#' Creates the parameter files in the article
#' Now every parameter setting has its own seed
#' @return The filenames of all parameter files created
#' @export
#' @author Richel Bilderbeek
create_parameter_files_article <- function() {
filenames <- NULL
b_index <- 0
seed <- 100
for (b in c(0.2, 0.4)) {
lambda_index <- 0
for (lambda in c(0.1, 0.3, 1.0, 1000000)) {
mu_index <- 0
for (mu in c(0.0, 0.1, 0.2)) {
if (mu > b) next
r_index <- 0
for (r in c(0.05)) {
l_index <- 0
for (l in c(1000, 10000)) {
for (replicate in seq(1, 20)) {
filename <- paste0(
"article_",
b_index, "_",
lambda_index, "_",
mu_index, "_",
r_index, "_",
l_index, "_",
seed, ".RDa"
)
filenames <- c(filenames, filename)
save_parameters_to_file(
rng_seed = seed,
sirg = b,
siri = b,
scr = lambda,
erg = mu,
eri = mu,
age = 15,
mutation_rate = r,
n_alignments = 2,
sequence_length = l,
nspp = 1000,
n_beast_runs = 2,
filename = filename,
fixed_crown_age = TRUE
)
# Every simulation has its unique seed
seed <- seed + 1
} # l
l_index <- l_index + 1
} # l
r_index <- r_index + 1
} # r
mu_index <- mu_index + 1
} # mu
lambda_index <- lambda_index + 1
} # lambda
b_index <- b_index + 1
} # b
filenames
}
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