From 3a64b8760765a93d3914cc2be8531b650123b660 Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Tue, 7 Nov 2017 10:43:19 +0100
Subject: [PATCH 01/13] Adding weighted average smoothing function

---
 R/smoothIntensity-methods.R    |  6 ++++++
 R/smoothingFilters-functions.R | 19 +++++++++++++++++++
 man/smoothIntensity-methods.Rd | 11 ++++++-----
 3 files changed, 31 insertions(+), 5 deletions(-)

diff --git a/R/smoothIntensity-methods.R b/R/smoothIntensity-methods.R
index 2721ecc..60efc1d 100644
--- a/R/smoothIntensity-methods.R
+++ b/R/smoothIntensity-methods.R
@@ -23,6 +23,12 @@ setMethod(f="smoothIntensity",
                     halfWindowSize <- 2L
                   }
                   .movingAverage
+                },
+                "MovingWeightedAverage" = {
+                  if (missing(halfWindowSize)) {
+                    halfWindowSize <- 2L
+                  }
+                  .movingWeightedAverage
                 }
   )
 
diff --git a/R/smoothingFilters-functions.R b/R/smoothingFilters-functions.R
index c8c556c..6ddce79 100644
--- a/R/smoothingFilters-functions.R
+++ b/R/smoothingFilters-functions.R
@@ -1,3 +1,22 @@
+## .movingWeightedAverage
+## runs a weighted 2-side moving average where 
+## the weight is calculated as:
+## w=1/(2**i)   where i is the distance from the center of the window
+##
+## params:
+##  y: double, intensity values
+##  halfWindowSize integer, half window size.
+##
+## returns:
+##  double
+##
+.movingWeightedAverage<-function(y, halfWindowSize=2L) {
+  windowSize <- 2L * halfWindowSize + 1L
+  myweigths<-1/2**abs(-halfWindowSize:halfWindowSize)
+  myweigths<-myweigths/sum(myweigths)
+  .filter(y, hws=halfWindowSize,
+          coef=matrix(myweigths, nrow=windowSize, ncol=windowSize))
+}
 
 ## .movingAverage
 ##  runs a simple 2-side moving average.
diff --git a/man/smoothIntensity-methods.Rd b/man/smoothIntensity-methods.Rd
index bdeb3c7..54a7af3 100644
--- a/man/smoothIntensity-methods.Rd
+++ b/man/smoothIntensity-methods.Rd
@@ -10,14 +10,14 @@ This method smoothes the intensity values of a
 }
 \usage{
 \S4method{smoothIntensity}{MassSpectrum}(object,
-  method=c("SavitzkyGolay", "MovingAverage"), halfWindowSize,
+  method=c("SavitzkyGolay", "MovingAverage","MovingWeightedAverage"), halfWindowSize,
   \dots)
 }
 \arguments{
   \item{object}{\code{\linkS4class{AbstractMassObject}} object or a
     \code{list} of \code{\linkS4class{AbstractMassObject}} objects.}
   \item{method}{used smoothing method, one of \code{"SavitzkyGolay"} or
-    \code{"MovingAverage"}.}
+    \code{"MovingAverage"} or \code{"MovingWeightedAverage"}.}
   \item{halfWindowSize}{half window size. The resulting
     window reaches from \code{mass[currentIndex-halfWindowSize]} to
     \code{mass[currentIndex+halfWindowSize]} (window size is
@@ -26,15 +26,16 @@ This method smoothes the intensity values of a
     selected \code{method}.}
   \item{\dots}{arguments to be passed to \code{method}. \code{SavitzkyGolay} has
     an additional \code{polynomialOrder} argument (default: \code{3}) to control
-    the order of the filter. Unused for \code{MovingAverage}}
+    the order of the filter. Unused for \code{MovingAverage} and \code{MovingWeightedAverage}}
 }
 \details{
   \code{halfWindowSize}: Depends on the selected \code{method}.
   For the \code{SavitzkyGolay} the \code{halfWindowSize} should be smaller than
   \emph{FWHM} of the peaks (full width at half maximum; please find details in
   Bromba and Ziegler 1981).
-  In general the \code{halfWindowSize} for the \code{MovingAverage} has to be
-  much smaller than for \code{SavitzkyGolay} to conserve the peak shape.
+  In general the \code{halfWindowSize} for the \code{MovingAverage} and the
+  \code{MovingWeightedAverage} has to be   much smaller than for
+  \code{SavitzkyGolay} to conserve the peak shape.
 }
 \author{
 Sebastian Gibb \email{mail@sebastiangibb.de}

