Update documentation

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: polyMatrix
-Version: 0.9.11
+Version: 0.9.16
 Title: Infrastructure for Manipulation Polynomial Matrices 
 Description: 
   Implementation of class "polyMatrix" for storing a matrix of polynomials and implements 
@@ -20,7 +20,7 @@ Type: Package
 Authors@R: c(
     person("Tamas", "Prohle", email="prohlet@ludens.elte.hu", role="aut"),
     person("Peter", "Prohle", email="prohlep@math.elte.hu", role="aut"),
-    person("Nikolai", "Ryzhkov", email="namezys@gmail.com", role=c("aut", "cre")),
+    person("Nikolai", "Ryzhkov", email="namezys@gmail.com", role=c("aut", "cre"), comment = c(ORCID = "0000-0003-4896-280X")),
     person("Ildiko", "Laszlo", role="aut", comment = c(ORCID = "0000-0003-2324-8183")),
     person("Ulas Onat", "Alakent", role="ctb")
     )

R/class_polyMatrix.R

@@ -1,5 +1,5 @@
 # Title     : Main class of polymatrix
-# Objective : Definition of class
+# Objective : The definition of the class
 # Created by: namezys
 # Created on: 2020. 10. 16.
 
@@ -15,15 +15,15 @@ setOldClass(P)
     return("Negative number of columns")
   }
   if(ncol(object@coef) %% object@ncol != 0) {
-    return("Invalid coefficient matrix size")
+    return("Invalid matrix size and size of coef")
   }
   return(TRUE)
 }
 
-#' A class to represent matrix of polinomials
+#' A class to represent a matrix of polynomials
 #'
 #' @slot coef A matrix of coefficients which are joined into one matrix from lower degree to higher
-#' @slot ncol Actual number of columns in the polynomial matrix
+#' @slot ncol The actual number of columns in the polynomial matrix
 #'
 #' @examples
 #'
@@ -41,7 +41,7 @@ polyMatrixClass <- setClass(
 )
 
 .clean.coef <- function(coef, ncol) {
-  # clean up coef matrix by removing zero tails
+  # cleans up coef matrix by removing zero tails
   stopifnot(ncol(coef) %% ncol == 0)
   nr <- nrow(coef)
   d <- ncol(coef) / ncol - 1
@@ -73,23 +73,25 @@ polyMatrixClass <- setClass(
 
 #' Create polyMatrix object
 #'
-#' This function will create polynomial object fromm
+#' This function will create a polynomial object from
 #' coefficient matrix or signle value
 #'
 #' A coefficient matrix is a matrix which contains
-#' matrices of coefficients from lower degree to higher
+#' matrices of coefficients starting from lower degree to higher ones,
 #' side-by-side
 #'
-#' @param data an matrix in case of creation from coefficient matrices or an numer/polynomial
-#' @param nrow A numer of rows of matrix.
-#'             If data is a matrix, default value is the number of rows of data matrix.
-#'             In other case, it's a required parameter
-#' @param ncol Must be positibe.
-#'             If data is a matrix, default value is the number of columns of data matrix.
-#'             In other ccase, it's a required parameter.
-#' @param degree Degree of polynomials in coefficient matrix. Can't be negative.
-#'        If data is polynomail, degree can be evaluated automatcal.
-#'        In other case, default value is 0.
+#' @param data A matrix containing matrices of coefficients
+#'  or a number or a polynomial
+#' @param nrow The numer of rows of a polynomial matrix. Must be postive.
+#'  If data is a matrix, the default value is the number of rows of matrix `data`.
+#'  In other cases it is a required parameter.
+#' @param ncol A number of columns of a polynomial matrix. Must be positive.
+#'  If data is a matrix, the default value is the number of columns of matrix `data`.
+#'  In other cases it is a required parameter.
+#' @param degree Degree of polynomials in the coefficient matrix. Must be zero or positive.
+#'  If data is polynomial, degree can be evaluated automatcal.
+#'  In other case, default value is 0.
+#'
 #' @return new polynomial matrix of polyMatrix class
 #' @export
 polyMatrix <- function(data, nrow, ncol, degree) {
@@ -104,7 +106,7 @@ polyMatrix <- function(data, nrow, ncol, degree) {
       ncol <- 1
     }
     if(!missing(degree) && degree < length(data) - 1) {
-      stop("Polynomail has higher degree than requested")
+      stop("Polynomial has higher degree than requested")
     }
     degree <- length(data) - 1
     nrow <- as.integer(nrow)
@@ -158,7 +160,7 @@ polyMatrix <- function(data, nrow, ncol, degree) {
 #' Check if object is polyMatrix
 #'
 #' @param x an \R object
-#' @return TRUE if object is a polonial matrix
+#' @return TRUE if object is a polynomial matrix
 #' @examples
 #' is.polyMatrix(c(1, 2, 3))
 #' is.polyMatrix(polyMatrix(0, 2, 2))
@@ -176,4 +178,4 @@ is.polyMatrix <- function(x) {
     }
   }
   return(polynom::as.polylist(result))
-}
+}

