Day 1
0930 - 1030: [lecture] introduction to workshop and phylogenetic trees
1030 - 1130: R demos (Intro to trees in R and Simulating nucleotide substitution models)
1130 - 1230: [lecture] introduction to ancestral character estimation (ace in R)
1230 - 1330: lunch (bring your own!)
1330 - 1430: R demo: ancestral character estimation in R
1430 - 1530: [live coding session] Introduction to stochastic character mapping – simulating event times
1530 - 1630: R demos (simulating stochastic character mapping; fitting models with stochastic character mapping)
Day 2
0930 - 1030: [lecture] Review of ancestral character estimation and stochastic character mapping
1030 - 1130: [live coding session] Birth death models
1130 - 1230: [lecture] Intro to state-dependent speciation and extinction (SSE) models
1230 - 1330: lunch
1330 - 1430: [mix of live coding and demo session] simulating state-dependent speciation and extinction (SSE) models
1430 - 1530: [mix of live coding and demo session] fitting state-dependent speciation and extinction (SSE) models
1530 - 1600: [live coding and demo session] ancestral state reconstruction with SSE models
1600 - 1630: End of day review
Day 3
0930 - 1030: [lecture] multi-type birth death (MTBD) models
1030 - 1130: [live coding session] setting up a MTBD BEAST2 run
1130 - 1230: [live coding session] setting up a BEAST2 run on a remote server
1230 - 1330: lunch
1330 - 1430: Demo session: analyzing BEAST2 output (premade in the oven)
1430 - 1530: [lecture] structured coalescent models
1530 - 1600: [live coding session] setting up a structured coalescent BEAST2 run
1600 - 1630: Recap of day
Day 4
0930 - 1030: [live demo session] Examine BEAST2 server run
1030 - 1130: [lecture] Bayesian stochastic search variable selection
1130 - 1230: [live demo session] setting up BSSVS in BEAST2
1230 - 1330: lunch
1330 - 1430: [lecture] SAASI
1430 - 1530: [live demo sesssion] comparing discrete trait analysis and phylodynamics
1530 - 1630: Recap, conclusions and closing
