These scripts support the POPAN abundance estimation described in Van Cise et al. 2021 (Endangered Species Research, DOI: https://doi.org/10.3354/esr01117). Descriptions of each script can be found below.
This Rmarkdown file compiles all analysis scripts in the project. It also includes manuscript text and code for figures and tables included in the manuscript.
This script initiates data input for the program MARK and uses RMark to run POPAN model and generate parameter estimates in MARK.
This script reads in photo identification data from the Cascadia Research Collective database, cleans and filters the data, and stratifies indviduals by sighting location.
This script tests whether sampling effort in each stock differs significantly from random. Analysis modified from original code provided by K. Alexandra Curtis (alex.curtis@noaa.gov), shared March 6, 2020.
This script tests whether individual inter-annual movements are significantly smaller than stock inter-annual movements. Analysis modified from original code provided by K. Alexandra Curtis (alex.curtis@noaa.gov), shared March 6, 2020.
This script generates summaries of effort, e.g. number of observations, number of individuals observed, median observations per individual.
This script estimates the proportion of highly distinctive animals in the population, used for downstream correction of abundance estimates.
This script estimates the proportion of times an individual is resighted within the same subarea where as its original sighting location.