## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----check_empty_cache_at_start, include = FALSE------------------------------ # This is only needed to pass the CRAN Windows build. # # This vignette is tested to clean up nicely on GitHub Actions # and r-hub on Windows # beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders() ## ----load_babette, results='hide', warning=FALSE, error=FALSE, message=FALSE---- library(babette) ## ----------------------------------------------------------------------------- inference_model <- create_test_inference_model() ## ----------------------------------------------------------------------------- beast2_options <- create_beast2_options(verbose = TRUE) ## ----------------------------------------------------------------------------- if (is_beast2_installed()) { out <- bbt_run_from_model( fasta_filename = get_babette_path("anthus_aco_sub.fas"), inference_model = inference_model, beast2_options = beast2_options ) bbt_delete_temp_files( inference_model = inference_model, beast2_options = beast2_options ) } ## ----------------------------------------------------------------------------- if (is_beast2_installed()) { library(ggplot2) p <- ggplot( data = out$estimates, aes(x = Sample) ) p + geom_line(aes(y = TreeHeight), color = "green") p + geom_line(aes(y = YuleModel), color = "red") p + geom_line(aes(y = birthRate), color = "blue") } ## ----------------------------------------------------------------------------- if (is_beast2_installed()) { traces <- remove_burn_ins( traces = out$estimates, burn_in_fraction = 0.2 ) esses <- t( calc_esses( traces, sample_interval = inference_model$mcmc$tracelog$log_every ) ) colnames(esses) <- "ESS" knitr::kable(esses) } ## ----------------------------------------------------------------------------- if (is_beast2_installed()) { sum_stats <- t( calc_summary_stats( traces$posterior, sample_interval = inference_model$mcmc$tracelog$log_every ) ) colnames(sum_stats) <- "Statistic" knitr::kable(sum_stats) } ## ----fig.width=7, fig.height=7------------------------------------------------ if (is_beast2_installed()) { plot_densitree(out$anthus_aco_sub_trees, width = 2) } ## ----check_empty_cache_at_end, include = FALSE-------------------------------- # This is only needed to pass the CRAN Windows build. # # This vignette is tested to clean up nicely on GitHub Actions # and r-hub on Windows # beastier::remove_beaustier_folders() beastier::check_empty_beaustier_folders()