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2015_Analysis_Compare2010&2015.xlsx is an Excel file created by MBM-AK to test statistical differences between the 2010 and 2015 Alaska Trumpeter Swan Survey results.
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These .csv tables, YYYY_Survey_Area.csv (where YYYY = survey year), list the U.S. Geological Survey 1:63,360 scale quadrangle maps that comprised the survey areas of the 1968-2015 Alaska Trumpeter Swan Surveys. Each year’s survey area consisted of a set of the 1:63,360 scale maps, where each map represented a potential sampling unit. The 1968-2005 surveys were designed to census the entire survey area, and thus all of the maps were surveyed in these years. The 2010 and 2015 surveys were stratified random samples (optimally allocated to minimize cost for a fixed variance); therefore, only a selected set of 100 maps were surveyed in these years. (Note: additional .csv tables are available in the survey’s project archive...
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This is the collection of raw data was collected during MBM-AK TLSA annual molting goose surveys. Partial quality control has been completed for these data: following each survey, the observer listened to their survey recording that documented counts along transects and then transcribed these findings into these raw datasets (‘raw_data’). The observer listened to their recording a second time in order to confirm that their transcriptions were correct. Further quality control and tidying was completed for these raw data using R scripts noted by the file extension ‘.Rmd’ located in the ‘GitHub_Annual_Report_Code’ folder. Ultimately, these scripts produced final datasets (‘final_data’) containing data used in annual...
Categories: Data; Types: Map Service, OGC WFS Layer, OGC WMS Layer, OGC WMS Service; Tags: ALPINE/TUNDRA, ANIMALS/VERTEBRATES, ARCTIC TUNDRA, BIOLOGICAL CLASSIFICATION, BIOLOGICAL RECORDS, All tags...
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EstimatesTableWBPHS_20220125.csv is a table of bird abundance estimates by year and species, 1957-2021. It was produced by MBM-AK using AKaerial R code and the WBPHS_AK QC transcribed dataset. The date in the file name (format = YYYYMODA, where YYYY = year, MO = month, and DA = day) represents the date that the R code was run to produce the table. A data dictionary and details on analysis methods are provided at NEED TO ADD REFERENCE TO CHUCK’S R CODE/GITHUB WITH LINK.
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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 dataset, BoatSum.csv, contains the bird and marine mammal data that was collected during boat-based surveys in the summers of 1997-2001 to double-sample portions of the aerial summer Southeast Alaska Nearshore Waterbird Survey.
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This dataset, AirSum.csv, contains the raw transcribed bird and marine mammal data collected during the 1997-2002 aerial summer Southeast Alaska Nearshore Waterbird Survey. Note that this dataset contains records of species that were omitted in the final, quality-controlled data (SummerSimplified.csv), due to detection issues or inappropriateness of the survey design for those species.
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The daily flight tracks of the 1997-2002 aerial summer Southeast Alaska Nearshore Waterbird Survey were recorded to an onboard computer using the custom survey software RECORD (John I. Hodges, FWS-MBM-Alaska, retired). The tracks were recorded by capturing the plane’s location from a GPS every five seconds as long as the software was running. The software was started at some time between the aircraft’s engine start and the start of the survey, and was shut down at some time between the end of the survey and engine shut-down. The tracks thus include the aircraft’s flight to and from the airport base. The 29 track files are named TRMMDDYY_AIR.csv, where MM = month, DD = day, and YY = year.
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Estimates_By_Year_2010to2015.csv summarizes the Alaska Trumpeter Swan Survey abundance estimates by survey year, 2010 and 2015. Estimates are rounded to the nearest integer.
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The Alaska Trumpeter Swan Survey used U.S. Geological Survey (USGS) 1:63,360 scale quadrangle maps as sampling units (plots). USGS identifies each 1:63,360 map with a combination of two identifiers: 1) the 1:250,000 quadrangle in which it occurs, and 2) the 1:63,360 quadrangle map itself. Similarly, in the swan survey files, the 1:63,360 map is identified by the combination of the “Map” and “Quad” fields. The Map field identifies the 1:250,000 quad by its USGS numeric code; the Quad field identifies the 1:63.360 map by its appropriate letter-number. USGS_Map_Index.tif is a map version of the USGS map index, saved in an image format (.tif).
