This software involves files to fit the physiologically-guided abundance (PGA) model ('fish_predictions_pga.R'), a naive model ('fish_predictions_naive.R'), and a PGA model using simulated data ('PGA_sim.R'). Each R file calls as associated .stan file that contains the model code that is executed by stan when running the R code ('fish_prediction.stan', 'fish_prediction_naive.stan', and 'fish_prediction_sim.stan', respecively.). The R scripts are currently setup to fit the model to bluegill data, but this can be changed to either yellow perch or cisco within the R scrip. The data for fitting the models can be found at https://hdl.handle.net/11299/228403.