merging

.Rbuildignore

+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

+Package: rterahertz
+Type: Package
+Title: R-Terahertz
+Version: 0.1.0
+Authors@R: 
+    person(given = "Ahmad",
+           family = "Alkadri",
+           role = c("aut", "cre"),
+           email = "ahmad.alkadri@outlook.com")
+Description: This package is a collection of functions used for working with THz data.
+    Specifically, it is used for working with the raw THz data obtained during the
+    research cooperation between LMGC (Laboratoire de Mechanics et Genie Civil) and
+    L2C (Laboratoire de Charles Coulomb) of the University of Montpellier, France.
+    Currently in active development due to the active state of the research.
+Imports: ggplot2,reshape2,plotly
+Depends: R (>= 3.0.0)
+License: CeCILL
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 6.1.1

NAMESPACE

+exportPattern("^[[:alpha:]]+")

R/matrixlineextractions.R

+#' Function for extracting the odd-numbered lines of a matrix.
+#'
+#' @description A function for extracting the odd-numbered lines (1,3,5,etc.) of a matrix
+#'
+#' @usage extractmatline_odd(m)
+#'
+#' @param m A matrix object
+#'
+#' @return The same matrix without the values of its even-numbered lines
+#'
+#' @examples
+#' m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+#' m_oddlines <- extractmatline_odd(m)
+
+extractmatline_odd <- function(m){
+  
+  #m = data de scan THz
+  
+  m <- as.matrix(m)
+  
+  colnames(m) <- 1:ncol(m)
+  
+  row.names(m) <- 1:nrow(m)
+  
+  nrow_m <- nrow(m)
+  
+  nrow_odd <- seq(1,nrow_m,by=2)
+  
+  m_odd <- m[nrow_odd,]
+  
+  return(m_odd)
+}
+
+#' Function for extracting the even-numbered lines of a matrix.
+#'
+#' @description A function for extracting the even-numbered lines (2,4,6,etc.) of a matrix
+#'
+#' @usage extractmatline_even(m)
+#'
+#' @param m A matrix object
+#'
+#' @return The same matrix without the values of its odd-numbered lines
+#'
+#' @examples
+#' m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+#' m_evenlines <- extractmatline_even(m)
+
+extractmatline_even <- function(m){
+  
+  #m = data de scan THz
+  
+  m <- as.matrix(m)
+  
+  colnames(m) <- 1:ncol(m)
+  
+  row.names(m) <- 1:nrow(m)
+  
+  nrow_m <- nrow(m)
+  
+  nrow_even <- seq(2,nrow_m,by=2)
+  
+  m_even <- m[nrow_even,]
+  
+  return(m_even)
+}
+
+#' Function for extracting the odd-numbered lines of a matrix.
+#'
+#' @description A function for extracting the odd-numbered lines (1,3,5,etc.) of a matrix
+#'
+#' @usage extrairematligne_odd(m)
+#'
+#' @param m A matrix object
+#'
+#' @return The same matrix without the values of its even-numbered lines
+#'
+#' @examples
+#' m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+#' m_oddlines <- extrairematligne_odd(m)
+
+extrairematligne_odd <- function(m){
+  
+  #m = data de scan THz
+  
+  m <- as.matrix(m)
+  
+  colnames(m) <- 1:ncol(m)
+  
+  row.names(m) <- 1:nrow(m)
+  
+  nrow_m <- nrow(m)
+  
+  nrow_odd <- seq(1,nrow_m,by=2)
+  
+  m_odd <- m[nrow_odd,]
+  
+  return(m_odd)
+}
+
+#' Function for extracting the even-numbered lines of a matrix.
+#'
+#' @description A function for extracting the even-numbered lines (2,4,6,etc.) of a matrix
+#'
+#' @usage extrairematligne_even(m)
+#'
+#' @param m A matrix object
+#'
+#' @return The same matrix without the values of its odd-numbered lines
+#'
+#' @examples
+#' m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+#' m_evenlines <- extrairematligne_even(m)
+
+extrairematligne_even <- function(m){
+  
+  #m = data de scan THz
+  
+  m <- as.matrix(m)
+  
+  colnames(m) <- 1:ncol(m)
+  
+  row.names(m) <- 1:nrow(m)
+  
+  nrow_m <- nrow(m)
+  
+  nrow_even <- seq(2,nrow_m,by=2)
+  
+  m_even <- m[nrow_even,]
+  
+  return(m_even)
+}
\ No newline at end of file