From 0f619da90fb56c68988589d4eaa38229e44569bc Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Tue, 7 Nov 2017 10:48:24 +0100
Subject: [PATCH 02/13] Adding more explanation to the man pages for the
 weighted average smoothing

---
 man/smoothIntensity-methods.Rd | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/man/smoothIntensity-methods.Rd b/man/smoothIntensity-methods.Rd
index 54a7af3..6bc14d1 100644
--- a/man/smoothIntensity-methods.Rd
+++ b/man/smoothIntensity-methods.Rd
@@ -26,7 +26,8 @@ This method smoothes the intensity values of a
     selected \code{method}.}
   \item{\dots}{arguments to be passed to \code{method}. \code{SavitzkyGolay} has
     an additional \code{polynomialOrder} argument (default: \code{3}) to control
-    the order of the filter. Unused for \code{MovingAverage} and \code{MovingWeightedAverage}}
+    the order of the filter. Unused for \code{MovingAverage} and 
+    \code{MovingWeightedAverage}}.
 }
 \details{
   \code{halfWindowSize}: Depends on the selected \code{method}.
@@ -36,6 +37,10 @@ This method smoothes the intensity values of a
   In general the \code{halfWindowSize} for the \code{MovingAverage} and the
   \code{MovingWeightedAverage} has to be   much smaller than for
   \code{SavitzkyGolay} to conserve the peak shape.
+  \code{MovingWeightedAverage} uses a simple weight function \code{1/2**i} where 
+  i is the distance from the center of the window, calculated as 
+  \code{1/2**abs(-halfWindowSize:halfWindowSize)} in R and normalized to the 
+  total sum of the weights.
 }
 \author{
 Sebastian Gibb \email{mail@sebastiangibb.de}

From 078c7af368a4cac4319bdb8c0ddaedeadc5d9a65 Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Tue, 7 Nov 2017 10:54:38 +0100
Subject: [PATCH 03/13] Minor edits to the man pages

---
 man/smoothIntensity-methods.Rd | 1 +
 1 file changed, 1 insertion(+)

diff --git a/man/smoothIntensity-methods.Rd b/man/smoothIntensity-methods.Rd
index 6bc14d1..deefc7e 100644
--- a/man/smoothIntensity-methods.Rd
+++ b/man/smoothIntensity-methods.Rd
@@ -44,6 +44,7 @@ This method smoothes the intensity values of a
 }
 \author{
 Sebastian Gibb \email{mail@sebastiangibb.de}
+Sigurður Smárason (WeightedAverage smoothing)
 }
 \references{
 A. Savitzky and M. J. Golay. 1964.

From 6e4d408d786754a75c9e46642f9be6d0d302ee8c Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Tue, 7 Nov 2017 11:48:34 +0100
Subject: [PATCH 04/13] Fixed allowed methods for smoothing

---
 R/smoothIntensity-methods.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/smoothIntensity-methods.R b/R/smoothIntensity-methods.R
index 60efc1d..24a538a 100644
--- a/R/smoothIntensity-methods.R
+++ b/R/smoothIntensity-methods.R
@@ -2,7 +2,7 @@
 setMethod(f="smoothIntensity",
           signature=signature(object="MassSpectrum"),
           definition=function(object,
-                              method=c("SavitzkyGolay", "MovingAverage"),
+                              method=c("SavitzkyGolay", "MovingAverage","MovingWeightedAverage"),
                               halfWindowSize, ...) {
   ## empty spectrum?
   if (.isEmptyWarning(object)) {

From 7626ea05f46b7b14364fa6d6f04c9d535a529929 Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Tue, 7 Nov 2017 12:09:28 +0100
Subject: [PATCH 05/13] Fixing non-ascii charcters in the .Rd file

