From 5b39d7d0d627061d3e1e07c30af61abea866129b Mon Sep 17 00:00:00 2001
From: Andreas Peterseil <andreas.peterseil@rcb.at>
Date: Sun, 5 May 2019 14:55:37 +0200
Subject: [PATCH 1/9] Fix #1: Included replacement of extremely low values

---
 R/windsorize.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/windsorize.R b/R/windsorize.R
index b4e15e6..2132c34 100644
--- a/R/windsorize.R
+++ b/R/windsorize.R
@@ -3,8 +3,9 @@
 #' Do some windsorization.
 #' @export
 windsorize <- function(x, p = .90) {
-  q <- quantile(x, p)
-  x[x >= q] <- q
+  q <- quantile(x, 0.5 * ( 1 + p * c(-1,1) ) )
+  x[x >= q[2] ] <- q[2]
+  x[x <= q[1] ] <- q[1] 
   x
 }
 

From 23a38fe7bbef15218105f5a556df4063c056b256 Mon Sep 17 00:00:00 2001
From: Andreas Peterseil <andreas.peterseil@rcb.at>
Date: Sun, 5 May 2019 14:58:42 +0200
Subject: [PATCH 2/9] Fix #3: Error is thrown in input is emptry or contains
 NAs

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

diff --git a/R/windsorize.R b/R/windsorize.R
index 2132c34..d6cbac1 100644
--- a/R/windsorize.R
+++ b/R/windsorize.R
@@ -3,6 +3,7 @@
 #' Do some windsorization.
 #' @export
 windsorize <- function(x, p = .90) {
+  stopifnot(length(x)>0 && sum(is.na(x))==0)
   q <- quantile(x, 0.5 * ( 1 + p * c(-1,1) ) )
   x[x >= q[2] ] <- q[2]
   x[x <= q[1] ] <- q[1] 

From fe77e6ac0f0e11f0e427b7da928216c18decd9a9 Mon Sep 17 00:00:00 2001
From: Andreas Peterseil <andreas.peterseil@rcb.at>
Date: Sun, 5 May 2019 15:00:50 +0200
Subject: [PATCH 3/9] Fix #5: transform_log added

---
 R/transform_log.R | 1 +
 1 file changed, 1 insertion(+)
 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..8c6138d
--- /dev/null
+++ b/R/transform_log.R
@@ -0,0 +1 @@
+transform_log<-function(x) log(x)
\ No newline at end of file

From d80308d183910bdce2357257ebca23a4964eda99 Mon Sep 17 00:00:00 2001
From: Andreas Peterseil <andreas.peterseil@rcb.at>
Date: Sun, 5 May 2019 15:05:21 +0200
Subject: [PATCH 4/9] Fix #5: added check of input in transform_log

---
 R/transform_log.R | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/R/transform_log.R b/R/transform_log.R
index 8c6138d..45ca6ef 100644
--- a/R/transform_log.R
+++ b/R/transform_log.R
@@ -1 +1,10 @@
-transform_log<-function(x) log(x)
\ No newline at end of file
+transform_log<-function(x){
+  if(length(x)==0){
+    stop("x must have positive length")
+  }else if(sum(x<=0)>0){
+    stop("x must not contain non-positive values")
+  }else if(sum(is.na(x))>0){
+    stop("x must not contain any NA")
+  } 
+  log(x)
+} 
\ No newline at end of file

From 8352e552cb99e1093a064137478ada866ae4bcc0 Mon Sep 17 00:00:00 2001
From: Andreas Peterseil <andreas.peterseil@rcb.at>
Date: Sun, 5 May 2019 15:06:55 +0200
Subject: [PATCH 5/9] Fix #3: Error is thrown in input is emptry or contains
 NAs