R/class_polyMatrixCharPolynomial.R

@@ -1,4 +1,4 @@
-# Title     : Class of characteristic polinomail of polynomail matrix
+# Title     : Class of characteristic polynomial of a polynomial matrix
 # Objective : We use polyMatrix to store polynomial coefficients
 # Created by: namezys
 # Created on: 2021. 05. 05.
@@ -8,14 +8,14 @@ PMCP <- "polyMatrixCharPolynomial"
 
 .check.polyMatrixCharClass <- function (object) {
   if (nrow(object@coef) != 1) {
-    return("Char polynomial matrix should contrains only one row")
+    return("Char polynomial matrix should contain only one row")
   }
   return(TRUE)
 }
 
-#' A class to repesent characteristic polynomial of polynomial matrix
+#' A class to repesent characteristic polynomial of a polynomial matrix
 #'
-#' Characteristic polynomial of polynomial matrix is polynomial with polynomial coefficients
+#' Characteristic polynomial of a polynomial matrix is a polynomial with polynomial coefficients
 #' @export
 polyMatrixCharClass <- setClass(
   PMCP,

R/method_adjoint.R

@@ -1,12 +1,12 @@
-# Title     : cofactor and adjoint matrix
+# Title     : cofactor and the adjoint matrix
 # Created by: namezys
 # Created on: 2021. 04. 29.
 
-#' Cofactor of matrix
+#' Cofactor of a matrix
 #'
-#' @param x an matrix
-#' @param r,c the row and column
-#' @return cofactor which is number or polynomial
+#' @param x a matrix
+#' @param r,c the rows and columns
+#' @return cofactor which is a number or a polynomial
 #'
 #' @seealso [adjoint()]
 #'
@@ -39,15 +39,15 @@ cofactor <- function(x, r, c) {
   return(result)
 }
 
-#' Adjugate or classical adjoint of a square matrix
+#' Adjungate or classical adjoint of a square matrix
 #'
-#' The adjugate or classical adjoint of a square matrix is the transpose of its cofactor matrix.
-#' It is also occasionally known as adjunct matrix,[ though this nomenclature appears to have decreased in usage.
+#' The adjungate or classical adjoint of a square matrix is the transpose of its cofactor matrix.
+#' It is also occasionally known as adjunct matrix, though this nomenclature appears to have been decreased in usage.
 #'
-#' @param x an matrix
+#' @param x a matrix
 #'
 #' @export
 setGeneric("adjoint", .adjoint.generic)
-#' @describeIn adjoint adjugate of polynomial matrix
+#' @describeIn adjoint adjungate of polynomial matrix DON'T UNDERSTAND!!!
 #' @export
 setMethod("adjoint", signature(x = PM), .adjoint.polyMatrix)

R/method_bind.R

@@ -1,18 +1,18 @@
-# Title     : row and column bind
-# Objective : because core function use only "..." we have to redefine method to allow to use with polyMatrix in any
-# poisition
+# Title     : row and column binding
+# Objective : because core functions use only "..." we have to redefine the method
+#             in order to allow us to use with polyMatrix in any poisition  of argument liist
 # Created by: namezys
 # Created on: 2020. 10. 23.
 
