Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
89
datasets available to search
ShareScore release 0.9.0
Dataset results
89 results for “Bayesian estimation”
Bayesian Estimation of Diagnostic Performance for Cardiovascular Autonomic Neuropathy
ClinicalTrials.gov study NCT02459522. IPD Sharing: Not stated. Countries: 1. Publications: 4.
Bayesian Estimation of Diagnostic Performance of Diabetic Cardiovascular Autonomic Neuropathy Without a Gold Standard
ClinicalTrials.gov study NCT02461381. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Bayesian models' outputs for: A new method to explicitly estimate the shift of optimum along gradients in multispecies studies
Open the record for dataset details and reuse information.
Data from: Bayesian adaptive Markov Chain Monte Carlo estimation of genetic parameters
Open the record for dataset details and reuse information.
Data from: Estimating age and age class of harvested hog deer from eye lens mass using frequentist and Bayesian methods
Open the record for dataset details and reuse information.
Data from: Bayesian phylogenetic estimation of clade ages supports trans-atlantic dispersal of cichlid fishes
Open the record for dataset details and reuse information.
Data from: Bayesian estimates of male and female African lion mortality for future use in population management
Open the record for dataset details and reuse information.
Data from: Assessing conservation risks to populations of an anadromous Arctic salmonid, the northern Dolly Varden (Salvelinus malma malma), via estimates of effective and census population sizes and approximate Bayesian computation
Open the record for dataset details and reuse information.
Data from: A Bayesian method for the joint estimation of outcrossing rate and inbreeding depression
Open the record for dataset details and reuse information.
Data from: Abundance estimation with sightability data: a Bayesian data augmentation approach
Open the record for dataset details and reuse information.
Data from: Bayesian divergence-time estimation with genome-wide SNP data of sea catfishes (Ariidae) supports Miocene closure of the Panamanian isthmus
Open the record for dataset details and reuse information.
Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards
Open the record for dataset details and reuse information.
Data from: Evaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale
The evolutionary timescale of angiosperms has long been a key question in biology. Molecular estimates of this timescale have shown considerable variation, being influenced by differences in taxon sampling, gene sampling, fossil calibrations, evolutionary models, and choices of priors. Here, we analyze a data set comprising 76 protein-coding genes from the chloroplast genomes of 195 taxa spanning 86 families, including novel genome sequences for 11 taxa, to evaluate the impact of models, priors, and gene sampling on Bayesian estimates of the angiosperm evolutionary timescale. Using a Bayesian relaxed molecular-clock method, with a core set of 35 minimum and two maximum fossil constraints, we estimated that crown angiosperms arose 221 (251-192) Ma during the Triassic. Based on a range of additional sensitivity and subsampling analyses, we found that our date estimates were generally robust to large changes in the parameters of the birth-death tree prior and of the model of rate variation across branches. We found an exception to this when we implemented fossil calibrations in the form of highly informative gamma priors rather than as uniform priors on node ages. Under all other calibration schemes, including trials of seven maximum age constraints, we consistently found that the earliest divergences of angiosperm clades substantially predate the oldest fossils that can be assigned unequivocally to their crown group. Overall, our results and experiments with genome-scale data suggest that reliable estimates of the angiosperm crown age will require increased taxon sampling, significant methodological changes, and new information from the fossil record.
Data from: Bayesian estimation of species divergence times using correlated quantitative characters
Discrete morphological data have been widely used to study species evolution, but the use of quantitative (or continuous) morphological characters is less common. Here, we implement a Bayesian method to estimate species divergence times using quantitative characters. Quantitative character evolution is modelled using Brownian diffusion with character correlation and character variation within populations. Through simulations, we demonstrate that ignoring the population variation (or population "noise") and the correlation among characters leads to biased estimates of divergence times and rate, especially if the correlation and population noise are high. We apply our new method to the analysis of quantitative characters (cranium landmarks) and molecular data from carnivoran mammals. Our results show that time estimates are affected by whether the correlations and population noise are accounted for or ignored in the analysis. The estimates are also affected by the type of data analysed, with analyses of morphological characters only, molecular data only, or a combination of both; showing noticeable differences among the time estimates. Rate variation of morphological characters among the carnivoran species appears to be very high, with Bayesian model selection indicating that the independent-rates model fits the morphological data better than the autocorrelated-rates model. We suggest that using morphological continuous characters, together with molecular data, can bring a new perspective to the study of species evolution. Our new model is implemented in the MCMCtree computer program for Bayesian inference of divergence times.
Data from: Bayesian estimation of speciation and extinction from incomplete fossil occurrence data
The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.
