update ltp to latest version

R/trees.R

@@ -196,3 +196,79 @@ ltp2 <- function(remove_zero_tips = TRUE) {
     )
 }
 
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+#' Get living tree project (LTP) tree or data v3
+#'
+#' \code{ltp3} gets the LTP tree or data.
+#'
+#' @return A list with a phylo (the ltp tree) and a data.frame (tip_data)
+#' objects.
+#' @export
+#'
+ltp3 <- function() {
+    tree_fname <- system.file(
+        'extdata', 'LTP_all_08_2023.newick', package = 'taxPPro'
+    )
+    tip_data_fname <- system.file(
+        'extdata', 'LTP_all_08_2023.tip_data', package = 'taxPPro'
+    )
+    node_data_fname <- system.file(
+        'extdata', 'LTP_all_08_2023.node_data', package = 'taxPPro'
+    )
+    tree <- ape::read.tree(tree_fname)
+    tip_data <- utils::read.table(
+        file = tip_data_fname, header = TRUE, sep = '\t', row.names = NULL
+    ) |>
+        purrr::modify(as.character) |>
+        as.data.frame() |>
+        dplyr::select(-.data$taxname)
+    rownames(tip_data) <- tip_data$tip_label
+
+    node_data <- utils::read.table(
+        file = node_data_fname, header = TRUE, sep = '\t', row.names = NULL
+    ) |>
+        purrr::modify(as.character) |>
+        as.data.frame()
+
+    # tip_data <- tip_data |>
+    #     dplyr::group_by(taxid) |>
+    #     dplyr::slice_head(n = 1) |>
+    #     dplyr::ungroup() |>
+    #     as.data.frame()
+    # ntips4 <- nrow(tip_data)
+    # tree <- ape::keep.tip(phy = tree, tip = tip_data$tip_label)
+    # message('Dropping ', ntips3 - ntips4, ' tips because of duplicated taxids.')
+    # tip_data <- tip_data[tree$tip.label,]
+    # message('Tips remaining: ', length(tree$tip.label))
+
+    # tip_data <- tip_data |>
+    #     dplyr::mutate(
+    #         NCBI_ID = dplyr::case_when(
+    #             .data$Rank == 'genus' ~ paste0('g__', taxid),
+    #             .data$Rank == 'species' ~ paste0('s__', taxid),
+    #             .data$Rank == 'strain' ~ paste0('t__', taxid),
+    #             TRUE ~ NA
+    #         )
+    #     )
+
+    list(
+        tree = tree, tip_data = tip_data, node_data = node_data
+    )
+}
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