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324 results for “test cases”
Data from: Testing the role of mating preference in a case of incomplete ecological speciation with gene flow
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Data from: Exploring patterns of beta-diversity to test the consistency of biogeographical boundaries: a case study across forest plant communities of Italy
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Data from: Testing adaptive hypotheses of convergence with functional landscapes: a case study of bone-cracking hypercarnivores
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Data from: Bringing habitat information into statistical tests of local adaptation in quantitative traits: a case study of nine-spined sticklebacks
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Data from: Sexually dimorphic dorsal coloration in a jumping spider: testing a potential case of sex-specific mimicry
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Supplementary material 8 from: Zizka VMA, Weiss M, Leese F (2020) Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding and Metagenomics 4: e51925. https://doi.org/10.3897/mbmg.4.51925
Table S1. Number of macroinvertebrate individuals per sample and season
PHASTA incompressible test case for 48 processes
<p>Input files and execution instructions for a PHASTA incompressible 'crossflow' flow case using 48 processes. The expected results are listed in the included README.md.</p>
Improving Traceability Recovery Between Bug Reports and Manual Test Cases
<p>Vídeo backup da apresentação SBES 2020.</p> <p>Artigo: Improving Traceability Recovery Between Bug Report and Manual Test Cases.</p>
Data from: Testing for ecological limitation of diversification: a case study using parasitic plants
Imbalances in phylogenetic diversity could be the result of variable unbounded diversification rates, differing limits on diversity, or a combination of the two. We propose an approach to distinguish between rates and limits as the primary cause of phylogenetic imbalance, using parasitic plants as a model. With sister-taxon comparisons, we show that parasitic plant lineages are typically much less diverse than their autotrophic sisters. We then use age estimates for taxa used in the sister-taxon comparisons to test for correlations between clade age and diversity. We find that parasitic plant diversity is not significantly correlated with the age of the lineage, whereas there is a strong positive correlation between the age and diversity of autotrophic sister lineages. The Ericaceae sister-pair Monotropoideae (parasitic) and Arbutoideae (autotrophic) are sufficiently well samples at the species level to allow more parametric comparisons of diversification patterns. Model-fitting for this group supports ecological limitation in Monotropoideae and unconstrained diversification in Arbutoideae. Thus, differences in diversity between parasitic plants and their autotrophic sisters might be caused by a mixture of ecological limitation and unbounded diversification. A combination of sister-taxon comparisons of diversity and age, coupled with model-fitting of well-sampled phylogenies of focal taxa, provides a powerful test of likely causes of asymmetry in the diversity of lineages.
Data from: An examination of the accuracy of a sequential PCR and sequencing test used to detect the incursion of an invasive species: the case of the red fox in Tasmania
1. Polymerase Chain Reaction (PCR) diagnostic tests are increasingly applied to the identification of wildlife. Yet rigorous verification is rare and the estimation of test accuracy (the probability that true positive and true negative samples are correctly identified – test sensitivity and specificity, respectively), particularly in combination with sequencing, is uncommon. This is important because PCR-based tests are prone to contamination in sampling and the laboratory. 2. Here, we use an experimental case–control approach to estimate the sensitivity and specificity of a sequential PCR-based wildlife detection test used to identify incursions of red foxes into Tasmania from predator faeces (scats). 3. Our results show that the sensitivity of the fox test is high (~94%) for the PCR-based test on its own, but this decreases to ~84% when combined with the DNA sequencing step. In contrast, the specificity increases from ~96% in the PCR only test to ~99.6% after inclusion of the DNA sequencing step. 4. The intense public scrutiny of the fox eradication program in Tasmania, has undoubtedly influenced the application of a sequential PCR test that maximises specificity at the expense of sensitivity and so increases the risk that scats containing fox DNA would not be detected. This could lead to the establishment of foxes in Tasmania as a consequence. 5. Synthesis and applications. Importantly, the estimation of the sensitivity and specificity of sequential tests enables decisions about the risk associated with mistaken identification (i.e. false negatives vs false positives) to be quantified for decision makers. The cost of false negative errors should be balanced against the costs of false positive errors, which could include the expenditure incurred in the application of unnecessary management actions were foxes not in fact present. Understanding the risks and costs associated with both false negative and false positive errors is therefore a key component to the decision making process for the management of the Tasmanian fox incursion.
