ScrewTrapR is a package for estimating juvenile salmonid abundances using capture-mark-recapture data collected at rotary screw traps using two primary hierarchical Bayesian models; apenalized-spline model (Bonner & Schwarz, 2011), and multi-year model (Oldemeyer et al. 2018). ScrewTrapR contains three functions (Merge_RST_Obs_Ops, Chinook_Format(), and Steelhead_Format()) for merging and formatting raw juvenile salmonid data from the Idaho Department of Fish and Game's JTRAP database into the appropriate capture-mark-recapture format needed for the hierarchical Bayesian model functions. Following, there are several functions that implement the various hierarchical Bayesian models and produce different life-stage and cohort summaries dependent on the species.
Additionally, this package is complimentary to theScrew_Trap_ExploreR shiny web application which allows biologists and practitioners to upload raw rotary screw trap data, visualize data, and provide recommendations regarding which model, stratification, life-stage date designation, etc. are most appropriate based on data characteristics. The formated data file and R script exported from the Screw_Trap_ExploreR web app allow for seamless implementation of the model functions contained within the ScrewTrapR package.
Before you install ScrewTrapR, you first need to install the latest version of Just Another Gibbs Sampler (JAGS). Make sure your R version is compatible with the version of JAGS you install. The README file associated with JAGS when this package was initially developed (July, 2023), states:
If you are using R to interface with JAGS then you must ensure that you download the correct binary:
If you are using R 4.2.0 or later then install JAGS-4.3.2.exe
If you are using R 4.1.3 or earlier then install JAGS-4.3.0.exe
You can check your R version by simply running:
R.version.string
Last, if you are using an Integrated Development Environment (IDE) for your coding in R (e.g. RStudio), be sure to check the IDE is using the intended version of R. You can check (and change) the selected R version in RStudio by going to the "Tools->Global Options->General->R Version" box.
To install ScrewTrapR you can use Hadley Wickham's devtools package. To install and load the devtools package use:
install.packages("devtools")
library(devtools)
NOTE: To use devtools, you may also have to download and install Rtools (although you shouldn't). The latest version on Rtools can be found at https://cran.r-project.org/bin/windows/Rtools/
Once devtools is successfully installed, use the following to install ScrewTrapR:
devtools::install_github("Mount-Hood-Environmental/ScrewTrapR")
If you are interested in making contributions to ScrewTrapR, consider getting a GitHub account, fork this repository, clone to a local directory, modify, and send me a pull request. I can then review any changes and merge.