R/plottingfunctions.R

+#' Function for visualizing the THz image matrix using plotly
+#'
+#' @description A wrapper for plot_ly() function, useful for visualizing the THz matrix data quickly.
+#'
+#' @usage plotlyTHz(m)
+#'
+#' @param m THz matrix data, obtained through the THz scan
+#'
+#' @return An imaging of said matrix
+#'
+#' @examples
+#' m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+#' plotlyTHz(m)
+
+plotlyTHz <- function(m){
+  
+  # m is the matrix of the data obtained through the THz imaging
+  
+  plotly::plot_ly(
+    
+    x = 1:ncol(m),
+    
+    y = 1:nrow(m),
+    
+    z = (as.matrix(m)), type = "heatmap"
+    
+  )
+  
+}
+
+#' Function for visualizing the THz image matrix using ggplot2
+#'
+#' @description A wrapper for ggplot() function, useful for visualizing the THz matrix data quickly.
+#'
+#' @usage plotTHz(m)
+#'
+#' @param m THz matrix data, obtained through the THz scan
+#'
+#' @return An imaging of said matrix
+#'
+#' @examples
+#' m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+#' plotTHz(m)
+
+plotTHz <- function(m){
+  
+  #m is the matrix of the data obtained through the THz imaging
+  
+  m <- as.matrix(m)
+  
+  colnames(m) <- 1:ncol(m)
+  
+  row.names(m) <- 1:nrow(m)
+  
+  m <- reshape2::melt(m)
+  
+  names(m) <- c("Y","X","Val")
+  
+  m$Y <- as.numeric(m$Y)
+  
+  m$X <- as.numeric(m$X)
+  
+  ggplot2::ggplot(data = m, ggplot2::aes(x = X, y = Y, fill = Val))+
+    ggplot2::geom_tile()
+  
+}

man/extractmatline_even.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/matrixlineextractions.R
+\name{extractmatline_even}
+\alias{extractmatline_even}
+\title{Function for extracting the even-numbered lines of a matrix.}
+\usage{
+extractmatline_even(m)
+}
+\arguments{
+\item{m}{A matrix object}
+}
+\value{
+The same matrix without the values of its odd-numbered lines
+}
+\description{
+A function for extracting the even-numbered lines (2,4,6,etc.) of a matrix
+}
+\examples{
+m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+m_evenlines <- extractmatline_even(m)
+}

man/extractmatline_odd.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/matrixlineextractions.R
+\name{extractmatline_odd}
+\alias{extractmatline_odd}
+\title{Function for extracting the odd-numbered lines of a matrix.}
+\usage{
+extractmatline_odd(m)
+}
+\arguments{
+\item{m}{A matrix object}
+}
+\value{
+The same matrix without the values of its even-numbered lines
+}
+\description{
+A function for extracting the odd-numbered lines (1,3,5,etc.) of a matrix
+}
+\examples{
+m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+m_oddlines <- extractmatline_odd(m)
+}

man/extrairematligne_even.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/matrixlineextractions.R
+\name{extrairematligne_even}
+\alias{extrairematligne_even}
+\title{Function for extracting the even-numbered lines of a matrix.}
+\usage{
+extrairematligne_even(m)
+}
+\arguments{
+\item{m}{A matrix object}
+}
+\value{
+The same matrix without the values of its odd-numbered lines
+}
+\description{
+A function for extracting the even-numbered lines (2,4,6,etc.) of a matrix
+}
+\examples{
+m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+m_evenlines <- extrairematligne_even(m)
+}

man/extrairematligne_odd.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/matrixlineextractions.R
+\name{extrairematligne_odd}
+\alias{extrairematligne_odd}
+\title{Function for extracting the odd-numbered lines of a matrix.}
+\usage{
+extrairematligne_odd(m)
+}
+\arguments{
+\item{m}{A matrix object}
+}
+\value{
+The same matrix without the values of its even-numbered lines
+}
+\description{
+A function for extracting the odd-numbered lines (1,3,5,etc.) of a matrix
+}
+\examples{
+m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+m_oddlines <- extrairematligne_odd(m)
+}

man/plotTHz.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plottingfunctions.R
+\name{plotTHz}
+\alias{plotTHz}
+\title{Function for visualizing the THz image matrix using ggplot2}
+\usage{
+plotTHz(m)
+}
+\arguments{
+\item{m}{THz matrix data, obtained through the THz scan}
+}
+\value{
+An imaging of said matrix
+}
+\description{
+A wrapper for ggplot() function, useful for visualizing the THz matrix data quickly.
+}
+\examples{
+m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+plotTHz(m)
+}

man/plotlyTHz.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plottingfunctions.R
+\name{plotlyTHz}
+\alias{plotlyTHz}
+\title{Function for visualizing the THz image matrix using plotly}
+\usage{
+plotlyTHz(m)
+}
+\arguments{
+\item{m}{THz matrix data, obtained through the THz scan}
+}
+\value{
+An imaging of said matrix
+}
+\description{
+A wrapper for plot_ly() function, useful for visualizing the THz matrix data quickly.
+}
+\examples{
+m <- matrix(rnorm(100, mean = 0, sd = 1), nrow = 10, ncol = 10)
+plotlyTHz(m)
+}

rterahertz.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace