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Surface Water Quality Monitoring Data collected in South Florida Coastal Waters (FCE LTER), Florida, USA, June 1989-ongoing
The Southeast Environmental Research Center at Florida International University operates a network of 331 fixed sampling sites distributed throughout the estuarine and coastal ecosystems of south Florida. The purpose of this network is to address concerns in regional water quality which cross and overlap separate political boundaries. Funding has come from different sources with individual programs being added as funding became available. Biscayne Bay, Florida Bay, Whitewater Bay, Ten Thousand Islands, Rookery Bay, Estero Bay, and Pine Island Sound are sampled monthly while the Florida Keys National Marine Sanctuary (FKNMS) and the southwest shelf are sampled quarterly. Variables currently being measured include surface and bottom temperature, salinity, dissolved oxygen, nitrate, nitrite, ammonium, total nitrogen, total organic nitrogen, total phosphorus, soluble reactive phosphorus, total organic carbon, total silicate, chlorophyll a, alkaline phosphatase activity, turbidity, and light extinction. The purpose of this network is to address concerns in regional water quality which cross and overlap separate political boundaries. One of the products is a quasi-synoptic big picture of nutrient and phytoplankton biomass distributions over the South Florida Coastal Waters. The SERC network will, in time, provide us with the data necessary to determine whether conditions within the estuaries and sanctuary are improving or declining.
Rainfall Stable Isotopes collected at Florida International University-MMC (FCE LTER), Miami, Florida, USA, October 2007 - ongoing
δ18O and δ2H values for precipitation collected at the Modesto A. Maidique Campus of Florida International University (FIU) relative to Vienna Standard Mean Ocean Water. Rainfall was collected from the roof of AHC-1 building (25.75772 ºN, 80.37108 ºW) from October 2007 to November 2022 using an Aerochemitrics wet/dry collector. Since December 2022, rainfall has been collected using a Palmex Rain Collector located in the FIU Organic Garden (25.75490 ºN, 80.37985 ºW). Oxygen and hydrogen isotope ratios were measured on a Los Gatos Research DLT-100 Liquid-Water Isotope Analyzer in the Hydrogeology laboratory at FIU since the project inception.
Quantitative and qualitative aspects of dissolved organic carbon leached from plant biomass in Taylor Slough, Shark River and Florida Bay (FCE) for samples collected in July 2004
Plant biomass was collected from Taylor Slough, Shark River and Florida Bay in Everglades National Park. Samples were taken to the lab and incubated with Milli-Q water in the dark for a period of 36 days. NaN3 was added to half the bottles to test the role of microbial activity on the leaching rates and composition of leachate. Every three days the water was decanted and replaced with fresh Milli-Q water. The decanted samples were filtered and analyzed for DOC concentration, sugar content, and total phenol content.
Fish and consumer data collected from Northeast Shark Slough, Everglades National Park (FCE) from September 2006 to September 2008
Three 1m2 throwtrap sites were selected randomly within a few meters of the location. All fish and macroinvertebrates were sampled within each trap using a seine; the trap is determined to be clear of fish and macroinvertebrates once three empty seines are recovered. The count is reset whenever a fish or invertebrate is caught. Once the trap is determined to be clear, five sweeps are done using a couple of nets. The count resets whenever fish is caught, while an extra sweep is added whenever an invertebrate is captured. The trap is finally cleared once the fifth sweep doesn't capture any organisms. All captured organisms are anesthesized in a plastic cup filled with water and MS222; they are then preserved using a 10% formaldehyde solution for identification and archiving in the lab
Periphyton and Associated Environmental Data Relative from Samples Collected from the Greater Everglades, Florida, USA from September 2005 to November 2014
This data package contains peripihyton and environmental data collected annually during the wet season between 2005 and 2014 from sites distributed throughout the greater Everglades ecosystem. This project is part of the Comprehensive Everglades Restoration Program's Monitoring and Assessment Plan intended to document baseline variability in periphyton attributes for assessing the effectiveness of restoration projects. A total of 200 primary sampling units (PSU) of 800 m x 800 m are nested in 32 landscape units and each year, random coordinates are 'drawn' within each PSU and one sampleable draw is visited in each. Sampled periphyton is processed for diatoms, slides are prepared, and 500 frustules are enumerated and identified to the lowest possible taxonomic resolution per slide. Taxon abundances are then relativized to the total count. These data accompany environmental, periphyton biomass, and soft algal abundance datasets.
