swap argument order

NEWS.md

@@ -10,6 +10,8 @@
 
 ### breaking changes
 
+* Reverse argument order for variable indices to `(source, target)` (#85).
+
 * Impose geometric constraint `k >= E+1` in `ops` generic (#81).
 
 * Euclidean/Manhattan distances now automatically compensate for dimensions skipped due to `NA/NaN`, aligned with base R `dist()` function (#79).

R/ops.R

@@ -49,7 +49,7 @@
 #' @return A list.
 #' \describe{
 #'   \item{\code{param}}{The selected optimal parameter combination.}
-#'   \item{\code{xmap}}{A data.frame containing cross-mapping performance across parameter settings.}
+#'   \item{\code{causality}}{A data.frame containing results across parameter settings.}
 #' }
 #'
 #' @export
@@ -58,7 +58,7 @@
 #'
 #' @examples
 #' crash = sf::read_sf(system.file("case/crash.gpkg", package = "pc"))
-#' pc::ops(crash, 1, 2, E = 3:10, maximize = "positive", threads = 1)
+#' pc::ops(crash, 2, 1, E = 3:10, maximize = "positive", threads = 1)
 #'
 methods::setMethod("ops", "data.frame", .ops_ts)
 

R/pc.R

@@ -89,12 +89,12 @@
 #'
 #' @examples
 #' crash = sf::read_sf(system.file("case/crash.gpkg", package = "pc"))
-#' p1 = pc::pc(crash, 1, 2, E = 3, k = 7, threads = 1)
+#' p1 = pc::pc(crash, 2, 1, E = 3, k = 7, threads = 1)
 #' print(p1)
 #' plot(p1)
 #' 
 #' # convergence diagnostics
-#' p2 = pc::pc(crash, 1, 2, libsizes = seq(10,172,40), E = 3, k = 7, threads = 1)
+#' p2 = pc::pc(crash, 2, 1, libsizes = seq(10,172,40), E = 3, k = 7, threads = 1)
 #' print(p2)
 #' plot(p2)
 #'