Code and parameter values for Lichti, Dalgleish, and Steele (2020) Interactions among shade, caching behavior, and predation risk may drive seed trait evolution in scatter-hoarded plants. Diversity 12:416.

ABSTRACT: Although dispersal is critical to plant life history, the relationships between seed traits and dispersal success in animal-dispersed plants remain unclear due to complex interactions among the effects of seed traits, habitat structure, and disperser behavior. We propose that in plants dispersed by scatter-hoarding granivores, seed trait evolution may have been driven by selective pressures that arise from interactions between seedling shade intolerance and predator-mediated caching behavior. Using an optimal foraging model that accounts for cache concealment, hoarder memory, and perceived predation risk, we show that hoarders can obtain cache-recovery advantages by placing caches in moderately risky locations that force potential pilferers to engage in high levels of vigilance. Our model also demonstrates that the level of risk needed to optimally protect a cache increases with the value of the cached food item. If hoarders perceive less sheltered, high-light conditions to be more risky and use this information to protect their caches, then shade-intolerant plants may increase their fitness by producing seeds with traits valued by hoarders. Consistent with this hypothesis, shade tolerance in scatter-hoarded tree species is inversely related to the value of their seeds as perceived by a scatter-hoarding rodent.

Files in this repository: The following files should be placed in the working directory for you current R session.

1. hoarding_model_optimization.R - Contains the functions and code used to run the analyses in this paper and generate Figures 1-3 and S1-S3. Running this script will automatically source hoarding_model_07232020-1635.R and upload the parameter values in parameters.xlsx and initial_values.xlsx.
2. hoarding_model_07232020-1635.R - This file contains the core functions for the model, including functions needed to load parameterization files into R. Any required packages will automatically be loaded, and if necessary, installed. This code has been borrowed from a related project that aims to model dynamic seed-hoarder-predator interactions in a differential equation framework.
3. parameters.xlsx - an Excel workbook that contains 19 spreadsheets with different parameter values. The top row of each sheet provides a brief description of the contents, and the first sheet contains metadata.
4. initial_values.xlsx - An Excel workbook with 9 spreadsheets, containing initial values for dynamic versions of the model. Many of these values are overridden by hoarding_model_optimization.R (see line ). The file is provided for compatibility with the setup() function in hoarding_model_06062020-1600.R.