Relative Abundance Diatom Data from Periphyton Samples Collected from the Greater Everglades, Florida USA from September 2005 to November 2014
This data package contains relative diatom taxon abundances collected annually during the wet season between 2005 and 2014 from sites distributed throughout the greater Everglades ecosystem. This project is part of the Comprehensive Everglades Restoration Program's Monitoring and Assessment Plan intended to document baseline variability in periphyton attributes for assessing the effectiveness of restoration projects. A total of 200 primary sampling units (PSU) of 800 m x 800 m are nested in 32 landscape units and each year, random coordinates are 'drawn' within each PSU and one sampleable draw is visited in each. Sampled periphyton is processed for diatoms, slides are prepared, and 500 frustules are enumerated and identified to the lowest possible taxonomic resolution per slide. Taxon abundances are then relativized to the total count. These data accompany environmental, periphyton biomass, and soft algal abundance datasets. Post-2014 data are available upon request to the project PI, Evelyn Gaiser.
Vegetation data collected from Northeast Shark River Slough, Everglades National Park, Florida, USA, September 2006 - April 2025
This project was established in 2006 to document the pattern of abundance of key ecological indicators (e.g., surface water, soil, floc, periphyton and sawgrass) across the NESRS landscape. A total of 30 sites were established and monitored in 2006, 2007 and 2008. After the completion of 1-mile bridge in 2012, additional 10 new sites were established to observe the ecological impact of 1-mile bridge (known as Bridge & Census sites). In 2015, additional 40 sites were established along eight transects (T1-T8, known as near canal sites) in ENP marshes starting at, and roughly perpendicular to the L-29 canal. The purpose of these sites was to monitor the potential effects of Modified Water Deliveries (MWD) operations on changing nutrient concentrations and ratios in key ecological compartments due to increased downstream discharges from the L-29 canal beneath the 1-mile and 2.6-mile bridges and culverts along Tamiami Trail. Data collection is complete.
Mollusc population size distribution monitoring: Fall 2013 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2013 report of infaunal and epifaunal mollusk species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-1407. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population abundance monitoring: Fall 2014 mid-marsh and creekbank infaunal and epifaunal mollusc abundance based on collections from GCE marsh, monitoring sites 1-10
This data set is the Fall 2014 estimate of infaunal and epifaunal mollusc abundance at the GCE-LTER marsh sites used for population monitoring. Species abundance was determined by hand-collecting all the infaunal and epifaunal molluscs from within quadrats of known area in mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, fixed in ethanol, transferred to and preserved in ethanol, counted and measured (size data is reported separately). The counts were converted to number per square meter. Gastropod species are listed first, followed by bivalve species. Size distribution data for these collections may be found in the GCE-LTER data set INV-GCEM-1507a.
Mollusc population size distribution monitoring: Fall 2014 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2014 report of infaunal and epifaunal mollusc species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-1507. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population abundance monitoring: Fall 2015 mid-marsh and creekbank infaunal and epifaunal mollusc abundance based on collections from GCE marsh, monitoring sites 1-10
This data set is the Fall 2015 estimate of infaunal and epifaunal mollusc abundance at the GCE-LTER marsh sites used for population monitoring. Species abundance was determined by hand-collecting all the infaunal and epifaunal molluscs from within quadrats of known area in mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, fixed in ethanol, transferred to and preserved in ethanol, counted and measured (size data is reported separately). The counts were converted to number per square meter. Gastropod species are listed first, followed by bivalve species. Size distribution data for these collections may be found in the GCE-LTER data set INV-GCEM-1607a.
Mollusc population size distribution monitoring: Fall 2015 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2015 report of infaunal and epifaunal mollusc species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-1607. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population abundance monitoring: Fall 2017 mid-marsh and creekbank infaunal and epifaunal mollusc abundance based on collections from GCE marsh, monitoring sites 1-10
This data set is the Fall 2017 estimate of infaunal and epifaunal mollusc abundance at the GCE-LTER marsh sites used for population monitoring. Species abundance was determined by hand-collecting all the infaunal and epifaunal molluscs from within quadrats of known area in mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, fixed in ethanol, transferred to and preserved in ethanol, counted and measured (size data is reported separately). The counts were converted to number per square meter. Gastropod species are listed first, followed by bivalve species. Size distribution data for these collections may be found in the GCE-LTER data set INV-GCEM-1807a.
Mollusc population abundance monitoring: Fall 2018 mid-marsh and creekbank infaunal and epifaunal mollusc abundance based on collections from GCE marsh, monitoring sites 1-10
This data set is the Fall 2018 estimate of infaunal and epifaunal mollusc abundance at the GCE-LTER marsh sites used for population monitoring. Species abundance was determined by hand-collecting all the infaunal and epifaunal molluscs from within quadrats of known area in mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, fixed in ethanol, transferred to and preserved in ethanol, counted and measured (size data is reported separately). The counts were converted to number per square meter. Gastropod species are listed first, followed by bivalve species. Size distribution data for these collections may be found in the GCE-LTER data set INV-GCEM-1907a.
