From 4b04d9a2d531ddef42d11f52b4e198d2a5ac9e9b Mon Sep 17 00:00:00 2001
From: "Andrew G. Brown" <andrew.g.brown@usda.gov>
Date: Fri, 10 Mar 2023 09:00:23 -0800
Subject: [PATCH] Add custom print method for data.tree subclass
 `SoilTaxonNode` #43

---
 NAMESPACE        |  1 +
 R/taxonTree.R    | 53 +++++++++++++++++++++++++++++++++++++++++++-----
 man/taxonTree.Rd |  2 +-
 3 files changed, 50 insertions(+), 6 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index e0d8f47..2feef8b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(print,SoilTaxonNode)
 export(FormativeElements)
 export(GreatGroupFormativeElements)
 export(OrderFormativeElements)
diff --git a/R/taxonTree.R b/R/taxonTree.R
index cc90234..d5673fa 100644
--- a/R/taxonTree.R
+++ b/R/taxonTree.R
@@ -1,4 +1,3 @@
-
 #' Create a `data.tree` Object from Taxon Names
 #'
 #' @param taxon A vector of taxon names
@@ -7,7 +6,7 @@
 #' @param verbose Print tree output? Default: `TRUE`
 #' @param ... Additional arguments to `data.tree::as.Node.data.frame()`
 #'
-#' @return A `data.tree` object (invisibly). A text representation of the tree is printed when `verbose=TRUE`.
+#' @return A `SoilTaxonNode` (subclass of `data.tree` `Node`) object (invisibly). A text representation of the tree is printed when `verbose=TRUE`.
 #' @export
 #' @importFrom stats complete.cases
 #' @examplesIf !inherits(requireNamespace("data.tree", quietly = TRUE), 'try-error')
@@ -28,19 +27,63 @@ taxonTree <- function(taxon,
   }
 
   level <- tolower(trimws(level))
-  lowest_level <- max(match(level, level_hierarchy(family = FALSE)))
-  x <- unique(do.call('c', getChildTaxa(taxon, level = level[length(level)])))
+
+  # get child taxa at most detailed `level`
+  lh <- level_hierarchy(family = FALSE)
+  lowest_level <- max(match(level, lh))
+  x <- unique(do.call('c', getChildTaxa(taxon,
+                                        level = as.character(lh[lowest_level]))))
   y <- getTaxonAtLevel(x, level = level)
+
+  # we build the tree from the terminal/leaf node information
+  #  parent taxa are included based on `level`
   y <- y[order(taxon_to_taxon_code(x)),]
   y <- y[stats::complete.cases(y),]
 
+  # create data.tree node
   y$pathString <- apply(data.frame(root, as.data.frame(lapply(level, function(z) {
     paste0("/", y[[z]])
   }))), MARGIN = 1, FUN = paste0, collapse = "")
-
   n <- data.tree::as.Node(y, ...)
+
+  # allow for S3 dispatch for "soil  taxonomic data.tree objects" SoilTaxonNode
+  attr(n, "class") <- c("SoilTaxonNode", attr(n, "class"))
+
   if (isTRUE(verbose)) {
     print(n, limit = NULL)
   }
+
   invisible(n)
 }
+
+#' @export
+print.SoilTaxonNode <- function(x,
+                                special.chars = "|",
+                                optional = FALSE,
+                                traversal = c("pre-order", "post-order", "in-order", "level", "ancestor"),
+                                pruneFun = NULL,
+                                filterFun = NULL,
+                                format = FALSE,
+                                inheritFromAncestors = FALSE,
+                                ...) {
+  res <- as.data.frame(x,
+                       optional = optional,
+                       traversal = traversal,
+                       pruneFun = pruneFun,
+                       filterFun = filterFun,
+                       format = format,
+                       inheritFromAncestors = inheritFromAncestors)
+
+  # replace unicode markup
+  special.chars.default <- c("\u00a6", "\u00b0")
+  if (is.null(special.chars) || length(special.chars) == 0) {
+    special.chars <- "|"
+  }
+
+  special.chars <- rep(special.chars, 2)[1:2]
+  for (i in 1:2) {
+    res$levelName <- gsub(special.chars.default[i], special.chars[i], res$levelName)
+  }
+
+  cat(res$levelName, sep = "\n")
+}
diff --git a/man/taxonTree.Rd b/man/taxonTree.Rd
index 1db6987..5178deb 100644
--- a/man/taxonTree.Rd
+++ b/man/taxonTree.Rd
@@ -24,7 +24,7 @@ taxonTree(
 \item{...}{Additional arguments to \code{data.tree::as.Node.data.frame()}}
 }
 \value{
-A \code{data.tree} object (invisibly). A text representation of the tree is printed when \code{verbose=TRUE}.
+A \code{SoilTaxonNode} (subclass of \code{data.tree} \code{Node}) object (invisibly). A text representation of the tree is printed when \code{verbose=TRUE}.
 }
 \description{
 Create a \code{data.tree} Object from Taxon Names