## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", eval = FALSE ) ## ----------------------------------------------------------------------------- # library(bifrost) # library(ape) # library(phytools) # library(mvMORPH) # # set.seed(1) # # # Simulate a tree # tr <- pbtree(n = 50, scale = 1) # # # Simulate multivariate traits under a single-regime BM1 model (no shifts) # sigma <- diag(0.1, 2) # 2 x 2 variance-covariance matrix for two traits # theta <- c(0, 0) # ancestral means for the two traits # # sim <- mvSIM( # tree = tr, # nsim = 1, # model = "BM1", # param = list( # ntraits = 2, # sigma = sigma, # theta = theta # ) # ) # # # mvSIM returns either a matrix or a list of matrices depending on mvMORPH version # X <- if (is.list(sim)) sim[[1]] else sim # rownames(X) <- tr$tip.label # # # Run bifrost's greedy search for shifts # res <- searchOptimalConfiguration( # baseline_tree = tr, # trait_data = X, # formula = "trait_data ~ 1", # min_descendant_tips = 10, # num_cores = 1, # shift_acceptance_threshold = 20, # conservative GIC threshold # IC = "GIC", # plot = FALSE, # store_model_fit_history = FALSE, # verbose = FALSE # ) # # # For this single-regime BM1 simulation, we typically expect no inferred shifts # res$shift_nodes_no_uncertainty # res$optimal_ic - res$baseline_ic # str(res$VCVs) ## ----workflow_diagram, echo=FALSE, eval=TRUE, results='asis'------------------ svg_uri <- knitr::image_uri("quick-start/bifrost-workflow.svg") cat(sprintf( '

Workflow diagram showing setup, baseline scoring, greedy search, post-processing, and output steps in bifrost.

', svg_uri ))