R/bca.R
In RAPLER/dst-1: Using the Theory of Belief Functions
Defines functions
bca
Documented in
bca
#' Basic chance assignment mass function
#'
#' Function \code{bca} is used to define subsets of a finite set \eqn{\Theta} of possible values and to assign their corresponding mass value.\cr
#' The set \eqn{\Theta} is called the frame of discernment. Each subset \eqn{A} of \eqn{Theta} with a positive mass value is called a focal element or a proposition. The associated mass value is a number of the \code{(0,1]} interval, called "basic chance assignment" (the basic probability assignment of Shafer's book). All other subsets that have not received a positive mass value are assumed to have a mass value of zero.
#'
#' There is two ways of defining the bca: a (0,1) matrix or a list of subsets labels.
#' @aliases bpa
#' @param tt Mandatory. A (0,1)-matrix or a boolean matrix. The number of columns must match the number of elements (values) of the frame of discernment \eqn{\Theta}. Each row is a subset of \eqn{\Theta}. The last row is the frame \eqn{\Theta}, represented by a vector of 1's.
#' @param ssnames A list of subsets names which will be obtained from the column names of the tt matrix.
#' @param m A numeric vector of length equal to the number of rows of the matrix \code{tt}. Values of \code{m} must lie in the interval \code{(0,1]} and must add to one. The mass \code{m(k)} represents the chance value allotted to the proposition represented by the row \code{k} of the matrix \code{tt}.
#' @param qq Commonality functions from the frame of discernment to \eqn{[0,1]}
#' @param W2c A binary matrix of support.
#' @param method = NULL: Use Fast Zeta Transform ("fzt") or Efficient Zeta Transform ("ezt")
#' @param include_all = FALSE Put TRUE to include all elements with 0 mass in the bca.
#' @param cnames A character vector containing the names of the elements of the frame of discernment \eqn{\Theta}. The length must be equal to the number of elements of \eqn{\Theta}. The names are first searched in the \code{valuenames} parameter. If NULL, column names of the matrix \code{tt} are taken if present. Otherwise, names are generated.
#' @param con The measure of conflict can be provided. 0 by default.
#' @param idvar The number given to the variable. A number is necessary to manage relations between variables and make computations on a graph. 0 if omitted.
#' @param infovar A two-column matrix containing variable identification numbers and the number of elements of the variable. Generated if omitted.
#' @param varnames The name of the variable. Generated if omitted.
#' @param valuenames A list of the names of the variables with the name of the elements of their frame of discernment.
#' @param inforel Not used here. Defined within function \code{\link{bcaRel}}.
#' @return y An object of class \code{bcaspec} called a bca for "basic chance assignment": \itemize{
#' \item tt The table of focal elements. Rownames of the matrix of focal elements are generated from the column names of the elements of the frame. See \code{\link{nameRows}} for details.
#' \item qq Commonality functions from the frame of discernment to \eqn{[0,1]}
#' \item spec A two column matrix. First column contains numbers given to the subsets, 1 to \code{nrow(tt)}. Second column contains the mass values of the subsets.
#' \item con The measure of conflict.
#' \item infovar The number of the variable and the size of the frame of discernment.
#' \item varnames The name of the variable.
#' \item valuenames A list of length 1 consisting of the name of the variable with the names of the elements of the frame of discernment (the column names of the \code{tt} matrix).
#' \item ssnames A list of subsets names done from the column names of the tt matrix.
#' \item inforel Set at 0. used in function \code{\link{bcaRel}}.
