remove .topHatR

sgibb · Apr 11, 2014 · 413f9d1 · 413f9d1
1 parent 35a02d3
commit 413f9d1
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Showing 3 changed files with 2 additions and 19 deletions.
diff --git a/NEWS b/NEWS
@@ -73,6 +73,8 @@ INTERNAL CHANGES
   in 0.2.
 * `.lowerConvexHullR`: removed. It was replaced by a C version of
   `.estimateBaselineConvexHull` in 0.3.
+* `.topHatR`: removed. It was never used and replaced by a C version of
+  `.estimateBaselineTopHat` in 1.6.
 
 
 CHANGES IN MALDIquant VERSION 1.9 [2014-01-14]:

diff --git a/R/estimateBaseline-functions.R b/R/estimateBaseline-functions.R
@@ -109,19 +109,3 @@
   return(cbind(x, y))
 }
 
-## R only: obsolete because too slow
-.topHatR <- function(x, y, halfWindowSize=100L) {
-
-  .stopIfNotIsValidHalfWindowSize(halfWindowSize=halfWindowSize, n=length(x))
-
-  windowSize <- 2L*halfWindowSize+1L
-
-  windows <- embed(c(rep(y[1L], halfWindowSize), y,
-                     rep(tail(y, 1L), halfWindowSize)), windowSize)
-  e <- apply(windows, 1L, min)
-  windows <- embed(c(rep(e[1L], halfWindowSize), e,
-                     rep(tail(e, 1L), halfWindowSize)), windowSize)
-  y <- apply(windows, 1L, max)
-  return(cbind(x, y))
-}
-
diff --git a/tests/testthat/test_estimateBaseline-methods.R b/tests/testthat/test_estimateBaseline-methods.R
@@ -75,11 +75,8 @@ test_that("estimateBaselineTopHat", {
   m[, 2] <- c(rep(8, 3), 7:1, rep(6, 5), 5:1)
   m1 <- m
   m1[, 2] <- c(rep(9, 2), 8:1, rep(8, 3), 7:1)
-  ## C implementation
   expect_identical(MALDIquant:::.estimateBaselineTopHat(1:20, i, 1), m1)
   expect_identical(MALDIquant:::.estimateBaselineTopHat(1:20, i, 2), m)
-  ## obsolete (slow) R implementation
-  expect_equal(MALDIquant:::.topHatR(1:20, i, 2), m)
 
   ## user method
   colnames(m) <- c("mass", "intensity")