AndreaBozzo/ceres-open-data-index huggingface dataset:
Data and code from: Virome of <i>Solenopsis invicta</i> (Hymenoptera: Formicidae): intercontinental differences in the native and introduced ranges

<p dir="ltr">This dataset contains all the raw data and R statistical software code needed to reproduce the maps and statistical analyses presented in the associated manuscript, titled “Virome of <i>Solenopsis invicta</i> (Hymenoptera: Formicidae): intercontinental differences in the native and introduced ranges.” In the manuscript, results are presented from a survey of viruses in 430 red imported fire ant nests at a total of 82 sites in its native range in Argentina and introduced range in the United States. A series of maps and graphs are generated to qualitatively describe the distribution of twenty different viruses, including prevalence of different social forms (monogyne and polygyne colonies) in each continent, and viral abundance by location and by season. In addition, we present a generalized linear mixed model that models the probability of virus presence as a function of viral species, continent, and social form. We investigate spatial patterning in model residuals and we compare the odds of each social form by virus within each continent and the odds of presence of each virus between the two continents. Raw data is provided in CSV form, and code is provided as an RMarkdown notebook along with its rendered HTML output. In addition, a GEOJSON file is included with the spatial coordinates of the study sites.</p><h3>Files</h3><ul><li><b>Virome survey S_invicta.csv</b>: All raw data, including site-level covariates and coordinates of colony locations within each site. Column "GP9" indicates the social form of the sampled colony (Monogyne or Polygyne) and all following columns indicate presence (1) or absence (0) of 18 different viruses</li><li><b>fire_ant_virome_code_supplement.Rmd</b>: RMarkdown notebook with all code needed to import and process the data, generate maps and other figures, fit statistical models, and produce figures and tables with statistical model predictions.</li><li><b>fire_ant_virome_code_supplement.html</b>: Rendered output from code notebook</li><li><b>fire_ant_sampling_sites.geojson</b>: Spatial coordinates of the 82 sampling sites (unprojected latitude-longitude)</li></ul><p></p>

Tags: biopesticide, fire-ant, formicidae, microbial-control, picornavirales, red-imported-fire-ant, single-stranded-rna-virus, solenopsis-invicta, source-code, virome, virus
Organization: Department of Agriculture
Data from: Strategies for mitigating greenhouse gas emissions from US dairy farms toward a net zero goal

<p dir="ltr">Representative dairy farms in major dairy regions of the United States were modeled using the Integrated Farm System Model to quantify potential reductions in greenhouse gas emissions using various mitigation strategies. Important data and information describing these 14 farms are documented in this table. These data include the farm location, number of cows and heifers maintained, milk produced, feeds and nutrient contents fed, crop areas, crop yields, fertilizer and lime application rates, irrigation water applied, milking and housing facilities, manure collection, storage and application methods used, and soil characteristics. Simulated output information for feed consumption, nutrient losses, fossil energy use, water use, and greenhouse gas emissions are listed for each farm. These data are published as supplementary information for the article “Strategies for mitigating greenhouse gas emissions from US dairy farms toward a net zero goal” published in the Journal of Dairy Science.</p>

Tags: dairy-farm, greenhouse-gas-mitigation, ifsm, integrated-farm-system-model
Organization: Department of Agriculture
Data from: A site suitability analysis for castor (Ricinus communis L.) production during Brazil's second harvest accounting for potential disease

<p>Raster data providing site suitability results for the production of castor throughout Brazil. The pixel value range from 1 (currently not suitable) to 10 (highly suitable) for a suitability ranking in the given pixel location. The site suitability for castor was conducted using data associated with agronomic and disease characteristics. The various characteristics were subject to a weighted overlay analysis in conjunction with an analytical hierarchy process. The raster was the result of these analytics.</p>

Tags: ars, brazil, castor, data-gov, gray-mold, np211, np215, np216, oil-seed-crop, raster-data, site-suitability, theme-geospatial
Organization: Department of Agriculture
USDA Beltsville Agricultural Research Center (BARC) Gridded Yield Data Archive, version 1

