From daad0485d3c84cdae0cf1756b02886a19749b0da Mon Sep 17 00:00:00 2001
From: Jeff Kimbrel <jakpot@gmail.com>
Date: Fri, 29 Sep 2023 07:54:38 -0700
Subject: [PATCH] moved add_taxonomy from method to function

---
 DESCRIPTION           |  2 +-
 R/add_taxonomy.R      | 31 +++++++++++++++++++++++++++++++
 R/qsip_feature_data.R | 35 +++--------------------------------
 man/add_taxonomy.Rd   |  6 +++---
 4 files changed, 38 insertions(+), 36 deletions(-)
 create mode 100644 R/add_taxonomy.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 2200910b..2f7b71f2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: qSIP2
 Title: qSIP Analysis
-Version: 0.4.5.9004
+Version: 0.4.5.9005
 Authors@R: 
     person("Jeff", "Kimbrel", , "kimbrel1@llnl.gov", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))
diff --git a/R/add_taxonomy.R b/R/add_taxonomy.R
new file mode 100644
index 00000000..a62e483d
--- /dev/null
+++ b/R/add_taxonomy.R
@@ -0,0 +1,31 @@
+#' Add a taxonomy table to qSIP abundance data
+#'
+#' @param feature_object An object of `qsip_feature_data` class
+#' @param taxa A taxa table
+#' @param id The column name for the taxa ids that match the ids in the
+#' abundance table
+#'
+#' @export
+#'
+#' @keywords abundance
+
+add_taxonomy <- function(feature_object, taxa, feature_id) {
+
+  taxa = taxa |>
+    dplyr::rename("feature_id" := feature_id)
+
+
+  feature_object_ids = feature_object@data['feature_id']
+  taxa_ids = taxa['feature_id']
+
+  if (length(setdiff(feature_object_ids, taxa_ids)) > 0) {
+    stop("Some ids found in the abundance object are not found in the taxa table")
+  } else if (length(setdiff(taxa_ids, feature_object_ids)) > 0) {
+    setdiff(taxa_ids, feature_object_ids)
+    stop("Some ids found in the taxa table are not found in the abundance object")
+  } else {
+
+    feature_object@taxonomy = taxa
+    feature_object
+  }
+}
diff --git a/R/qsip_feature_data.R b/R/qsip_feature_data.R
index 6ed58936..7e9ce386 100644
--- a/R/qsip_feature_data.R
+++ b/R/qsip_feature_data.R
@@ -16,7 +16,9 @@ qsip_feature_data <- S7::new_class(
     feature_id = S7::class_character,
     taxonomy = S7::class_data.frame
     ),
-  constructor = function(data, feature_id, taxonomy = data.frame()) {
+  constructor = function(data,
+                         feature_id,
+                         taxonomy = data.frame()) {
 
     # rename columns to standardized names
     data = data |>
@@ -41,35 +43,4 @@ qsip_feature_data <- S7::new_class(
 
 
 
-#' Add a taxonomy table to qSIP abundance data
-#'
-#' @param x An object of `qsip_feature_data` class
-#' @param taxa A taxa table
-#' @param id The column name for the taxa ids that match the ids in the
-#' abundance table
-#'
-#' @export
-#'
-#' @keywords abundance
-
-add_taxonomy <- S7::new_generic("add_taxonomy", "x")
-
-S7::method(add_taxonomy, qsip_feature_data) <- function(x, taxa, feature_id) {
-
-  x_ids = x@data |> dplyr::pull(feature_id)
-  taxa_ids = taxa |> dplyr::pull(feature_id)
-
-  if (length(setdiff(x_ids, taxa_ids)) > 0) {
-    stop("some ids found in the abundance object are not found in the taxa table")
-  } else if (length(setdiff(taxa_ids, x_ids)) > 0) {
-    setdiff(taxa_ids, x_ids)
-    stop("some ids found in the taxa table are not found in the abundance object")
-  } else {
-
-    # rename taxa id column to the object level ID
-    x@taxonomy = taxa |>
-      dplyr::rename("feature_id" := feature_id)
 
-    x
-  }
-}
diff --git a/man/add_taxonomy.Rd b/man/add_taxonomy.Rd
index 34d7e387..f726a3dc 100644
--- a/man/add_taxonomy.Rd
+++ b/man/add_taxonomy.Rd
@@ -1,13 +1,13 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/qsip_feature_data.R
+% Please edit documentation in R/add_taxonomy.R
 \name{add_taxonomy}
 \alias{add_taxonomy}
 \title{Add a taxonomy table to qSIP abundance data}
 \usage{
-add_taxonomy(x, ...)
+add_taxonomy(feature_object, taxa, feature_id)
 }
 \arguments{
-\item{x}{An object of \code{qsip_feature_data} class}
+\item{feature_object}{An object of \code{qsip_feature_data} class}
 
 \item{taxa}{A taxa table}