AndreaBozzo/ceres-open-data-index huggingface dataset:
Model code to build and run an integrated population model for the endangered Cape Sable Seaside Sparrow

The Cape Sable Seaside Sparrow (CSSS; Ammospiza maritima mirabilis) is an endangered species that has experienced population declines of more than 60% since the 1990s. The CSSS is restricted in geographic extent to a relatively small area of remaining marl prairie in the southern Florida Everglades and remains in six subpopulation areas (named A-F). There has been over two decades of field research conducted on the CSSS across its six subpopulations, but a statistically robust analysis of the bird’s demographic parameters utilizing all data has yet to be completed. To address this gap, we conducted demographic analysis of the CSSS population using an integrated population model (IPM). The IPM provides a flexible framework to incorporate three separate CSSS data types (range-wide counts, mark-recapture, productivity) into a single model to estimate demographic processes and population trajectories. We calculated: (1) annual estimates of annual population size, survival, and productivity; (2) coefficient estimates of hydrologic and environmental variables on survival and productivity; (3) estimates of annual population growth and its correlation with demographic rates; and (4) a population viability analysis (PVA) that includes predicted population size and demographic rates 10 years into the future, and probabilities of extinction and quasi-extinction. This data release contains the code to run the IPM and PVA in addition to providing the parameter estimates from the model.

Tags: biota, ecology, endangered-species, everglades, everglades-national-park, population-dynamics, southern-florida, statistical-modeling, usgs-65011717d34ed30c20583625, wetland-restoration, wildlife-population-management
Organization: Department of the Interior
Simulating changes in the distribution of ammonium and ammonia versus physical and chemical conditions using PHREEQC with applications to toxicity to fish

Two sets of PHREEQC input and output files are provided that illustrate the distribution of aqueous ammonium and ammonia as a function of physical (temperature) and chemical (pH and solution composition) conditions. One set of simulations calculates the distribution of aqueous ammonia and aqueous ammonium over a range of temperatures and pH values in different solution compositions. The other set of simulations illustrates how aqueous ammonia concentrations in a water body change over time owing to changes in pH and temperature, how ammonia concentrations potentially toxic to salmonids (trout and salmon) can occur owing to changes in pH and temperature, and how these changes in ammonia concentration can be calculated from "continuous" records of pH and temperature provided by sensors. The ammonia concentrations toxic to salmonids are based on recommendations from the U.S. Environmental Protection Agency (EPA). The model data generated with these simulations were used to prepare selected figures in Edwards, Thea M., Puglis, Holly J., Kent, Douglas B., López Durán, Jonathan, Bradshaw, Lillie, Farag, Aïda M., Ammonia and Aquatic Ecosystems – A Review of Global Sources, Biogeochemical Cycling, and Effects on Fish, Science for the Total Environment, in review. Detailed instructions on how to download the software (PHREEQC), to run the files, and to generate the model data are provide in three read-me files. The top-level readme file (Top-level_read_me_Ammonium_Speciation_computation_files.txt) has a summary description of the data release; description of the contents; description of the software; instructions for installing the software; instructions for running the software to generate the model data; instructions for reading the output file containing the model data; acknowledgements; and a list of references. The read-me file Read-me_Ammonia_Speciation_vs_pH_temperature.txt provides a description of the simulations used to illustrate the fraction of total dissolved ammonium present as ammonia over a range of pH values and temperatures at three different solution compositions. The read-me file Read-me_Compare_ammonia_concentrations_to_EPA_Acute_CMC.txt provides a description of the simulations used to compare ammonia concentrations calculated from stream-water chemistry, including a large number of pH and temperature measurements provided by a sensor, with ammonia concentrations that are potentially toxic to salmonids.

Tags: ammonia, ammonium, biota, nutrients, toxicity, usgs-6500f7f1d34ed30c205835c2
Organization: Department of the Interior
Microsatellite genetic marker genotypes from southern mule deer (Odocoileus hemionus fuliginatus) sampled in San Diego County, California

Collection of microsatellite genetic data from multiple projects involving southern mule deer (Odocoileus hemionus fuliginatus) in San Diego County, California. Samples were collected 2005-2007, 2010, 2012-2013, 2015, and 2018-2020.