<p dir="ltr">[Note, 1/20/2026: Farm management PDF files added.]</p><p dir="ltr">The USDA Beltsville Agricultural Research Center (BARC) Gridded Yield Data Archive is a multi-year, gridded yield data archive derived from yield monitor data acquired from over 40 production fields in Beltsville, MD. Production of the archive involved the projection of the yield monitor data into a geographic coordinate system suitable for mapping, the identification and removal of data outliers, and the production of gridded, spatially interpolated yield maps using block Kriging. All map products were produced in common, nonproprietary file formats for easy access.</p><p dir="ltr">This research was a contribution from the Long-Term Agroecosystem Research (LTAR) network. LTAR is supported by the United States Department of Agriculture.</p>

Tags: agricultural-veterinary-and-food-sciences-agriculture-land-and-farm-management-agricultural-lan, agricultural-veterinary-and-food-sciences-agriculture-land-and-farm-management-agricultural-spa, agriculture, agroecosystems-environment-management, agroecosystems-environment-plant-and-animal-harvest-yield-and-quality, barc, continent-north-america-united-states-of-america, crop-yield, data-archive, earth-science-biosphere-terrestrial-ecosystems-agricultural-lands, earth-sciences-physical-geography-and-environmental-geoscience, farm-management, farming, kriging, long-term-agricultural-experiments, maps-multimedia-gis-data-and-images, ope3, plants-crops-crop-production, precision-agriculture, productivity, remote-sensing, yield-monitor
Organization: Department of Agriculture
Data and code from: Denitrification genes play minor roles in fumonisin production and virulence in <i>Fusarium verticillioides</i>

<p dir="ltr">This dataset contains all data and code necessary to reproduce the analyses, tables, and figures presented in the associated manuscript.</p><p dir="ltr">The following files are included:</p><ul><li>Fumonisin_Bioassay_Rice_Trial_1.xlsx (and Trial_2.xlsx, Trial_3.xlsx): results from the three experimental runs of the fumonisin bioassay</li><li>Seedling_Disease_Assay_Trial_1.xlsx (and Trial_2.xlsx, Trial_3.xlsx): results from the three experimental runs of the seedling growth and disease assay</li><li>fumonisin_bioassay.Rmd: RMarkdown notebook with annotated R code needed to analyze the fumonisin bioassay data</li><li>fumonisn_bioassay.html: rendered HTML output of the fumonisin bioassay notebook</li><li>seedling_disease_assay.Rmd: RMarkdown notebook with annotated R code needed to analyze the seedling disease assay data</li><li>seedling_disease_assay.html: rendered HTML output of the seedling disease assay notebook</li><li>data_description.pdf: metadata document with column descriptions for each of the spreadsheets</li></ul><p dir="ltr">The following software and package versions were used:</p><ul><li>R version 4.3.1</li><li>CmdStan version 2.33.1</li><li>R packages:</li><li><ul><li>brms version 2.20.4</li><li>cmdstanr version 0.5.3</li><li>emmeans version 1.8.9</li><li>tidybayes version 3.0.4</li><li>bayestestR version 0.13.2</li></ul></li></ul><p><br></p>

Tags: denitrification, disease, fumonisin, fungi, fusarium-verticillioides, nitrogen-cycle, software-code, virulence
Organization: Department of Agriculture
Data from: Assessing agroecosystem resilience in annual cropping systems with ecometabolomics

<p dir="ltr">Plant ecometabolomics is a growing field of study which allows broader understanding of the metabolomic dynamics within and between plants and their ecosystem. Plants constantly respond to environmental cues, producing plant secondary metabolites (PSMs) to communicate with and adapt to their everchanging ecosystems. Plant secondary metabolites allow plants to withstand biotic and abiotic stressors and are mediators of interactions between their above and belowground ecosystem. However, the way PSMs are affected by and respond to agricultural management is poorly understood. As part of the Long-Term Agroecosystem Research (LTAR) Network, we assessed ecometabolomic profiles of corn (<i>Zea mays</i> L.) leaves and roots between contrasting prevailing (prevailing practice, PP) and alternative (alternative practice, AP) cropping practices which utilized cover crops and cover crop interseeding. The ecometabolomic profiles of corn leaves and roots were 90% and 71%, respectively, richer in PSMs in the AP than PP treatments. Our untargeted metabolomic analyses resulted in 124 annotated features, with 68 features significantly different between AP and PP treatments. We detected 43 features annotated as PSMs, 39 of which were greater (p ≤ 0.10) in the AP than PP treatments. This research shows that our agricultural management practices influence the way plants respond within their agroecosystem. Increased production of PSMs allows plants to better adapt to various abiotic and biotic stresses, enhancing the resilience of plants within their ecosystem.</p>

