updated comparisons code to properly

handle just the comparisons we are defining we want to do
MoseleyBioinformaticsLab · Jul 24, 2024 · 7897bd1 · 7897bd1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ICIKendallTau
 Title: Calculates information-content-informed Kendall-tau
-Version: 1.2.1
+Version: 1.2.2
 Authors@R: c(
     person(
       given = c("Robert", "M"), 

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# ICIKendallTau 1.2.2
+
+- Fixed a bug where passing a two vector list is **supposed** to restrict the comparisons to just those provided, but instead did all possible pairwise comparisons between the two things and all others available.
+
 # ICIKendallTau 1.2.0
 
 - Refactored much of `ici_kendalltau`, making the code more consistent and easier to extend, as well as providing more informative error messages. Thanks to @njtierney for suggestions.

diff --git a/R/kendalltau.R b/R/kendalltau.R
@@ -212,9 +212,15 @@ setup_comparisons = function(samples,
         # of the sets against each of the lists. Again, this returns TRUE where
         # they match. Because we want the things where they
         # are both TRUE (assuming l1[1] goes with l2[1]), we use the AND at the end.
-        l1_include = (named_comparisons$s1 %in% include_only[[1]]) | (named_comparisons$s2 %in% include_only[[1]])
-        l2_include = (named_comparisons$s1 %in% include_only[[2]]) | (named_comparisons$s2 %in% include_only[[2]])
-        named_comparisons = named_comparisons[(l1_include & l2_include), ]
+        l1_l2 = paste0(include_only[[1]], "-", include_only[[2]])
+        l2_l1 = paste0(include_only[[2]], "-", include_only[[1]])
+
+        all_include = c(l1_l2, l2_l1)
+        all_compare = paste0(named_comparisons$s1, "-", named_comparisons$s2)
+
+        keep_compare = all_compare %in% all_include
+        named_comparisons = named_comparisons[keep_compare, ]
+
       } else {
         cli::cli_abort(message = c(
           '{.arg {include_arg}} must be a vector, a data.frame with two columns, or list of two vectors.',
@@ -238,7 +244,7 @@ setup_comparisons = function(samples,
   n_each = ceiling(n_todo / ncore)
 
   which_core = rep(seq(1, ncore), each = n_each)
-  which_core = which_core[1:nrow(named_comparisons)]
+  which_core = which_core[seq_len(nrow(named_comparisons))]
 
   named_comparisons$core = which_core
   if (which %in% "icikt") {

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/ici-kendalltau.html b/docs/articles/ici-kendalltau.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/testing-for-left-censorship.html b/docs/articles/testing-for-left-censorship.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,8 +1,8 @@
-pandoc: 3.1.12.3
+pandoc: 3.1.11
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   ici-kendalltau: ici-kendalltau.html
   testing-for-left-censorship: testing-for-left-censorship.html
-last_built: 2024-07-18T22:16Z
+last_built: 2024-07-24T14:30Z
 
diff --git a/docs/reference/add_uniform_noise.html b/docs/reference/add_uniform_noise.html
diff --git a/docs/reference/calculate_matrix_medians.html b/docs/reference/calculate_matrix_medians.html
diff --git a/docs/reference/cor_fast.html b/docs/reference/cor_fast.html
diff --git a/docs/reference/cor_matrix_2_long_df.html b/docs/reference/cor_matrix_2_long_df.html
diff --git a/docs/reference/disable_logging.html b/docs/reference/disable_logging.html
diff --git a/docs/reference/enable_logging.html b/docs/reference/enable_logging.html
diff --git a/docs/reference/ici_kendalltau.html b/docs/reference/ici_kendalltau.html
diff --git a/docs/reference/ici_kendalltau_ref.html b/docs/reference/ici_kendalltau_ref.html
diff --git a/docs/reference/ici_kt.html b/docs/reference/ici_kt.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/kt_fast.html b/docs/reference/kt_fast.html
diff --git a/docs/reference/log_memory.html b/docs/reference/log_memory.html
diff --git a/docs/reference/log_message.html b/docs/reference/log_message.html
diff --git a/docs/reference/long_df_2_cor_matrix.html b/docs/reference/long_df_2_cor_matrix.html
diff --git a/docs/reference/missing_dataset.html b/docs/reference/missing_dataset.html