-#' Combine polynial matrices by rows or coluns
+#' Combine polynomial matrices by rows or columns
 #'
-#' @param ... (generalzed) vectors or mmatrices.
-#'   If any of objects are polynomail matrix
-#' @param deparse.level details in base function, polynomial matrices doesn't use it
+#' @param ... (generalized) vectors or matrices.
+#'   If any of the objects is a polynomail matrix
+#' @param deparse.level details in the base function, polynomial matrices doesn't use this argument
 #'
-#' @return if at least one argument is a polynomail matrix,
-#'   the result will be combined polynomial matrix.
-#'   Overwise, base package implementatioon [base::cbind()] or [base::rbind()]
+#' @return if at least one argument is a polynomial matrix,
+#'   the result will be a combined polynomial matrix.
+#'   Otherwise, the base package implementation [base::cbind()] or [base::rbind()]
 #'   will be called.
 #'
 #' @seealso [base::cbind()]
@@ -42,7 +42,7 @@ cbind <- function(..., deparse.level = 1) {
     if(is.null(nr)) {
       nr <- vnr
     } else if(!is.null(vnr) && nr != vnr) {
-      stop("number of rows of matrices must match")
+      stop("the number of rows of the matrices must match")
     }
     vnc <- ncol(i)
     if(is.null(vnc)) {
@@ -69,7 +69,7 @@ cbind <- function(..., deparse.level = 1) {
   return(res)
 }
 
-#' @describeIn cbind row based bind
+#' @describeIn cbind row based bind  DON'T UNDERSTAND.. !!!
 #'
 #' @export
 rbind <- function(..., deparse.level = 1) {
@@ -97,7 +97,7 @@ rbind <- function(..., deparse.level = 1) {
     if(is.null(nc)) {
       nc <- vnc
     } else if(!is.null(vnc) && nc != vnc) {
-      stop("number of columns of matrices must match")
+      stop("the number of columns of the matrices must match")
     }
     vnr <- nrow(i)
     if(is.null(vnr)) {
@@ -122,4 +122,4 @@ rbind <- function(..., deparse.level = 1) {
     r <- r + vnr
   }
   return(res)
-}
+}

R/method_charpolynom.R

@@ -65,18 +65,18 @@
   return(polyMatrixCharClass(coef=.char.step(x, diag(1, nrow(x), ncol(x)))))
 }
 
-#' Characteristic polynomial of matrix
+#' Characteristic polynomial of a matrix
 #'
 #' @param x an matrix
 #'
 #' @export
 setGeneric("charpolynom", function(x) {
-  stop("Matrix object is exppected")
+  stop("Matrix object is expected")
 })
 #' @describeIn charpolynom for numerical matrix it is a polynomial with numerical coefficients
 #'
 #' @return When the input is a numerical matrix of `matrix` class
-#'         then the value is a `polynomial` object.
+#'         the value is a `polynomial` object.
 #'
 #' @examples
 #'
@@ -92,13 +92,13 @@ setMethod("charpolynom", signature(x="matrix"), .charpolynom.matrix)
 setMethod("charpolynom", signature(x=P), function (x) {
   return(charpolynom(polyMatrix(x)))
 })
-#' @describeIn charpolynom for polynomial matrix it has polynomial coefficients
+#' @describeIn charpolynom for polynomial matrix has polynomial coefficients
 #'
 #' @details
 #' The characteristic polynom of a polynomial matrix is a polynom with polynomial coefficients.
 #'
 #' @return When the input is a `polyMatrix` object
-#'         then a value is `polyMatrixCharClass` class object,
+#'         then the value is `polyMatrixCharClass` class object,
 #'
 #' @seealso [polyMatrixCharClass]
 #' @export

R/method_coef.R

@@ -1,10 +1,10 @@
-# Title     : Get coeffisient matrix by using "[[" operator
+# Title     : Gets coefficient matrix by using "[[" operator
 # Created by: namezys
 # Created on: 2020. 10. 16.
 
