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Filters: Tags: Waders/Gulls/Auks and Allies (X) > Types: OGC WMS Service (X)

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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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The Yukon-Kuskokwim Delta (YKD) Aerial Breeding Pair Survey provides data on the spring abundance of targeted waterfowl species nesting on the YKD coastal zone in western Alaska. This region supports millions of waterbirds that comprise one of the largest and most important waterfowl breeding grounds in North America, including species of concern such as the red-throated loon (Gavia stellata), emperor goose (Chen canagica), Pacific black brant (Branta bernicla nigricans), common eider (Somateria mollissima), black scoter (Melanitta nigra), long-tailed duck (Clangula hyemalis), and the threatened spectacled eider (Somateria fischeri). The YKD goose, swan, and crane survey was first implemented in 1985 to monitor...
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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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 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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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 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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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 R code (eggs.R) inputs the quality controlled nest card data and (1) performs additional quality control on the egg code data, (2) reformat the eggs data into a tidy file of egg observations, (3) summarizes egg data into yearly means of initiation and hatch date based on incubation model, and (4) writes csv files for tidy egg data (eggs.csv) and yearly nest stats (yearstats.csv).
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 data set provides the coordinates of plot centers, the area of each plot, plot type, and search history of the plot. Plots in this data set are linked through the combination of plot number and year provided in this file. Plot search history indicates if a plot was searched for nests. Plot shape and area has varied through time. After 1985, plot were selected by stratified random sampling, and after 1998 by simple random sampling from the area defined in ‘YKD Nest Plot Study Area Boundary.’ Plot shape has also varied but after 1998 was generally 1/4 by 1/2 mile.
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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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...
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This is an SQLite GeoPackage simple feature vector database of spectacled eider relative densities predicted from a generalized additive model across the Arctic Coastal Plain. These density are “relative” because year- or observer-specific detection is not incorporated. However, the estimation model include observer as a random effect and predictions are made after removing the effect of observer (i.e., at the average observer). Each year is a separate layer named by year. Predictions are gridded into cells 750m per side but are trimmed to the ACP survey area, so some cells are smaller. For each year, the variable ‘fit’ gives the expected density, ‘se.fit’ gives the standard error of the fit, ‘Sample.Label’ is an...
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This is an SQLite GeoPackage simple feature multilinestring vector database of the Arctic Coastal Plain survey transects in coordinate reference system EPSG:4326. There is one layer for each year 2007 to 2023, although in general the there is a four panel rotation that varies each year. All years are provided because implementation of the panel design varied through time. The field”Year” given the calendar year that the transects were implemented, “Stratum” gives the strata name, “Transect” gives the transect identifier, and the “geom” field gives the simple feature Well Known Text geometry data. Note that these transect are the idealized design and are not an exact record of the true flight path or survey effort....
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This R code uses the nest card data (“Nest_Cards_1985_2019_QC.csv”), cumulative observer experience data (“cumnest.csv”), and the output from the detection model to produce nest population estimates for focal species or species groups. Model results used are the the maximum likelihood estimates and covariance matrix from Program Mark for “model 7” or from a Bayesian posterior distribution based on a generalized linear mixed model for detection with random effects for plot, year, and crew. Results from “model 7” are produced only to provide population estimates based on legacy methods as reported in past reports. For final estimates, results from the Bayesian posterior should be used. Result from either model cannot...
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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The Spectacled Recovery Plan identified annual nesting surveys as the primary method to assess recovery status for Alaska’s Yukon-Kuskokwim Delta (YKD) subpopulation. In addition to documenting population status for spectacled eiders, the survey provides annual information on egg production, nesting effort, phenology, and habitat use for three other focal species including cackling geese, emperor geese, and greater white-fronted geese. Numbers of nests of the four species are stable or increasing in the short-term (2007-2016) and long-term (1985-2016). In 2016, the estimated number of spectacled eider nests (9,464) was the second highest in the history of the survey, but nest success was poor and clutch size very...
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 is an SQLite GeoPackage simple feature multipolygon vector database of the Arctic Coastal Plain survey area transect density strata. There is only one layer that gives the strata boundaries in EPSG:4326. The field “Statra” gives the strata name and the “geom” field gives the simple feature Well Known Text geometry data. See the GitHub site for more information. This product was produced from the file ACPmapping.R and is simplified from the original strata files distributed at https://www.sciencebase.gov/catalog/item/65419a58d34ee4b6e05bd001.
map background search result map search result map Arctic Coastal Plain Waterfowl and Waterbird Spatial and Temporal Trends Arctic Coastal Plain Aerial Survey Design Strata Arctic Coastal Plain Aerial Survey Design Transects Arctic Coastal Plain Aerial Survey Approximate Fight Lines Arctic Coastal Plain Aerial Survey Spectacled Eider Density Estimates, 2007-2023 Alaska Yukon Delta Nest Distance Sampling Pilot Project Alaska Yukon Delta Mean initiation and hatch from Egg Data 1985 - 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 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 Plot Location, Size, and Search Historic Data 1985 - 2019 Alaska Yukon Delta Nest Population Estimation Code Using R Alaska Yukon Delta Tidy Eggs data R Code Alaska Yukon Delta Tidy Egg Data 1985 - 2019 Alaska Yukon Delta Nest Population Size and Potential Production of Geese and Spectacled Eiders on the Yukon-Kuskokwim Delta, Alaska, 1985-2016 Alaska Yukon-Kuskokwim Delta Aerial Breeding Pair Survey Alaska Yukon Delta Nest Distance Sampling Pilot Project Alaska Yukon Delta Mean initiation and hatch from Egg Data 1985 - 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 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 Plot Location, Size, and Search Historic Data 1985 - 2019 Alaska Yukon Delta Nest Population Estimation Code Using R Alaska Yukon Delta Tidy Eggs data R Code Alaska Yukon Delta Tidy Egg Data 1985 - 2019 Alaska Yukon Delta Nest Population Size and Potential Production of Geese and Spectacled Eiders on the Yukon-Kuskokwim Delta, Alaska, 1985-2016 Alaska Yukon-Kuskokwim Delta Aerial Breeding Pair Survey Arctic Coastal Plain Waterfowl and Waterbird Spatial and Temporal Trends Arctic Coastal Plain Aerial Survey Design Strata Arctic Coastal Plain Aerial Survey Design Transects Arctic Coastal Plain Aerial Survey Approximate Fight Lines Arctic Coastal Plain Aerial Survey Spectacled Eider Density Estimates, 2007-2023