add depth screening function to guide user to checkHzDepthLogic()

R/SoilProfileCollection-setters.R

@@ -90,6 +90,18 @@ setReplaceMethod("depths", "data.frame",
   return(depth)
 }
 
+.checkDepthOrder <- function(x, depthcols) {
+  if (any(x[[depthcols[2]]] < x[[depthcols[1]]], na.rm = TRUE)) {
+    warning("One or more horizon bottom depths are shallower than top depth. Check depth logic with aqp::checkHzDepthLogic()", call. = FALSE)
+  }
+}
+
+.screenDepths <- function(x, depthcols = horizonDepths(x)) {
+  .checkNAdepths(x[[depthcols[1]]], "top")
+  .checkNAdepths(x[[depthcols[2]]], "bottom")
+  .checkDepthOrder(x, depthcols)
+}
+
 # create 0-length spc from id and horizon depth columns (`idn`, `hzd`)
 #  - allows template horizon (`hz`) and site (`st`) data to be provided (for additional columns)
 .prototypeSPC <- function(idn, hzd, 
@@ -178,6 +190,9 @@ setReplaceMethod("depths", "data.frame",
   data[[depthcols[1]]] <- .checkNAdepths(data[[depthcols[1]]], "top")
   data[[depthcols[2]]] <- .checkNAdepths(data[[depthcols[2]]], "bottom")
 
+  # warn if bottom depth shallower than top (old style O horizons, data entry issues, etc.)
+  .checkDepthOrder(data, depthcols)
+
   tdep <- data[[depthcols[1]]]
 
   # calculate ID-top depth order, re-order input data

R/collapseHz.R

@@ -144,6 +144,8 @@ collapseHz <- function(x,
   idn <- idname(x)
   hzd <- horizonDepths(x)
 
+  .screenDepths(x, hzd)
+
   # use exact match of existing genhz labels as default in lieu of pattern
   if (is.null(pattern) & missing(by)) {
     by <- GHL(x, required = TRUE)

tests/testthat/test-collapseHz.R

@@ -69,11 +69,12 @@ test_that("collapseHz works", {
 
   # works on SPC with filled profile (1 horizon with NA depths)
   all_na <- subsetHz(jacobs2000_gen[1,], TRUE)
-  all_na$top <- NA
-  all_na$bottom <- NA
+  all_na$top <- NA_real_
+  all_na$bottom <- NA_real_
   expect_warning(na_nonna <- c(all_na, jacobs2000_gen[2:5,]))
-  expect_silent(f <- collapseHz(all_na, by = "genhz"))
-  expect_silent(n <- collapseHz(na_nonna, by = "genhz"))
+  expect_warning(f <- collapseHz(all_na, by = "genhz"), "contain NA")
+  na_nonna$top[2] <- 19
+  expect_warning(n <- collapseHz(na_nonna, by = "genhz"), "bottom depths are shallower than top")
   expect_equal(nrow(n), 14)