---
 R/windsorize.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/windsorize.R b/R/windsorize.R
index d6cbac1..238f06a 100644
--- a/R/windsorize.R
+++ b/R/windsorize.R
@@ -3,7 +3,11 @@
 #' Do some windsorization.
 #' @export
 windsorize <- function(x, p = .90) {
-  stopifnot(length(x)>0 && sum(is.na(x))==0)
+  if(length(x)==0){
+    stop("x must be of positive length")
+  }else if(sum(is.na(x))>0){
+    stop("x must not contain any NA")
+  }
   q <- quantile(x, 0.5 * ( 1 + p * c(-1,1) ) )
   x[x >= q[2] ] <- q[2]
   x[x <= q[1] ] <- q[1] 

From 8a551e48f082745bed7a22c4e7ba29f9bc862cce Mon Sep 17 00:00:00 2001
From: Andreas Peterseil <andreas.peterseil@rcb.at>
Date: Sun, 5 May 2019 15:19:55 +0200
Subject: [PATCH 6/9] Fix #3: Error is thrown in input is emptry or contains
 NAs git commit -m Fix

---
 NAMESPACE            |  6 +++++-
 R/meanimpute.R       |  5 +++++
 R/transform_log.R    |  7 +++++++
 R/windsorize.R       |  8 ++++++--
 man/meanimpute.Rd    |  9 +++++++++
 man/transform_log.Rd | 20 ++++++++++++++++++++
 man/windsorize.Rd    | 15 +++++++++++++--
 7 files changed, 65 insertions(+), 5 deletions(-)
 create mode 100644 man/transform_log.Rd

diff --git a/NAMESPACE b/NAMESPACE
index d75f824..934d9b3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1 +1,5 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(meanimpute)
+export(transform_log)
+export(windsorize)
diff --git a/R/meanimpute.R b/R/meanimpute.R
index cc7cf5e..d09ca51 100644
--- a/R/meanimpute.R
+++ b/R/meanimpute.R
@@ -1,4 +1,9 @@
 #' Meanimputation
+#'
+#' @param x A numeric vector containing the data
+#' @return the input vector with its NA values replaced by the mean
+#' @examples
+#' log(1:5)
 #' @export
 meanimpute <- function(x) {
   x[is.na(x)] <- mean(x, na.rm = TRUE)
diff --git a/R/transform_log.R b/R/transform_log.R
index 45ca6ef..db716d8 100644
--- a/R/transform_log.R
+++ b/R/transform_log.R
@@ -1,3 +1,10 @@
+#' Log transforms data.
+#'
+#' @param x A numeric vector containing the data
+#' @return A numeric vector whose entries are the logarithms of the input.
+#' @examples
+#' log(1:5)
+#' @export
 transform_log<-function(x){
   if(length(x)==0){
     stop("x must have positive length")
diff --git a/R/windsorize.R b/R/windsorize.R
index 238f06a..dba1fda 100644
--- a/R/windsorize.R
+++ b/R/windsorize.R
@@ -1,6 +1,10 @@
-#' Windsorize
+#' Windsorizes data.
 #'
-#' Do some windsorization.
+#' @param x A numeric vector containing the data.
+#' @param p A numeric value denoting the a probability
+#' @return A numeric vector containing the windsorized data, i.e. extreme values are replaced by the quantiles derived from \code{p}.
+#' @examples
+#' windsorize(c(92 , 19 , 101 , 58 , 1053 , 91 , 26 , 78 , 10 , 13 , -40 , 101 , 86 , 85 , 15 , 89 , 89 , 28 , -5 , 41))
 #' @export
 windsorize <- function(x, p = .90) {
   if(length(x)==0){
diff --git a/man/meanimpute.Rd b/man/meanimpute.Rd
index 8139e8f..5984f37 100644
--- a/man/meanimpute.Rd
+++ b/man/meanimpute.Rd
@@ -6,6 +6,15 @@
 \usage{
 meanimpute(x)
 }
+\arguments{
+\item{x}{A numeric vector containing the data}
+}
+\value{
+the input vector with its NA values replaced by the mean
+}
 \description{
 Meanimputation
 }
+\examples{
+log(1:5)
+}
diff --git a/man/transform_log.Rd b/man/transform_log.Rd
new file mode 100644
index 0000000..b7d9dce
--- /dev/null
+++ b/man/transform_log.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/transform_log.R
+\name{transform_log}
+\alias{transform_log}
+\title{Log transforms data.}
+\usage{
+transform_log(x)
+}
+\arguments{
+\item{x}{A numeric vector containing the data}
+}
+\value{
+A numeric vector whose entries are the logarithms of the input.
+}
+\description{
+Log transforms data.
+}
+\examples{
+log(1:5)
+}
diff --git a/man/windsorize.Rd b/man/windsorize.Rd
index 832c3cb..ed90eb5 100644
--- a/man/windsorize.Rd
+++ b/man/windsorize.Rd
@@ -2,10 +2,21 @@
 % Please edit documentation in R/windsorize.R
 \name{windsorize}
 \alias{windsorize}
-\title{Windsorize}
+\title{Windsorizes data.}
 \usage{
 windsorize(x, p = 0.9)
 }
+\arguments{
+\item{x}{A numeric vector containing the data.}
+
+\item{p}{A numeric value denoting the a probability}
+}
+\value{
+A numeric vector containing the windsorized data, i.e. extreme values are replaced by the quantiles derived from \code{p}.
+}
 \description{
-Do some windsorization.
+Windsorizes data.
+}
+\examples{
+windsorize(c(92 , 19 , 101 , 58 , 1053 , 91 , 26 , 78 , 10 , 13 , -40 , 101 , 86 , 85 , 15 , 89 , 89 , 28 , -5 , 41))
 }

