README.md

In lucasnell/clonewars: Clonal Evolution in Aphid Metapopulations

gameofclones

This R package simulates aphid–parasitoid eco-evolutionary dynamics.

Installation

To install this package:

remotes::install_github("lucasnell/gameofclones")

Package functions

Each exported function has its own documentation, but here are some basic descriptions of each:

• clonal_line: Create an object to store information about an aphid clonal line. Outputs an aphid object, which you can combine using c() to create a multiAphid object.
• inv_logit and logit: Convenience functions for proportion data
• rel_res_fitness: Calculate relative fitness for resistance vs susceptible aphids using calculations from Ives et al. (2020).
• restart_experiment: Restart simulations from sim_experiments or restart_experiment. This function's main purpose is to allow for very flexible perturbations. Outputs a cloneSimsRestart object.
• rm_tibs: Convert tibbles in a cloneSims or cloneSimsRestart object into normal data frames.
• sim_experiments: This is the main function for simulations. It defaults to simulating experiments where we have two habitat patches, one with and one without parasitoids. Outputs a cloneSims object.

Usage

With all the defaults, you could simulate a resistant and susceptible clone (with a cost for resistance) in two patches (only one with parasitoids) for 250 days with the following:

# set initial densities:
adults32 <- cbind(c(0,0,0,0,32), rep(0, 5))

line_s <- clonal_line("susceptible", adults32)
line_r <- clonal_line("resistant", adults32,
                      resistant = TRUE,
                      surv_juv_apterous = "low",
                      surv_adult_apterous = "low",
                      repro_apterous = "low")
sims <- sim_experiments(c(line_s, line_r))
print(sims)

lucasnell/clonewars documentation built on Oct. 12, 2023, 4:39 p.m.