update phangorn

waldronlab · Sep 21, 2023 · 085cda7 · 085cda7
1 parent cbb141b
commit 085cda7
Show file tree

Hide file tree

Showing 3 changed files with 1,003 additions and 1 deletion.
diff --git a/inst/scripts/phagorn.R b/inst/scripts/phagorn.R
@@ -1,5 +1,8 @@
+library(phangorn)
 
 x <- m3
+
+
 x[x > 0] <- 1
 x <- x[,sort(colnames(x))]
 rownames(x) <- NULL
@@ -13,6 +16,7 @@ for (i in seq_along(output)) {
 }
 rownames(y) <- output
 
+
 trait_mat <- m3[, sort(colnames(m3))]
 trait_mat[trait_mat > 0] <- 1
 trait_v <- vector('character', nrow(trait_mat))
@@ -46,10 +50,29 @@ system.time(
     {
         ## This one takes too long
         fit <- pml(mpa_tree, myData)
-        fit <- optim.pml(fit, model = NULL, control = pml.control(trace=0))
+        # fit <- optim.pml(fit, model = NULL, control = pml.control(trace=0))
     }
 )
 
+system.time(
+    anc.ml <- ancestral.pml(fit, "ml")
+)
+
+
+system.time(
+    anc.ml <- ancestral.pml(fit, "ml")
+)
+
+system.time(
+    anc.bayes <- ancestral.pml(fit, "bayes")
+)
+
+
+
+
+
+
+
 anc_pars_data <- vector('list', length(anc_pars))
 for (i in seq_along(anc_pars_data)) {
     anc_pars_data[[i]] <- as.data.frame(unname(anc_pars[[i]]))