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575 results for “Modeling Codes”
Code and data for RCEMIP-II: Mock-Walker Simulations as Phase II of the Radiative-Convective Equilibrium Model Intercomparison Project
<p>Model configuration code and post-processed data for simulations with SAM6.11.2 (Khairoutdinov and Randall, 2003) and CAM6 (https://github.com/ESCOMP/CESM/releases/tag/release-cesm2.1.3) needed to reproduce figures in the protocol paper for RCEMIP-II (Wing et al., 2023):</p> <p>Wing, A. A., Silvers, L. G., and Reed, K. A.: RCEMIP-II: Mock-Walker Simulations as Phase II of the Radiative-Convective Equilibrium Model Intercomparison Project, Geosci. Model Dev. Discuss. [preprint], https://doi.org/10.5194/gmd-2023-235, in review, 2023.</p> <p>SAM6.11.2 data (SAM6.11.2-lambda6000.zip and SAM6.11.2-lambda6144.zip):</p> <ul> <li>lambda6000: simulations with wavelength 6000 km</li> <li>lambda6144: simulations with wavelength 6144 km</li> <li>Each simulation, for a given mean SST ($SST) and delta SST ($dT) has the following data files <ul> <li>crh_avg_$SST_$dT.mat: column relative humidity averaged over the short (y) dimension, as a function of x and time.</li> <li>mockwalker2048x128x74_3km_12s_$SST_$dT.nc: domain-averaged 0D (function of t) and 1D (function of z and t) data <ul> <li>The "long" simulations, which have a domain that is twice as long as normal, instead have files with names mockwalker4096x128x74_3km_12s_$SST_$dT.nc</li> <li>The "wide" simulations, which have a domain that is twice as wide as normal, instead have files with names mockwalker2048x256x74_3km_12s_$SST_$dT.nc</li> <li>The "longwide" simulations, which have a domain that is twice as long and twice as wide as normal, instead have files with names mockwalker4096x256x74_3km_12s_$SST_$dT.nc</li> </ul> </li> <li>SAM_CRM_MW_$SST_$dT_1D_cldfrac_avg.nc: domain cloud fraction profile (function of z and t) following cfv2 definition of Stauffer and Wing (2022)</li> </ul> </li> </ul> <p>SAM6.11.2 configuration files (SAM6.11.2-lambda6000-config.zip and SAM6.11.2-lambda6144.zip):</p> <ul> <li>lambda6000: simulations with wavelength 6000 km</li> <li>lambda6144: simulations with wavelength 6144 km</li> <li>Each simulation, for a given mean SST and delta SST has the following configuration files <ul> <li>snd: Initial sounding</li> <li>prm: Namelist parameters</li> <li>grd: Vertical grid</li> <li>domain.f90: Domain size and number of subdomains</li> <li>simpleocean.f90: SST specification</li> </ul> </li> </ul> <p>CAM6 data (CAM6.zip):</p> <ul> <li>Each simulation, for a given mean SST ($SST) and delta SST ($dT) has the following data files <ul> <li>MockWalk54_humidity_HCF_$dT_$SST.nc: column relative humidity averaged over 4 longitude points, as a function of latitude and time.</li> <li>CAM6_MockW_$dT_cos_$SST_3_yr_HCF_0D_rlut_avg.nc: domain-averaged longwave flux at the top of the atmosphere</li> <li>CAM6_MockW_$dT_cos_$SST_3_yr_HCF_0D_rsut_avg.nc: domain-averaged upwelling shortwave flux at the top of the atmosphere</li> <li>CAM6_MockW_$dT_cos_$SST_3_yr_HCF_0D_rsdt_avg.nc: domain-averaged downwelling shortwave flux at the top of the atmosphere</li> <li>CAM6_MockW_$dT_cos_$SST_3_yr_HCF_1D_cldfrac_avg.nc: domain-averaged cloud fraction profile (function of z and t)</li> </ul> </li> </ul> <p>CAM6 configuration files (CAM6-MW295dT1p25-config.tar, CAM6-MW300dT1p25-config.tar, CAM6-MW305dT1p25-config.tar): Contains model initialization and configuration files for simulations with delta SST = 1.25 K. Simulations with other delta SST values need only change the delta SST parameter. </p>
Data and codes for Landslide hazard spatiotemporal prediction based on data-driven models: Estimating where, when and how large landslide may be
<p>Data and codes for Landslide hazard spatiotemporal prediction based on data-driven models: Estimating where, when and how large landslide may be</p>
Raw data and R code for statistical analyses from: Sensory trap leads to reliable communication without a shift in nonsexual responses to the model cue
