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This R code (Nest_Cards_QC.R) is used to process the raw legacy nest card data (1985 - 2019) and produce the quality controlled legacy nest card data for analysis and sharing. This code does not quality control the double searched plots (R2 plots in 1995-99), which is done in the file ‘PrepData.R’. Basic operations include transforming missing value to a common code, transforming other variable to match the data dictionary for nest cards, and resolving non-unique observer initials. The code requires the raw data (“1985-2019_Nest Cards_10-24-19_cleaned.xlsx”) and the table of observer names (“Observer Names_1985-2019_10-24-19.xlsx”). The code writes the QC nest card file “Nest_Cards_1985_2019_QC.csv”. Mostly obseration...
Categories: Data, Software; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, All tags...
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This is the quality controlled YKD salinity data for fixed and random plots 2006 - 2019. These data are quality controlled using the R code in the file ‘YKDsalinity_QC.R’ to produce the data used for analysis and sharing (‘YKDsalinity_QC.R’). These data should be what is used for analysis or distributed on request.
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Poorly-labeled boxes of rock, sediment, and fossil specimens collected by individual workers at different times. Also, numerous samples of Cenozoic volcanic ashes that may be of unrealized future value as a reference collection. Hand specimens exist in our collections, but they are completely uncataloged and are improperly stored. This collection may be discarded as additional space restrictions are imposed.
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Lithology logs from oil and gas wells and stratigraphic tests in various formats, particularly strip logs and lithologic logs of cuttings produced by stratigraphy consulting firms.
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Annual assessment of nesting populations of geese on the Yukon-Kuskokwim Delta (YKD) provides information for biologists, participants in cooperative goose management plans, and Pacific Flyway technical committees. A ground-based sampling procedure has been used since 1986 to estimate the number of total nests, active nests, and eggs for cackling geese, emperor geese, greater white-fronted geese, and spectacled eiders. Annual information on the size of the nesting population and potential number of young produced contributes long term data needed to understand goose and eider population ecology and better manage these species. The survey has been the primary method of measuring recovery status for the western population...
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R code that takes in the nest capture history data (chdata.csv), reformats it for model fitting in Program Mark via the R package RMark. A series of models of increasing complexity are fit and compared using AIC. Output is written to text files for each model but is generally not used or saved. Code can be run to generate model results and R workspaces/ object to inspect parameter estimates. The primary purpose of this code is to explore model structures for predicting detection and as an attempt to reproduce historically used parameter estimates in past nest plot reports (e.g., Fischer et al. 2017 and earlier). Results from ‘Model 7’ are most similar to detection estimates used in the past.
Categories: Data, Software; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, BIOLOGICAL CLASSIFICATION, BIOLOGICAL CLASSIFICATION, All tags...
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These are the observer names, observer initials, year, and unique observer number for all observe that collected data on the YKD nest plot project from 1985 to 2019. This data is used with the nest card data to in various ways, but primarily to calculate cumulative observer experience for nest detection rates. This file is also used for quality control and reconciling non-unique observer initials across years.
Categories: Data; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, All tags...
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This R code (YKDsalinity_QC.R) is used to process the raw legacy salinity data for fixed and random plots (2006 - 2019) and produce the quality controlled legacy salinity data for analysis and sharing (YKDsalinity_QC.csv). Basic operations include transforming missing value to a common code, transforming other variables to match the data dictionary, and cleaning spatial location issues. Of special note is that this QC process discover significant error in location data due to a variety of reasons so the random plot centers are added to the data table and should be used for analysis. The code requires the raw data (“Official_YKD.SALINITY.DATA.MASTER.2020.csv”), a definition of the nest plot study area (“NestPlotStudyAreaBoundary.geojson”),...
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This is the YKD egg observation data reformatted from the nest card data (‘Nest_Cards_1985_2019_QC.csv’). The file eggs.R is used to produce this data set, and then this is further summarized into yearly stats on mean initiation and hatch dates to produce the file yearstats.csv.
Categories: Data; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, All tags...
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From 1995 to 1999, a subset of nest plots were searched twice by field crews to estimate nest detection probability by mark-recapture methods. Over the five years, 30 plots were searched twice and over 2700 unique nests were found. From these data, nest detection probability is estimated using a Huggins-type mark recapture model where individual-level covariate effects of nest and observer attributes were estimated. These estimates are then used to predict nest detection rates in other years based on covariates of nests and observers. Nest detection rates are then applied to annual plot search to estimate nest populations for each species in the sampled area.
Categories: Data, Project; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, All tags...
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Paper maps, including many original-draft or working copies.
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This multi-layer GeoPackage contains the Alaska Arctic Coastal Plain Aerial Breeding Pair Survey design transects from 2007 to present. The original transects were created as shapefiles and imported to this SQLite database. Transects were saved as individual polylines named according to the year they were created (e.g., “main.ACP_2007_Trans,” “main.ACP_2008_Trans,” “main.ACP_2009_Trans,” etc.). These aerial transects were developed systematically from randomly-selected start points and created along constant lines of latitude. The inter-transect spacing in the low, medium, high, and very-high density strata varies so that areas with higher waterfowl density are surveyed more intensively. The current four-year rotating...
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R code that takes in the nest capture history data (chdata.csv), reformats it for model fitting in the Bayesian MCMC software JAGS via the R package jagsUI. Various generalized linear mixed models are fit using a Huggins two occasion capture history model structure as in Program Mark. A series of models of increasing complexity are fit and compared using DIC. Model text is written to text files for each model but is generally not used or saved. Posteriors are saved as Rworkspaces or written to text files for use in population estimation (nostpop.R). Code can be run to generate model results and R workspaces/objects to inspect parameter estimates. The primary purpose of this code is to compare various mixed model...