Data from: Using phylogenomic data to explore the effects of relaxed clocks and calibration strategies on divergence time estimation: primates as a test case
Primates have long been a test case for the development of phylogenetic methods for divergence time estimation. Despite a large number of studies, however, the timing of origination of crown Primates relative to the K-Pg boundary and the timing of diversification of the main crown groups remain controversial. Here we analysed a dataset of 372 taxa (367 Primates and 5 outgroups, 3.4 million aligned base pairs) that includes nine primate genomes. We systematically explore the effect of different interpretations of fossil calibrations and molecular clock models on primate divergence time estimates. We find that even small differences in the construction of fossil calibrations can have a noticeable impact on estimated divergence times, especially for the oldest nodes in the tree. Notably, choice of molecular rate model (auto-correlated or independently distributed rates) has an especially strong effect on estimated times, with the independent rates model producing considerably more ancient age estimates for the deeper nodes in the phylogeny. We implement thermodynamic integration, combined with Gaussian quadrature, in the program MCMCTree, and use it to calculate Bayes factors for clock models. Bayesian model selection indicates that the auto-correlated rates model fits the primate data substantially better, and we conclude that time estimates under this model should be preferred. We show that for eight core nodes in the phylogeny, uncertainty in time estimates is close to the theoretical limit imposed by fossil uncertainties. Thus, these estimates are unlikely to be improved by collecting additional molecular sequence data. All analyses place the origin of Primates close to the K-Pg boundary, either in the Cretaceous or straddling the boundary into the Palaeogene.
Data from: Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using 'early but risky' fossil constraints in addition to 'safe but late' constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown-group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical re-assessment of their phylogenetic position.
Data from: Potential and pitfalls of eukaryotic metagenome skimming: A test case for lichens
Whole genome shotgun sequencing of multi species communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here we investigate to what extent such metagenome skimming approaches are applicable for in-depth genomic characterizations of eukaryotic communities, e.g. lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from this data. To facilitate a project specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all-purpose overlap assembler, and SPAdes, a multi-sized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide range of coverage ratios. Testing assemblers on a real-world metagenome skimming data from the lichen Lasallia pustulata demonstrates the applicability of twin sets for guiding method selection. Furthermore, it reveals that the assembly outcome for the photobiont Trebouxia sp. falls behind the a-priori expectation given the simulations. Although the underlying reasons remain still unclear this highlights that further studies on this organism require special attention during sequence data generation and downstream analysis.
Automated Test Case Generation - Master Thesis
<p>This is the dataset used and created within my master thesis.</p>
Measurement Data for "LIRPA: Parallelized List Reductions for Language Agnostic Test Case Reducers"
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Semgrep*: Further Improving Static Application Security Testing (SAST) Tools: An Industry Case-Study
<p>Scripts to download and build data.</p> <p> </p> <p>Yaml files for additional SAST rules.</p>
TGenAI: LLM-based Approach for Functional Test Case Generation for IoT System
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Dataset Package for the paper "Single and Multi-objective Test Cases Prioritization for Self-driving Cars in Virtual Environments"
<p><br> #Dataset Package for the paper "Automated Test Cases Prioritization for Self-driving Cars in Virtual Environments"</p> <p><br> Description of the content:</p> <p><br> 1) "1_datasets" folder contains all the datasets concerning the test scenarios considered in the study. <br> <br> - AsFault supports two SDC software as test subjects while generating test cases, which we use to generate our test suites.<br> - BeamNG.AI. <br> - DeepDriving<br> - STRUCTURE: We report test subjects considered and organized with sub-folders for each of the supported two SDC software (i.e., Driving AIs):<br> - fullroad<br> - BeamNG_AI<br> - Driver_AI<br> 2) "2_SDC-source-code" contains all code and scripts composing the MATLAB/R prototypical implementation of SDC-pririotizer: </p> <p> - STRUCTURE:<br> - runSearch.m<br> - runGreedy.m<br> - plotResults.m<br> - permutationMutation.m<br> - mainGreedy.m<br> - permutationCrossover.m<br> - main.m<br> - initialPopulation.m<br> - fitness.m<br> - featureSelection.m<br> - faultDetectionRatePlots.m<br> - faultDetection.m<br> - (folder) r-script<br> - (folder) python<br> <br> 3) "3_study-data" folder contains all the main experimental data concerning the study conducted, RQs and all generated figures and main row-data reported in section results<br> <br> - results.csv<br> - greedy_results.csv<br> - (folder) tables<br> - (folder) figures<br> - (folder) DriverAI<br> - (folder) BeamNG_RF_1_5<br> - (folder) BeamNG_RF_1 </p>
Results from the test of the MCDA-MSS with the 56 case studies from the energy systems analysis literature
<p>Results from the test of the MCDA-MSS with the 56 case studies from the energy systems analysis literature</p>
Test cases for SERGHEI v1.0
<p>Test cases for verification of the shallow water module of SERGHEI v1.0.</p>
ScienceDex guides
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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.