<p>The sensory trap model of signal evolution suggests that males manipulate females into mating using traits that mimic cues used in a nonsexual context. Despite much empirical support for sensory traps, little is known about how females evolve in response to these deceptive signals. Female sea lamprey (<em>Petromyzon marinus</em>) evolved to discriminate a male sex pheromone from the larval odor it mimics and orient only towards males during mate search. Larvae and males release the attractant 3-keto petromyzonol sulfate (3kPZS), but spawning females avoid larval odor using the pheromone antagonist, petromyzonol sulfate (PZS), which larvae but not males, release at higher rates than 3kPZS. We tested the hypothesis that migratory females also discriminate between larval odor and the male pheromone and orient only to larval odor during anadromous migration, when they navigate within spawning streams using larval odor before they begin mate search. In-stream behavioral assays revealed that, unlike spawning females, migratory females do not discriminate between mixtures of 3kPZS and PZS applied at ratios typical of larval versus male odorants. Our results indicate females discriminate between the sexual and nonsexual sources of 3kPZS during but not outside of mating and show sensory traps can lead to reliable sexual communication without females shifting their responses in the original context.</p>
Models (atmospheric and atomic) for the P-CORONA code together with some sample runs.
<p>The dataset comprises some sample example runs with all necessary input parameters and corresponding outputs expected from P-CORONA, along with a few atomic and atmospheric models. Description of the files included is given in the README.txt file.</p> <p>The P-CORONA code can be obtained at <a href="https://gitlab.com/polmag/P-CORONA">https://gitlab.com/polmag/P-CORONA</a> and its documentation at <a href="https://polmag.gitlab.io/P-CORONA/">https://polmag.gitlab.io/P-CORONA/</a></p> <p>The version of P-CORONA used to generate this dataset (which corresponds to the commit #85d7552 in <a href="https://gitlab.com/polmag/P-CORONA">https://gitlab.com/polmag/P-CORONA</a>) can be found at: <a href="https://doi.org/10.5281/zenodo.15195460">https://doi.org/10.5281/zenodo.15195460</a></p>
Dataset and R-codes for Publication: "Best performances of visible-near infrared models in soils with little carbonate - a field study in Switzerland" (accepted version)
<p><span>In this upload you can find the R-codes and dataset for the Publication: </span></p> <p><span>"Best performances of visible-near infrared models in soils with little carbonate - a field study in Switzerland" by Simon Oberholzer Laura Summerauer, Markus Steffens and Chinwe Ifejika Speranza accepted in SOIL (https://doi.org/10.5194/egusphere-2023-1087)</span></p> <p><span>To reproduce the results of the manuscript, start with the R-file “ResampleandPreprocess.R” to prepare spectral data and then continue with the R-file “PLSRmodelling_GroupedCV.R” for the modelling.</span></p> <p><span>The R-files “control_train.R” and “rep_grouped_kfold_CV.R” are helper-functions for the grouped cross-validation. The file metadata.csv explains the column names in the spectral data (spcdata.RDS).</span></p>
Data and code for the article "Advancing Fine Branch Biomass Estimation with LiDAR and Structural Models"
<p>This is the repository for the data and code to reproduce the article "Advancing Fine Branch Biomass Estimation with LiDAR and Structural Models".</p> <p>Summary:</p> <p><span><span>·</span></span><span><span><span> </span><em>Background and Aims</em></span></span></p> <p><span><span>Lidar is a promising tool for fast and accurate measurements of trees. There are several approaches to estimate aboveground woody biomass using lidar point clouds. One of the most widely used methods involves fitting geometric primitives (<em>e.g.</em> cylinders) to the point cloud, thereby reconstructing both the geometry and topology of the tree. However, current algorithms are not suited for accurate estimation of the volume of finer branches, because of the unreliable point dispersions from <em>e.g. </em>beam footprint compared to the structure diameter.</span></span></p> <p><span><span>·</span></span><span><span><span> </span><em>Methods</em></span></span></p> <p><span><span>We propose a new method that couples point cloud-based skeletonization and multi-linear statistical modelling based on structural data to make a model (structural model) that accurately estimates the aboveground woody biomass of trees from high-quality lidar point clouds, including finer branches. The structural model was tested at segment, axis, and branch level, and compared to a cylinder fitting algorithm and to the pipe model theory.