Commits

Casey Dunn  committed 285bd9f

updated to work with new version of geiger

  • Participants
  • Parent commits 30d3ab2

Comments (0)

Files changed (2)

File regularization.pdf

Binary file modified.

File simulation.r

 # Run the phylogenetic analyses
 tree_text <- "(((Species_A:10.0,Species_B:10.0)I:40.0,(Species_C:40.0,Species_D:40.0)J:10.0)K:10.0,(Species_E:45.0,(Species_F:30.0,(Species_G:15.0,Species_H:15.0)O:15.0)N:15.0)M:15.0)L:0.0;"
 phy <- read.tree( text=tree_text )
-Z <- sim.char(phy, trueCovariance, nsims = 1, model = "brownian", root.state = 1)
+Z <- sim.char(phy, trueCovariance, nsim = 1, model = "BM", root = 1)
 W <- Z[,,1]	# Grab one simulation
 contrasts <- apply( W, 2, function(a) pic(a, phy) )
 
 
 # Set up plotting parameters
 # Color plots
-mycols <- tim.colors(100)
+# mycols <- tim.colors(100)
 # Greyscale plots
-# mycols <- gray(1:100 / 100)
+mycols <- gray(1:100 / 100)
 
 mybreaks <- seq(-1, 1, length.out=101)