 #' @describeIn polyMatrix get coefficient matrix by degree
 #'
-#' @param i the degree to extract matrix of coefficient
+#' @param i the degree of the matrix of coefficient to be extracted
 #' @examples
 #'
 #' # get coefficient matrix for degree 0
@@ -21,23 +21,23 @@
 #' @export
 setMethod("[[", signature(x = PM, i = "numeric"), function(x, i) {
   if(length(i) != 1) {
-    stop("Only one coefficient matrix can be gotten")
+    stop("Only one coefficient matrix can be gotten at once")
   }
   if(i > degree(x) || i < 0) {
     stop("degree out of bounds")
   }
   return(x@coef[, seq_len(ncol(x)) + ncol(x) * i])
 })
-#' @describeIn charpolynom get polynomial coefficient of characteristic
+#' @describeIn charpolynom get polynomial coefficient of characteristic polynomial
 #'
-#' @param i the degree to extract polinomial coefficient
+#' @param i the degree of the polynomial coefficient to be extract
 #' @export
 setMethod("[[", signature(x = PMCP), function(x, i) {
   if(length(i) != 1) {
-    stop("Only one coefficient matrix can be gotten")
+    stop("Only one coefficient matrix can be gotten at once")
   }
   if(i + 1 > ncol(x@coef) || i < 0) {
     stop("degree out of bounds")
   }
   return(x@coef[1, i + 1])
-})
+})

R/method_degree.R

@@ -2,7 +2,7 @@
 # Created by: namezys
 # Created on: 2020. 10. 17.
 
-#' Gets maximum degree of polynomial objects
+#' Gets the maximum degree of polynomial objects
 #'
 #' Returns the maximum degree as an integer number.
 #'
@@ -11,8 +11,7 @@
 #' for polynomial objects.
 #'
 #' @details
-#' By default, this function raises
-#' error for unknown type of object.
+#' By default, this function raises error for unknown type of object.
 #'
 #' @export
 setGeneric("degree", function(x) {
@@ -22,7 +21,7 @@ setGeneric("degree", function(x) {
 #' @describeIn degree a scalar argument always has zero degree
 #'
 #' @details
-#' A numerical scalar has zero degree.
+#' A numerical scalar can be treated as a polynomial with zero degree.
 #'
 #' @examples
 #'
@@ -32,7 +31,7 @@ setGeneric("degree", function(x) {
 #' @export
 setMethod("degree", signature(x = NUM), function(x) {
   if(length(x) != 1) {
-    stop("Numeric suquence is unsupported")
+    stop("Numeric sequence is unsupported")
   }
   return(0)
 })
@@ -77,12 +76,12 @@ setMethod("degree", signature(x = P), function(x) { length(x) - 1 })
 #'
 #' @export
 setMethod("degree", signature(x = PM), function(x) { as.integer(ncol(x@coef) / x@ncol - 1) })
-#' @describeIn charpolynom the degree of char polynomail of polynomial matrix
+#' @describeIn charpolynom the degree of char polynomial of polynomial matrix
 #'
 #' @export
 setMethod("degree", signature(x = PMCP), function(x) { as.integer(ncol(x@coef) - 1) })
 
-#' Degree of each item of matrix
+#' Degree of each item of the matrix
 #'
 #' Returns a matrix obtained by applying a function [degree()]
 #' for each element of the matrix.
@@ -94,7 +93,7 @@ setMethod("degree", signature(x = PMCP), function(x) { as.integer(ncol(x@coef) -
 #'
 #' @details
 #' Degree of each item is calculated using [degree()] which is defined for polynomials
-#' as the highest degree of the terms with non-zero coefficient.
+#' as the highest degree of the terms with non-zero coefficients.
 #'
 #' For convenience this function is defined for any object,
 #' but returns zero for non polynomial objects.

R/method_det.R

@@ -1,10 +1,10 @@
-# Title     : deteminant of polyMatrix
+# Title     : determinant of polyMatrix
 # Created by: namezys
 # Created on: 2021. 04. 02.
 
 .number.nonzero.item.in.row <- function(pm, r)
 {
-  # We should it very fast, use coef matrix directly
+  # We should do it very fast, use coef matrix directly
   positions <- ncol(pm) * 0:degree(pm)
   result <- 0
   for(i in seq_len(ncol(pm))) {