model_numbers <- 17:19
for (model_number in model_numbers) {
model_res <- dplyr::filter(ordered_results_paleo_minus_outliers, model == model_number)
pars_res_df <- data.frame(
age = model_res$age,
lambda_c0 = model_res$lambda_c0,
mu_0 = model_res$mu_0,
K_0 = model_res$K_0,
gamma_0 = model_res$gamma_0,
lambda_a0 = model_res$lambda_a0,
x = model_res$x,
y = model_res$y,
z = model_res$z,
alpha = model_res$alpha,
beta = model_res$beta,
d_0 = model_res$d_0,
loglik = model_res$loglik
)
areas <- list()
distances <- list()
datalist <- archipelagos41_paleo[[1]]
arch_to_remove <- c("Lord_Howe", "Norfolk", "Chagos", "Seychelles_Inner")
datalist <- datalist[which(!names(archipelagos41_paleo[[1]]) %in% arch_to_remove)]
for (archipelago in names(datalist)) {
area <- c()
distance <- c()
for (time_slice in pars_res_df$age) {
area <- c(area, archipelagos41_paleo[[time_slice]][[archipelago]][[1]]$area)
distance <- c(distance, archipelagos41_paleo[[time_slice]][[archipelago]][[1]]$distance_continent)
}
areas[[archipelago]] <- area
distances[[archipelago]] <- distance
}
base_rates <- list()
for (archipelago in names(datalist)) {
base_rates[[archipelago]] <- get_base_rates(
archipelago_data = archipelagos41_paleo[[1]][[archipelago]][[1]],
M = 1000,
pars_res_df = pars_res_df,
model = model_number,
area = areas[[archipelago]],
distance = distances[[archipelago]]
)
}
for (archipelago in names(datalist)) {
base_rates[[archipelago]]$age <- pars_res_df$age
}
# out_diff <- facet_archipelagos(base_rates, standardisation = "difference")
# out_ratio <- facet_archipelagos(base_rates, standardisation = "ratio")
out <- facet_archipelagos(base_rates, standardisation = FALSE)
save_paper_plot(plot_to_save = out[[1]], file_name = paste0("combined_1_minus_outliers", "_m_", model_number))
save_paper_plot(plot_to_save = out[[2]], file_name = paste0("combined_2_minus_outliers", "_m_", model_number))
save_paper_plot(plot_to_save = out[[3]], file_name = paste0("combined_3_minus_outliers", "_m_", model_number))
save_paper_plot(plot_to_save = out[[4]], file_name = paste0("combined_4_minus_outliers", "_m_", model_number))
}
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