Tags: biological-population-management, biota, dna-sequencing, environment, genetics, genotype, polymerase-chain-reaction, population-and-community-ecology, usgs-6500f3ffd34ed30c205835bd, wildlife-population-management
Organization: Department of the Interior
Bartram's Stonecrop (Graptopetalum bartramii) survey data from southern Arizona, 2020-2021

These data were compiled for the U.S. Fish and Wildlife Service to assist them with updating the current status of the species Bartram's Stonecrop (Graptopetalum bartramii). Objective(s) of our study were to survey selected sites within the of Bartram's Stonecrop for future management and protection. These data represent summary population counts at selected known sites for the Federally listed Threatened plant species, Bartram's Stonecrop (Graptopetalum bartramii). These data were collected in the southern Arizona portion of the species' range, stratified across Sky Island Mountain ranges from the Rincon Mountains south to the Atascosa Highlands, just north of the Mexican border. Sites were selected to represent a range of local population sizes and physiographic and vegetative conditions, to provide data on population trends across this portion of the species' limited range. These data were collected by the U.S. Geological Survey / Southwest Biological Science Center from on-site field surveys. These data can be used to assess population trends of Bartram's Stonecrop at selected sites within its range.

Tags: adobe-canyon, alamo-canyon, arizona, atascosa-highlands, atascosa-mountains, bartrams-stonecrop, biogeography, biota, bond-canyon, box-canyon, carlink-canyon, cave-canyon, cave-creek, cochise-county, data-release, dragoon-mountains, field-activity-logs, field-inventory-and-monitoring, flux-canyon, gardner-canyon, graptopetalum-bartramii, italian-spring, jordan-canyon, josephine-canyon, madera-canyon, mexican-border, miller-canyo, mountain-range, pajarito-mountains, patagonia-mountains, physiographic-condition, plants-organisms, population-and-community-ecology, population-count, population-size, population-status, population-trends, rincon-mountains, santa-rita-mountains, size-class, sky-islands, southern-arizona, species-range, species-status, stronghold-canyon-east, survey-sites, sycamore-canyon, threatened-and-endangered-species, threatened-plant, u-s-fish-and-wildlife, usgs-6500db18d34ed30c20580a45, vegetative-condition
Organization: Department of the Interior
Four Band Image Mosaic of the Colorado River Corridor in Arizona--2021, including Accuracy Assessment Data

In May 2021, the Grand Canyon Monitoring and Research Center (GCMRC) of the U.S. Geological Survey’s (USGS), Southwest Biological Science Center (SBSC) acquired airborne multispectral high resolution data for the Colorado River in Grand Canyon in Arizona, USA. The imagery data consist of four bands (Band 1 – red, Band 2 – green, Band 3 – blue, and Band 4 – near infrared) with a ground resolution of 20 centimeters (cm). These image data are available to the public as 16-bit GeoTIFF files, which can be read and used by most geographic information system (GIS) and image-processing software. The spatial reference of the image data are in the State Plane (SP) map projection using the central Arizona zone (FIPS 0202) and the North American Datum of 1983 (NAD83) National Adjustment of 2011 (NA2011). The airborne data acquisition was conducted under contract by Fugro Earthdata Inc (Fugro) using two fixed wing aircraft from May 29th to June 4th, 2021 at flight altitudes from approximately 2,440 to 3,350 meters above mean sea level. Fugro produced a corridor-wide mosaic using the best possible flight line images with the least amount of smear, the smallest shadow extent, and clearest, most glint-free water possible. The mosaic delivered by Fugro was then further corrected by GCMRC for smear, shadow extent and water clarity as described in the process steps of this metadata and for previous image acquisitions in Durning et al. (2016) and Davis (2012). 47 ground controls points (GCPs) were used to conduct an independent spatial accuracy assessment by GCMRC. The accuracy calculated from the GCPs is reported at 95% confidence as 0.514 m and a Root Mean Square Error (RMSE) of 0.297 m.

