fix: fix entropy unit tests and add general method

DESCRIPTION

@@ -72,7 +72,7 @@ VignetteBuilder: knitr
 BugReports: https://github.com/RforMassSpectrometry/Spectra/issues
 URL: https://github.com/RforMassSpectrometry/Spectra
 biocViews: Infrastructure, Proteomics, MassSpectrometry, Metabolomics
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown=TRUE)
 Collate:
     'hidden_aliases.R'

NAMESPACE

@@ -78,6 +78,7 @@ exportMethods(containsNeutralLoss)
 exportMethods(dataOrigin)
 exportMethods(dataStorage)
 exportMethods(dropNaSpectraVariables)
+exportMethods(entropy)
 exportMethods(export)
 exportMethods(filterAcquisitionNum)
 exportMethods(filterDataOrigin)
@@ -153,12 +154,14 @@ importFrom(MsCoreUtils,coefMA)
 importFrom(MsCoreUtils,coefSG)
 importFrom(MsCoreUtils,coefWMA)
 importFrom(MsCoreUtils,common)
+importFrom(MsCoreUtils,entropy)
 importFrom(MsCoreUtils,group)
 importFrom(MsCoreUtils,i2index)
 importFrom(MsCoreUtils,join)
 importFrom(MsCoreUtils,join_gnps)
 importFrom(MsCoreUtils,localMaxima)
 importFrom(MsCoreUtils,ndotproduct)
+importFrom(MsCoreUtils,nentropy)
 importFrom(MsCoreUtils,noise)
 importFrom(MsCoreUtils,ppm)
 importFrom(MsCoreUtils,rbindFill)

R/Spectra.R

@@ -659,9 +659,10 @@ NULL
 #'   documentation of [isotopologues()] for more information. The approach
 #'   and code to define the parameters for isotope prediction is described
 #'   [here](https://github.com/EuracBiomedicalResearch/isotopologues).
-#'   
-#' - `entropy`: calculates the entropy of each spectra based on the metrics suggested by 
-#'    Li et al. (https://doi.org/10.1038/s41592-021-01331-z).
+#'
+#' - `entropy`: calculates the entropy of each spectra based on the metrics
+#'    suggested by Li et al. (https://doi.org/10.1038/s41592-021-01331-z).
+#'   See also [nentropy()] in the *MsCoreUtils* package for details.
 #'
 #' - `estimatePrecursorIntensity`: defines the precursor intensities for MS2
 #'   spectra using the intensity of the matching MS1 peak from the
@@ -928,6 +929,9 @@ NULL
 #' @param neutralLoss for `containsNeutralLoss`: `numeric(1)` defining the value
 #'     which should be subtracted from the spectrum's precursor m/z.
 #'
+#' @param normalized for `entropy`: `logical(1)` whether the normalized entropy
+#'     should be calculated (default). See also [nentropy()] for details.
+#'
 #' @param object For `Spectra`: either a `DataFrame` or `missing`. See section
 #'     on creation of `Spectra` objects for details. For all other methods a
 #'     `Spectra` object.
@@ -2647,12 +2651,19 @@ setMethod("combinePeaks", "Spectra", function(object, tolerance = 0, ppm = 20,
 #' @rdname Spectra
 #'
 #' @importFrom MsCoreUtils entropy nentropy
+#'
+#' @export
 setMethod("entropy", "Spectra", function(object, normalized = TRUE) {
-  if (normalized) entropy_fun <- nentropy
-  else entropy_fun <- entropy
-  unlist(.peaksapply(
-    object, FUN = function(pks, ...) entropy_fun(pks[, "intensity"])), 
-    use.names = FALSE
-  )
-})
-
+    if (length(object)) {
+    if (normalized) entropy_fun <- nentropy
+    else entropy_fun <- entropy
+    unlist(.peaksapply(
+        object, FUN = function(pks, ...) entropy_fun(pks[, "intensity"])),
+        use.names = FALSE
+        )
+    } else numeric()
+})
+#' @rdname Spectra
+setMethod("entropy", "ANY", function(object, ...) {
+    MsCoreUtils::entropy(object)
+})

tests/testthat/test_Spectra.R

@@ -1788,16 +1788,15 @@ test_that("entropy,Spectra works", {
   sps <- Spectra()
   res <- entropy(sps)
   expect_identical(res, numeric())
-  
+
   df <- DataFrame(msLevel = c(1L, 2L), centroided = TRUE)
-  df$intensity <- list(c(5, 9, 3), c(9, 8, 2))
   df$mz <- list(1:3, 1:3)
+  df$intensity <- list(c(5, 9, 3), c(9, 8, 2))
   sps <- Spectra(df)
-
-  res <- entropy(sps)
-  expect_identical(res, c(17, 19))
-
-  sps <- replaceIntensitiesBelow(sps, threshold = 4)
-  res <- entropy(sps)
-  expect_identical(res, c(14, 17))
-})
+
+  res <- entropy(sps, normalized = TRUE)
+  expect_identical(res, vapply(df$intensity, MsCoreUtils::nentropy, numeric(1)))
+
+  res <- entropy(sps, normalized = FALSE)
+  expect_identical(res, vapply(df$intensity, MsCoreUtils::entropy, numeric(1)))
+})