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236 results for “Modeling Methods”
Analyzing disparity and rates of morphological evolution with model-based phylogenetic comparative methods
<p>Understanding variation in rates of evolution and morphological disparity is a goal of macroevolutionary research. In a phylogenetic comparative methods framework, we present three explicit models for linking the rate of evolution of a trait to the state of another evolving trait. This allows testing hypotheses about causal influences on rates of phenotypic evolution with phylogenetic comparative data. We develop a statistical framework for fitting the models with generalized least-squares regression, and use this to discuss issues and limitations in the study of rates of evolution more generally. We show that the power to detect effects on rates of evolution is low in that even strong causal effects are unlikely to explain more than a few percent of observed variance in disparity. We illustrate the models and issues by testing if rates of beak-shape evolution in birds are influenced by brain size, as may be predicted from a Baldwin effect in which presumptively more behaviorally flexible large-brained species generate more novel selection on themselves leading to higher rates of evolution. From an analysis of morphometric data for 645 species we find evidence that both macro- and microevolution of the beak are faster in birds with larger brains, but with the caveat that there are no consistent effects of relative brain size.</p>
Flow-field correction method to constrain AMOC in coupled model (IPSL-CM6A-LR)
<p>We use the standard version of IPSL-CM6A-LR (Boucher et al., 2020). The ocean component of IPSL-CM6A-LR is the NEMO oceanic model Version 3.6. The dynhpg.F90 file is a modified version of the routine that implements the flow-field correction method, and the namelist_ORCA1_cfg is the modified namelist used to activate the flow field correction, set the parameters, and read the input temperature, salinity, and mask. The mask specifies the region where this method is applied.</p> <p>To implement this method using the IPSL coupled model, consider following these steps:</p> <p>1. Install the standard configuration in a path<br> 2. Copy the provided dynhpg.F90 in modipsl/modeles/NEMOGCM/CONFIG/ORCA1_LIM3_PISCES/MY_SRC<br> 3. Compile<br> 3. Copy and modify the namelist_ORCA1_cfg in modipsl/config/IPSLCM6/testffc/PARAM</p> <p>The input conservative temperature (in degC), absolute salinity (in g/kg), and mask are provided to the model for the flow field correction are available in the following files:</p> <p>data_sal_sa_1.5LFC.nc (salinity) <br> data_sal_sa_weak1.5LFC.nc (salinity)<br> data_tem_bigthetao_1.5LFC.nc (temperature)<br> data_tem_bigthetao_weak1.5LFC.nc (temperature)<br> rhdmsk_data_bothBC2.v2.nc (mask)</p> <p>Note that data_sal_sa_1.5LFC.nc and data_tem_bigthetao_1.5LFC.nc are used to constrain the AMOC to the strong state in Jiang et al., (2023). data_sal_sa_weak1.5LFC.nc and data_tem_bigthetao_weak1.5LFC.nc are used to constrain it to the weak state in Jiang et al., (2023).</p> <p>Finally, some of the main simulated outputs are given. All the outputs are the annual mean ensemble mean (3 members) data lasting for 100 years. The initial states of the 3 members are sampled in the years of 1850, 2000 and 2080 of the CMIP6 piControl simulation available on ESGF, corresponding to neutral, strong, and weak AMOC states respectively.</p> <p>heatc_strong_3runs_1Y.nc (ocean heat content in J/m2)<br> sos_strong_3runs_1Y.nc (sea surface salinity in psu)<br> tos_strong_3runs_1Y.nc (sea surface temperature in degC)<br> precip_strong_3runs_1Y.nc (precipitation in kg/(s*m2))<br> diaptrW_strong_3runs_1Y.nc (meridional streamfunction in Sv)<br> slp_strong_3runs_1Y.nc (sea level pressure in Pa)<br> geop500_strong_3runs_1Y.nc (geopotential height at 500 hPa in m)<br> nettop0_strong_3runs_1Y.nc (clear-sky solar radiation at the top of atmosphere in W/m2)<br> nettop_strong_3runs_1Y.nc (net downward flux at the top of atmosphere in W/m2)<br> t2m_strong_3runs_1Y.nc (air temperature at 2-m in K)<br> vitu850_strong_3runs_1Y.nc (zonal wind at 850 hPa in m/s)<br> cld_strong_3runs_1Y.nc (low-level and high-level cloudiness, unitless)<br> tauuo_strong_3runs_1Y.nc (surface downward stress in the x-direction in N/m2)<br> tauvo_strong_3runs_1Y.nc (surface downward stress in the y-direction in N/m2)</p> <p>The files listed above are the results from simulations where the AMOC is constrained to the strong state (i.e., using the input data_tem_bigthetao_1.5LFC.nc and data_sal_sa_1.5LFC.nc). Similarly, the same fields from simulations where