---
 man/smoothIntensity-methods.Rd | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/man/smoothIntensity-methods.Rd b/man/smoothIntensity-methods.Rd
index deefc7e..a00e6c3 100644
--- a/man/smoothIntensity-methods.Rd
+++ b/man/smoothIntensity-methods.Rd
@@ -10,7 +10,8 @@ This method smoothes the intensity values of a
 }
 \usage{
 \S4method{smoothIntensity}{MassSpectrum}(object,
-  method=c("SavitzkyGolay", "MovingAverage","MovingWeightedAverage"), halfWindowSize,
+  method=c("SavitzkyGolay", "MovingAverage","MovingWeightedAverage"),
+  halfWindowSize,
   \dots)
 }
 \arguments{
@@ -37,14 +38,14 @@ This method smoothes the intensity values of a
   In general the \code{halfWindowSize} for the \code{MovingAverage} and the
   \code{MovingWeightedAverage} has to be   much smaller than for
   \code{SavitzkyGolay} to conserve the peak shape.
-  \code{MovingWeightedAverage} uses a simple weight function \code{1/2**i} where 
-  i is the distance from the center of the window, calculated as 
+  \code{MovingWeightedAverage} uses a simple weight function \code{1/2**i}
+  where i is the distance from the center of the window, calculated as 
   \code{1/2**abs(-halfWindowSize:halfWindowSize)} in R and normalized to the 
   total sum of the weights.
 }
 \author{
 Sebastian Gibb \email{mail@sebastiangibb.de}
-Sigurður Smárason (WeightedAverage smoothing)
+Sigurdur Smarason (WeightedAverage smoothing)
 }
 \references{
 A. Savitzky and M. J. Golay. 1964.
@@ -71,6 +72,9 @@ data("fiedler2009subset", package="MALDIquant")
 s <- smoothIntensity(fiedler2009subset, method="MovingAverage",
                      halfWindowSize=2)
 ## or
+s <- smoothIntensity(fiedler2009subset, method="MovingWeightedAverage",
+                     halfWindowSize=2)
+## or
 s <- smoothIntensity(fiedler2009subset, method="SavitzkyGolay",
                      halfWindowSize=10)
 }

From 7958942b519b5516760f75319736604da8a98d9d Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Tue, 7 Nov 2017 12:44:22 +0100
Subject: [PATCH 06/13] Added unit tests for weighted moving average smoothing

---
 tests/testthat/test_smoothIntensity-methods.R    | 5 +++++
 tests/testthat/test_smoothingFilters-functions.R | 8 ++++++++
 2 files changed, 13 insertions(+)

diff --git a/tests/testthat/test_smoothIntensity-methods.R b/tests/testthat/test_smoothIntensity-methods.R
index 084fc4e..464da50 100644
--- a/tests/testthat/test_smoothIntensity-methods.R
+++ b/tests/testthat/test_smoothIntensity-methods.R
@@ -20,6 +20,11 @@ test_that("smoothIntensity", {
   expect_equal(intensity(smoothIntensity(s, method="MovingAverage",
                                          halfWindowSize=2)),
                MALDIquant:::.movingAverage(i, halfWindowSize=2))
+  expect_equal(length(smoothIntensity(s, method="MovingWeightedAverage",
+                                      halfWindowSize=2)), 40)
+  expect_equal(intensity(smoothIntensity(s, method="MovingWeightedAverage",
+                                         halfWindowSize=2)),
+               MALDIquant:::MovingWeightedAverage(i, halfWindowSize=2))
 })
 
 test_that("smoothIntensity works with list of MassSpectrum objects", {
diff --git a/tests/testthat/test_smoothingFilters-functions.R b/tests/testthat/test_smoothingFilters-functions.R
index 1fd9afb..1961f60 100644
--- a/tests/testthat/test_smoothingFilters-functions.R
+++ b/tests/testthat/test_smoothingFilters-functions.R
@@ -8,6 +8,14 @@ test_that(".movingAverage", {
   expect_equal(MALDIquant:::.movingAverage(1:10, 3), values)
 })
 
+test_that(".movingWegithedAverage", {
+  values <- c(rep(3, 3), 4:7, rep(8, 3))
+  expect_equal(MALDIquant:::.movingWeightedAverage(1:10, halfWindowSize=2), values)
+
+  values <- c(rep(4, 4), 5:6, rep(7, 4))
+  expect_equal(MALDIquant:::.movingWeightedAverage(1:10, 3), values)
+})
+
 test_that(".movingAverage throws errors", {
   expect_error(MALDIquant:::.movingAverage(1:10, halfWindowSize=0),
                "too small")

