#' Create a set of testing experiments
#' @inheritParams default_params_doc
#' @param has_candidates if there are candidate experiments yes/no
#' @param rng_seed the RNG seed used in inference
#' @export
create_test_razzo_experiments <- function(
has_candidates = TRUE,
folder_name = peregrine::get_pff_tempfile(),
rng_seed = 1
) {
experiments <- create_razzo_experiments(
has_candidates = has_candidates,
folder_name = folder_name,
rng_seed = rng_seed
)
# Shorten the MCMC
for (i in seq_along(experiments)) {
experiments[[i]]$inference_model$mcmc$chain_length <- 3e3
experiments[[i]]$inference_model$mcmc$store_every <- 1e3
experiments[[i]]$inference_model$mcmc$tracelog$filename <-
get_tracelog_filename(
folder_name = folder_name,
model_type = experiments[[i]]$inference_conditions$model_type
)
experiments[[i]]$inference_model$mcmc$tracelog$log_every <- 1000
experiments[[i]]$inference_model$mcmc$treelog$filename <-
get_treelog_filename(
folder_name = folder_name,
model_type = experiments[[i]]$inference_conditions$model_type
)
experiments[[i]]$inference_model$mcmc$treelog$log_every <- 1000
experiments[[i]]$est_evidence_mcmc$chain_length <- 3e3
experiments[[i]]$est_evidence_mcmc$store_every <- 1e3
}
if (isTRUE(has_candidates)) {
experiments <- experiments[1:3]
# Different site models
experiments[[2]]$inference_model$site_model <-
beautier::create_hky_site_model()
experiments[[3]]$inference_model$site_model <-
beautier::create_tn93_site_model()
experiments[[2]]$inference_model$clock_model <-
beautier::create_strict_clock_model()
experiments[[3]]$inference_model$clock_model <-
beautier::create_strict_clock_model()
experiments[[2]]$inference_model$tree_prior <-
beautier::create_yule_tree_prior()
experiments[[3]]$inference_model$tree_prior <-
beautier::create_yule_tree_prior()
}
# Experiments' filenames are correctly set up by 'create_razzo_experiments'
experiments
}
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