From 10961870aa1fc54700af3999e44179b460c54c1b Mon Sep 17 00:00:00 2001
From: MarkoBarzic <markbarzic@gmail.com>
Date: Mon, 6 May 2019 22:17:52 +0200
Subject: [PATCH 1/7] issue #30- adding importFrom("stats","quantile") to
 NAMESPACE

---
 NAMESPACE | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NAMESPACE b/NAMESPACE
index d75f824..c1a7cea 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1 +1,2 @@
 exportPattern("^[[:alpha:]]+")
+importFrom("stats", "quantile")

From 9514ba40b4ce4cca8df5703b0c8c25f3298b3024 Mon Sep 17 00:00:00 2001
From: MarkoBarzic <markbarzic@gmail.com>
Date: Mon, 6 May 2019 22:27:25 +0200
Subject: [PATCH 2/7] issue #30- function argument documented, issue #31-
 detailed description of a function added

---
 R/meanimpute.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/meanimpute.R b/R/meanimpute.R
index cc7cf5e..f7f79e5 100644
--- a/R/meanimpute.R
+++ b/R/meanimpute.R
@@ -1,4 +1,5 @@
 #' Meanimputation
+#' @param x A vector
 #' @export
 meanimpute <- function(x) {
   x[is.na(x)] <- mean(x, na.rm = TRUE)

From cd2ebaac92bbafd09bcc53cbd353d5ce1db71e92 Mon Sep 17 00:00:00 2001
From: MarkoBarzic <markbarzic@gmail.com>
Date: Mon, 6 May 2019 22:28:53 +0200
Subject: [PATCH 3/7] issue #32- added function Log transform

---
 R/transform_log.R | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 R/transform_log.R

diff --git a/R/transform_log.R b/R/transform_log.R
new file mode 100644
index 0000000..c9045b9
--- /dev/null
+++ b/R/transform_log.R
@@ -0,0 +1,18 @@
+#' transform_log 
+#' Transform numerical values into their log values
+#' @param x A vector
+#' @return logarithm of x
+#' @examples
+#' transform_log(c(NA,0,-1,exp(2)))
+#'@export 
+transform_log<-function(x){
+  if(!is.numeric(x))stop("function is expecting only numeric values")
+  x_nan<-is.na(x)
+  x[x_nan]<-1
+  ifelse(x<0,"OK", warning("input vector contains negative values, turned into NA"))
+  y<-log(x[x>=0])
+  x[x>=0]<-y
+  x[x<0]<-NA
+  x[x_nan]<-NA
+  x
+}
\ No newline at end of file

From d258cdc6012921539be7da37f63715c7cd4b69a4 Mon Sep 17 00:00:00 2001
From: MarkoBarzic <markbarzic@gmail.com>
Date: Mon, 6 May 2019 22:48:39 +0200
Subject: [PATCH 4/7] issues #28-#31- corrected function, updated documentation

---
 R/windsorize.R | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/R/windsorize.R b/R/windsorize.R
index b4e15e6..85044f8 100644
--- a/R/windsorize.R
+++ b/R/windsorize.R
@@ -1,10 +1,23 @@
 #' Windsorize
 #'
-#' Do some windsorization.
+#'
+#' Transform all outliner data to
+#' (1-p)/2 percentile value for lower outliers and 
+#' (1+p)/2 for higher outliers.
+#' 
+#' @param x A vector.
+#' @param p A quantile.
+#' @return inuput vector x with trimmed outliers by (1-p) percentile.
+#' @examples 
+#' windsorize(rnorm(100,0,1))
 #' @export
 windsorize <- function(x, p = .90) {
-  q <- quantile(x, p)
-  x[x >= q] <- q
+  if(is.null(x))stop("vector is empty")
+  y<-x[!is.na(x)]
+  if(length(y)==0)stop("vector contains only NAs")
+  q_max <- quantile(y, (1+p)/2)
+  q_min<- quantile(y,(1-p)/2)
+  x[x >= q_max] <- q_max
+  x[x<= q_min]<-q_min
   x
-}
-
+}
\ No newline at end of file

From e1239727fb82af4859a8be0ccf92c024e20daaff Mon Sep 17 00:00:00 2001
From: MarkoBarzic <markbarzic@gmail.com>
Date: Mon, 6 May 2019 22:51:07 +0200
Subject: [PATCH 5/7] #31-added description of the function

---
 R/meanimpute.R    | 1 +
 man/meanimpute.Rd | 3 +++
 2 files changed, 4 insertions(+)

diff --git a/R/meanimpute.R b/R/meanimpute.R
index f7f79e5..9023102 100644
--- a/R/meanimpute.R
+++ b/R/meanimpute.R
@@ -1,4 +1,5 @@
 #' Meanimputation
+#' Calculates mean of a given vector, ignores NA values.
 #' @param x A vector
 #' @export
 meanimpute <- function(x) {
diff --git a/man/meanimpute.Rd b/man/meanimpute.Rd
index 8139e8f..77f2fbc 100644
--- a/man/meanimpute.Rd
+++ b/man/meanimpute.Rd
@@ -6,6 +6,9 @@
 \usage{
 meanimpute(x)
 }
+\arguments{
+\item{x}{A vector}
+}
 \description{
 Meanimputation
 }

From 37de5d53053862404501f67077a979e0eb5c7212 Mon Sep 17 00:00:00 2001
From: MarkoBarzic <markbarzic@gmail.com>
Date: Mon, 6 May 2019 22:52:07 +0200
Subject: [PATCH 6/7] #31-added explanations for function windsorize

---
 man/windsorize.Rd | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/man/windsorize.Rd b/man/windsorize.Rd
index 832c3cb..dcabd36 100644
--- a/man/windsorize.Rd
+++ b/man/windsorize.Rd
@@ -6,6 +6,19 @@
 \usage{
 windsorize(x, p = 0.9)
 }
+\arguments{
+\item{x}{A vector.}
+
+\item{p}{A quantile.}
+}
+\value{
+inuput vector x with trimmed outliers by (1-p) percentile.
+}
 \description{
-Do some windsorization.
+Transform all outliner data to
+(1-p)/2 percentile value for lower outliers and 
+(1+p)/2 for higher outliers.
+}
+\examples{
+windsorize(rnorm(100,0,1))
 }

From 3706cdc513a25c4e1dd99e1c20e1e2852142777a Mon Sep 17 00:00:00 2001
From: MarkoBarzic <markbarzic@gmail.com>
Date: Mon, 6 May 2019 22:54:40 +0200
Subject: [PATCH 7/7] #32 #31- added explanation for function Log transform

---
 man/transform_log.Rd | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 man/transform_log.Rd

diff --git a/man/transform_log.Rd b/man/transform_log.Rd
new file mode 100644
index 0000000..c42f726
--- /dev/null
+++ b/man/transform_log.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/transform_log.R
+\name{transform_log}
+\alias{transform_log}
+\title{transform_log 
+Transform numerical values into their log values}
+\usage{
+transform_log(x)
+}
+\arguments{
+\item{x}{A vector}
+}
+\value{
+logarithm of x
+}
+\description{
+transform_log 
+Transform numerical values into their log values
+}
+\examples{
+transform_log(c(NA,0,-1,exp(2)))
+}