the AMOC is constrained to the weak state (i.e., using the input data_tem_bigthetao_weak1.5LFC.nc and data_sal_sa_weak1.5LFC.nc) are:</p> <p>heatc_weak_3runs_1Y.nc (ocean heat content in J/m2)<br> sos_weak_3runs_1Y.nc (sea surface salinity in psu)<br> tos_weak_3runs_1Y.nc (sea surface temperature in degC)<br> precip_weak_3runs_1Y.nc (precipitation in kg/(s*m2))<br> diaptrW_weak_3runs_1Y.nc (meridional streamfunction in Sv)<br> slp_weak_3runs_1Y.nc (sea level pressure in Pa)<br> geop500_weak_3runs_1Y.nc (geopotential height at 500 hPa in m)<br> nettop0_weak_3runs_1Y.nc (clear-sky solar radiation at the top of atmosphere in W/m2)<br> nettop_weak_3runs_1Y.nc (net downward flux at the top of atmosphere in W/m2)<br> t2m_weak_3runs_1Y.nc (air temperature at 2-m in K)<br> vitu850_weak_3runs_1Y.nc (zonal wind at 850 hPa in m/s)<br> cld_weak_3runs_1Y.nc (low-level and high-level cloudiness, unitless)<br> tauuo_weak_3runs_1Y.nc (surface downward stress in the x-direction in N/m2)<br> tauvo_weak_3runs_1Y.nc (surface downward stress in the y-direction in N/m2)</p> <p> </p>
Calibration of Absorbing Boundary Layers for Geoacoustic Wave Modeling in Pseudo-Spectral Time-Domain Methods
<p>Mesh.zip contains three folders each of them having seven meshes for each ABL. These data are required for reproducing TEST 3 which can be downloaded from https://github.com/carlosSpa/PSTD_ABL.git</p>
Combining formal methods and Bayesian approach for inferring discrete-state stochastic models from steady-state data
<p>Model, data, and a script to a paper of respective name</p>
Data from: genetic resources of macroalgae: development of an efficient method using microsatellite markers in non-model organisms
<p><span>Red and brown seaweeds are species with high ecological and economic importance. Here we report the feasibility of cost-effective molecular marker development in 6 species from different clades. Microsatellites markers of two brown seaweed species <em>Alaria esculenta</em>, <em>Pylaiella littoralis</em>, and of four red seaweed species <em>Calliblepharis jubata</em>, <em>Gracilaria gracilis</em>, <em>Gracilaria dura </em>and <em>Palmaria palmata</em> were identified and characterized using genomic sequences of Double-Digest Restriction site Associated DNA (ddRAD). A total of 64,623,186 reads were generated from two runs of multiplexed Illumina Miseq sequencing for which 30,636 reads containing microsatellites and 15,443 microsatellite loci with primers pairs were found. Five hundred seventy-six primers pairs were selected for amplification trials and levels of polymorphism. From the 338 that gave a positive amplification, 142 primers pairs were polymorphic. For genetic analyses two or three populations per species from 13 different geographic locations were used. A total of 28 usable polymorphic markers for <em>A. esculenta</em>, 18 for <em>P. littoralis</em>, 11 for <em>C. jubata</em>, 14 for <em>G. gracilis</em>, 21 for <em>G. dura </em>and 13 for <em>P. palmata </em>were developed. The overall number of alleles per locus ranged from 2 to 22. These 105 new microsatellite markers will be useful for further studies of population genetics, breeding programs and conservation genetics of these species. Compared with traditional approaches, our study yielded thousands of microsatellite loci in a short tim</span><span>e with affordable costs in six different species. This study based on ddRAD-sequencing for the development of microsatellite markers provides preliminary data u</span><span>sing a few individuals from two distinct populations on the genetic structure and reproduction mode of a non-model species as shown </span>with the detection of clonality for the two red algae, <em>C. jubata </em>and <em>G. dura</em> and the detection of highly genetically divergent populations corresponding probably to different cryptic species under the name of<em> P. littoralis</em>.</p>
A Data-facilitated Numerical Method for Richards Equation to Model Water Flow Dynamics in Soil Dataset
<p>This dataset contains the reference solutions used for training the two neural networks in 1-, 2- and 3-D cases for the article:"A Data-facilitated Numerical Method for Richards Equation to Model Water Flow Dynamics in Soil" by Zeyuan Song and Zheyu Jiang, submitted to the journal Water Resources Research. </p> <p>This dataset which describes the relationship between the pressure head and number of particles used to train two MLPs in D-GRW based solvers consists of three files, i.e., 1-, 2- and 3-D case study. There are two parts, original reference solutions and reference solutions, corresponding to the original solutions generated by coarse mesh solvers and solutions after data augmentation process, respectively.The dataset is generated by GRW based solvers and simulation results (e.g., Celia's finite difference method). Original reference solutions admit GRW proportionality assumption. We initialize the number of particles by multiplying the initial condition and 1E10. </p>
