系統發育關聯檢驗

Question

我需要在兩個變量之間進行相關性檢驗（返回r，t和p.value），這兩個變量說明了個體之間的系統發育關聯結構。有沒有簡單的方法來做到這一點在R？

Answer 1

從ape包，具體?ape::pic（「系統發育獨立對比」）：

library(ape) 
cat("((((Homo:0.21,Pongo:0.21):0.28,", 
     "Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);", 
     file = "ex.tre", sep = "\n") 
tree.primates <- read.tree("ex.tre") 
X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) 
Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259) 
names(X) <- names(Y) <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago") 
pic.X <- pic(X, tree.primates) 
pic.Y <- pic(Y, tree.primates) 
cor.test(pic.X, pic.Y) 

# Pearson's product-moment correlation 
# 
# data: pic.X and pic.Y 
# t = -0.85623, df = 2, p-value = 0.4821 
# alternative hypothesis: true correlation is not equal to 0 
# 95 percent confidence interval: 
# -0.9874751 0.8823934 
# sample estimates: 
# cor 
# -0.5179156 

如果你打算做太多這樣的工作，你可能希望得到天堂的Analysis of Phylogenetics and Evolution with R，看phylogenetics task view