Tags: agricultural-resilience, ecometabolomics, ltar, zea-mays
Organization: Department of Agriculture
Data from: Framework to Develop an Open-Source Forage Data Network to Improve Primary Productivity and Enhance System Resiliency

<p>A compilation of experimental forage data from 108 unique locations across the United States, with harvest dates ranging from 1958 to 2022. This dataset contains a subset of the data compiled in the initial stages of development of the <em>Forage Data Hub</em>. In particular, these are the 37,970 data entries used for the forage system resiliency analysis presented in the primary article.</p>
<p>Resources in this dataset:</p>
<ul>
<li>
<p>Resource Title: FDH Data Dictionary
File Name: FDH_Data_Dictionary.csv
Resource Description: Data dictionary for the data compiled as a result of the efforts described in Ashworth et al. (2023) - Framework to Develop an Open-Source Forage Data Network to Improve Primary Productivity and Enhance System Resiliency (in review). Includes descriptions for the data fields in the FDH Data data file.</p>
</li>
<li>
<p>Resource Title: FDH Data
File Name: FDH_Data_03-04-2023.csv
Resource Description: Data compiled as a result of the efforts described in Ashworth et al. (2023) - Framework to Develop an Open-Source Forage Data Network to Improve Primary Productivity and Enhance System Resiliency (in review). Includes a lightly preprocessed version of the data housed in the Forage Data Hub as of March 4th, 2023.</p>
</li>
</ul><p></p>

Tags: annual-forage-systems, ars, biomass-yield, data-gov, diverse-forage-systems, dry-matter-yield, forage, np212, perennial-forage-systems
Organization: Department of Agriculture
Organic farming impact on soil health indicators across 9 yr of management in a US Midwest Mollisol

<p dir="ltr">This dataset contains soil health indicator data across 9-yr (2012-2020) from an experiment evaluating conventional corn-soybean, organic corn-soybean-oat/alfalfa-alfalfa, and an organic perennial pasture near Boone, IA. The soil samples were collected annually and analyzed using standard methods. The soil properties used as soil health indicators were: microbial biomass C, potentially mineralizable C and N, pH, wet-aggregate stability, and concentrations of organic C, total N, inorganic N (NH4 and NO3), P, and K. Such data were collected to answer key farmer questions regarding changes in soil health under organic farming. Data were presented in Ruis et al. (2025), Soil Science Society of America Journal (<a href="https://doi.org/10.1002/saj2.20795" rel="noreferrer" target="_blank">https://doi.org/10.1002/saj2.20795</a>).</p>

Tags: alfalfa, corn, nutrients, organic-farming, ph, soil-aggregation, soil-biology, soil-fertility, soil-health, soil-properties, soil-structure, soybean, total-nitrogen
Organization: Department of Agriculture
Data from: Comparison of sediment transport and bedforms from steady and unsteady flow hydrographs of similar flow rate