From fc5cedccb45bfe49c43998fd43aef3ac310d132d Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Tue, 7 Nov 2017 14:14:59 +0100
Subject: [PATCH 07/13] Fixed weighted average smoothing function and related
 unit tests

---
 R/smoothingFilters-functions.R                   | 2 +-
 tests/testthat/test_smoothIntensity-methods.R    | 2 +-
 tests/testthat/test_smoothingFilters-functions.R | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/smoothingFilters-functions.R b/R/smoothingFilters-functions.R
index 6ddce79..7305b32 100644
--- a/R/smoothingFilters-functions.R
+++ b/R/smoothingFilters-functions.R
@@ -15,7 +15,7 @@
   myweigths<-1/2**abs(-halfWindowSize:halfWindowSize)
   myweigths<-myweigths/sum(myweigths)
   .filter(y, hws=halfWindowSize,
-          coef=matrix(myweigths, nrow=windowSize, ncol=windowSize))
+          coef=matrix(myweigths, nrow=windowSize, ncol=windowSize, byrow = TRUE))
 }
 
 ## .movingAverage
diff --git a/tests/testthat/test_smoothIntensity-methods.R b/tests/testthat/test_smoothIntensity-methods.R
index 464da50..bfc46a5 100644
--- a/tests/testthat/test_smoothIntensity-methods.R
+++ b/tests/testthat/test_smoothIntensity-methods.R
@@ -24,7 +24,7 @@ test_that("smoothIntensity", {
                                       halfWindowSize=2)), 40)
   expect_equal(intensity(smoothIntensity(s, method="MovingWeightedAverage",
                                          halfWindowSize=2)),
-               MALDIquant:::MovingWeightedAverage(i, halfWindowSize=2))
+               MALDIquant:::.movingWeightedAverage(i, halfWindowSize=2))
 })
 
 test_that("smoothIntensity works with list of MassSpectrum objects", {
diff --git a/tests/testthat/test_smoothingFilters-functions.R b/tests/testthat/test_smoothingFilters-functions.R
index 1961f60..df98dbd 100644
--- a/tests/testthat/test_smoothingFilters-functions.R
+++ b/tests/testthat/test_smoothingFilters-functions.R
@@ -8,8 +8,8 @@ test_that(".movingAverage", {
   expect_equal(MALDIquant:::.movingAverage(1:10, 3), values)
 })
 
-test_that(".movingWegithedAverage", {
-  values <- c(rep(3, 3), 4:7, rep(8, 3))
+test_that(".movingWeightedAverage", {
+  values <- c(rep(3,3),4:7,rep(8,3))
   expect_equal(MALDIquant:::.movingWeightedAverage(1:10, halfWindowSize=2), values)
 
   values <- c(rep(4, 4), 5:6, rep(7, 4))

From c6418e03527f3910602d7644f3ecb9d2f283fda5 Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Tue, 7 Nov 2017 14:25:07 +0100
Subject: [PATCH 08/13] Added one more test to see ensure that missing
 halfWindowSize results in 2L being used

---
 tests/testthat/test_smoothIntensity-methods.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/testthat/test_smoothIntensity-methods.R b/tests/testthat/test_smoothIntensity-methods.R
index bfc46a5..b29a777 100644
--- a/tests/testthat/test_smoothIntensity-methods.R
+++ b/tests/testthat/test_smoothIntensity-methods.R
@@ -25,6 +25,9 @@ test_that("smoothIntensity", {
   expect_equal(intensity(smoothIntensity(s, method="MovingWeightedAverage",
                                          halfWindowSize=2)),
                MALDIquant:::.movingWeightedAverage(i, halfWindowSize=2))
+  expect_equal(intensity(smoothIntensity(s, method="MovingWeightedAverage",
+                                         halfWindowSize=2)),
+               intensity(smoothIntensity(s, method="MovingWeightedAverage")))
 })
 
 test_that("smoothIntensity works with list of MassSpectrum objects", {

From 74b2afd9e14295f7e46b3fc502df06075f51f3f3 Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Wed, 8 Nov 2017 12:11:42 +0100
Subject: [PATCH 09/13] Changed MovingAverage to incorporate weigthed
 MovingAverage as well

