请完善上述代码，自动遍历读取基因树文件夹下所有.treefile文件

好的，我会为你更新代码，使其自动遍历读取基因树文件夹下的所有.treefile文件。请使用以下代码：

library(ape)
species_tree <- read.tree("species_tree.treefile")

# 定义一个函数来比较树拓扑结构差异
compare_trees <- function(gene_tree_file, species_tree) {
  gene_tree <- read.tree(gene_tree_file)
  diff_count <- comparePhylo(gene_tree, species_tree, force.rooted = TRUE)
  return(diff_count)
}

# 定义一个函数来批量比较基因树和物种树的差异
batch_compare_trees <- function(gene_tree_folder, species_tree) {
  gene_tree_files <- list.files(path = gene_tree_folder, pattern = ".treefile", full.names = TRUE)
  diff_counts <- numeric(length(gene_tree_files))
  for (i in seq_along(gene_tree_files)) {
    gene_tree_file <- gene_tree_files[i]
    diff_counts[i] <- compare_trees(gene_tree_file, species_tree)
  }
  return(diff_counts)
}

# 设置基因树文件夹路径
gene_tree_folder <- "path/to/gene/tree/folder" # 替换为你的基因树文件夹路径

# 执行批量比较
diff_counts <- batch_compare_trees(gene_tree_folder, species_tree)

# 统计不一致的基因树数量
inconsistent_count <- sum(diff_counts != 0)
print(paste("有", inconsistent_count, "个基因树与物种树不一致。"))

请将`species_tree.treefile`替换为你的物种树文件路径，将`"path/to/gene/tree/folder"`替换为你的基因树文件夹路径。执行这段代码后，它将自动遍历读取基因树文件夹下的所有.treefile文件，并统计有多少个基因树与物种树的拓扑结构不一致。