Merge branch 'hyndman-suggestions' into develop

* hyndman-suggestions:
  Updated NEWS.md
  Refactoring
  Increment version number to 1.0.0.9001
  Added TODOs
  Updated docs
  Implemented faster `chackoStatistic()`
  Improved validation of `x`

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: permChacko
 Title: Chacko Test for Order-Restriction with Permutation
-Version: 1.0.0.9000
+Version: 1.0.0.9001
 Date: 2024-04-17
 Authors@R:
     c(
@@ -25,7 +25,8 @@ Description: Implements an extension of the Chacko chi-square test for
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
+Imports: methods
 Suggests:
     knitr,
     rmarkdown,

NAMESPACE

@@ -9,5 +9,6 @@ export(chacko66_sec5)
 export(permChacko)
 export(reduceVector)
 export(ruxton221207)
+importFrom(methods,is)
 importFrom(stats,pchisq)
 importFrom(stats,weighted.mean)

NEWS.md

@@ -1,5 +1,8 @@
 # permChacko (development version)
 
+* Improved validation
+* Optimized `chackoStatistic()`
+
 # permChacko 1.0.0
 
 * Improved printing of hypothesis ([issue #11](https://github.com/ocbe-uio/permChacko/issues/11)).

R/chackoStatistic.R

@@ -1,10 +1,8 @@
-chackoStatistic <- function(x_t, n, k) {
-  x_bar <- x_t[, "x"]
-  t <- x_t[, "t"]
-  m <- length(unique(x_bar))
-  power_sum <- 0
-  for (j in seq_len(m)) {
-    power_sum <- power_sum + t[[j]] * (x_bar[[j]] - n / k) ^ 2
-  }
-  return(k / n * power_sum)
+chackoStatistic <- function(x_t, n, k, uniqueness_method = 1) {
+  m <- length(unique(x_t[, "x"])) # TODO: check what Chacko really means by m
+  x_t_unique <- switch(uniqueness_method,
+    x_t[seq_len(m), , drop = FALSE],  # current implementation
+    x_t[!duplicated(x_t[, "x"]), , drop = FALSE], # new idea (hidden)
+  )
+  k / n * sum(x_t_unique[, "t"] * (x_t_unique[, "x"] - n / k) ^ 2)
 }

R/permChacko-package.R

@@ -1,7 +1,4 @@
 #' @keywords internal
 #' @aliases permChacko-package
+#' @importFrom methods is
 "_PACKAGE"
-
-## usethis namespace: start
-## usethis namespace: end
-NULL

R/permChacko.R

@@ -24,7 +24,7 @@
 #' permChacko(chacko66_sec5)
 #' @export
 permChacko <- function(x, n_perm = 1000L, verbosity = 0) {
-  if (!is.null(dim(x))) stop("Input must be a vector")
+  if (!is(x, "numeric")) stop("Input must be a vector")
   if (verbosity >= 1L) message("Reducing original vector")
   # Ordering and reducing vector
   x_t <- reduceVector(x, verbosity)[["x_t"]]

R/reduceVector.R

@@ -21,7 +21,7 @@
 #' reduceVector(chacko66_sec5)
 #' reduceVector(chacko66_sec5, verbosity = 1)
 reduceVector <- function(x, verbosity = 0L) {
-  if (!is.null(dim(x))) stop("Input must be a vector")
+  if (!is(x, "numeric")) stop("Input must be a vector")
   x_t <- cbind("x" = unname(x), "t" = unname(x) ^ 0L)
   reductions <- 0L
   while (nrow(x_t) > 1L && isMonotoneIncreasing(x_t[, "x"])) {