Merge branch 'develop' into paper

.Rbuildignore

@@ -7,3 +7,5 @@
 ^Meta$
 paper
 Makefile
+^CRAN-SUBMISSION$
+^cran-comments\.md$

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 0.2.0
+Date: 2023-11-07 08:27:25 UTC
+SHA: 543f1ca2fb82489effd0178f2be3f9fec5e9f68b

DESCRIPTION

@@ -1,6 +1,7 @@
 Package: permChacko
 Title: Chacko Test for Order-Restriction with Permutation
-Version: 0.1.0.9014
+Version: 0.2.0.9000
+Date: 2023-11-07
 Authors@R:
     c(
         person(

NEWS.md

@@ -1,5 +1,9 @@
 # permChacko (development version)
 
+* Improved printing of hypothesis ([issue #11](https://github.com/ocbe-uio/permChacko/issues/11)).
+
+# permChacko 0.2.0
+
 * Replaced `verbose` with `verbosity` in functions to allow for more control over the output ([issue #3](https://github.com/ocbe-uio/permChacko/issues/3)).
 * Exported `reduceVector()` ([issue #4](https://github.com/ocbe-uio/permChacko/issues/4)).
 * Added package documentation ([issue #5](https://github.com/ocbe-uio/permChacko/issues/5)).

R/print.R

@@ -13,8 +13,8 @@ print.chacko_test <- function(x, ...) {
         "  Numeric p-value         : %f (%d permutations)\n",
         "  Tabular p-value         : %f\n"
       ),
-      paste0("p", seq_along(x$observed_data), collapse = " == "),
-      paste0("p", seq_along(x$observed_data), collapse = " <= "),
+      printHypothesis("p", seq_along(x$observed_data), "=="),
+      printHypothesis("p", seq_along(x$observed_data), "<="),
       x[["statistic"]], p_values[["analytic"]],
       p_values[["numeric"]], x[["n_perm"]], p_values[["tabular"]]
     )
@@ -35,3 +35,16 @@ print.reduced_vector <- function(x, details = TRUE, ...) {
     )
   )
 }
+
+printHypothesis <- function(x_name, x_indices, operator = "==") {
+  operator <- paste0(" ", operator, " ")
+  if (length(x_indices) < 6) {
+    return(paste0(x_name, x_indices, collapse = operator))
+  } else {
+    first_idx <- 1:2
+    last_idx <- seq(length(x_indices) - 1, length(x_indices))
+    first_x <- paste0(x_name, x_indices[first_idx], collapse = operator)
+    last_x <- paste0(x_name, x_indices[last_idx], collapse = operator)
+    paste0(first_x, operator, "...", operator, last_x)
+  }
+}

README.md

@@ -1,7 +1,7 @@
 
 # permChacko
 
-permChacko is an R package that implements a modified version of the Chacko (1966) algorithm for order restriction.
+permChacko is an R package that implements a modified version of the [Chacko (1966)](https://www.jstor.org/stable/25051572) algorithm for order restriction.
 
 ## Installation
 
@@ -32,10 +32,16 @@ library(permChacko)
 permChacko(chacko66_sec3) # example 5 from Chacko (1966)
 ```
 
-# Contributing and support
+## Contributing and support
 
 If you find a bug or have a feature request, please open an issue [here](https://github.com/ocbe-uio/permChacko/issues). If you would like to contribute with code, please see [here](https://github.com/ocbe-uio/permChacko/contribute) for a list of good issues for newcomers.
 
+## References
+
+Chacko, V. J. "Testing homogeneity against ordered alternatives." The Annals of Mathematical Statistics (1963): 945-956. https://www.jstor.org/stable/2238476
+
+Chacko, V. J. (1966). Modified Chi-Square Test for Ordered Alternatives. Sankhyā: The Indian Journal of Statistics, Series B (1960-2002), 28(3/4), 185–190. http://www.jstor.org/stable/25051572
+
 ## Badges
 
 <!-- badges: start -->

cran-comments.md

@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.

tests/testthat/test-print-and-summary.R

@@ -19,3 +19,7 @@ test_that("print.chacko_test() works as expected", {
 test_that("summary.reduced_vector() works as expected", {
   expect_output(summary(reduceVector(rpois(7, 7))), "has been reduced 3 times")
 })
+test_that("Hypothesis suppression works as expected", {
+  expect_output(print(permChacko(4:1)), "p1 == p2 == p3 == p4")
+  expect_output(print(permChacko(6:1)), "p1 == p2 == ... == p5 == p6")
+})