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#' Determine if a tip is present on a tree
#' @description Determine which tips that are not on the tree, puts them in a dataframe if they
#' do not have congeners on the tree
#' @param absent_list Vector of taxa in the total dataset that are not on the tree
#' @param tree Starting tree; object of type phylo
#' @return not_found_df Dataframe objects expressing the tips that are not
#' on the tree, and don"t have congeners
#' @examples
#' no_congeners <- treestartr:::get_lost(absent_list, tree)
get_lost <- function(absent_list, tree){
absent_df <- make_absentdf(absent_list)
tree_df <- make_treedf(tree)
tree_gen <- data.frame(matrix(ncol = 2, nrow = length(absent_list)))
not_gen <- data.frame(matrix(ncol = 2, nrow = length(absent_list)))
x <- c("genera", "fullnames")
colnames(tree_gen) <- x
colnames(not_gen) <- x
not_found_gen <- list()
not_found_full <- list()
for (row in seq_len(nrow(absent_df))) {
gen <- absent_df[row, "genera"]
full <- absent_df[row, "fullnames"]
not_found_gen[[row]] <- gen[which(!gen %in% tree_df$genera)]
not_found_full[[row]] <- full[which(!gen %in% tree_df$genera)]
}
not_found_gen <- not_found_gen[lapply(not_found_gen, length) > 0]
not_found_full <- not_found_full[lapply(not_found_full, length) > 0]
not_found_df <- do.call(rbind.data.frame, Map('c', not_found_full,
not_found_gen))
names(not_found_df ) <- c("full_name", "genera")
return(not_found_df)
}
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