#' }
#' @author Claude Boivin
#' @export
#' @examples
#' tt<- t(matrix(c(1,0,1,1),ncol = 2))
#' m<- c(.9,.1)
#' cnames <- c("yes","no")
#' bca(tt, m)
#' bca(tt, m, cnames)
#' tt1<- t(matrix(c(1,0,1,1),ncol = 2))
#' colnames(tt1) <- c("yes", "no")
#' m <- c(.9, .1)
#' bca(tt=tt1, m, idvar = 1)
#' x <- bca(tt=matrix(c(0,1,1,1,1,0,1,1,1),nrow = 3,
#' byrow = TRUE), m = c(0.2,0.5, 0.3), include_all = TRUE,
#' cnames = c("a", "b", "c"), idvar = 1)
#' y <- bca(tt=matrix(c(1,0,0,1,1,1),nrow = 2,
#' byrow = TRUE), m = c(0.6,0.4),
#' cnames = c("a", "b", "c"),varnames = "y", idvar = 1)
#' vacuous <- bca(matrix(c(1,1,1), nrow = 1), m = 1, cnames = c("a","b","c"), ssnames = c("a","b","c"))
#' @references \itemize{
#' \item Shafer, G., (1976). A Mathematical Theory of Evidence. Princeton University Press, Princeton, New Jersey, p. 38: Basic probability assignment.
#' \item Guan, J. W. and Bell, D. A., (1991). Evidence Theory and its Applications. Elsevier Science Publishing company inc., New York, N.Y., p. 29: Mass functions and belief functions
#' }
bca<-function(tt = NULL, m, qq = NULL, W2c = NULL, method = NULL, include_all = FALSE, cnames = NULL, con = NULL, ssnames = NULL, idvar = NULL, infovar = NULL, varnames = NULL, valuenames = NULL, inforel=NULL) {
#
# Local variables: ztable, zdup, zframe, znames, str1, str2, tt_all, m_all
# Functions calls: nameRows, DoSSnames
#
# 1, Empty section
#
# 2. Determine names of columns of tt matrix and fix some parameters
#
# 2 Check inputs: bca constructed with a (0,1) description matrix
# Check on tt
if (is.null(tt)) {
stop("Error in input arguments: description matrix tt is missing.")
}
#
# Check column names
if (is.null(cnames)) {
cnames <- colnames(tt, do.NULL = FALSE, prefix = "col")
}
#
# Check for duplicates column names
ztable <- outer(cnames, cnames, "==")
zdup <- apply(ztable, 2, sum)
if (sum(zdup) != ncol(tt)) {
stop("Error in input arguments: Duplicate names in column names of tt matrix or in column names supplied.")
}
#
# Check mass vector
#
if((abs(sum(m)-1)>0.000001) | (length(tt[,1])!=length(m)) ) {
stop("Error in input arguments: check your input data.")
}
else {
colnames(tt) <- cnames # for the case where tt matrix had no column names
rownames(tt) <- nameRows(tt)
if (is.null(con)) { con <- 0 }
if (is.null(idvar)) { idvar <- 0 }
#
# including all elements of the frame in the bca
# encode the complete tt matrix
#
if (include_all == TRUE) {
n_frame <- ncol(tt)
tt_all <- t(sapply(1:2^n_frame,FUN = function(x) {encode(rep(2,n_frame), x-1)}) )
colnames(tt_all) <- colnames(tt)
rownames(tt_all) <- nameRows(tt_all)
}
#
# 3. Build infovar parameter
#
if (is.null(infovar)) {
infovar <- matrix(c(idvar, ncol(tt)), ncol = 2)
}
colnames(infovar) <- c("varnb", "size")
idvar <- infovar[,1]
#
# 4. Build varnames and valuenames (former = infovaluenames)
#
# check and use varnames if provided
if (include_all == TRUE) {
if (is.null(valuenames) | missing(valuenames)) {
valuenames <- split(colnames(tt_all), rep(paste(rep("v",length(idvar)),c(1:length(idvar)),sep=""), infovar[,2]))
}
}
else {
if (is.null(valuenames) | missing(valuenames)) {
valuenames <- split(colnames(tt), rep(paste(rep("v",length(idvar)),c(1:length(idvar)),sep=""), infovar[,2]))
}
}
if (!is.null(varnames)) {
if (is.numeric(varnames)) {
stop("Names of variables must start with a letter.")