---
 R/smoothIntensity-methods.R                   |  8 +----
 R/smoothingFilters-functions.R                | 34 ++++++-------------
 man/smoothIntensity-methods.Rd                | 25 +++++++-------
 tests/testthat/test_smoothIntensity-methods.R | 20 ++++++-----
 .../test_smoothingFilters-functions.R         | 10 ++----
 5 files changed, 38 insertions(+), 59 deletions(-)

diff --git a/R/smoothIntensity-methods.R b/R/smoothIntensity-methods.R
index 24a538a..2721ecc 100644
--- a/R/smoothIntensity-methods.R
+++ b/R/smoothIntensity-methods.R
@@ -2,7 +2,7 @@
 setMethod(f="smoothIntensity",
           signature=signature(object="MassSpectrum"),
           definition=function(object,
-                              method=c("SavitzkyGolay", "MovingAverage","MovingWeightedAverage"),
+                              method=c("SavitzkyGolay", "MovingAverage"),
                               halfWindowSize, ...) {
   ## empty spectrum?
   if (.isEmptyWarning(object)) {
@@ -23,12 +23,6 @@ setMethod(f="smoothIntensity",
                     halfWindowSize <- 2L
                   }
                   .movingAverage
-                },
-                "MovingWeightedAverage" = {
-                  if (missing(halfWindowSize)) {
-                    halfWindowSize <- 2L
-                  }
-                  .movingWeightedAverage
                 }
   )
 
diff --git a/R/smoothingFilters-functions.R b/R/smoothingFilters-functions.R
index 7305b32..6f27895 100644
--- a/R/smoothingFilters-functions.R
+++ b/R/smoothingFilters-functions.R
@@ -1,40 +1,26 @@
-## .movingWeightedAverage
-## runs a weighted 2-side moving average where 
-## the weight is calculated as:
-## w=1/(2**i)   where i is the distance from the center of the window
-##
-## params:
-##  y: double, intensity values
-##  halfWindowSize integer, half window size.
-##
-## returns:
-##  double
-##
-.movingWeightedAverage<-function(y, halfWindowSize=2L) {
-  windowSize <- 2L * halfWindowSize + 1L
-  myweigths<-1/2**abs(-halfWindowSize:halfWindowSize)
-  myweigths<-myweigths/sum(myweigths)
-  .filter(y, hws=halfWindowSize,
-          coef=matrix(myweigths, nrow=windowSize, ncol=windowSize, byrow = TRUE))
-}
-
 ## .movingAverage
 ##  runs a simple 2-side moving average.
 ##
 ## params:
 ##  y: double, intensity values
-##  halfWindowSize integer, half window size.
-##
+##  halfWindowSize integer, half window size
+##  weighted boolean, if TRUE then applies weighted average, otherwise unweighted average.
 ## returns:
 ##  double
 ##
-.movingAverage <- function(y, halfWindowSize=2L) {
+.movingAverage <- function(y, halfWindowSize=2L, weighted=FALSE) {
   .stopIfNotIsValidHalfWindowSize(halfWindowSize, n=length(y))
   windowSize <- 2L * halfWindowSize + 1L
+  if (weighted) {
+    weights <- 1 / 2^abs(-halfWindowSize:halfWindowSize)
+  } else {
+    weights <- rep.int(1L, windowSize)
+  }
   .filter(y, hws=halfWindowSize,
-          coef=matrix(1L / windowSize, nrow=windowSize, ncol=windowSize))
+          coef=matrix(weights/sum(weights), nrow=windowSize, ncol=windowSize, byrow=TRUE))
 }
 