Tags: aerial-photography, airborne-imagery, airborne-multispectral-high-resolution-data, arizona, bright-angel-creek, colorado-river, data-release, diamond-creek, digital-aerial-imagery, esri-shapefile, four-band-image-mosaic, geographic-information-systems, geospatial-datasets, geotiff, glen-canyon-dam, grand-canyon, havasu-creek, image-collections, image-mosaics, imagerybasemapsearthcover, infrared-imaging, kanab-creek, lake-mead, lake-powell, lees-ferry, leica-ads80-82, little-colorado-river, marble-canyon, multispectral-imaging, natural-color, near-infrared, orthoimagery, page, paria-river, peach-springs, pearce-ferry, remote-sensing, shinumo-creek, study-areas, tapeats-creek, united-states, usgs-6500d687d34ed30c205801b2
Organization: Department of the Interior
Climate Impact Meteorological Stations (CLIM-MET) data from Canyonlands National Park, Utah

These CLIM-MET stations are meteorological/geological stations that is designed to function in remote areas for long periods of time without human intervention. These stations measure meteorological and wind-erosion parameters under varying climatic and land-use conditions to detect and describe ongoing landscape changes. These data represent multiple years of local detailed landscape and environmental change observations. These data were collected in and close to Canyonlands National Park, Utah from 1 August 2016 to 31 December 2022. These data were collected by U.S. Geological Survey researchers utilizing site visits and automated data collection data loggers. These data can be used to inform studies of local and regional landscape change as well as to provide input into regional climatic models.

Tags: air-temperature, atmospheric-and-climatic-processes, atmospheric-deposition-chemical-amp-particulate, barometric-pressure, battery-voltage, canyonlands-national-park, climate, climate-change, climate-trends, climatologymeteorologyatmosphere, corral-pocket, data-logger, data-release, downwelling-shortwave-flux, dryland-systems, elevation, elevational-gradient, environment, evapotranspiration, field-inventory-and-monitoring, field-monitoring-stations, latitudinal-gradient, lavender-canyon, location, lost-canyon, meteorological-data, meteorology, net-radiation, peak-windspeed, photosynthetic-photon-flux-density, precipitation-atmospheric, precipitation-gauge, relative-humidity, sensit-kinetic-energy-count, sensit-particle-count, soil-moisture, solar-radiation, spatial-location, terrestrial-ecosystems, time-series-datasets, topography, upwelling-shortwave-flux, usgs-6500d4e2d34ed30c2057fbdc, utah, virgin-peak, volumetric-water-content, weather-events, weather-station, wind, wind-direction, wind-speed
Organization: Department of the Interior
Depth to frozen soil measurements at APEX, 2008-2023

Depth to frozen soil measurements taken by a variety of collaborators at the Alaskan Peatland EXeriment (APEX) bog/permafrost plateau site. Data is from 2018 - 2023.

Tags: alaska, boundaries, fairbanks-c-3, permafrost, usgs-6500d067d34ed30c2057fa42
Organization: Department of the Interior
Groundwater level trends for 110 U.S. Geological Survey observation wells in the Delaware River Basin.

This data release contains groundwater level trend results from 110 U.S. Geological Survey (USGS) observation wells in and near the Delaware River Basin. Mean annual groundwater level elevations from water years 2000-2020 were computed from mean daily recorded groundwater levels and discretely measured groundwater levels.  Both time series were analyzed using the Mann-Kendall test for monotonic trend and the Thiel-Sen slope.  Wells are completed in both confined and unconfined aquifers.  Data include well identification number, latitude, longitude, aquifer type, trend slopes and p-values for both mean annual time series at 110 wells.

Tags: delaware-river-basin, environment, groundwater, trends, usgs-6500ba4ed34ed30c2057f9d1
Organization: Department of the Interior
Field Observations of Surface Rupture and Fault Displacement in the 2023 M7.8 Pazarcık, Türkiye Earthquake

Field observations of surface rupture extent and fault displacement are critical to improving our understanding of rupture processes in the 6 February 2023 earthquakes in the Kahramanmaraş region of Türkiye. This data release includes two primary datasets depicting the 2023 M7.8 Pazarcık, Türkiye earthquake rupture: 1) surface rupture mapping (lines) and 2) measurements of left-lateral and vertical fault displacement (points). These observations were made in the field, northwest of Pazarcık, Türkiye along the East Anatolian (EAF) and Narlı faults between 2 and 11 June 2023. Surface-rupture mapping consists of field observations along a 28-km-long reach of the central EAF and northern 5 km of the Narlı fault that lacked previous remote observations. An additional dataset includes observations of no surface rupture. Displacement data include 68 field observations of left-laterally and vertically displaced natural or cultural features, with 62 measurements along the central EAF and 6 measurements on the Narlı fault. Collectively, these data support scientific and humanitarian response efforts, provide field observations for comparison to remote data, and help improve our understanding of the geologic context of the 2023 Kahramanmaraş region earthquakes.

