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Alaska Yukon Delta Nest Plot Survey Legacy Nest Card Quality Control R Code

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...

Alaska Yukon Delta Detection Model Fitting Code Using R and RMark

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...

Alaska Yukon Delta Nest Plot Survey Detection Model Fitting Code Using R and JAGS

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...

Alaska Yukon Delta Tidy Eggs data R Code

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).

Alaska Yukon Delta Nest Population Estimation Code Using R

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...