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2010_Analysis_Trends.xlsx is an Excel file created by MBM-AK to analyze data from the 1968-2010 Alaska Trumpeter Swan Surveys to assess trends in the numbers of adult (i.e., white) swans, total swans (i.e., adults and cygnets), and broods, and the percentage of cygnets in the total swan population.
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This collection comprises the log files that accompany the quality-controlled (QC) WBPHS-AK transcribed bird-observation data files. The log files were produced when the original (“raw”) transcribed data were run through the QC process via the “Greenlight” script within the R package “AKaerial” (available at github.com/USFWS/AKaerial). The log files describe any changes that were made to the raw transcribed data during the QC process. There is one log file for each QC transcribed data file: WBPHS_YYYY_QCLog_OOO.html, where YYYY=Year and OOO=Observer initials.
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The standard operating procedures (SOP) document for the overall WBPHS, including the Alaska strata, was updated by USFWS Division of Migratory Bird Management Branch of Migratory Bird Surveys on 21 April 2022. This SOP applies to all survey crews, including Alaska’s.
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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 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)....
map background search result map search result map Southeast Alaska Nearshore Summer Boat Data 1997-2002 Southeast Alaska Nearshore Summer Air Raw Transcribed Data 1997-2002 Southeast Alaska Nearshore Summer Flight Tracks 1997-2002 Alaska Trumpeter Swan Survey 2015 Analysis - Compare 2010 & 2015 Alaska Trumpeter Swan Survey 2015 Analysis - Abundance Estimates Alaska Trumpeter Swan Survey Areas 1968-2015: CSV Tables Alaska Trumpeter Swan Survey Estimates by Year 2010-2015 Alaska Trumpeter Swan Survey 2010 Analysis - Trends USGS_Map_Index.tif for Alaska Trumpeter Swan Survey Teshekpuk Lake Alaska Molting Goose Raw Aerial Survey Data Waterfowl Breeding Population Habitat Survey Alaska Abundance Estimate data Waterfowl Breeding Population Habitat Survey Alaska Quality Control Log Files Waterfowl Breeding Population Habitat Survey Standard Operating Protocol Update 04-21-2022 Arctic Coastal Plain Waterfowl and Waterbird Spatial and Temporal Trends 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 Survey Legacy Nest Card Data 1985 - 2019 Alaska Yukon Delta Nest Plot Survey Observer Names 1985 - 2019 Alaska Yukon Delta Tidy Egg Data 1985 - 2019 Teshekpuk Lake Alaska Molting Goose Raw Aerial Survey Data 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 Survey Legacy Nest Card Data 1985 - 2019 Alaska Yukon Delta Nest Plot Survey Observer Names 1985 - 2019 Alaska Yukon Delta Tidy Egg Data 1985 - 2019 Southeast Alaska Nearshore Summer Boat Data 1997-2002 Southeast Alaska Nearshore Summer Air Raw Transcribed Data 1997-2002 Southeast Alaska Nearshore Summer Flight Tracks 1997-2002 Arctic Coastal Plain Waterfowl and Waterbird Spatial and Temporal Trends Waterfowl Breeding Population Habitat Survey Alaska Abundance Estimate data Waterfowl Breeding Population Habitat Survey Alaska Quality Control Log Files Alaska Trumpeter Swan Survey 2015 Analysis - Compare 2010 & 2015 Alaska Trumpeter Swan Survey 2015 Analysis - Abundance Estimates Alaska Trumpeter Swan Survey Areas 1968-2015: CSV Tables Alaska Trumpeter Swan Survey Estimates by Year 2010-2015 Alaska Trumpeter Swan Survey 2010 Analysis - Trends USGS_Map_Index.tif for Alaska Trumpeter Swan Survey Waterfowl Breeding Population Habitat Survey Standard Operating Protocol Update 04-21-2022