Tags: biota, displacement, earthquake, fault, kahramanmara, surface-rupture, turkiye, usgs-6500acacd34ed30c2057f960
Organization: Department of the Interior
Undersized Fire Mapping Program (ver. 10.0, January 2025)

This map layer is a thematic raster image of MTBS burn severity classes for all inventoried fires occurring in CONUS during calendar year 2022 that do not meet standard MTBS size criteria. These data are published to augment the data that are available from the MTBS program. This product was produced using the methods of the Monitoring Trends in Burn Severity Program (MTBS), however these fires do not meet the size criteria for a standard MTBS assessment. The MTBS Program assesses the frequency, extent, and magnitude (size and severity) of all large wildland fires (wildfires and prescribed fires) in the conterminous United States (CONUS), Alaska, Hawaii, and Puerto Rico for the period 1984 and beyond. MTBS typically maps fires using an initial assessment (immediately after the fire) or an extended assessment (peak of green the season after the fire) for low-biomass and high-biomass fires respectively. Refer to MTBS.gov for more information on MTBS methods and criteria. Standard MTBS mappings must meet the size criteria of at least 500 acres for the eastern states and territories and 1,000 acres for the western states and territories to be eligible for mapping. Undersized MTBS fires are those fires that do not meet the standard MTBS size criteria but are otherwise mapped using standard MTBS methodologies.

Tags: ak, alaska, burn-severity, burned-area, continental-u-s, conus, differenced-normalized-burn-ratio, fire-location, fire-occurrence, hawaii, hi, imagerybasemapsearthcover, landsat, location, normalized-burn-ratio, pr, prescribed-fire, puerto-rico, sentinel, united-states, us, usgs-64cd014fd34ef477cf3a69d7, wildfire, wildland-fire
Organization: Department of the Interior
Geologic Map Schema (GeMS) version of Wentworth, C.M., Knudsen, K.L., and Witter, R.C., 2023, Quaternary deposits of the 9-county San Francisco Bay Region

This is a conversion of Wentworth and others (2023)[DAS1] to the Geologic Map Schema (GeMS) for inclusion in the National Geologic Map Database.  The original publication was in the Alacarte schema commonly used for geologic map databases prior to the release of the now mandatory GeMS.  The GIS layers in this release have the same scientific content as the source data release.  The source data release lacks description of map units, however, so those have been copied verbatim from the two principal sources for that work (Witter and others, 2006 [DAS2]; Knudsen and others, 2000 [DAS3]).

Tags: geologic-maps, quaternary, unconsolidated-deposits, usgs-6500a888d34ed30c2057f94a
Organization: Department of the Interior
Water chemistry data for samples collected at groundwater sites in the Placerita Oil Field study area, June 2018–November 2018, Los Angeles County, California

The California State Water Resources Control Board (State Water Board) initiated the Oil and Gas Regional Monitoring Program (RMP) to assess effects of oil and gas development on groundwater designated for any beneficial use. The U.S. Geological Survey (USGS) is the technical lead in conducting the RMP through the California Oil, Gas, and Groundwater (COGG) Program, working in cooperation with the State Water Board, and in partnership with other State and local agencies. The USGS collected and analyzed groundwater for the Placerita Oil Field study area, the area within the Placerita Oil Field administrative boundary and the surrounding three-mile buffer zone in Los Angeles County, California. Sixteen groundwater samples were collected from June 2018 through November 2018 from three public-supply wells, two monitoring wells, three irrigation wells, two oil-field water supply wells, and one domestic well. Samples were collected using established groundwater data-collection protocols and procedures. Samples were analyzed for (1) water-quality indicators, (2) major and minor ions, (3) nutrients,  (4) trace elements, (5) volatile organic compounds (VOCs), (6) naturally-occurring radioactive material (radium isotopes), (7) geochemical and age-dating tracers, (8) dissolved organic carbon (DOC) characteristics, (9) dissolved standard and hydrocarbon gases (methane through hexane), (10) dissolved noble gases and atmospheric gases, and (11) low molecular weight organic acids. In total, 229 constituents, water-quality indicators, or properties were measured. Quality-control (QC) samples were used to assess the quality of laboratory results. QC samples were collected for all oil fields assessed by the Regional Monitoring Program during the general time period (within three months) of groundwater samples that were collected for the Placerita Oil Field study area and include four replicates, three field blanks, one equipment blank, four source-solution blanks, three laboratory-matrix spikes, and two samples collected to verify results of environmental samples that arrived at the laboratory above the recommended temperature for preventing degradation of VOCs and nutrients.

