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 and do not reproduce legacy results because of slight differences in nest card data and nest matching quality control procedures from past applications. Differences also arise because this code propagates variance in detection estimates through to population estimates that was not done in legacy estimates. The method for variance propagation for both model results is done through use of a bootstrap procedure. This code is currently under active development and subject to revision.
