r-comparative-phylogeneticslisted

# R Comparative Phylogenetics ## Execution Environment R code runs via the `run_r_script` tool, which: - Locates `Rscript` at `/opt/homebrew/bin/Rscript` (fallback: `which Rscript`) - Creates a timestamped working directory under `data/r_runs/YYYYMMDD_HHMMSS/` unless `working_dir` is specified explicitly - Prepends `agent/r_runtime/preamble.R` to every script - Saves the full script as `working_dir/script.R` for reproducibility - Returns JSON: `stdout`, `stderr`, `exit_code`, `working_dir`, `plot_paths`, `created_files` Always tell Heath the `working_dir` path so he can inspect plots and outputs directly. For long analyses, write intermediate results to disk rather than holding everything in the R session. ### Preamble (auto-prepended) ```r options(warn = 1, stringsAsFactors = FALSE) set.seed(42) suppressPackageStartupMessages({ # Loaded by default; per-run libraries appended after }) ``` `stringsAsFactors = FALSE` is always active — do not fight it. `set.seed(42)` is set globally; override inside your script if a different seed is needed for a specific analysis. --- ## Mandatory Preflight: Data Resource Resolution Before emitting any R code that reads a lab database, call `require_data_resource(key)`. Use the returned `OK|<path>` string verbatim. ```r # After require_data_resource("coleoptera_karyotypes") returns # "OK|/Users/blackmon/Desktop/GitHub/coleoguy.github.io/data/karyotypes-coleoptera.csv" dat <- read.csv("/Users/blackmon/Desktop/GitHub/coleoguy.gi