+
 ## .savitzkyGolay
 ##  runs a savitzky golay filter
 ##
diff --git a/man/smoothIntensity-methods.Rd b/man/smoothIntensity-methods.Rd
index a00e6c3..171988a 100644
--- a/man/smoothIntensity-methods.Rd
+++ b/man/smoothIntensity-methods.Rd
@@ -10,7 +10,7 @@ This method smoothes the intensity values of a
 }
 \usage{
 \S4method{smoothIntensity}{MassSpectrum}(object,
-  method=c("SavitzkyGolay", "MovingAverage","MovingWeightedAverage"),
+  method=c("SavitzkyGolay", "MovingAverage"),
   halfWindowSize,
   \dots)
 }
@@ -18,7 +18,7 @@ This method smoothes the intensity values of a
   \item{object}{\code{\linkS4class{AbstractMassObject}} object or a
     \code{list} of \code{\linkS4class{AbstractMassObject}} objects.}
   \item{method}{used smoothing method, one of \code{"SavitzkyGolay"} or
-    \code{"MovingAverage"} or \code{"MovingWeightedAverage"}.}
+    \code{"MovingAverage"}.}
   \item{halfWindowSize}{half window size. The resulting
     window reaches from \code{mass[currentIndex-halfWindowSize]} to
     \code{mass[currentIndex+halfWindowSize]} (window size is
@@ -27,21 +27,20 @@ This method smoothes the intensity values of a
     selected \code{method}.}
   \item{\dots}{arguments to be passed to \code{method}. \code{SavitzkyGolay} has
     an additional \code{polynomialOrder} argument (default: \code{3}) to control
-    the order of the filter. Unused for \code{MovingAverage} and 
-    \code{MovingWeightedAverage}}.
+    the order of the filter. Unused for \code{MovingAverage}. 
+    \code{MovingAverage} has an additional \code{weighted} argument (default: 
+    \code{FALSE}) to indicate if the average should be equal weight (default) or
+    if it should have weights depending on the distance from the center as 
+    calculated as \code{1/2^abs(-halfWindowSize:halfWindowSize)} with the sum 
+    of all weigths normalized to 1.
 }
 \details{
   \code{halfWindowSize}: Depends on the selected \code{method}.
   For the \code{SavitzkyGolay} the \code{halfWindowSize} should be smaller than
   \emph{FWHM} of the peaks (full width at half maximum; please find details in
   Bromba and Ziegler 1981).
-  In general the \code{halfWindowSize} for the \code{MovingAverage} and the
-  \code{MovingWeightedAverage} has to be   much smaller than for
-  \code{SavitzkyGolay} to conserve the peak shape.
-  \code{MovingWeightedAverage} uses a simple weight function \code{1/2**i}
-  where i is the distance from the center of the window, calculated as 
-  \code{1/2**abs(-halfWindowSize:halfWindowSize)} in R and normalized to the 
-  total sum of the weights.
+  In general the \code{halfWindowSize} for the \code{MovingAverage} has to be
+  much smaller than for \code{SavitzkyGolay} to conserve the peak shape.
 }
 \author{
 Sebastian Gibb \email{mail@sebastiangibb.de}
@@ -72,8 +71,8 @@ data("fiedler2009subset", package="MALDIquant")
 s <- smoothIntensity(fiedler2009subset, method="MovingAverage",
                      halfWindowSize=2)
 ## or
-s <- smoothIntensity(fiedler2009subset, method="MovingWeightedAverage",
-                     halfWindowSize=2)
+s <- smoothIntensity(fiedler2009subset, method="MovingAverage",
+                     halfWindowSize=2, weights=TRUE)
 ## or
 s <- smoothIntensity(fiedler2009subset, method="SavitzkyGolay",
                      halfWindowSize=10)
diff --git a/tests/testthat/test_smoothIntensity-methods.R b/tests/testthat/test_smoothIntensity-methods.R
index b29a777..a3741c8 100644
--- a/tests/testthat/test_smoothIntensity-methods.R
+++ b/tests/testthat/test_smoothIntensity-methods.R
@@ -20,14 +20,18 @@ test_that("smoothIntensity", {
   expect_equal(intensity(smoothIntensity(s, method="MovingAverage",
                                          halfWindowSize=2)),
                MALDIquant:::.movingAverage(i, halfWindowSize=2))
-  expect_equal(length(smoothIntensity(s, method="MovingWeightedAverage",
-                                      halfWindowSize=2)), 40)
-  expect_equal(intensity(smoothIntensity(s, method="MovingWeightedAverage",
-                                         halfWindowSize=2)),
-               MALDIquant:::.movingWeightedAverage(i, halfWindowSize=2))
-  expect_equal(intensity(smoothIntensity(s, method="MovingWeightedAverage",
-                                         halfWindowSize=2)),
-               intensity(smoothIntensity(s, method="MovingWeightedAverage")))
+  expect_equal(length(smoothIntensity(s, method="MovingAverage",
+                                      halfWindowSize=2, weighted=TRUE)), 40)
+  expect_equal(intensity(smoothIntensity(s, method="MovingAverage",
+                                         halfWindowSize=2, weighted=TRUE)),
+               MALDIquant:::.movingAverage(i, halfWindowSize=2, weighted=TRUE))
+  expect_equal(intensity(smoothIntensity(s, method="MovingAverage",
+                                         halfWindowSize=2, weighted=TRUE)),
+               intensity(smoothIntensity(s, method="MovingAverage", 
+                                          weighted=TRUE)))
+  expect_equal(intensity(smoothIntensity(s, method="MovingAverage", 
+                                          halfWindowSize=2)),
+               intensity(smoothIntensity(s, method="MovingAverage")))
 })
 
