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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,
Water availability, distribution, quality and quantity are critical habitat elements for fish and other water-dependent species. Furthermore, the availability of water is also a pre-requisite for a number of human activities. The density of weather and hydrology observation sites on the North Slope is orders of magnitude less than in other parts of the U.S., making it difficult to document hydrologic trends and develop accurate predictive models where water is a key input. The information that does exist is scattered among many entities, and varies in format. This multi-year data rescue effort project brings together these scarce and scattered hydrology data sets, including high-priority datasets held by the Bureau...
Categories: Data;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ARCHIVING,
ARCHIVING,
Academics & scientific researchers,
Arctic Landscape Conservation Cooperative data.gov,
CATALOGING,
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,
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”),...
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: BIOSPHERE,
BIOSPHERE,
BIOSPHERE,
DATA INTEROPERABILITY,
DATA INTEROPERABILITY,
Viable sockeye salmon populations are critical to the economy, culture, and freshwater ecosystems of Bristol Bay in Western Alaska, and it is unclear how populations might respond to warming temperatures during the critical life history stages of spawning and embryo incubation. The overarching goal of the project is to understand how temperature might influence population-specific patterns of embryo incubation, timing of hatching and fry emergence, and sockeye salmon embryo survival. By combining analyses of data from two large lake systems in the Kvichak watershed, laboratory rearing experiments to elucidate functional relationships, and simulation modeling, this project quantifies biological responses to changing...
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,
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,
Water availability, distribution, quality and quantity are critical habitat elements for fish and other water-dependent species. Furthermore, the availability of water is also a pre-requisite for a number of human activities. The density of weather and hydrology observation sites on the North Slope is orders of magnitude less than in other parts of the U.S., making it difficult to document hydrologic trends and develop accurate predictive models where water is a key input. The information that does exist is scattered among many entities, and varies in format. This multi-year data rescue effort project brings together these scarce and scattered hydrology data sets, including high-priority datasets held by the Bureau...
Categories: Data;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ARCHIVING,
ARCHIVING,
Academics & scientific researchers,
Arctic Landscape Conservation Cooperative data.gov,
CATALOGING,
This report is structured around the specific objectives in the format of three stand-alone manuscripts that are in the process of submission to peer-reviewed journals. The first manuscript includes objectives 1-2, the second manuscript addresses objective 3, and the final manuscript objective 4. The overarching goal of the proposal was to understand how both recently experienced and projected water temperatures might influence population-specific patterns of embryo incubation, timing of hatching and fry emergence, and survival of sockeye salmon embryos. Additionally, we sought to explore the potential for adaptation in a heritable threshold life history trait that shapes whether an individual migrates to the ocean...
Water availability, distribution, quality and quantity are critical habitat elements for fish and other water-dependent species. Furthermore, the availability of water is also a pre-requisite for a number of human activities. The density of weather and hydrology observation sites on the North Slope is orders of magnitude less than in other parts of the U.S., making it difficult to document hydrologic trends and develop accurate predictive models where water is a key input. The information that does exist is scattered among many entities, and varies in format. This multi-year data rescue effort project brings together these scarce and scattered hydrology data sets, including high-priority datasets held by the Bureau...
Categories: Data;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ARCHIVING,
ARCHIVING,
Academics & scientific researchers,
Arctic Landscape Conservation Cooperative data.gov,
CATALOGING,
An important unresolved question is how populations of coldwater-dependent fishes will respond to rapidly warming water temperatures. For example, the culturally and economically important group, Pacific salmon (Oncorhynchus spp.), experience site-specific thermal regimes during early development that could be disrupted by warming. To test for thermal local adaptation and heritable phenotypic plasticity in Pacific salmon embryos, we measured the developmental rate, survival, and body size at hatching in two populations of sockeye salmon (Oncorhynchus nerka) that overlap in timing of spawning but incubate in contrasting natural thermal regimes. Using a split half-sibling design, we exposed embryos of 10 families...
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,
This R code (PrepData.R) is used to process the quality controlled legacy nest card data (1985 - 2019) together with the observer names data to produce a capture history data set plot searched twice in 1995 to 1999. Second searches of plot are defined by the PLOTTYPE = “R2” in the nest cards data. Matches are define by the PREVIOUSOBS and PREVIOUSNEST field in the nest card data set but a large number of quality control issue arise in this process and are resolve as detailed in this code. This code produces a data file “chdata.csv” that defines the capture history for each nest and is used as input to Program MARK and JAGS for model fitting and detection estimation. Basic operations include reconciling species and...
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,
Water availability, distribution, quality and quantity are critical habitat elements for fish and other water-dependent species. Furthermore, the availability of water is also a pre-requisite for a number of human activities. The density of weather and hydrology observation sites on the North Slope is orders of magnitude less than in other parts of the U.S., making it difficult to document hydrologic trends and develop accurate predictive models where water is a key input. The information that does exist is scattered among many entities, and varies in format. This multi-year data rescue effort project brought together scarce and scattered hydrology data sets, including high-priority datasets held by the Bureau of...
Categories: Data,
Project;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ARCHIVING,
ARCHIVING,
Academics & scientific researchers,
CATALOGING,
CATALOGING,
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