Run article code as vignette

.gitignore

@@ -38,3 +38,4 @@ tests/testthat/Rplots.pdf
 vignettes/examples_cache/
 vignettes/examples_files/
 vignettes/*.fas
+vignettes/article_cache/

vignettes/article.Rmd

@@ -0,0 +1,122 @@
+---
+title: "rbeast2: BEAUti 2, BEAST2 and Tracer for R"
+author: "Richel J.C. Bilderbeek"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{rbeast2: BEAUti 2, BEAST2 and Tracer for R}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r create_files, include = FALSE}
+file.copy(rbeast2::get_path("anthus_aco.fas"), "test_output_0.fas")
+file.copy(rbeast2::get_path("anthus_aco.fas"), "my_fasta.fas")
+file.copy(rbeast2::get_path("anthus_aco.fas"), "my_alignment.fas")
+file.copy(rbeast2::get_path("anthus_aco.fas"), "anthus_aco.fas")
+file.copy(rbeast2::get_path("anthus_nd2.fas"), "anthus_nd2.fas")
+```
+
+This vignette does the same as the code in the article.
+
+```{r}
+library(rbeast2)
+mcmc <- create_mcmc(chain_length = 2000, store_every = 1000)
+```
+
+```{r cache=TRUE}
+out <- run_beast2("anthus_aco.fas", mcmc = mcmc)
+```
+
+
+```{r cache=TRUE}
+out <- run_beast2(
+  "anthus_aco.fas",
+  site_models = create_hky_site_model(),
+  clock_models = create_rln_clock_model(),
+  tree_priors = create_bd_tree_prior(),
+  mcmc = mcmc
+)
+```
+
+
+```{r cache=TRUE}
+out <- run_beast2(
+  c("anthus_aco.fas", "anthus_nd2.fas"),
+  site_models = list(
+    create_tn93_site_model(), 
+    create_gtr_site_model()
+  ),
+  mcmc = mcmc
+)
+```
+
+```{r cache=TRUE}
+out <- run_beast2(
+  "anthus_aco.fas",
+  tree_priors = create_yule_tree_prior(
+    birth_rate_distr = create_exp_distr()    
+  ),
+  mcmc = mcmc
+)
+```
+
+```{r cache=TRUE}
+out <- run_beast2(
+  "anthus_aco.fas",
+  tree_priors = create_yule_tree_prior(
+    birth_rate_distr = create_exp_distr(
+      mean = create_mean_param(value = 1.0)
+    )    
+  ),
+  mcmc = mcmc
+)
+```
+
+```{r cache=TRUE}
+out <- run_beast2(
+  "anthus_aco.fas",
+  posterior_crown_age = 15,
+  mcmc = mcmc
+)
+```
+
+
+```{r}
+traces <- remove_burn_ins(out$estimates)
+```
+
+
+```{r}
+esses <- calc_esses(
+  traces, 
+  sample_interval = 1000
+)
+```
+
+```{r}
+sum_stats <- calc_summary_stats(
+  traces, 
+  sample_interval = 1000
+)
+```
+
+
+```{r cache=TRUE}
+plot_densitree(out$anthus_aco_trees)
+```
+
+```{r 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")
+```