</span></span></p> <p><span><span>·</span></span><span><span><span> </span><em>Key Results</em></span></span></p> <p><span><span>The model accurately predicted the biomass with 1.6% nRMSE at the segment scale from a k-fold cross-validation. It also gave satisfactory results when up-scaled to the branch level with a significantly lower error (13% nRMSE) and bias (-5%) compared to conventional cylinder fitting to the point cloud (nRMSE: 92%, bias: 82%), or using the pipe model theory (nRMSE: 31%, bias: -27%).</span></span></p> <p><span><span>The model was then applied to the whole-tree scale and showed that the sampled trees had more than 1.7km of structures on average and that 96% of that length was coming from the twigs (<em>i.e.</em> <5 cm diameter). Our results showed that neglecting twigs can lead to a significant underestimation of tree aboveground woody biomass (-21%).</span></span></p> <p><span><span>·</span></span><span><span><span> </span><em>Conclusions</em></span></span></p> <p><span><span>The structural model approach is an effective method that allows a more accurate estimation of the volumes of smaller branches from lidar point clouds. This method is versatile but requires manual measurements on branches for calibration. Nevertheless, once the model is calibrated, it can provide unbiased and large-scale estimations of tree structure volumes, making it an excellent choice for accurate 3D reconstruction of trees and estimating standing biomass.</span></span></p>
RAM-SCB ROPE Dataset and Machine Learning Models with Code
<p>This repository contains the machine learning datasets and programs used in the development of the RAM-SCB ROPE.</p>
Code generation for classical-quantum software systems modelled in UML - Dataset and EGL Transformation
<p>This dataset contains all the elements necessary for carry out the EGL transformation from UML models to Hybrid and Quantum code, as well as to carry its validation. </p> <blockquote> <p><em>Quantum computing is gaining an increasing interest since it can solve certain problems exponentially faster than classical computing. Thus, many organizations are researching and launching investments for integrating quantum software into their existing systems. Software modernization (as based on Model-Driven Engineering) has been proposed to migrate from/to the so-called hybrid software systems, which integrate classical and quantum software. In that process, both, reverse engineering and restructuring phases, have already been investigated. However, forward engineering phase for generating hybrid source code from high-level design models has not yet been addressed. Thus, this research proposes a quantum code generation technique from extended UML design models. It consists of a set of Model-to-Text transformations (defined through Epsilon Generation Language) to generate both Python and Qiskit code, which respectively integrate classical and quantum code. The transformation has been validated through a multi-case study with 7 hybrid software systems modelled in UML, which demonstrated that the transformation is effective and efficient. The implication of this work is that the software modernization process for hybrid software systems can be completed by tackling forward engineering phase, and that Model-Driven Engineering can therefore globally facilitate industry adoption of quantum software.</em></p> </blockquote>
Code and datasets for "Controls on sediment transport from a glacierized catchment in the Swiss Alps established through inverse modeling of geomorphic processes"
<p>Code and datasets for:</p> <p>Delaney I., M. A. Werder, D. Felix, I. Albayrak, R. M. Boes, D. Farinotti, 2024, Controls on sediment transport from a glacierized catchment in the Swiss Alps established through inverse modeling of geomorphic processes. Water Resources Research. </p> <p>For more information, contact Ian Delaney (ianarburua.delaney@unil.ch).</p>
Data and R code for machine learning modelling of favourite places and routes of outdoor recreation
<p>This is a script showing the analysis used in a paper submitted for review in Landscape and Urban Planning, titled "Seeing through their eyes: Revealing recreationists’ landscape preferences through viewshed analysis and machine learning", by Carl Lehto, Marcus Hedblom, Anna Filyushkina and Thomas Ranius. </p> <p>The zip file contains an R script, data saved in .rds format and a R workspace. </p>
Data and Code for "A Novel Emergent Constraint Approach for Refining Regional Climate Model Projections of Flood Timing" Paper Submission to AGU GRL
