Add thicknessOf()

DESCRIPTION

@@ -15,6 +15,6 @@ URL: https://github.com/ncss-tech/aqp, https://ncss-tech.github.io/AQP/
 BugReports: https://github.com/ncss-tech/aqp/issues
 Language: en-US
 Encoding: UTF-8
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 VignetteBuilder: knitr

R/thicknessOf.R

@@ -2,12 +2,13 @@
 #'
 #' This function calculates the cumulative (`method="cumulative"`, default) or maximum difference between (`method="minmax"`) horizons within a profile that match a defined pattern (`pattern`) or, more generally, any set of horizon-level logical expressions encoded in a function (`FUN`).
 #' 
-#' @param x A SoilProfileCollection
-#' @param pattern character. A pattern to match in `hzdesgn`; used with the default `FUN` definition for regular expression pattern matching on horizons.
-#' @param hzdesgn character. A column containing horizon designations or other horizon-level character label used to identify matches; used with the default `FUN` definition.
-#' @param method character. Either `"cumulative"` (default) or `"minmax"`. See details.
-#' @param na.rm logical. Omit `NA` values in summaries of thickness and in matching? Default: `FALSE`
-#' @param FUN function. A function that returns a _logical_ vector equal in length to the number of horizons in `x`. See details.
+#' @param x A _SoilProfileCollection_
+#' @param pattern _character_. A pattern to match in `hzdesgn`; used with the default `FUN` definition for regular expression pattern matching on horizons.
+#' @param hzdesgn _character_. A column containing horizon designations or other horizon-level character label used to identify matches; used with the default `FUN` definition.
+#' @param method _character_. Either `"cumulative"` (default) or `"minmax"`. See details.
+#' @param prefix _character_. Column prefix for calculated `"thickness"` result, and `"min"`/`"max"` column results for `method="minmax"`. Default: `""`.
+#' @param FUN _function_. A function that returns a _logical_ vector equal in length to the number of horizons in `x`. See details.
+#' @param na.rm _logical_. Omit `NA` values in summaries of thickness and in matching? Default: `FALSE`
 #' @param ... Additional arguments passed to the matching function `FUN`.
 #'
 #' @return A _data.frame_-like object (corresponding to the `aqp_df_class()` of `x`) with one row per profile in `x`. First column is always the profile ID which is followed by `"thickness"`. In `method="minmax"` the upper and lower boundaries used to calculate `"thickness"` are also returned as `"tmin"` and `"tmax"` columns, respectively.
@@ -29,24 +30,26 @@
 #' thicknessOf(jacobs2000, "Bt")
 #' 
 #' # maximum bottom depth minus minimum top depth of horizon designations matching "Bt"
-#' thicknessOf(jacobs2000, "Bt", method = "minmax")
+#' thicknessOf(jacobs2000, "Bt", prefix = "Bt_", method = "minmax")
 #' 
 #' # cumulative thickness of horizon designations matching "A|B"
-#' thicknessOf(jacobs2000, "A|B")
+#' thicknessOf(jacobs2000, "A|B", prefix = "AorB_")
 #' 
 #' # maximum bottom depth minus minimum top depth of horizon designations matching "A|B"
-#' thicknessOf(jacobs2000, "A|B", method = "minmax")
+#' thicknessOf(jacobs2000, "A|B", method = "minmax", prefix = "AorB_")
 #' # note that the latter includes the thickness of E horizons between the A and the B
 #' 
 #' # when using a custom function (be sure to accept ... and consider the effect of NA values)
 #' 
 #' # calculate cumulative thickness of horizons containing >18% clay
-#' thicknessOf(jacobs2000, FUN = function(x, ...) !is.na(x[["clay"]]) & x[["clay"]] > 18)
+#' thicknessOf(jacobs2000, prefix = "claygt18_", 
+#'             FUN = function(x, ...) !is.na(x[["clay"]]) & x[["clay"]] > 18)
 #' 
 thicknessOf <- function(x, 
                         pattern = NULL, 
                         hzdesgn = guessHzDesgnName(x, required = TRUE), 
                         method = "cumulative",
+                        prefix = "",
                         FUN = function(x, pattern, hzdesgn, ...) grepl(pattern, x[[hzdesgn]]),
                         na.rm = FALSE,
                         ...) {
@@ -66,12 +69,13 @@ thicknessOf <- function(x,
     h$.internalTHK <- x[[hzd[2]]] - x[[hzd[1]]]
     res <- h[, list(thickness = sum(.internalTHK[.internalHZM], na.rm = na.rm)), by = lid]
   } else if (method == "minmax") {
-    res <- h[, list(tmin = suppressWarnings(min(.SD[[1]][.internalHZM], na.rm = na.rm)),
-                    tmax = suppressWarnings(max(.SD[[2]][.internalHZM], na.rm = na.rm))),
+    res <- h[, list(`min` = suppressWarnings(min(.SD[[1]][.internalHZM], na.rm = na.rm)),
+                    `max` = suppressWarnings(max(.SD[[2]][.internalHZM], na.rm = na.rm))),
               by = lid, .SDcols = c(hzd, ".internalHZM")]
-    res$thickness <- res$tmax - res$tmin
+    res$thickness <- res$`max` - res$`min`
     res$thickness[!is.finite(res$thickness)] <- 0L
   } else stop("unknown thickness method: ", shQuote(method), call. = FALSE)
+  colnames(res)[2:ncol(res)] <- paste0(prefix, colnames(res)[2:ncol(res)])
   .as.data.frame.aqp(res, aqp_df_class(x))
 }
 

tests/testthat/test-thicknessOf.R

@@ -4,17 +4,18 @@ test_that("thicknessOf works", {
   ## method="cumulative"
 
   # cumulative thickness of horizon designations matching "A|B"
-  x1 <- thicknessOf(jacobs2000, "A|B")
+  x1 <- thicknessOf(jacobs2000, "A|B", prefix = "AorB_")
   expect_equal(nrow(x1), length(jacobs2000))
-  expect_equal(x1$thickness, c(131, 117, 136, 20, 54, 110, 43))
+  expect_equal(x1$AorB_thickness, c(131, 117, 136, 20, 54, 110, 43))
 
   ## method="minmax"
 
   # maximum bottom depth minus minimum top depth of horizon designations matching "A|B"
-  x2 <- thicknessOf(jacobs2000, "A|B", method = "minmax")
+  x2 <- thicknessOf(jacobs2000, "A|B", method = "minmax", prefix = "AorB_")
   expect_equal(ncol(x2), 4)
-  expect_equal(x2$thickness, c(156, 145, 175, 20, 135, 168, 140))
-  expect_true(all(x2$thickness >= x1$thickness))
+  expect_equal(x2$AorB_min, rep(0, nrow(x2)))
+  expect_equal(x2$AorB_thickness, c(156, 145, 175, 20, 135, 168, 140))
+  expect_true(all(x2$AorB_thickness >= x1$AorB_thickness))
 
   ## custom logical function