<p dir="ltr">This is the dataset that was used to make the figures for the publication entitled "Comparison of sediment transport and bedforms from steady and unsteady flow hydrographs of similar flow rate"</p><p dir="ltr">The citation for the publication is: Wren, D. G.<b>,</b> McAlpin, T. O., and Langendoen, E. L. Comparison of sediment transport and bedforms for equilibrium flows to unsteady hydrograph flows at the same flow rates. Journal of Hydraulic Engineering. (In preparation).</p><p dir="ltr">Flow rates and depths in natural rivers and streams can change rapidly with time due to runoff from rainfall and snowmelt. These changing conditions complicate the prediction of sediment transport, bed topography, and flow depth. Due to the difficulty in collecting field data during unsteady flow events, it is necessary to use laboratory flume experiments to study sediment transport and bedform properties during unsteady flows. The goal of the work described here was to isolate the effects of hydrograph flows on bedform dimensions, water surface slope, and sediment transport relative to the same flow rates in equilibrium conditions for steady flows while also comparing results across the various flowrates. For three repeated hydrographs of 1-, 3-, and 6-hour periods, quantities measured at four different flow rates during the hydrographs will be compared to equilibrium conditions for each flow rate. The development of bedforms during rising and peak flow rates competed with the destruction of bedforms during falling flow rates. When bedform growth was greater than decay, bedform sizes, water surface slopes, and transport rates during falling flow rates were typically greater than for equilibrium steady conditions at the same flow rate, while they were typically smaller than equilibrium bedforms for rising flow rates.</p>

Tags: bedforms, hydrographs, sediment-transport, unsteady-flows
Organization: Department of Agriculture
Data from: Above-ground plant properties are not leading indicators of grazing-induced soil carbon accrual in the Northern Great Plains

<p dir="ltr">This is digital research data corresponding to a manuscript, Above-ground plant properties are not leading indicators of grazing-induced soil carbon accrual in the Northern Great Plains, published in <a href="https://doi.org/10.1016/j.ecolind.2023.111509" rel="noreferrer" target="_blank">Ecological Indicators</a>.  </p><p dir="ltr">Little is known about how grazing-induced shifts in plant properties correspond with shifts in soil organic carbon (SOC) stocks. To help fill this gap, we used data from a field experiment to test whether above-ground plant properties (i.e. biomass, species richness) act as leading indicators of grazing-induced SOC accrual in the Northern Great Plains, USA.</p><p dir="ltr">Our 5-yr bovine grazing experiment had a randomized complete block design and pre-treatment data. Moderate summer grazing (control) is widely used in the Northern Great Plains, and treatments that may alter grassland vegetation and SOC included: severe summer grazing, moderate fall grazing, and severe fall grazing. The four grazing treatments were applied to 20 paddocks (60 × 30 m) arranged in a randomized complete block design with 5 replications. Grazing intensities approximated recommended (i.e. moderate; 1 animal unit month [AUM] × ha<sup>-1</sup> × year<sup>-1</sup>) and severe (1.5 AUM × ha<sup>-1</sup> × year<sup>-1</sup>) stocking rates. Summer grazing occurred during the third week of June and fall grazing was after killing frosts at the end of October.</p><p dir="ltr">This study's dataset is of a subset of data for this grazing experiment. Given the study aim's, the dataset included a single measure of SOC stock (0-60 cm depth increment) and three plant properties (current-year above-ground biomass, older dead above-ground biomass, and plant species richness). SOC data were for 2013 and 2018 while plant data were for 2014 and 2017. Additional details can be found in the readme file, open access manuscript, and manuscript's supplement.</p>

Tags: carbon-dioxide-removal, carbon-ranching, carbon-sequestration, climate-change, co-benefits, grassland, grazing-experiment, livestock-grazing, mixed-grass-prairie, natural-climate-solution, northern-great-plains, soil-carbon, soil-carbon-sequestration-scs
Organization: Department of Agriculture
Data from: Ammonia emissions and corn yield response from injected versus surface‐applied liquid‐separated anaerobic digestate

<p dir="ltr">Anaerobic digestion and digestate solid-liquid separation are manure treatment strategies used on commercial dairy farms. These treatment strategies typically result in increased total ammoniacal nitrogen concentration (TAN) and pH, and reduced dry matter content, which tend to increase ammonia (NH3) emissions following field application. We hypothesized that shallow disk injection of liquid-separated, anaerobically digested dairy manures, compared to surface application without incorporation on no-till farmland, would reduce ammonia-nitrogen concentration (NH3-N) emissions and conserve manure-nitrogen (manure-N) for crop production. Six corn (Zea mays L.) silage studies were established on commercial dairy farms across Pennsylvania in 2021-2023 with side-by-side field-scale treatment comparison strips replicated five times per farm. We quantified the impact of liquid-separated, anaerobically digested manure application methods on: i) NH3 emissions for 24 hours after application, ii) in-season soil nitrate-nitrogen (nitrate-N), iii) cornstalk nitrate at harvest, iv) corn silage production, and iv) returns on investment.</p>

