add markdown for phytools

vignettes/articles/phytools.Rmd

@@ -0,0 +1,52 @@
+---
+title: "phytools"
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup, message=FALSE}
+library(phytools)
+```
+
+Load data:
+
+```{r}
+data("primate.tree")
+data("primate.data")
+tree <- primate.tree
+data <- primate.data
+rm(primate.tree)
+rm(primate.data)
+activity <- data$Activity_pattern
+names(activity) <- rownames(data)
+m <- to.matrix(activity, levels(activity))
+m[,] <- rep(1/ncol(m), ncol(m))
+labs <- rownames(m)[which(grepl('Galago', rownames(m)))]
+for (i in seq_along(labs)) {
+    m[labs[i],] <- c(0, 0, 1)
+}
+fit <- fitMk(
+    tree = tree, x = m, model = 'ARD', pi = "fitzjohn", logscale = TRUE, 
+    lik.func = "pruning"
+)
+ace <- ancr(fit, tips = TRUE)
+res <- ace$ace
+
+```
+
+
+
+
+
+
+```{r}
+plot(ace, args.plotTree = list(direction = "upwards"))
+tips <- sapply(labs, function(x, y) which(y == x), y = tree$tip.label)
+add.arrow(tree, tips, arrl = 3, offset = 2, lwd = 2, col = palette()[4])
+```
+