This repository stores the code and data used to perform the analysis presented in Accounting for uncertainty when estimating drivers of imperfect detection: An integrated approach illustrated with snorkel surveys for riverine fishes by authors B. Staton, C. Justice, S. White, E. Sedell, L. Burns, and M. Kaylor (published in Fisheries Research)
This repository is organized into two parts, reflecting the two main aspects of the analyses presented in the manuscript:
grande-ronde: contains data and code for fitting, summarizing, and generating plots based on the empirical application of the integrated model to Grande Ronde salmonid snorkel survey/mark-recapture datasim-eval: contains code for simulating data following various scenarios, fitting two models to each data set, and summarizing the output across many replicates
JAGS is required fit the models. This is also a prerequisite for installing the R package jagsUI, so should be done first. JAGS version 4.3.0 was used to fit the models for the analysis - it can be found here.
All analyses were conducted in R (or JAGS, called through R), so you must have R installed to run this code. R version 4.0.2 was used to run the code for the manuscript, but any recent version (i.e., after 4.0.0) should work fine. It can be found here.
Several packages are used by this code: running the 00-packages.R script found in each of the grande-ronde and sim-eval subdirectories will ensure that all of these packages are installed on your computer and loads them. Thus, a source("00-packages.R") call is placed at the top portion of most of the scripts found in thess subdirectories. The table below shows the R packages that were used, as well as their versions (newer or older versions of most packages should be fine).
| Package Name | Version Used | Install From | How Used |
|---|---|---|---|
scales |
1.1.1 | CRAN | Creating transparent colors |
jagsUI |
1.5.1 | CRAN | Calling JAGS from within R |
stringr |
1.4.0 | CRAN | Basic string manipulations |
reshape2 |
1.4.4 | CRAN | Basic data reformatting (e.g., long to wide) |
postpack |
0.5.3 | CRAN | Posterior summarization |
posterior |
1.0.0 | CRAN | Posterior diagnostics |