Match tree extraction to tskit's 0-based indexing

bodkan · May 11, 2023 · 554e13e · 554e13e
1 parent 087cbc2
commit 554e13e
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Showing 4 changed files with 19 additions and 18 deletions.
diff --git a/R/tree-sequences.R b/R/tree-sequences.R
@@ -1430,9 +1430,9 @@ ts_descendants <- function(ts, x, verbose = FALSE, complete = TRUE) {
 #'
 #' @param ts Tree sequence object of the class \code{slendr_ts}
 #' @param i Position of the tree in the tree sequence. If \code{mode = "index"},
-#'   an i-th tree will be returned (in one-based indexing), if \code{mode =
-#'   "position"}, a tree covering an i-th base of the simulated genome will be
-#'   returned.
+#'   an i-th tree will be returned (in zero-based indexing as in tskit), if
+#'   \code{mode = "position"}, a tree covering the i-th base of the simulated genome will be
+#'   returned (again, in tskit's indexing).
 #' @param mode How should the \code{i} argument be interpreted? Either "index"
 #'   as an i-th tree in the sequence of genealogies, or "position" along the
 #'   simulated genome.
@@ -1453,19 +1453,19 @@ ts_descendants <- function(ts, x, verbose = FALSE, complete = TRUE) {
 #' # load the tree-sequence object from disk
 #' ts <- ts_load(slendr_ts, model, simplify = TRUE)
 #'
-#' # extract the first tree in the tree sequence
-#' tree <- ts_tree(ts, i = 1)
+#' # extract the zero-th tree in the tree sequence
+#' tree <- ts_tree(ts, i = 0)
 #'
-#' # extract the tree at a position 100000bp in the tree sequence
+#' # extract the tree at a position in the tree sequence
 #' tree <- ts_tree(ts, i = 100000, mode = "position")
 #' @export
 ts_tree <- function(ts, i, mode = c("index", "position"), ...) {
   check_ts_class(ts)
   mode <- match.arg(mode)
   if (mode == "index")
-    tree <- ts$at_index(index = i - 1, ...)
+    tree <- ts$at_index(index = i, ...)
   else
-    tree <- ts$at(position = i - 1, ...)
+    tree <- ts$at(position = i, ...)
   attr(tree, "tree_sequence") <- ts
   tree
 }

diff --git a/man/ts_phylo.Rd b/man/ts_phylo.Rd
diff --git a/man/ts_tree.Rd b/man/ts_tree.Rd
diff --git a/vignettes/vignette-09-paper.Rmd b/vignettes/vignette-09-paper.Rmd
@@ -499,7 +499,8 @@ ggsave("/Users/mp/Documents/postdoc/slendr-paper/preprint_models_v0.5/ex3.pdf",
 ```{r, ex4, time_it = TRUE, eval = eval_chunk, fig.keep='none'}
 ts_small <- ts_simplify(ts, simplify_to = c("EUR_578", "YAM_75", "ANA_163", "EHG_208"))
 
-tree <- ts_phylo(ts_small, i = 20 / scaling)
+# tskit uses zero-based indexing
+tree <- ts_phylo(ts_small, i = 19 / scaling)
 nodes <- ts_nodes(tree)
 edges <- ts_edges(tree)