tags, DNA and otolith microstructure analysis, to estimate the relative influence of individual traits (life history strategy, body size at departure, and growth during migration), population-specific strategies, and interannual variability on the phenology of marine migrations in juvenile sockeye salmon Oncorhynchus nerka. 4. We show that the timing and duration of juvenile sockeye salmon migrations were correlated with both life history strategy and body size, while migration duration was also correlated with departure timing and growth rates during migration. Even after accounting for the effect of individual traits, several populations exhibited distinct migration phenologies. Finally, we observed substantial interannual and residual variation, suggesting stochastic environmental conditions moderate the influence of carry-over effects that develop prior to departure, as well as population-specific strategies. 5. Migratory phenologies are shaped by complex interactions between drivers acting at multiple ecological and temporal scales. Given evidence that intraspecific diversity can stabilize ecological systems, conservation efforts should seek to maintain migratory variation among populations and preserve locally adapted phenotypes; however, variation within populations, which may buffer systems from environmental stochasticity, should also be regularly assessed and preserved.
Brownian Motion or Mean Reversion? A Parameter Based Approach to Stochastic Process Selection
<p>Data set and supporting files for article "Brownian Motion or Mean Reversion? A Parameter Based Approach to Stochastic Process Selection"</p> <ul> <li>ADF Tests log commodities SA (Excel and PDF files) – EViews outputs (18) of Augmented Dickey-Fuller tests run on all 9 Seasonally Adjusted time series (S A) with trend and intercept, and with only intercept.</li> <li>Commodities data historical x Inflation (Excel file) – Time series used in the paper in 3 versions: <ul> <li>In historical monthly averages prices US$,</li> <li>In December 2018 US$ prices (with US inflation adjustment in appropriate tab),</li> <li>In December 2018 US$ prices Seasonally Adjusted (S A) from EViews output.</li> </ul> </li> <li>commodities log SA data Ev1 (Excel file) – for the log of 9 commodities time series in Dec 2018 values, after STL decomposition in EViews: original series, seasonally adjusted, seasonal factor and trend</li> <li>commodities log SA Regressions (Excel and PDF files) - EViews outputs of OLS regression on log of seasonally adjusted times series: Dx = α + β x.</li> <li>GBMVaratAVG, GBMVaratPaths, MRMVaratAVG, MRMVaratPaths (Matlab codes) – Matlab codes for Variance ratio tests for GBM and MRM, sample paths (200) and averages of 2,500 paths.</li> <li>Series Seasonal data decomposition (PDF file) – graphical display of seasonal decomposition of log of 9 price series into: original series, trend, seasonal factor, remainder, and seasonally adjusted.</li> <li>Variance Ratio Comm SA (Excel file) - EViews outputs of variance ratio tests run of seasonal adjusted log of 9 price series in Dec 2018 values. </li> <li>ADF Tests log commodities SA (Excel and PDF files) – EViews outputs (18) of Augmented Dickey-Fuller tests run on all 9 Seasonally Adjusted time series (S A) with trend and intercept, and with only intercept.</li> <li>Commodities data historical x Inflation (Excel file) – Time series used in the paper in 3 versions: <ul> <li>In historical monthly averages prices US$,</li> <li>In December 2018 US$ prices (with US inflation adjustment in appropriate tab),</li> <li>In December 2018 US$ prices Seasonally Adjusted (S A) from EViews output.</li> </ul> </li> <li>commodities log SA data Ev1 (Excel file) – for the log of 9 commodities time series in Dec 2018 values, after STL decomposition in EViews: original series, seasonally adjusted, seasonal factor and trend</li> <li>commodities log SA Regressions (Excel and PDF files) - EViews outputs of OLS regression on log of seasonally adjusted times series: Dx = α + β x.</li> <li>GBMVaratAVG, GBMVaratPaths, MRMVaratAVG, MRMVaratPaths (Matlab codes) – Matlab codes for Variance ratio tests for GBM and MRM, sample paths (200) and averages of 2,500 paths.</li> <li>Series Seasonal data decomposition (PDF file) – graphical display of seasonal decomposition of log of 9 price series into: original series, trend, seasonal factor, remainder, and seasonally adjusted.</li> <li>Variance Ratio Comm SA (Excel file) - EViews outputs of variance ratio tests run of seasonal adjusted log of 9 price series in Dec 2018 values. </li> </ul>
Data from: Individual variation, population-specific behaviours, and stochastic processes shape marine migration phenologies
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.