From 57dd0b20fdc18311f60db72a2e120467192d063a Mon Sep 17 00:00:00 2001
From: Michael McLaren <m.mclaren42@gmail.com>
Date: Sat, 12 Sep 2020 15:50:47 -0400
Subject: [PATCH] Change internal var names to avoid conflicts

See Issue #51.
---
 DESCRIPTION        |  2 +-
 NEWS.md            |  6 +++---
 R/merge_taxa_vec.R | 22 +++++++++++-----------
 3 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0dca77a..3d9ed66 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: speedyseq
 Title: Faster implementations of phyloseq functions
-Version: 0.3.2.9003
+Version: 0.4.0
 Authors@R: 
     person(given = "Michael",
            family = "McLaren",
diff --git a/NEWS.md b/NEWS.md
index f9067f7..312959f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,6 @@
-# speedyseq 0.3.3
+# speedyseq 0.4.0
 
-* Add `merge_samples2()` and the helper `unique_or_na()` as an alternative to
+* New `merge_samples2()` and helper `unique_or_na()` provides an alternative to
   `phyloseq::merge_samples()` that better handles categorical sample variables.
   The `funs` argument specifies which summary is used to merge each sample
   variable within groups. The default is `unique_or_na()`, which collapses the
@@ -22,7 +22,7 @@ sample_data(ps0) %>% head
 
 * Add `tibble::glimpse()` methods for `sample_data` and `phyloseq` objects
 
-* Fixed bug in `merge_taxa_vec()` when only one tax rank
+* Minor bug fixes to `merge_taxa_vec()`
 
 # speedyseq 0.3.2
 
diff --git a/R/merge_taxa_vec.R b/R/merge_taxa_vec.R
index 50eb831..8059fbb 100644
--- a/R/merge_taxa_vec.R
+++ b/R/merge_taxa_vec.R
@@ -148,10 +148,10 @@ setMethod("merge_taxa_vec", "otu_table",
 setMethod("merge_taxa_vec", "taxonomyTable",
   function(x, group, reorder = FALSE, tax_adjust = 1L) {
     stopifnot(ntaxa(x) == length(group))
-    # Temporary stopgap to avoid hidden  errors if "taxon" or "group" are in
-    # the tax table
-    if (any(c("taxon", "group") %in% rank_names(x))) {
-      stop("Currently requires that 'taxon' and 'group' are not in `rank_names(x)`")
+    # Temporary stopgap to avoid hidden errors if internal variable names are
+    # in the tax table
+    if (any(c(".taxon", ".group") %in% rank_names(x))) {
+      stop("Currently requires that '.taxon' and '.group' are not in `rank_names(x)`")
     }
     # drop taxa with `is.na(group)`
     if (anyNA(group)) {
@@ -172,23 +172,23 @@ setMethod("merge_taxa_vec", "taxonomyTable",
     # ranks and making new tax table
     reduced <- x %>% 
       as("matrix") %>%
-      data.table::as.data.table(keep.rownames = "taxon") %>%
-      .[, group := group] %>%
+      data.table::as.data.table(keep.rownames = ".taxon") %>%
+      .[, .group := group] %>%
       .[,
         # Reduce to one row per group; compute new names and bad ranks
-        by = group, .SDcols = rank_names(x),
+        by = .group, .SDcols = rank_names(x),
         c(
           # New taxa names are the first taxon in each group
-          .(taxon = taxon[1]), 
+          .(.taxon = .taxon[1]), 
           lapply(.SD, bad_or_unique, bad = bad_string)
         )
       ]
     if (reorder)
-      data.table::setorder(reduced, group)
+      data.table::setorder(reduced, .group)
     # For last step, convert to data frame with rownames as taxon names; but
     # must be a matrix before final call to tax_table
-    reduced <- reduced[, !"group"] %>%
-        tibble::column_to_rownames("taxon")
+    reduced <- reduced[, !".group"] %>%
+        tibble::column_to_rownames(".taxon")
     # If only one tax rank, just convert bad_string -> NA; else, need to
     # propagate bad ranks downwards and convert to NAs
     if (identical(length(rank_names(x)), 1L)) {