Protocols

Stage-mass-structured IPMs incorporating seasonal demographic transitions and environmental stochasticity for population viability analysis. Uses prospective perturbation analysis and stochastic proje...

High-resolution integrated hydrological modeling using coupled PRMS-MODFLOW system to simulate surface water and groundwater interactions extending 400 m into subsurface. Model accounts for complex te...

Hydrological modeling approach that stratifies mountain watersheds by elevation zones to quantify water budget components and assess climate change impacts on streamflow and groundwater storage.

Integrated groundwater flow and reactive transport modeling using PHT-USG coupled with MODFLOW-USG for geochemical reactions and PHREEQC for reaction modeling. Includes parameter estimation using PEST...

Size-structured population model that incorporates climate effects on vital rates to project population dynamics and calculate population growth rates. Uses continuous size distributions and matrix pr...

Application of METE mathematical framework to predict species-area relationships and species-abundance distributions based on community state variables and entropy maximization principles.

Bayesian statistical approach to simultaneously estimate individual lifetime means and variances in social traits from longitudinal data. Controls for age effects and repeated measures while quantifyi...

Daily water and energy budget modeling at 100-m grid resolution using the US Geological Survey Precipitation-Modeling Runoff System (PRMS) with climate forcing from SNOTEL stations and LiDAR snow obse...

Standard metagenomics pipeline involving assembly with MEGAHIT, binning with multiple tools, dereplication, and taxonomic classification using GTDB-tk.

Used raster analysis in ArcGIS to identify suitable ground squirrel habitat by combining landcover and canopy height data, then calculated distance-from-cover metrics using buffer operations. This met...

Maximum likelihood phylogenetic analysis of full genome sequences using MUSCLE alignment and Tamura-Nei evolutionary model to determine relationships between outbreak isolates and assess overwintering...

Development and analysis of a seven-dimensional nonlinear differential equation system modeling tiger salamander population dynamics across life stages and morphological forms. The model incorporates ...

A brokering framework that uses OGC standards to integrate heterogeneous environmental datasets from multiple sources into synthesized time-series data accessible through Python and web interfaces.

Used Community Land Model to simulate evapotranspiration components at high spatiotemporal resolution over a mountainous watershed with detailed soil layering and vegetation parameterization. Model se...

Coupled integrated hydrologic and particle tracking modeling approach that simulates groundwater flow using ParFlow-CLM and age distributions using EcoSLIM, with matrix diffusion effects incorporated ...

Development and application of a 2-D multiphase reactive transport model using PFLOTRAN to simulate coupled hydrological and biogeochemical processes in shale weathering. The model integrates variably...

A novel approach combining LSTM neural networks with process-based ecological understanding to predict evapotranspiration and ecosystem respiration. The method integrates temporal pattern recognition ...

Machine learning approach for snow cover mapping using PlanetScope imagery with multiple model configurations incorporating spectral, topographic, and vegetation variables. Performance evaluation acro...

Oxford Nanopore long-read sequencing followed by assembly using both FLYE and NECAT assemblers, with iterative polishing using Racon and Medaka, then merging assemblies using Quickmerge and HaploMerge...

Monte Carlo simulation comparing observed reproductive pair relatedness to expected relatedness under random mating to test for inbreeding avoidance.

A comprehensive statistical framework for quality assurance and quality control of meteorological time series data involving preliminary data exploration, quality assessment with outlier detection, an...

High-resolution Weather Research and Forecasting model simulations using different microphysical parameterizations to assess precipitation sensitivity in complex mountain terrain. Three different micr...

Conversion of reflectance spectra into bee and bird visual spaces using established photoreceptor sensitivity models. Uses color hexagon model for bees and receptor-noise limited model for birds to ca...

Three-dimensional geological modeling using implicit modeling with radial basis functions to generate subsurface structure. Model incorporates strike, dip, and fault information from geological survey...

Swiss avalanche dynamics program used to calculate runout distance, flow thickness, velocity and impact pressure by modeling avalanche flow physics with calibrated friction parameters.

Numerical experiments to test whether sum of SARs for taxonomic subgroups equals the SAR for the entire assemblage under METE predictions.

Use of Bias Correction and Spatial Disaggregation downscaled CMIP5 climate projections processed through VIC hydrologic model to generate future streamflow scenarios.

BEAST analysis using linked mitochondrial and nuclear gene sequences with HKY substitution models and birth-death priors to estimate species-level phylogenetic relationships.

A resource allocation model combining growth rate, flowering time, and optimal control theory to predict phenological shifts under climate change. The model incorporates species-specific climate thres...

Application of uniform temperature increases to historical climate sequences to assess hydrological response to warming. Seasonal warming scenarios applied independently to test timing effects on wate...

A method that uses species' current climate ranges to predict extinction risk under future climate scenarios by assuming all individuals within a species share the same climate envelope.

Calculation of site-specific wetness indices using mean annual precipitation and temperature data to characterize local climate conditions for experimental sites.

Automated system for retrieving, normalizing, and processing heterogeneous environmental data using ODM2 datamodel with web interface and API access for real-time predictions.

Systematic comparison of first-order kinetic vs. dormancy-based models for predicting soil CO2 respiration under varying moisture conditions using multi-scale experimental datasets.

Development of power-law scaling relationships between environmental variables and DOM chemodiversity using ordinary least squares regression on log-transformed data.

Deep machine learning algorithm trained with ~29,000 images to automatically detect and flag time-lapse images potentially containing hummingbirds for manual verification.

Iterative numerical procedure for solving dynamic macroecological theory equations by cycling through MaxEnt structure function calculation, state variable updates, and Lagrange multiplier optimizatio...

Offline energy-only PET calculation using ERA5-Land reanalysis net radiation estimates, with optional snow albedo adjustment using MODIS observations.

Development of deterministic and stochastic population models incorporating empirical estimates of selection, heritability, and phenotypic plasticity to project population persistence under climate ch...

Bioinformatics pipeline for processing raw sequencing reads through quality filtering, mapping, variant calling, and SNP filtering using GATK v4.0 and associated tools.

Mapping species distributions across elevational gradients using abundance data, GPS coordinates, and digital elevation models. Includes range core calculation using abundance-weighted elevation avera...

Application of general mixed Yule/coalescent models to identify species boundaries in molecular phylogenies by detecting transitions between inter- and intraspecific branching rates.

Calculation of potential solar radiation at study sites using topographic variables including sun angle, latitude, ground slope, local shading, and day length.

Computer simulation of population genetic changes during bottlenecks using BOTTLESIM software combined with multiple analytical approaches to detect bottleneck signatures.

Forward modeling approach using HeFTy software to simulate time-temperature conditions and map out thermal history of samples by matching predicted ages to measured thermochronological data.

Back-trajectory analysis to determine air mass origins and transport pathways for correlating with microplastic deposition patterns.

Combines process-based mass conservation equations with empirical curvature relationships to predict soil thickness. Applies different methods based on erosional vs depositional terrain classification...

Standard molecular phylogenetic approach using ITS sequences to reconstruct evolutionary relationships and calculate phylogenetic distances between plant species. Includes sequence alignment, tree inf...

Process-based dynamic global ecosystem modeling using IBiS to simulate terrestrial carbon storage responses to climate change, CO2 fertilization, and plant migration constraints. Uses leaf-level calcu...

Machine learning approach using USGS LOADEST software to develop concentration time-series models by combining discharge and concentration data. Used to extrapolate long-term trends and fill data gaps...