All-atom models of SU10 and P68 viral genomes. Supplementary to the "Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses".
<p>The dataset contains mmCIF formatted all-atom models of SU10 and P68 viral genomes and the python script used for refinement of the initial MMB-generated coordinates.</p>
Calibration of a pedestrian ingress model based on CCTV surveillance data using machine learning methods: data and code
<p>The package includes a dataset of trajectories obtained from a real-time pedestrian traffic detector at the vaccination centre and the code needed to validate the analyses described in the paper entitled Calibration of a pedestrian ingress model based on CCTV surveillance data using machine learning methods. Version 1.0.1 is a patch that corrects path to data.</p>
Dataset: Modular Impedance Matrix Method for Transient Modeling in Pipe Network Systems
<p>Unsteady flow is an important engineering problem in urban pipe network systems, requiring pressure and flow rate management analyses and reliable drinking water quality maintenance. Efficiently solving the hyperbolic partial differential equation and integrating it with various boundary conditions under the complex layout scenarios of pipe networks is a challenging issue for pipeline modelers. Frequency-domain modeling with a time-domain response was developed as an alternative to the traditional method of characteristics. However, this solution requires a substantial array size for large pipe network systems, significantly affecting applicability in field pipe network systems. This study proposes an innovative transient analysis method, the modular impedance matrix method, to solve the most labor- and cost-intensive computational issues affecting the unsteady flow analysis of large, complicated pipe networks. This method was applied to a field pipe network system and its performance compared to existing approaches. The algorithm of the proposed method fundamentally solved the computational problems associated with other methods, and its modular scheme allowed feasible integration with an analytical formulation that can be tailored to the modeler's preferences. The modular impedance matrix method's strength can be amplified according to the size and complexity of the pipe network system owing to its unique complementary validation capability. </p>
Ultrasound-guided Nerve Block Training Model and Evaluation Method
ClinicalTrials.gov study NCT06219005. IPD Sharing: NO. Countries: 1. Publications: 2.
Interpretation Training to Reduce Anxiety: Evaluating Technology-based Delivery Models and Methods to Reduce Attrition
ClinicalTrials.gov study NCT03498651. IPD Sharing: YES. Countries: 1. Publications: 1.
Data from: Flexible methods for species distribution modeling with small samples
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Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models
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Data from: genetic resources of macroalgae: development of an efficient method using microsatellite markers in non-model organisms
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Data from: Exploring the multi-level impacts of a youth-led comprehensive sexuality education model in Madagascar using human-centered design methods
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Sensitivity analysis of the maximum entropy production method to model evaporation in boreal and temperate forests
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Analyzing disparity and rates of morphological evolution with model-based phylogenetic comparative methods
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Limitations of using surrogates for behaviour classification of accelerometer data: refining methods using random forest models in Caprids
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Data for: Information accessibility, accounting manipulation, and sustainable development of digital enterprises: Based on double moderating effect model and panel PSM-DID method
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Data for: A new threshold selection method for species distribution models with presence-only data: extracting the mutation point of the P/E curve by threshold regression
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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.