Please note that this work is currently in review at North American Journal of Fisheries Management. It is pre-decisional, and therefore should not be cited without consulting first with the author(s).
This work benefited greatly from this conversation on the Stan User Forum between <"https://discourse.mc-stan.org/u/Richard_Erickson">Richard Erickson and Christopher Peterson, and the examples in R. Eirckson's CarpLifeHistoryModels repository on GitHub. Examples in Monnahan et al. (2017) were also especially helpful for understanding and working with non-centered parameterizations.
von Bertalanffy growth models for triploid Grass Carp (Ctenopharyngodon idella) in Lake Gaston, North Carolina and Virginia. The growth model uses a non-centered parameterization of multivariate normal VBGF parameters. One model incorporates year-specific offsets using a hierarchical prior, and the other incorporates a continuous effect of hydrilla abundance on parameters L
Models are fit using Hamiltonian Monte Carlo sampling in Stan using the No-U-Turn Sampler (NUTS). To run the analysis, the user will need a recent version of R with rstan installed. Note that this may require installation of other software (Rtools v 3.5) or R packages. Help for installing and getting started with rstan and other (R)Stan resources can be found here.
Files are organized into subdirectories under the assumption that all workflow occurs through the use of an R project that relies on version history. Likewise, all file paths in R source files are coded as relative directories to make file read/write more streamlined.
grasscarp_models_stan.R: R script used for package loading, function declarations, data read and manipulation, and fitting VBGF models in Stan.This is the file to use for re-running the analysis.
data/: Subdirectory containing all data files necessary to conduct the analysis.
models/: Subdirectory containing Stan model(s) for estimating VBGF parameters.
results/: Output directory for results. Also contains plotting code for result of vonbert_hydrilla_mv.stan.