Tags: aquifers, california, geochemistry, groundwater, groundwater-aquifer, groundwater-quality, inlandwaters, los-angeles-county, placerita-oil-field, regional-monitoring-program, salinity, salinity-mapping, usgs-6500a15ed34ed30c2057f766, water-chemistry, water-quality-data
Organization: Department of the Interior
Physiological Analysis of Eleutherodactylus Specimens in West-Central Puerto Rico, 2021-2022

Amphibians are vulnerable to extinction owing, partly, to altered physiological processes induced by projected global warming and drying.  Understanding the mechanisms behind their responses is essential to formulate adaptation strategies for their conservation.  Puerto Rico harbors 15 endemic Eleutherodactylus frogs considered vulnerable to extinction due to poor vagility and sensitivity to environmental variability.  Herein are reported the effects of four temperature treatments (15, 20, 25, and 30 degrees Centigrade) on metabolic rates associated with specific dynamic action (SDA) and standard metabolic rates (SMR) of four representative species of Eleutherodactylus employing a respirometer.  All species in either experiment increased their excretion of CO2 with increasing temperature.  CO2 excretion rates were higher immediately post-ingestion, subsiding to low levels by the third day (72 hours).  SMR excretion rates of E. juanariveroi and E. antillensis increased up to 20 degrees Centigrade and then curbed.  Rates of E. coqui increased linearly, whereas rates of E. wightmanae increased markedly from 20 to 25 degrees Centigrade, perishing at 30 degrees Centigrade.  E. antillensis, E. wightmanae and E. juanariveroi exhibited a change in metabolic rates between 20 degrees Centigrade and 25 degrees Centigrade, the same range where occupancy shifts from lower to higher probability for all species.  Climate projections suggest that species will be exposed to 2-3 additional hours during evenings at ≥25 degrees Centigrade below 300 m, and about 1 hour at 400-500 m.  Species occurring in low elevations (≤400 m) may have to compensate for the additional energy expenditure induced by increased exposure and adjust their evening time budget.  A continuing warming trend could begin to infringe on habitats of high elevation specialists like E. wightmanae.

Tags: adaptation-strategy, biota, climate-change, coqui, coqui-churi, coqui-llanero, coqui-melodioso, eleutherodactylus, eleutherodactylus-antillensis, eleutherodactylus-coqui, eleutherodactylus-juanariveroi, eleutherodactylus-wightmanae, physiology, puerto-rico, specific-dynamic-action, standard-metabolic-rate, usgs-65009778d34ed30c2057f6e5, west-central-puerto-rico
Organization: Department of the Interior
Grass Carp (Ctenopharyngodon idella) egg capture data from Great Lakes tributaries, 2021-2022 (ver. 1.1, November 2023)

The data includes dates, places, and times of sampling events for eggs of invasive Grass Carp (Ctenopharyngodon idella) in tributaries to the Great Lakes in 2021 and 2022. Reference data on locations and dates sampled, gears used, and effort are included. Developmental stages for a subset of undamaged, fertilized eggs are provided. Tables include common fields to allow for integration into a relational database to aid data extraction and associating data among tables. First posted: September 2023 Revised: November 2023 (version 1.1)

Tags: biota, cuyahoga-river, fish, fish-spawning-and-larval-aggregation, grand-river-ohio-usa, grass-carp, great-lakes, huron-river-ohio-usa, invasive-carp, invasive-species, mathematical-modeling, maumee-river, portage-river, sandusky-river, st-joseph-river, streamflow, tittabawassee-river, usgs-64d1bc5ed34ef477cf3c07b4
Organization: Department of the Interior