This repository contains data and code to support the development of a population dynamics model for the Bay-Delta DPS of Longfin Smelt (Spirinchus thaleichthys). This model uses indices of Longfin Smelt abundance for three age-classes to estimate survival and reproduction parameters. This code was used in Appendix E of the Species Status Assessment (SSA) for the Bay-Delta DPS of Longfin Smelt. Further development of this project may also occur.
There are two main R scripts in this repository. The first (Data_Exploration_Figures.R) creates graphs that are used to visualize the relationships among age-classes and gear types. The second (PopModel_BH_LN.R) fits a state space model to estimate age-0 survival, age-1 survival, and two parameters for reproduction based on the Beverton-Holt model for density dependent populationg growth.
Data for this study were derived from the Interagency Ecological Program's long-term monitoring data. Specifically, this model uses data and abundance indices from the San Francisco Bay Study program.
Figure 1: Age-based conceptual model for Longfin Smelt population dynamics.
The code contained in this repository produced the figures and derived data that are also contained in this repository using R version 4.3.1 ("Beagle Scouts"). This repository is set up to work as an RStudio project; as such, file paths contained in the code are relative paths. This code will also work as a set of stand-alone R scripts, but the user may need to specify the locations of data files in a more explicity way.
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