CAMPSITE

The goal of CAMPSITE is to run simulation using the Competition And Multiple-Peak Selection Integrated Trait Evolution (CAMPSITE) model in R.

Installation

You can install the development version of CAMPSITE like so:

remotes::install_github("annakrystalli/CAMPSITE")

Example

This is a basic example which shows you how to solve a common problem:

library(CAMPSITE)
## basic example code
set.seed(20220327)

Create parameter object

Creates default parameter object. Supply parameter values as arguments to change

pars <- cs_pars(lambda1 = 0.3)

Run simulation

res <- cs_simulate(pars, ou = list(opt = 0, alpha4 = 0), root.value = 0, age.max = 10, 
                          age.ext = NULL, step_size = 0.01, bounds = c(-Inf, Inf), 
                          plot = TRUE, ylims = NULL, full_results = TRUE) 
#> ℹ Simulation initiated 
#> ✓ Simulation complete 
#> ✓ Building tree complete

Plot simulation

The default plotting method for the simulation results object plots the simulated evolution of lineages through trait space

res2 <- cs_simulate(pars = cs_pars(alpha1 = 0.1), ou = list(opt = NULL, alpha4 = NULL), root.value = 0, age.max = 10, 
                    age.ext = NULL, step_size = 0.01, bounds = c(-Inf, Inf), 
                    plot = FALSE, ylims = NULL, full_results = TRUE) 
#> Warning: no OU parameters supplied; continuing without OU process
#> ℹ Simulation initiated 
#> ✓ Simulation complete 
#> ✓ Building tree complete

plot(res2, incipient_col = harrypotter::hp(n = 6, option = "Ravenclaw")[6])

Summarising results

res_summaries <- cs_summarise_results(list(res, res2))

Plotting means of multiple selection x competion combinations

plot_tip_trait_distribution(res_summaries)

plot_var_vs_time(res_summaries, variable = "VAR", time = "int")

plot_var_vs_time(res_summaries, variable = "VAR", time = "step")

# plot individual result
plot_var_vs_time(cs_summarise_results(res), variable = "VAR", time = "step")

plot_var_vs_time(res_summaries, variable = "MNND", time = "step")

plot_var_vs_time(res_summaries, variable = "VNND", time = "step")

Simulating over parameter space

Simulate

The following code runs the replicate (3 for each combination) simulations across all combination of selection and competition values 0, 0.025 and 0.1 and saves the replicates for each combination in an appropriately named file in subdirectory sims/ of the working directory.

max_rep <- 3
selection_values <- c(0, 0.025, 0.1)
competition_values <- c(0, 0.025, 0.1)

params_grid <- tidyr::crossing(selection_values, competition_values)

future.apply::future_mapply(FUN = 
                              function(selection, competition, max_rep, age.max, ensure_valid, plot) {
                                cs_simulate_reps(pars = cs_pars(alpha1 = competition, 
                                                                alpha2 = competition,
                                                                alpha3 = selection),
                                                 ou = list(opt = 0, alpha4 = selection),
                                                 max_rep = max_rep, age.max = age.max,
                                                 out_filepath = file.path("sims", 
                                                                          paste0("comp-", competition, 
                                                                                 "_selec-", selection, 
                                                                                 "_reps-", max_rep, 
                                                                                 "_", Sys.Date(),
                                                                                 ".rds")),
                                                 ensure_valid = ensure_valid, plot = plot)
                              }, 
                            competition = params_grid$competition_values, 
                            selection = params_grid$selection_values, 
                            MoreArgs = list(
                              max_rep = max_rep,
                              age.max = 20,
                              ensure_valid = TRUE,
                              plot = FALSE),
                            future.seed=TRUE)

Summarise

Summarise all simluation results

summaries <- list.files(file.path("sims"), full.names = TRUE) %>%
  future.apply::future_lapply(FUN = function(x){
    readRDS(x) %>% cs_summarise_results
  }) %>% unlist(recursive = FALSE)

Plotting means and replicates of a single selection x competion combinations

Load and summarise replicates of a single selection x competion combinations

rep_filepath <- list.files(system.file("sims", package = "CAMPSITE"), 
                        full.names = TRUE)[1]
rep_filepath
#> [1] "/Library/Frameworks/R.framework/Versions/4.1/Resources/library/CAMPSITE/sims/comp0_selec0_reps3.rds"

rep_summaries <- rep_filepath %>%
  future.apply::future_lapply(FUN = function(x){
    readRDS(x) %>% cs_summarise_results }) %>% 
  unlist(recursive = FALSE)

plot_tip_trait_distribution_replicates(rep_summaries)

plot_var_vs_time_replicates(rep_summaries, variable = "VAR")

plot_var_vs_time_replicates(rep_summaries, variable = "MNND")

plot_var_vs_time_replicates(rep_summaries, variable = "VNND")

plot_diversification_replicates(rep_summaries)

plot_lineages_through_time_replicates(rep_summaries)