Mollusc population size distribution monitoring: Fall 2018 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2018 report of infaunal and epifaunal mollusc species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-1907. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Mollusc population abundance monitoring: Fall 2019 mid-marsh and creekbank infaunal and epifaunal mollusc abundance based on collections from GCE marsh, monitoring sites 1-10
This data set is the Fall 2019 estimate of infaunal and epifaunal mollusc abundance at the GCE-LTER marsh sites used for population monitoring. Species abundance was determined by hand-collecting all the infaunal and epifaunal molluscs from within quadrats of known area in mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, fixed in ethanol, transferred to and preserved in ethanol, counted and measured (size data is reported separately). The counts were converted to number per square meter. Gastropod species are listed first, followed by bivalve species. Size distribution data for these collections may be found in the GCE-LTER data set INV-GCEM-2007a.
Mollusc population size distribution monitoring: Fall 2019 mid-marsh and creekbank infaunal and epifaunal mollusc size distributions based on collections from GCE marsh monitoring sites 1-10
This data set is the Fall 2019 report of infaunal and epifaunal mollusc species size distributions at the GCE-LTER marsh sites used for population monitoring. Infaunal and epifaunal molluscs were hand-collected from within quadrats of known area from mid-marsh and creekbank zones (n = 4 quadrats per zone) at all sites. The molluscs were returned to the lab, preserved in ethanol, measured and counted (count data is reported separately). Length of each measurable individual was determined using calipers or an ocular micrometer mounted in a stereomicroscope. Species abundance and density data for these collections may be found in the GCE-LTER data set INV-GCEM-2007. Numbers of individuals of each species in the abundance data file may not correspond exactly to the numbers of individuals in the size data file because some individuals may not have been measureable.
Software Tools to Collect and Use Provenance in R
The software tools that scientists use to process and analyze data are typically optimized for performance and ease of use. Few if any such tools are designed to capture and record the details of what happens as the tool performs its task. This detailed information, and more generally the history of an item of data from its creation to its present state, is known as provenance. Provenance has the potential to make science more transparent, reliable, and reproducible. This project focused on collecting and using provenance for scripts written in the R statistical language, which is widely used by ecologists and environmental scientists for data analysis and visualization. Our tools include a provenance collector (rdtLite), which collects provenance as an R script executes (or during a console session), as well as other tools that use the collected provenance to document and visualize the execution or to support activites such as script debugging. The R packages included here are also available on CRAN. For more details, see the project website on GitHub (https://end-to-end-provenance.github.io).
Long-term climate indices (SPEI and scPDSI) derived from monthly meteorology data collected at USHCN stations in the northern Chihuahuan Desert of the United States, 1911-2021
Drought indices — Standardized Precipitation Evapotranspiration Index (SPEI) and the self-calibrating Palmer Drought Severity Index (scPDSI) —where derived from 9 United States Historical Climate Network (USHCN) stations on the Chihuahuan Desert in North America for this dataset. USHCN is a subset of the NOAA Cooperative Observer Program (COOP) Network, which consists of selected sites based on spatial coverages and completeness of data. Monthly precipitation depths, minimum, maximum and mean temperature were pulled from the dataset. These drought indices were derived using the SPEI package and scPDSI packages in R. Potential evapotranspiration was also calculated in R using the Thornthwaite method. All 9 sites are within the bounds of the Chihuahuan Desert in the state of New Mexico, with a single site (EL PASO) in the state of Texas.
Size-fractionated chlorophyll from water column bottle samples collected during NES-LTER Transect cruises, ongoing since 2017.
Size-fractionated chlorophyll a and phaeopigments are measured from discrete bottle samples collected during CTD-rosette casts on Northeast U.S. Shelf Long-Term Ecological Research (NES-LTER) Transect cruises (ongoing since 2017), as a proxy for phytoplankton biomass. Sampling frequency is approximately seasonal. Samples were processed by three lab groups using different methods. Size fractions in addition to whole seawater (>0.7 micron) include >5 , <10, >10, and >20 microns with some samples pre-filtered <200 microns. Pigments were analyzed using fluorometers in which fluorescence was measured versus a blank and a standard, and final concentrations were calculated in micrograms per liter (or mg per cubic meter). Some of the data are from cruises in collaboration with the Ocean Observatories Initiative (OOI).
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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.