Categories: Data, Software; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, ANIMALS/VERTEBRATES, BIOLOGICAL CLASSIFICATION, BIOLOGICAL CLASSIFICATION, All tags...
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This is a geojson file that define the spatial polygon of the YKD nest plot study area. From 1998 to current, nest plot centroids are randomly selected from this area with the constraint that plots cannot overlap plots from the previous 5 years. This area also define the area of inference for design-based calculations of nest population estimates. Before 1998, larger areas were sampled, so this file does not apply to those years.
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This project aims to estimate spatial and temporal trends of waterfowl and waterbirds on the Arctic Coastal Plain (ACP) of Alaska from 2007 to present. The main approach is motivated by Amundson et al. (2019) using space-time generalized additive models (GAMs, Wood 2017) but with some improvements to handle observer effects and to associate sampling effort to specific spatial locations along a sampled transect similar to Miller et al. (2013). As part of this effort, a major data quality control process was begun in March 2022 that led to the correction of many data errors and re-formatting of the original 2007 to 2023 data to make it more accessible and usable to outside partners (original raw data available here)....
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This is an SQLite GeoPackage simple feature linestring vector database of the Arctic Coastal Plain survey flow tracks in coordinate reference system EPSG:4326. There is one layer for each year 2007 to 2023. The field”Year” gives the calendar year that the transects were flown, “Stratum” gives the strata name, “NavTransect” gives the transect identifier used for navigation by the pilot (this is not necessarily the same as the design transect), and the “geom” field gives the simple feature Well Known Text geometry data of the approximate flight path recreated from bird observations. See the GitHub site https://github.com/USFWS/ACP-Mapping for more information. This product was produced from the file ACPmapping.R and...
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This collection contains test-hole cores through surficial sediments and shallow bedrock drilled by the Nebraska Geological Survey (Conservation and Survey Division), the Nebraska Department of Roads, the U.S. Army Corps of Engineers, and other organizations, including bedrock cores drilled by petroleum and mineral concerns. A portion of the cores in this collection originated from oil producing areas and areas with potential petroleum development within the Panhandle region of western Nebraska. These cores were drilled by oil companies between 1950-1969 and were later donated to the Nebraska Geological Survey (Conservation and Survey Division). With the assistance of the National Geological and Geophysical...
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In 2019 a pilot study was conducted to determine the feasibility of using distance sampling to estimate density and population size of goose and eider nests on the Yukon-Kuskokwim Delta (YKD). Distance sampling (Buckland et al. 2001) is a common and well-understood method to estimate wildlife population size or density, especially for sparse and hard-to-detect populations. A main advantage of distance sampling is that it accounts for imperfect detection and gives precise estimates for a given level of effort relative to other methods. The objectives for the pilot project in 2019 was to (1) determine if distance sampling is feasible on the YKD, (2) determine what aspects of the field protocol need to be changed or...
map background search result map search result map Collection of Cores from Nebraska Collection of Maps from Nebraska Collection of lithology logs from Nebraska Collection of Hand samples from Nebraska Alaska Arctic Coastal Plain Aerial Breeding Pair Survey Design Transect Geodata Arctic Coastal Plain Waterfowl and Waterbird Spatial and Temporal Trends Arctic Coastal Plain Aerial Survey Approximate Fight Lines Alaska Yukon Delta Nest Distance Sampling Pilot Project Alaska Yukon Delta Detection Model Fitting Code Using R and RMark Alaska Yukon Delta Double Observer Nest Plot Detection Alaska Yukon Delta Nest Plot Survey Detection Model Fitting Code Using R and JAGS Alaska Yukon Delta Nest Plot Distance Sampling Field Protocol Alaska Yukon Delta Nest Plot Survey Study Area Boundary 1998 - current Alaska Yukon Delta Nest Plot Survey Legacy Nest Card Quality Control R Code Alaska Yukon Delta Nest Plot Survey Legacy Nest Card Data 1985 - 2019 Alaska Yukon Delta Nest Plot Survey Observer Names 1985 - 2019 Alaska Yukon Delta Salinity Quality Control R Code Alaska Yukon Delta Pond Salinity Data 2006 - 2019 Alaska Yukon Delta Tidy Egg Data 1985 - 2019 Alaska Yukon Delta Nest Plot Survey Alaska Yukon Delta Nest Distance Sampling Pilot Project Alaska Yukon Delta Pond Salinity Data 2006 - 2019 Alaska Yukon Delta Detection Model Fitting Code Using R and RMark Alaska Yukon Delta Double Observer Nest Plot Detection Alaska Yukon Delta Nest Plot Survey Detection Model Fitting Code Using R and JAGS Alaska Yukon Delta Nest Plot Distance Sampling Field Protocol Alaska Yukon Delta Nest Plot Survey Study Area Boundary 1998 - current Alaska Yukon Delta Nest Plot Survey Legacy Nest Card Quality Control R Code Alaska Yukon Delta Nest Plot Survey Legacy Nest Card Data 1985 - 2019 Alaska Yukon Delta Nest Plot Survey Observer Names 1985 - 2019 Alaska Yukon Delta Salinity Quality Control R Code Alaska Yukon Delta Tidy Egg Data 1985 - 2019 Alaska Yukon Delta Nest Plot Survey Collection of Cores from Nebraska Collection of Maps from Nebraska Collection of lithology logs from Nebraska Collection of Hand samples from Nebraska Alaska Arctic Coastal Plain Aerial Breeding Pair Survey Design Transect Geodata Arctic Coastal Plain Waterfowl and Waterbird Spatial and Temporal Trends Arctic Coastal Plain Aerial Survey Approximate Fight Lines