 test_that("smoothIntensity works with list of MassSpectrum objects", {
diff --git a/tests/testthat/test_smoothingFilters-functions.R b/tests/testthat/test_smoothingFilters-functions.R
index df98dbd..260f661 100644
--- a/tests/testthat/test_smoothingFilters-functions.R
+++ b/tests/testthat/test_smoothingFilters-functions.R
@@ -3,18 +3,14 @@ context("smoothingFilters")
 test_that(".movingAverage", {
   values <- c(rep(3, 3), 4:7, rep(8, 3))
   expect_equal(MALDIquant:::.movingAverage(1:10, halfWindowSize=2), values)
+  expect_equal(MALDIquant:::.movingAverage(1:10, halfWindowSize=2, 
+    weighted=TRUE), values)
 
   values <- c(rep(4, 4), 5:6, rep(7, 4))
   expect_equal(MALDIquant:::.movingAverage(1:10, 3), values)
+  expect_equal(MALDIquant:::.movingAverage(1:10, 3, weighted=TRUE), values)
 })
 
-test_that(".movingWeightedAverage", {
-  values <- c(rep(3,3),4:7,rep(8,3))
-  expect_equal(MALDIquant:::.movingWeightedAverage(1:10, halfWindowSize=2), values)
-
-  values <- c(rep(4, 4), 5:6, rep(7, 4))
-  expect_equal(MALDIquant:::.movingWeightedAverage(1:10, 3), values)
-})
 
 test_that(".movingAverage throws errors", {
   expect_error(MALDIquant:::.movingAverage(1:10, halfWindowSize=0),

From 32b7c52661dbf25054ba49bea13a3a2a4f8fb220 Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Wed, 8 Nov 2017 12:29:41 +0100
Subject: [PATCH 10/13] Fixing a typo

---
 man/smoothIntensity-methods.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/smoothIntensity-methods.Rd b/man/smoothIntensity-methods.Rd
index 171988a..ad6dd60 100644
--- a/man/smoothIntensity-methods.Rd
+++ b/man/smoothIntensity-methods.Rd
@@ -32,7 +32,7 @@ This method smoothes the intensity values of a
     \code{FALSE}) to indicate if the average should be equal weight (default) or
     if it should have weights depending on the distance from the center as 
     calculated as \code{1/2^abs(-halfWindowSize:halfWindowSize)} with the sum 
-    of all weigths normalized to 1.
+    of all weigths normalized to 1.}
 }
 \details{
   \code{halfWindowSize}: Depends on the selected \code{method}.

From 42fbd58641a0fa8caf8efa3eaad46467d28d3003 Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Wed, 8 Nov 2017 12:34:43 +0100
Subject: [PATCH 11/13] Another typo

---
 man/smoothIntensity-methods.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/smoothIntensity-methods.Rd b/man/smoothIntensity-methods.Rd
index ad6dd60..df8d958 100644
--- a/man/smoothIntensity-methods.Rd
+++ b/man/smoothIntensity-methods.Rd
@@ -72,7 +72,7 @@ s <- smoothIntensity(fiedler2009subset, method="MovingAverage",
                      halfWindowSize=2)
 ## or
 s <- smoothIntensity(fiedler2009subset, method="MovingAverage",
-                     halfWindowSize=2, weights=TRUE)
+                     halfWindowSize=2, weighted=TRUE)
 ## or
 s <- smoothIntensity(fiedler2009subset, method="SavitzkyGolay",
                      halfWindowSize=10)

From 8cf324dfd604c8e2266796a893ed2388ee5481d2 Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Thu, 9 Nov 2017 09:51:19 +0100
Subject: [PATCH 12/13] added tests where weighted smoothing and unweigted
 smoothing differ code tyding in the function itself and in the man page

