fixes a missed instance of rows as samples

MoseleyBioinformaticsLab · Jan 27, 2024 · 080f0f7 · 080f0f7
1 parent 506c98f
commit 080f0f7
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Showing 28 changed files with 51 additions and 52 deletions.
diff --git a/R/kendalltau.R b/R/kendalltau.R
@@ -338,7 +338,6 @@ ici_kendalltau = function(data_matrix,
                              return_matrix = TRUE){
 
   do_log_memory = get("memory", envir = icikt_logger)
-  # assume row-wise (because that is what the description states), so need to transpose
   exclude_loc = matrix(FALSE, nrow = nrow(data_matrix), ncol = ncol(data_matrix))
 
   if (is.data.frame(data_matrix)) {

diff --git a/README.Rmd b/README.Rmd
@@ -59,10 +59,10 @@ The functions that implement this include:
   * The option `perspective` will control how the `NA` values influence ties.
   * When comparing samples, you likely want to use `perspective = "global"`.
 * `ici_kendallt`: Handles comparisons for a large matrix.
-  * Rows are samples, columns are features.
+  * Rows are features, columns are samples.
   * Implicitly parallel, but have to call:
-    * library(furrr)
-    * plan(multiprocess)
+    * `library(furrr)`
+    * `plan(multiprocess)`
   * Otherwise will only use a single core.
 
 ## Examples

diff --git a/README.md b/README.md
@@ -60,10 +60,10 @@ The functions that implement this include:
   - When comparing samples, you likely want to use
     `perspective = "global"`.
 - `ici_kendallt`: Handles comparisons for a large matrix.
-  - Rows are samples, columns are features.
+  - Rows are features, columns are samples.
   - Implicitly parallel, but have to call:
-    - library(furrr)
-    - plan(multiprocess)
+    - `library(furrr)`
+    - `plan(multiprocess)`
   - Otherwise will only use a single core.
 
 ## Examples
@@ -136,10 +136,10 @@ microbenchmark(
   times = 5
 )
 #> Unit: microseconds
-#>                           expr      min        lq      mean    median        uq       max
-#>  cor(x, y, method = "kendall") 13568.01 13818.243 14017.885 14090.436 14174.800 14437.933
-#>         ici_kt(x, y, "global")   261.84   272.733   304.271   287.571   335.669   363.542
-#>       ici_kt(x2, y2, "global") 14631.30 15614.509 16419.494 16340.620 17646.365 17864.673
+#>                           expr       min        lq       mean    median        uq       max
+#>  cor(x, y, method = "kendall") 11506.697 11670.094 12169.6628 12006.418 12482.883 13182.222
+#>         ici_kt(x, y, "global")   243.866   250.125   294.6542   275.104   320.058   384.118
+#>       ici_kt(x2, y2, "global") 13467.011 13739.312 14658.5050 14945.446 14987.140 16153.616
 #>  neval
 #>      5
 #>      5
@@ -202,7 +202,7 @@ r_4
 #> 3 s4 s4    0 1.0000000      0 1.000000 1.0000000
 #> 
 #> $run_time
-#> [1] 0.0196352
+#> [1] 0.01606894
 ```
 
 ## Code of Conduct

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/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
@@ -3,5 +3,5 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   ici-kendalltau: ici-kendalltau.html
-last_built: 2024-01-27T02:43Z
+last_built: 2024-01-27T15:25Z
 
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/pairwise_completeness.html b/docs/reference/pairwise_completeness.html