<p>This contains the emergent constraint code, the offline CMIP6 hydrology data, and the shapefiles for each region used in the paper "A Novel Emergent Constraint Approach for Refining Regional Climate Model Projections of Flood Timing" submitted to AGU GRL.</p>
The processing results, dataset and original codes of Coral reef PtCloud segmentation model (based on proposed underwater camera systems)
<p><strong># Data Introduction</strong><br>The proposed camera system includes three operation modes: Surface Mode, Horizontal Mode, and Curved Mode.</p> <ul> <li><strong>Surface Mode</strong>: Provides 3D reconstructions (point cloud), DEM, and orthophoto maps of the seabed (covering a line of 70m in length).</li> <li><strong>Horizontal Mode</strong>: Provides 3D reconstructions (point cloud and mesh) and orthophoto maps of a single transect line.</li> <li><strong>Curved Mode</strong>: Offers 3D reconstructions (mesh) of various targets, including artificial coral reefs, coral reefs with snails, and coral reefs with starfish.</li> </ul> <p>All mesh results are saved in <code>.FBX</code> format, and point cloud results are saved in <code>.TXT</code> format.</p> <p><strong># Code Introduction</strong><br>The backbone of our point cloud segmentation model is the KPConv model.<br>If you encounter any issues during code deployment, please refer to the original KPConv repository (<a href="https://github.com/HuguesTHOMAS/KPConv" target="_new" rel="noopener">Original Code: https://github.com/HuguesTHOMAS/KPConv</a>).<br>We provide our modified code (customized for our task) along with the complete point cloud dataset.</p>
Dataset and source code for "Explanation and optimizing multi-model blending algorithm using random variables theory"
<p>this dataset contain: </p> <ol> <li>2m temperature de-biased model forecast data on station location, ECMWF, NCEP, JP and CMA</li> <li>2m temperature observaton data, obs_t2m</li> <li>24H QPF model forecast data on station location, ECMWF, NCEP, CMA-GFS, in raw_data_r24.zip</li> <li>24H precipitation data, in raw_data_r24.zip</li> <li>source code (in python)</li> </ol> <p> </p> <p>how to use it: </p> <p>1. prepare data and python environment<br> 1.1 if you want to run [Station_FCST_MMWB.py] or [Station_FCST_MMWB_r24.py] , please download the station forecast and observation data<br> 1.2 neet meteva package to read/write micaps-3 format data: https://github.com/nmcdev/meteva<br> 1.3 need cartopy to draw picture FigS01. </p> <p>2. try the 2m temperature blending methods <optional><br> 2.1 unzip the [CMA.zip, ECMWF.zip, jp.zip, NCEP.zip, obs_t2m.zip] file into ./raw_data/<br> 2.2 run the Station_FCST_MMWB.py in python environment </p> <p>3. try the 24h QPF multi blending methods <optional><br> 3.1 unzip the [raw_data_r24.zip] file into ./raw_data_r24/<br> 3.2 run the Station_FCST_MMWB_r24.py in python environment</p> <p>4. draw figures<br> 4.1 run Fig01.py in python environment <br> 4.2 run Fig02.py in python environment <br> 4.3 run Fig03.py in python environment <br> 4.4 run FigA01.py in python environment <br> 4.5 run FigS01.py in python environment </p>
Substorm Dataset and code (Substorm Identification With The WINDMI Magnetosphere - Ionosphere Nonlinear Physics Model)
<p>The archive contains MATLAB Live Script (<code>.mlx</code>) and Simulink model (<code>.slx</code>) files.</p> <ul> <li> <p><strong><code>.mlx</code> files:</strong> MATLAB Live Scripts are interactive files that combine code, output, and formatted text in a single document. They are used for data analysis, visualization, and sharing workflows in an easy-to-read format. These files can be opened in MATLAB's Live Editor for an interactive coding experience.</p> </li> <li> <p><strong><code>.slx</code> files:</strong> Simulink model files are used in MATLAB's Simulink environment for graphical modeling and simulation of dynamic systems. They are particularly useful for designing and analyzing systems with time-dependent behaviors, such as control systems or physical processes.</p> </li> </ul>
Archived Model Output and Code for "Marine Boundary Layer Cloud Condensation Nuclei Bias over the Southern Ocean: Comparisons between the Community Atmosphere Model 6 and Field Observations "
<div> <p>This is an archive of CAM6 simulation output used in the paper Marine Boundary Layer Cloud Condensation Nuclei Bias over the Southern Ocean: Comparisons between the Community Atmosphere Model 6 and Field Observations, submitted to the AGU Journal. Codes used to read the nc file is also attached.</p> </div>