Data from: Estimating Bayesian phylogenetic information content
Measuring the phylogenetic information content of data has a long history in systematics. Here we explore a Bayesian approach to information content estimation. The entropy of the posterior distribution compared to the entropy of the prior distribution provides a natural way to measure information content. If the data have no information relevant to ranking tree topologies beyond the information supplied by the prior, the posterior and prior will be identical. Information in data discourages consideration of some hypotheses allowed by the prior, resulting in a posterior distribution that is more concentrated (has lower entropy) than the prior. We focus on measuring information about tree topology using marginal posterior distributions of tree topologies. We show that both the accuracy and the computational efficiency of topological information content estimation improve with use of the conditional clade distribution, which also allows topological information content to be partitioned by clade. We explore two important applications of our method: providing a compelling definition of saturation, and detecting conflict among data partitions that can negatively affect analyses of concatenated data.
Data from: Elevated substitution rate estimates from ancient DNA: model violation and bias of Bayesian methods
The increasing ability to extract and sequence DNA from non-contemporaneous tissue offers biologists the opportunity to analyze ancient DNA (aDNA) together with modern DNA (mDNA) to address the taxonomy of extinct species, evolutionary origins, historical phylogeography and biogeography. Perhaps more exciting are recent developments in coalescence-based Bayesian inference that offer the potential to use temporal information from aDNA and mDNA for the estimation of substitution rates and divergence dates as an alternative to fossil and geological calibration. This comes at a time of growing interest in the possibility of time dependency for molecular rate estimates. Here we provide a critical assessment of Bayesian MCMC analysis for the estimation of substitution rate using simulated samples of aDNA and mDNA. We conclude that the current models and priors employed in Bayesian MCMC analysis of heterochronous mtDNA are susceptible to an upward bias in the estimation of substitution rates due to model misspecification when the data comes from populations with less than simple demographic histories, including sudden short-lived population bottlenecks or pronounced population structure. However when model misspecification is only mild, then the 95% HPD intervals provide adequate frequentist coverage of the true rates.
A Bayesian framework for estimating parameters of a generic toxicokinetic model for the bioaccumulation of organic chemicals by benthic invertebrates: proof of concept with PCB153 and two freshwater species.
<p>R Codes and corresponding .csv data files for estimating toxicokinetic model parameters for both chironomids and gammarids exposed to PCB153.</p>
Data from: Conventional analysis of trial-by-trial adaptation is biased: empirical and theoretical support using a Bayesian estimator
Research on human motor adaptation has often focused on how people adapt to self-generated or externally-influenced errors. Trial-by-trial adaptation is a person's response to self-generated errors. Externally-influenced errors applied as catch-trial perturbations are used to calculate a person's perturbation adaptation rate. Although these adaptation rates are sometimes compared to one another, we show through simulation and empirical data that the two metrics are distinct. We demonstrate that the trial-by-trial adaptation rate, often calculated as a coefficient in a linear regression, is biased under typical conditions. We tested 12 able-bodied subjects moving a cursor on a screen using a computer mouse. Statistically different adaptation rates arise when sub-sets of trials from different phases of learning are analyzed from within a sequence of movement results. We propose a new approach to identify when a person's learning has stabilized in order to identify steady-state movement trials from which to calculate a more reliable trial-by-trial adaptation rate. Using a Bayesian model of human movement, we show that this analysis approach is more consistent and provides a more confident estimate than alternative approaches. Constraining analyses to steady-state conditions will allow researchers to better decouple the multiple concurrent learning processes that occur while a person makes goal-directed movements. Streamlining this analysis may help broaden the impact of motor adaptation studies, perhaps even enhancing their clinical usefulness.
The impact of estimator choice: Disagreement in clustering solutions across K estimators for Bayesian analysis of population genetic structure across a wide range of empirical datasets
<p class="CxSpFirst">The software program STRUCTURE is one of the most cited tools for determining population structure. To infer the optimal number of clusters from STRUCTURE output, the Δ<i>K</i> method is often applied. However, a recent study relying on simulated microsatellite data suggested that this method has a downward bias in its estimation of <i>K</i> and is sensitive to uneven sampling. If this finding holds for empirical datasets, conclusions about the scale of gene flow may have to be revised for a large number of studies. To determine the impact of method choice, we applied recently described estimators of <i>K</i> to re-estimate genetic structure in 41 empirical microsatellite datasets; 15 from a broad range of taxa and 26 focused on a diverse phylogenetic group, coral. We compared alternative estimates of <i>K</i> (Puechmaille statistics) with traditional (Δ<i>K</i> and posterior probability) estimates and found widespread disagreement of estimators across datasets. Thus, one estimator alone is insufficient for determining the optimal number of clusters regardless of study organism or evenness of sampling scheme. Subsequent analysis of molecular variance (AMOVA) between clustering solutions did not necessarily clarify which solution was best. To better infer population structure, we suggest a combination of visual inspection of STRUCTURE plots and calculation of the alternative estimators at various thresholds in addition to Δ<i>K</i>. Differences between estimators could reveal patterns with important biological implications, such as the potential for more population structure than previously estimated, as was the case for many studies reanalyzed here.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.