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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,
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,
The SeaDuckDetectoR is software designed to identify sea ducks and other avian species in aerial photographs. The program is run through R and RStudio. The product includes a .zip file “SeaDuckDetectoR.0.1.0.zip” with the files for installation, and a manual “SeaDuckDetectoR_Manual.docx” explaining how to run the program.
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ANIMALS/VERTEBRATES,
BIOLOGICAL CLASSIFICATION,
BIRDS,
EARTH SCIENCE,
Science Keywords,
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,
Originally created by Brad Shults, the GitHub repository was created for markdown code used to quality control survey data and create annual survey reports beginning in 2016. The repository can be found on GitHub (‘https://github.com/bsshults/Teshekpuk-Lake-Molt’). A copy of the master branch that was last committed by user “bsshults” (Brad Shults) on 2/24/20 was downloaded by Maggie Harings on 6/29/21 and stored on the Alaska Regional Data Repository (‘GitHub_Annual_Report_Code’). General file naming structure for repository files is: ‘TMGSurvey_Master_[surveyYear]’ Files ending in the file extension ‘.Rmd’ are used to conduct some quality control and data tidying for original survey data. These files contain comments...
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ALPINE/TUNDRA,
ANIMALS/VERTEBRATES,
ARCTIC TUNDRA,
BIOLOGICAL CLASSIFICATION,
BIOLOGICAL RECORDS,
Topock Marsh is a large wetland adjacent to the Colorado River and main feature of Havasu National Wildlife Refuge (Havasu NWR) in southern Arizona. In 2010, U.S. Fish and Wildlife Service (FWS) and Bureau of Reclamation began a project to improve water management capabilities at Topock Marsh and protect habitats and species. Initial construction required a drawdown, which caused below-average inflows and water depths in 2010-2011. Co-applicants Daniels and Haegele of FORT monitored Topock Marsh during the drawdown and immediately after, thus obtained information on immediate effects. However, stress from the drawdown may have a delayed effect on aquatic resources; additionally, significant changes to the infrastructure...
Categories: Data,
Software;
Types: ArcGIS REST Map Service,
ArcGIS Service Definition,
Downloadable,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: 2013,
AZ-04,
Applications and Tools,
Arizona,
CA-08,
This is an Rmarkdown file that maps the 2019 plot centers, creates plot polygons, and created the start and end coordinates of the distance sampling transects. Transect end points are written to a csv file for input in field GPS unit to guide field staff during surveys. Running this code will produce the file ‘transects.csv’.
This code produces the memo document and the tabular data files associated with the annual reporting memo.
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
BIOLOGICAL CLASSIFICATION,
BIOLOGICAL CLASSIFICATION,
BIRDS,
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,
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