Code and data for Porting the Meso-NH Atmospheric Model on Different GPU Architectures for the Next Generation of Supercomputers (version MESONH-v55-OpenACC)
<p>GeometricMG.pdf (source: https://bitbucket.org/em459/tensorproductmultigrid/src/master/Documentation/)<br>MESONH_Bench_HECTOR_ADASTRA_LEONARDO.tar.gz: code and data for Meso-NH bench<br>Performance.zip: code and data for figures related to performance<br>WeatherApplications.zip: namelists for running weather applications<br>OASIS3_WW3.tar.gz: OASIS and WW3 codes for running the Meso-NH WWW3 coupled simulation</p>
Code, Data, and Technical Note for SCREAM Beijing flood Convection-Permitting Regionally Refined Model 1.0 version
<p><a href="https://zenodo.org/api/records/15126670/draft/files/BeijingRRM-v0.1-SCREAM_push.tar.gz/content" target="_blank" rel="noopener noreferrer">BeijingRRM-v0.1-SCREAM_push.tar.gz</a> :</p> <p>The code used to generate all simulations for the paper entitled "Through the lens of a kilometer-scale climate model: 2023 Jing-Jin-Ji flood under climate change" submitted to Geophysical Research Letters. The SCREAM Beijing RRM source code is also available on GitHub at https://github.com/E3SM-Project/scream/tree/jzhang/RRM_tmp (last access: 28 Aug 2024) and a maint branch (BeijingRRM-v0.1; https://github.com/jsbamboo/scream/releases/tag/BeijingRRM-v0.1, last access: 28 Aug 2024). </p> <p><a href="https://zenodo.org/api/records/15126670/draft/files/files_scream-BeijingRRM-v1.0_storylines.zenodo.tar.gz/content" target="_blank" rel="noopener noreferrer">files_scream-BeijingRRM-v1.0_storylines.zenodo.tar.gz</a> : </p> <p>The runscripts, mapping files, masks used for analysis and figures in the paper. The simulation outputs and processed data are too large (3.3T) to upload to zenodo, and are available on the NERSC portal: https://portal.nersc.gov/archive/home/z/zhang73/www/files_scream-BeijingRRM-v1.0_storylines</p> <p><a href="https://zenodo.org/uploads/15126670" target="_blank" rel="noopener noreferrer">BeijingFlood_Doc.pdf</a> :</p> <p>The technical note documenting our practice in generating the SCREAM Beijing flood RRM configurations. Source page: https://acme-climate.atlassian.net/wiki/spaces/DOC/pages/4056318237/SCREAM+Beijing+Flood+RRM+Technical+Note</p>
Data and code to replicate: Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie
<p>Diet analysis integrates a wide variety of visual, chemical and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, e.g., highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package <i>mvtweedie</i> that extends capabilities of widely used packages in R (<i>mgcv</i> and <i>ggplot2</i>) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted puffins (<i>Fratercula cirrhata</i>) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980-2000) and then Pacific herring and capelin (2000-2020), while wolves (<i>Canis lupus ligoni</i>) in Southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines. </p>
Models of evolutionary rescue with plasticity and nonlinear environmental change: code and data
<p>Rapid environmental changes are putting numerous species at risk of extinction. For migration-limited species, persistence depends on either phenotypic plasticity or evolutionary adaptation (evolutionary rescue). Current theory on evolutionary rescue typically assumes linear environmental change. Yet accelerating environmental change may pose a bigger threat. Here we present the simulation code and data from a model of a species encountering an environment with accelerating or decelerating change, to which it can adapt through evolution or phenotypic plasticity (within-generational or transgenerational). We show that unless either form of plasticity is sufficiently strong or adaptive genetic variation is sufficiently plentiful, accelerating or decelerating environmental change increases extinction risk compared to linear environmental change for the same mean rate of environmental change. </p>
Representing surface heterogeneity in land-atmosphere coupling in E3SMv1 single-column model over ARM SGP during summertime - E3SM SCM data and code
<p>This dataset contains post-processed E3SM single-column model output and code used to produce the figures in the manuscript that we are targeting Geoscientific Model Development to submit. </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.