From b760efb013afda97eaafe2f612a904557b3e0f4c Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Fri, 18 Oct 2024 21:46:37 +0100
Subject: [PATCH] clean up

---
 R/gt_helper_functions.R | 20 --------------------
 R/gt_roh_window.R       |  4 ++--
 man/gt_roh_window.Rd    |  4 ++--
 3 files changed, 4 insertions(+), 24 deletions(-)

diff --git a/R/gt_helper_functions.R b/R/gt_helper_functions.R
index bc58f58c..aa0bc217 100644
--- a/R/gt_helper_functions.R
+++ b/R/gt_helper_functions.R
@@ -10,23 +10,3 @@
 .gt_get_bigsnp<-function(.x){
   attr(.x$genotypes,"bigsnp")
 }
-
-
-# a developer function to create various count summaries of a population, used to
-# compute more complex statistics (e.g. pairwise fst, etc.).
-.gt_pop_freqs <- function(.x){
-  counts <- bigstatsr::big_counts( .gt_get_bigsnp(.x)$genotypes,
-                                   ind.row =.gt_bigsnp_rows(.x),
-                                   ind.col = .gt_bigsnp_cols(.x))
-  sums_alt <- apply(counts,2,function(x) x[2]+2*x[3])
-  n <- apply(counts,2,function(x) sum(x[1:3])*2)
-  sums_ref <- n - sums_alt
-  freq_alt <- sums_alt/n
-  freq_ref <- 1- freq_alt
-  het_obs <- apply(counts,2,function(x) x[2]/sum(x[1:3]))
-  return (list(
-    freq_alt = freq_alt,
-    freq_ref = freq_ref,
-    n = n,
-    het_obs = het_obs))
-}
diff --git a/R/gt_roh_window.R b/R/gt_roh_window.R
index fc4d3d12..ae38bbb1 100644
--- a/R/gt_roh_window.R
+++ b/R/gt_roh_window.R
@@ -42,8 +42,8 @@
 #' @export
 #'
 #' @examples
-#' # don't run the example
-#' if (FALSE) {
+#' # run the example only if we have the package installed
+#' if (requireNamespace("detectRUNS", quietly = TRUE)) {
 #' sheep_ped <- system.file("extdata", "Kijas2016_Sheep_subset.ped",
 #'     package="detectRUNS")
 #' sheep_gt <- tidypopgen::gen_tibble(sheep_ped, backingfile = tempfile(),
diff --git a/man/gt_roh_window.Rd b/man/gt_roh_window.Rd
index a569ba0b..441d8801 100644
--- a/man/gt_roh_window.Rd
+++ b/man/gt_roh_window.Rd
@@ -74,8 +74,8 @@ group table. Otherwise, the group 'column' is filled with the same values as the
 column
 }
 \examples{
-# don't run the example
-if (FALSE) {
+# run the example only if we have the package installed
+if (requireNamespace("detectRUNS", quietly = TRUE)) {
 sheep_ped <- system.file("extdata", "Kijas2016_Sheep_subset.ped",
     package="detectRUNS")
 sheep_gt <- tidypopgen::gen_tibble(sheep_ped, backingfile = tempfile(),