Addition of function force_sorted()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MsCoreUtils
 Title: Core Utils for Mass Spectrometry Data
-Version: 1.15.4
+Version: 1.15.5
 Description: MsCoreUtils defines low-level functions for mass
     spectrometry data and is independent of any high-level data
     structures. These functions include mass spectra processing

NAMESPACE

@@ -21,6 +21,7 @@ export(estimateBaselineConvexHull)
 export(estimateBaselineMedian)
 export(estimateBaselineSnip)
 export(estimateBaselineTopHat)
+export(force_sorted)
 export(formatRt)
 export(getImputeMargin)
 export(gnps)

NEWS.md

@@ -1,5 +1,10 @@
 # MsCoreUtils 1.15
 
+## MsCoreUtils 1.15.5
+
+- Add function `force_sorted()` to adjust a vector to ensure increasing/sorted
+  values. 
+
 ## MsCoreUtils 1.15.4
 
 - Fix documentation of `ndotproduct`.

R/force_sorted.R

@@ -0,0 +1,71 @@
+#' @title Forcing a numeric vector into a monotonously increasing sequence.
+#'
+#' @description
+#' This function performs interpolation on the non-increasing parts of an
+#' input vector to ensure its values are monotonously increasing.
+#' If the values are non-increasing at the end of the vector, these values
+#' will be monotonously increasing by the value defined with parameter `by `
+#' from the last increasing value.
+#'
+#' @param x `numeric` vector.
+#'
+#' @param by `numeric(1)` value that will determine the monotonous increase in
+#'        case the values at the end of the vector are non-increasing and
+#'        therefore interpolation would not be possible. Default
+#'        to `by = .Machine$double.eps` which is the smallest positive
+#'        floating-point number x such that 1 + x != 1.
+#'
+#' @return A vector with continuously increasing values.
+#'
+#' @note
+#' NA values will not be replaced.
+#'
+#' @examples
+#' x <- c(NA, NA, NA, 1.2, 1.1, 1.14, 1.2, 1.3, NA, 1.04, 1.4, 1.6, NA, NA)
+#' sorted_vec <- force_sorted(x)
+#' is.unsorted(x, na.rm = TRUE)
+#'
+#' ## Vector non increasing at the end
+#' x <- c(1, 2, 1.5, 2)
+#' sorted_rtime <- force_sorted(x, by = 0.1)
+#' is.unsorted(x, na.rm = TRUE)
+#'
+#' ## We can see the values were not interpolated but rather replaced by the
+#' ## last increasing value `2` and increasing by 0.1.
+#' sorted_vec
+#'
+#' @export
+#'
+#' @rdname force_sorted
+force_sorted <- function(x, by = .Machine$double.eps) {
+    # Select only the non-NA values
+    if (!is.numeric(x) && !is.integer(x))
+        stop("'x' needs to be numeric or integer")
+    nna_idx <- which(!is.na(x))
+    vec_temp <- x[nna_idx]
+
+    while (any(diff(vec_temp) < 0)) {
+        idx <- which.max(diff(vec_temp) < 0)
+        # Find next biggest value
+        next_idx <- which(vec_temp > vec_temp[idx])[1L]
+
+        if (is.na(next_idx)) {
+            l <- idx:length(vec_temp)
+            vec_temp[l] <- seq(vec_temp[idx], by = by,
+                               length.out = length(l))
+            warning("Found decreasing values at the end of the vector. ",
+                    "Interpolation is not possible in this region. Instead, ",
+                    "replacing these values with a sequence that starts from ",
+                    "the last increasing value and increments by  ", by,
+                    ". See help for more details")
+            break
+        }
+        # Interpolation
+        idx_range <- idx:next_idx
+        vec_temp[idx_range] <- seq(vec_temp[idx], vec_temp[next_idx],
+                                   length.out = length(idx_range))
+    }
+    x[nna_idx] <- vec_temp
+    x
+}
+

tests/testthat/test_force_sorted.R

@@ -0,0 +1,20 @@
+test_that("forceSorting works", {
+    vec <- c(NA, NA, NA, 1.2, 1.1, 1.14, 1.2, 1.3, 1.1, 1.04, 1.4, 1.6, NA, NA)
+    # Expected result after interpolation
+    sorted <- c(NA, NA, NA, 1.2, 1.225, 1.25, 1.275, 1.3, 1.333, 1.367,
+                1.4, 1.6, NA, NA)
+    result <- force_sorted(vec)
+    expect_equal(result, sorted, tolerance = 0.001)
+
+    # Test with decreasing values at the end
+    vec <- c(NA, NA, NA, 1.2, 1.1, 1.14, 1.2, 1.3, 1.4, 1.04, 1.2, 1.04, NA)
+    expect_warning(result <- force_sorted(vec, by = 0.000001), "replacing")
+    sorted <- c(NA, NA, NA, 1.2, 1.225, 1.25, 1.275, 1.3, 1.4, 1.400001,
+                1.400002, 1.400003, NA)
+    expect_equal(result, sorted)
+
+    # Test with sorted values
+    vec <- c(NA, NA, NA, 1.2, 1.3, 1.42, 1.46, 1.49, 1.498, 1.5, 1.6, 1.66, NA)
+    result <- force_sorted(vec)
+    expect_equal(vec, result)
+})