dispersim is an R package for simulating pollen and seed dispersal in plant populations. It simulates individual-level effects (seed and pollen movement, survival) to generate population-level patterns. The simulation framework is flexible and designed to be both an exploratory tool and a means to perform large scale simulations parameterized with field data.
To install dispersim on your computer, you must first make sure the package 'devtools' is installed. This will allow you to install dispersim directly from github.
Here's an example of a typical workflow to run a basic simulation (code is given below)...
dispersim is very much still in active development, and certainly contains many bugs. If you're interested in contributing, have any comments or suggestions, please get in touch via github or email - [email protected]
library(dispersim) params <- list( # Landscape parameters x_max = 100, y_max = 100, boundary_setting = "unsuitable", # Expected number of steps and individuals expected_total_individuals = 100000, # Num of starting adults n_adults_init = 50, # Genetic parameters n_loci = 10, n_alleles_per_loci = 20, loci_names = makeLociNames(n_loci = 10), # Demographic parameters age_at_adult = 5, crop_size = 5, adult_survival = .8, seedling_survival = "random", # Random or distance dependent seedling_survival_prob = .5, seedling_survival_dist_location = 10, seedling_survival_dist_scale = 1, # Dispersal parameters. based in Weibull PDF seed_kernel_scale = 10, seed_kernel_shape = 1, pollen_kernel_scale = 10, pollen_kernel_shape = 1 ) # Create new simulation sim <- initSim(params = params) #> Checking parameter list for errors... #> No errors detected in parameter list... Everything looks great. #> Data frame initialized... #> Counter initialized... #> Registry initialized... #> Adults initialized... #> Loci for Adults initialized... #> Summary initialized... #> Simulation successfully inialized! # Run simulation forward in time runSim(sim, steps = 10) #> Beginning simulation... 10 total steps #> 10 % complete #> 20 % complete #> 30 % complete #> 40 % complete #> 50 % complete #> 60 % complete #> 70 % complete #> 80 % complete #> 90 % complete #> 100 % complete
#> --- Simulation complete! --- # Plot simulation landscape plotSim(sim)
# Plot dispersal kernels plotKernels(sim, type = "adult", step = 10)
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