Tags: ammonia-volatilisation, anaerobic-digestate, anaerobic-digestion, corn-silage, nitrogen, shallow-disk-injection, surface-broadcast
Organization: Department of Agriculture
USDA-ARS Colorado Sunflower Water Use and Productivity Dataset

<p dir="ltr">The USDA-Agricultural Research Service conducted a deficit irrigation and water productivity field trial for irrigated sunflower (<i>Helianthus annuus</i>) in northeastern Colorado in 2008 through 2016. Oil-type sunflower was irrigated at a wide range of amounts in a replicated field trial.  This dataset from that field trial is composed of 5 Excel workbooks. The dataset includes measurements of irrigation amount, precipitation, soil water storage, and plant responses; daily estimates of crop evapotranspiration; and seasonal crop water use and crop yield data. Soil parameters, hourly and daily weather data and photo images are also provided. The dataset can be useful to develop and evaluate sunflower crop models under varying conditions and levels of water stress.</p>

Tags: central-plains, crop-management, crop-water-productivity, deficit-irrigation, helianthus-annuus, irrigation-water-management, sunflower, water-use-efficiency
Organization: Department of Agriculture
Data from: Efficacy of long-lasting insecticide-incorporated netting in controlling preharvest and postharvest pest insects: a meta-analysis study

<p dir="ltr">This dataset aims to provide a comprehensive analysis of existing literature on the utilization of LLINs in the management of pre- and postharvest pest insect species (excluding those in urban systems and vectors). By synthesizing findings from a broad spectrum of studies, we aim to discern patterns relative to system and experimental design and develop a new synthesized understanding of the effectiveness of LLINs in agriculture. Moreover, our dataset intends to identify and address gaps in current knowledge. Through a meta-analytical approach, this review aims to distill key insights that can inform future research directions, and practical applications in the integrated management programs of pre- and postharvest insect pests.</p><p dir="ltr"><br></p><p dir="ltr">The goal of this dataset is to understand the efficacy of long-lasting insecticide netting in agriculture. We used databases such as Web of Science, Scopus, and Google Scholar to find studies related to LLIN. First, we carried out a literature search on the topic of insecticide netting. We used various Keyword combinations to identify a broad initial dataset, including various terms such as ‘netting’, ‘LLIN’ ‘insecticide netting’ in combination with either ‘insects’, ‘preharvest’, ‘postharvest’, and ‘agriculture’. Papers were individually checked to ensure they met criteria for inclusion in the meta-analysis, which included that 1) articles were published between 1990–2024, 2) the focus was on agricultural crops (not urban systems or vectored diseases), 3) netting was not solely used for exclusion (e.g., in the absence of an insecticidal ingredient), and 4) included a proper negative or stakeholder standard control. At the end, this left us with a total of 44 peer-reviewed publications (23 postharvest + 22 preharvest studies, one common study for pre and postharvest insects) with 285 data points on the efficacy of LLINs in agriculture. However, an additional required criterion was that all studies needed to present means, standard errors, and samples sizes for both controls and LLIN treatment. After this additional criterion, there was a final total of 31 peer-reviewed publications (19 postharvest + 12 preharvest studies). Additionally, potential publication bias was assessed by using funnel plots, and statistical tests were evaluated.</p>

Tags: agriculture, alpha-cypermethrin, cgahr, controlled-release-materials, deltamethrin, direct-lethality, field, fruit, global, halyomorpha-halys, integrated-pest-management, ipm, laboratory, llin, long-lasting-insecticide-incorporated-netting, long-lasting-insecticide-netting, meta-analysis, mortality, postharvest, preharvest, specialty-crops, stored-product-pests, stored-products, sublethal-doses, sublethal-effects, toxicology, usda, vegetables
Organization: Department of Agriculture