EOD

ropensci · Sep 22, 2018 · 8256c8a · 8256c8a
1 parent dfadc43
commit 8256c8a
Showing 1 changed file with 0 additions and 95 deletions.
diff --git a/vignettes/article.R b/vignettes/article.R
@@ -15,98 +15,3 @@ file.copy(babette::get_babette_path("anthus_nd2_sub.fas"), "anthus_nd2.fas")
 library(babette)
 mcmc <- create_mcmc(chain_length = 2000, store_every = 1000)
 
-## ----cache=FALSE---------------------------------------------------------
-out <- bbt_run(
-  fasta_filenames = "anthus_aco.fas", 
-  mcmc = mcmc
-)
-
-## ----cache=FALSE---------------------------------------------------------
-out <- bbt_run(
-  "anthus_aco.fas",
-  site_models = create_hky_site_model(),
-  clock_models = create_rln_clock_model(),
-  tree_priors = create_bd_tree_prior(),
-  mcmc = mcmc
-)
-
-## ----cache=FALSE---------------------------------------------------------
-out <- bbt_run(
-  c("anthus_aco.fas", "anthus_nd2.fas"),
-  site_models = list(
-    create_tn93_site_model(), 
-    create_gtr_site_model()
-  ),
-  mcmc = mcmc
-)
-
-## ----cache=FALSE---------------------------------------------------------
-out <- bbt_run(
-  "anthus_aco.fas",
-  tree_priors = create_yule_tree_prior(
-    birth_rate_distr = create_exp_distr()    
-  ),
-  mcmc = mcmc
-)
-
-## ----cache=FALSE---------------------------------------------------------
-out <- bbt_run(
-  "anthus_aco.fas",
-  tree_priors = create_yule_tree_prior(
-    birth_rate_distr = create_exp_distr(
-      mean = create_mean_param(value = 1.0)
-    )    
-  ),
-  mcmc = mcmc
-)
-
-## ----cache=FALSE---------------------------------------------------------
-out <- bbt_run(
-  "anthus_aco.fas",
-  posterior_crown_age = 15,
-  mcmc = mcmc
-)
-
-## ----cache=FALSE---------------------------------------------------------
-out <- bbt_run(
-  "anthus_aco.fas",
-  mrca_priors = create_mrca_prior(
-    alignment_id = get_alignment_id("anthus_aco.fas"),
-    taxa_names = get_taxa_names("anthus_aco.fas"),
-    mrca_distr = create_normal_distr(
-      id = 1,
-      mean = create_mean_param(value = 15.0, id = 2),
-      sigma = create_sigma_param(value = 0.01, id = 3)
-    )
-  ),
-  mcmc = mcmc
-)
-
-## ------------------------------------------------------------------------
-traces <- remove_burn_ins(
-  traces = out$estimates, 
-  burn_in_fraction = 0.2
-)
-
-## ------------------------------------------------------------------------
-esses <- calc_esses(
-  traces = traces, 
-  sample_interval = 1000
-)
-
-## ------------------------------------------------------------------------
-sum_stats <- calc_summary_stats(
-  traces = traces, 
-  sample_interval = 1000
-)
-
-## ----cache=FALSE---------------------------------------------------------
-plot_densitree(phylos = out$anthus_aco_trees)
-
-## ----cleanup, include = FALSE--------------------------------------------
-file.remove("test_output_0.fas")
-file.remove("my_fasta.fas")
-file.remove("my_alignment.fas")
-file.remove("anthus_aco.fas")
-file.remove("anthus_nd2.fas")
-