---
 R/smoothingFilters-functions.R                   |  2 +-
 man/smoothIntensity-methods.Rd                   |  2 +-
 tests/testthat/test_smoothingFilters-functions.R | 10 +++++++++-
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/R/smoothingFilters-functions.R b/R/smoothingFilters-functions.R
index 6f27895..2e929a8 100644
--- a/R/smoothingFilters-functions.R
+++ b/R/smoothingFilters-functions.R
@@ -17,7 +17,7 @@
     weights <- rep.int(1L, windowSize)
   }
   .filter(y, hws=halfWindowSize,
-          coef=matrix(weights/sum(weights), nrow=windowSize, ncol=windowSize, byrow=TRUE))
+          coef=matrix(weights / sum(weights), nrow=windowSize, ncol=windowSize, byrow=TRUE))
 }
 
 
diff --git a/man/smoothIntensity-methods.Rd b/man/smoothIntensity-methods.Rd
index df8d958..2951652 100644
--- a/man/smoothIntensity-methods.Rd
+++ b/man/smoothIntensity-methods.Rd
@@ -27,7 +27,7 @@ This method smoothes the intensity values of a
     selected \code{method}.}
   \item{\dots}{arguments to be passed to \code{method}. \code{SavitzkyGolay} has
     an additional \code{polynomialOrder} argument (default: \code{3}) to control
-    the order of the filter. Unused for \code{MovingAverage}. 
+    the order of the filter.  
     \code{MovingAverage} has an additional \code{weighted} argument (default: 
     \code{FALSE}) to indicate if the average should be equal weight (default) or
     if it should have weights depending on the distance from the center as 
diff --git a/tests/testthat/test_smoothingFilters-functions.R b/tests/testthat/test_smoothingFilters-functions.R
index 260f661..4d31989 100644
--- a/tests/testthat/test_smoothingFilters-functions.R
+++ b/tests/testthat/test_smoothingFilters-functions.R
@@ -4,11 +4,19 @@ test_that(".movingAverage", {
   values <- c(rep(3, 3), 4:7, rep(8, 3))
   expect_equal(MALDIquant:::.movingAverage(1:10, halfWindowSize=2), values)
   expect_equal(MALDIquant:::.movingAverage(1:10, halfWindowSize=2, 
-    weighted=TRUE), values)
+                weighted=TRUE), values)
 
   values <- c(rep(4, 4), 5:6, rep(7, 4))
   expect_equal(MALDIquant:::.movingAverage(1:10, 3), values)
   expect_equal(MALDIquant:::.movingAverage(1:10, 3, weighted=TRUE), values)
+
+  signal <- c(rep(1, 4), 6, 20, 6, rep(1, 4))
+  resAve <- c(2.0, 2.0, 2.0, 5.8, 6.8, 6.8, 6.8, 5.8, 2.0, 2.0, 2.0)
+  reswAve <- c(1.5, 1.5, 1.5, 3.9, 7.3,10.6, 7.3, 3.9, 1.5, 1.5, 1.5)
+  expect_equal(MALDIquant:::.movingAverage(signal, halfWindowSize=2, 
+                weighted=FALSE),resAve)
+  expect_equal(MALDIquant:::.movingAverage(signal, halfWindowSize=2, 
+                weighted=TRUE),reswAve)
 })
 
 

From 063c32eabf15aec6256b292f4a65b9d21153d484 Mon Sep 17 00:00:00 2001
From: siggismara <runningman69@gmail.com>
Date: Thu, 9 Nov 2017 09:55:54 +0100
Subject: [PATCH 13/13] updated the news with the weighted moving average

---
 NEWS | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/NEWS b/NEWS
index 478fece..26c0d06 100644
--- a/NEWS
+++ b/NEWS
@@ -1,5 +1,11 @@
 RELEASE HISTORY OF THE "MALDIquant" PACKAGE
 ===========================================
+CHANGES IN MALDIquant VERSION 1.17:
+--------------------------------------------------
+IMPROVEMENTS
+
+* Added weighted moving average as an option in moving average smoothing of spectra
+
 
 CHANGES IN MALDIquant VERSION 1.16.4 [2017-08-27]:
 --------------------------------------------------