Add MCMCtree workflow and SNaQ analysis scripts

- Updated `pixi.toml` to include new R package dependencies for MCMCtree workflow.
- Modified markdown file to remove unnecessary simulation data discussion.
- Introduced `.lintr` configuration for linting R scripts.
- Created `mcmctree.ctl` control file for MCMCtree analysis.
- Developed `mcmctree_workflow.r` script to orchestrate MCMCtree analysis with model testing and ESS checks.
- Added `06.snaq.jl` script for SNaQ analysis with plotting capabilities.
- Implemented `07.mcmctree.sh` bash script to run MCMCtree on multiple alignments in parallel.

This commit is contained in:

agent

2026-01-18 13:26:16 +08:00

parent 316017a575

commit 7f4e888e6a

11 changed files with 1068 additions and 23 deletions

.lintr

View File

@@ -0,0 +1,5 @@
 linters: linters_with_defaults(
     line_length_linter(80),
     commented_code_linter = NULL,
     indentation_linter(4, hanging_indent_style = "never")
   )