From c9d0d26d701acdec53cd38099acb309e56661953 Mon Sep 17 00:00:00 2001
From: Andreas Peterseil <andreas.peterseil@rcb.at>
Date: Sun, 5 May 2019 15:30:40 +0200
Subject: [PATCH 7/9] added test

---
 DESCRIPTION                         | 2 +-
 tests/testthat.R                    | 4 ++++
 tests/testthat/test-transform_log.R | 3 +++
 3 files changed, 8 insertions(+), 1 deletion(-)
 create mode 100644 tests/testthat.R
 create mode 100644 tests/testthat/test-transform_log.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 492ae33..cad592e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -10,7 +10,7 @@ License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Suggests: 
-    testthat,
+    testthat (>= 2.1.0),
     covr,
     rmarkdown
 RoxygenNote: 6.1.1
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..56f8508
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,4 @@
+dlibrary(testthat)
+library(datacleaner)
+
+test_check("datacleaner")
diff --git a/tests/testthat/test-transform_log.R b/tests/testthat/test-transform_log.R
new file mode 100644
index 0000000..42d45df
--- /dev/null
+++ b/tests/testthat/test-transform_log.R
@@ -0,0 +1,3 @@
+test_that("windsorize works", {
+  expect_equal(windsorize(3:10), c(3.35,4.00,5.00,6.00,7.00,8.00,9.00,9.65))
+})

From 0723c6b2c743275ecc79de045919282ae8a03957 Mon Sep 17 00:00:00 2001
From: Andreas Peterseil <andreas.peterseil@rcb.at>
Date: Sun, 5 May 2019 15:32:56 +0200
Subject: [PATCH 8/9] windsorize test: changed test

---
 tests/testthat/{test-transform_log.R => test-windsorize.R} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename tests/testthat/{test-transform_log.R => test-windsorize.R} (100%)

diff --git a/tests/testthat/test-transform_log.R b/tests/testthat/test-windsorize.R
similarity index 100%
rename from tests/testthat/test-transform_log.R
rename to tests/testthat/test-windsorize.R

From ed28c497c4e5a6ad61a60ff1818358014a7323db Mon Sep 17 00:00:00 2001
From: Andreas Peterseil <andreas.peterseil@rcb.at>
Date: Sun, 5 May 2019 15:34:16 +0200
Subject: [PATCH 9/9] removed typo

---
 tests/testthat.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat.R b/tests/testthat.R
index 56f8508..8adbfff 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,4 +1,4 @@
-dlibrary(testthat)
+library(testthat)
 library(datacleaner)
 
 test_check("datacleaner")