Merge pull request #21 from MoseleyBioinformaticsLab/updates

Updates

Author: rmflight

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ICIKendallTau
 Title: Calculates information-content-informed Kendall-tau
-Version: 1.1.3
+Version: 1.2.0
 Authors@R: c(
     person(
       given = c("Robert", "M"), 
@@ -21,13 +21,15 @@ LazyData: true
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 LinkingTo: Rcpp
 Imports: Rcpp, 
          purrr, 
          utils, 
          stringr,
-         stats
+         stats,
+         rlang,
+         cli
 Suggests: furrr, 
           future, 
           testthat (>= 3.0.0), 
@@ -44,4 +46,4 @@ URL: https://moseleybioinformaticslab.github.io/ICIKendallTau/
 BugReports:
         https://github.com/moseleybioinformaticslab/ICIKendallTau/issues
 Config/testthat/edition: 3
-Depends: R (>= 2.10)
+Depends: R (>= 3.5)

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(add_uniform_noise)
 export(calculate_matrix_medians)
+export(cor_fast)
 export(cor_matrix_2_long_df)
 export(disable_logging)
 export(enable_logging)
@@ -16,4 +17,5 @@ export(rank_order_data)
 export(show_progress)
 export(test_left_censorship)
 importFrom(Rcpp,sourceCpp)
+importFrom(stats,median)
 useDynLib(ICIKendallTau)

NEWS.md

@@ -1,3 +1,10 @@
+# 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.
+- Also refactored `kt_fast` to be more consistent and use more functions internally. **Note**: now returns matrix or data.frame regardless of whether passing simply two vectors or a matrix input.
+- Added `alternative` and `continuity` arguments to both `ici_kendalltau` and `kt_fast`.
+- Added `cor_fast` to allow running many iterations of `cor.test` on large matrix inputs if desired, with parallel processing to speed things up.
+
 # ICIKendallTau 1.1.3
 
 - makes `rank_order_data` take a sample class argument to enable splitting out by class.