added get_overlap_depths() function

NAMESPACE

@@ -7,6 +7,7 @@ export(SeriesDetrend)
 export(arco)
 export(check_pretreat)
 export(cpts_ar)
+export(get_overlap_depths)
 export(global_thresh)
 export(local_thresh)
 export(mgcv2tapas)
@@ -23,12 +24,15 @@ importFrom(changepoint,cpts)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
 importFrom(dplyr,all_of)
+importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,count)
+importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,pick)
 importFrom(dplyr,pull)
 importFrom(dplyr,relocate)
 importFrom(dplyr,select)

R/get_overlap_samples.R

@@ -0,0 +1,56 @@
+#' Get overlapping sample depths
+#'
+#' This function makes it easy to see which samples in the input file have
+#' overlapping sample depths. It may be used if the
+#' \code{tapas::check_pretreat()} function flags a warning for the presence of
+#' overlapping sample depths.
+#'
+#' @details
+#' The function checks if any \code{CmBot[i] > CmTop[i+1]}. If \code{TRUE},
+#' a data.frame with the overalpping samples is returned.
+#'
+#' @param series The input data frame. A matrix with the following columns:
+#'    \code{CmTop, CmBot, AgeTop, AgeBot, Volume},
+#'    and one or more columns with the data
+#'    that is being analysed (variables).
+#'
+#' @return A data frame including only the rows of the overlapping samples
+#' sorted in ascending order by depth. The rownames are inherited from the
+#' input data.frame, and mya thus help finding the flagged samples in raw data
+#' files.
+#'
+#' @seealso [check_pretreat()]
+#'
+#' @importFrom dplyr distinct arrange pick
+#'
+#' @export
+#'
+#' @author Walter Finsinger
+#'
+get_overlap_depths <- function(series) {
+
+
+  ## Gather data --------------------------------------------------------------
+  A <- series
+  cm <- A[ ,1]
+  cmB <- A[ ,2]
+
+
+  ## Check if the depth scale is continuous (cmBot[i] > cmTop[i+1]) ----------
+
+  ## Get difference between cmBot of sample[i] and cmTop of sample[i+1].
+  overlaps_index <- cmB[1:length(cmB) - 1] - cm[2:length(cm)]
+
+  # Get indices for overlapping samples
+  overlaps <- which(overlaps_index > 0)
+
+  # Get overlapping samples from input data.frame:
+  all_overlap_samples <- rbind(A[overlaps, ], A[overlaps + 1, ])
+
+  # Remove duplicates and sort in ascending order by top depth
+  overlap_samples <- dplyr::distinct(all_overlap_samples) %>%
+    dplyr::arrange(dplyr::pick(1))
+
+  # Return output
+  return(overlap_samples)
+}