Skip to content

Updating the correct data files in ClaSSE tutorial #100

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
basantakhakurel merged 1 commit into from
Nov 4, 2025
Merged

Updating the correct data files in ClaSSE tutorial #100

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 3 additions & 6 deletions tutorials/sse/classe.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,8 @@ prerequisites:
- sse/bisse
include_all: false
include_files:
- data/primates_activity_period.nex
- data/primates_mating_system.nex
- data/primates_solitariness.nex
- data/primates_tree.nex
- sse/data/primates_biogeo.tre
- sse/data/primates_biogeo.tsv
- scripts/mcmc_ClaSSE.Rev
index: true
---
Expand Down Expand Up @@ -343,7 +341,7 @@ anc_tree = ancestralStateTree(tree=observed_phylogeny, ancestral_state_trace_vec
Like before, we'll plot the ancestral states
using the `RevGadgets` `R` package.
Execute the script `plot_anc_states_ClaSSE.R` in `R`.
The results can be seen in Figure \ref{fig:results_ClaSSE}.
The results can be seen in ({% ref results_ClaSSE %}).
The maximum *a posteriori* (MAP) estimate for each node is shown as well as the posterior probability of the states represented by the size of the dots.

```{R}
Expand Down Expand Up @@ -387,4 +385,3 @@ daughter lineage in the Old World and one in the New World (green).
Modify this script to include cladogenetic
long distance dispersal and calculate Bayes factors to see which model fits the data better.
How does this affect the ancestral state estimate?
}