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  1. Abstract

    This paper summarizes the open community conventions developed by the Ecological Forecasting Initiative (EFI) for the common formatting and archiving of ecological forecasts and the metadata associated with these forecasts. Such open standards are intended to promote interoperability and facilitate forecast communication, distribution, validation, and synthesis. For output files, we first describe the convention conceptually in terms of global attributes, forecast dimensions, forecasted variables, and ancillary indicator variables. We then illustrate the application of this convention to the two file formats that are currently preferred by the EFI, netCDF (network common data form), and comma‐separated values (CSV), but note that the convention is extensible to future formats. For metadata, EFI's convention identifies a subset of conventional metadata variables that are required (e.g., temporal resolution and output variables) but focuses on developing a framework for storing information about forecast uncertainty propagation, data assimilation, and model complexity, which aims to facilitate cross‐forecast synthesis. The initial application of this convention expands upon the Ecological Metadata Language (EML), a commonly used metadata standard in ecology. To facilitate community adoption, we also provide a Github repository containing a metadata validator tool and several vignettes in R and Python on how to both write and read in the EFI standard. Lastly, we provide guidance on forecast archiving, making an important distinction between short‐term dissemination and long‐term forecast archiving, while also touching on the archiving of code and workflows. Overall, the EFI convention is a living document that can continue to evolve over time through an open community process.

     
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    Free, publicly-accessible full text available November 23, 2024
  2. Free, publicly-accessible full text available February 1, 2025
  3. Coulson, Tim (Ed.)
  4. Abstract. Monitoring leaf phenology tracks the progression ofclimate change and seasonal variations in a variety of organismal andecosystem processes. Networks of finite-scale remote sensing, such as thePhenoCam network, provide valuable information on phenological state at hightemporal resolution, but they have limited coverage. Satellite-based data withlower temporal resolution have primarily been used to more broadly measurephenology (e.g., 16 d MODIS normalizeddifference vegetation index (NDVI) product). Recent versions of the GeostationaryOperational Environmental Satellites (GOES-16 and GOES-17) can monitor NDVI attemporal scales comparable to that of PhenoCam throughout most of thewestern hemisphere. Here we begin to examine the current capacity of thesenew data to measure the phenology of deciduous broadleaf forests for thefirst 2 full calendar years of data (2018 and 2019) by fittingdouble-logistic Bayesian models and comparing the transition dates of the start, middle, and end of theseason to those obtained from PhenoCam and MODIS 16 dNDVI and enhanced vegetation index (EVI) products. Compared to these MODIS products, GOES was morecorrelated with PhenoCam at the start and middle of spring but had a largerbias (3.35 ± 0.03 d later than PhenoCam) at the end of spring.Satellite-based autumn transition dates were mostly uncorrelated with thoseof PhenoCam. PhenoCam data produced significantly more certain (allp values ≤0.013) estimates of all transition dates than any of thesatellite sources did. GOES transition date uncertainties were significantlysmaller than those of MODIS EVI for all transition dates (all p values ≤0.026), but they were only smaller (based on p value <0.05) than thosefrom MODIS NDVI for the estimates of the beginning and middle of spring. GOES willimprove the monitoring of phenology at large spatial coverages and providesreal-time indicators of phenological change even when the entire springtransition period occurs within the 16 d resolution of these MODISproducts. 
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  5. null (Ed.)
    Abstract. Canopy radiative transfer is the primary mechanism by which models relate vegetation composition and state to the surface energy balance, which is important to light- and temperature-sensitive plant processes as well as understanding land–atmosphere feedbacks.In addition, certain parameters (e.g., specific leaf area, SLA) that have an outsized influence on vegetation model behavior can be constrained by observations of shortwave reflectance, thus reducing model predictive uncertainty.Importantly, calibrating against radiative transfer outputs allows models to directly use remote sensing reflectance products without relying on highly derived products (such as MODIS leaf area index) whose assumptions may be incompatible with the target vegetation model and whose uncertainties are usually not well quantified.Here, we created the EDR model by coupling the two-stream representation of canopy radiative transfer in the Ecosystem Demography model version 2 (ED2) with a leaf radiative transfer model (PROSPECT-5) and a simple soil reflectance model to predict full-range, high-spectral-resolution surface reflectance that is dependent on the underlying ED2 model state.We then calibrated this model against estimates of hemispherical reflectance (corrected for directional effects) from the NASA Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and survey data from 54 temperate forest plots in the northeastern United States.The calibration significantly reduced uncertainty in model parameters related to leaf biochemistry and morphology and canopy structure for five plant functional types.Using a single common set of parameters across all sites, the calibrated model was able to accurately reproduce surface reflectance for sites with highly varied forest composition and structure.However, the calibrated model's predictions of leaf area index (LAI) were less robust, capturing only 46 % of the variability in the observations.Comparing the ED2 radiative transfer model with another two-stream soil–leaf–canopy radiative transfer model commonly used in remote sensing studies (PRO4SAIL) illustrated structural errors in the ED2 representation of direct radiation backscatter that resulted in systematic underestimation of reflectance.In addition, we also highlight that, to directly compare with a two-stream radiative transfer model like EDR, we had to perform an additional processing step to convert the directional reflectance estimates of AVIRIS to hemispherical reflectance (also known as “albedo”).In future work, we recommend that vegetation models add the capability to predict directional reflectance, to allow them to more directly assimilate a wide range of airborne and satellite reflectance products.We ultimately conclude that despite these challenges, using dynamic vegetation models to predict surface reflectance is a promising avenue for model calibration and validation using remote sensing data. 
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  6. The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON’s shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.

     
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