}
if (length(varnames) != (nrow(infovar)) ) {
stop("number of variable names not equal to number of variables") }
names(valuenames) <- varnames
}
if (is.null(varnames)) {
varnames <- names(valuenames)
}
#
# 5. Build specification matrix spec
#
spec <- cbind((1:nrow(tt)), m)
colnames(spec) <- c("specnb", "mass")
rownames(spec) <- rownames(tt)
#
# mass vector and spec matrix of all elements of the frame
if (include_all == TRUE) {
# 2. add elements with 0 mass to the bca
# masses
m_mat <- matrix(spec[,2])
rownames(m_mat) <- rownames(tt)
# compute expanded vector of masses
str1 <- rownames(tt_all)
str2 <-rownames(m_mat)
m_mat_pos <- outer(str1, str2, "==")
m_all <- m_mat_pos %*% m_mat
m <- m_all
spec <- cbind((1:nrow(tt_all)), m)
colnames(spec) <- c("specnb", "mass")
rownames(spec) <- rownames(tt_all)
}
#
# Update tt
#
if (include_all == TRUE) {
tt <- tt_all
}
#
# 6. inforel parameter
#
if (missing(inforel) | is.null(inforel)) {
inforel <- matrix(c(0, 0), ncol = 2)
}
colnames(inforel) <- c("relnb", "depth")
#
# 7 build subsets names
#
if (is.null(ssnames) == TRUE ) {
znames <- DoSSnames(tt)
}
else {
znames <- ssnames
}
# 7.1 build qq
if (is.null(qq) == TRUE ) {
qq <- commonality(tt,m,method,W2c)
}
#
# 8. Construction of the result
#
y<-list(con = con, tt = tt, qq=qq, spec = spec , infovar = infovar, varnames = varnames, valuenames = valuenames, ssnames = znames, inforel = inforel)
# end test
#
class(y) <- append(class(y), "bcaspec")
return(y)
}
}
RAPLER/dst-1 documentation built on Oct. 15, 2024, 9:24 p.m.
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Defines functions bca
Documented in bca
#' Basic chance assignment mass function
#'
#' Function \code{bca} is used to define subsets of a finite set \eqn{\Theta} of possible values and to assign their corresponding mass value.\cr
#' The set \eqn{\Theta} is called the frame of discernment. Each subset \eqn{A} of \eqn{Theta} with a positive mass value is called a focal element or a proposition. The associated mass value is a number of the \code{(0,1]} interval, called "basic chance assignment" (the basic probability assignment of Shafer's book). All other subsets that have not received a positive mass value are assumed to have a mass value of zero.
#'
#' There is two ways of defining the bca: a (0,1) matrix or a list of subsets labels.
#' @aliases bpa
#' @param tt Mandatory. A (0,1)-matrix or a boolean matrix. The number of columns must match the number of elements (values) of the frame of discernment \eqn{\Theta}. Each row is a subset of \eqn{\Theta}. The last row is the frame \eqn{\Theta}, represented by a vector of 1's.
#' @param ssnames A list of subsets names which will be obtained from the column names of the tt matrix.
#' @param m A numeric vector of length equal to the number of rows of the matrix \code{tt}. Values of \code{m} must lie in the interval \code{(0,1]} and must add to one. The mass \code{m(k)} represents the chance value allotted to the proposition represented by the row \code{k} of the matrix \code{tt}.
#' @param qq Commonality functions from the frame of discernment to \eqn{[0,1]}
#' @param W2c A binary matrix of support.
#' @param method = NULL: Use Fast Zeta Transform ("fzt") or Efficient Zeta Transform ("ezt")
#' @param include_all = FALSE Put TRUE to include all elements with 0 mass in the bca.
#' @param cnames A character vector containing the names of the elements of the frame of discernment \eqn{\Theta}. The length must be equal to the number of elements of \eqn{\Theta}. The names are first searched in the \code{valuenames} parameter. If NULL, column names of the matrix \code{tt} are taken if present. Otherwise, names are generated.
#' @param con The measure of conflict can be provided. 0 by default.
#' @param idvar The number given to the variable. A number is necessary to manage relations between variables and make computations on a graph. 0 if omitted.
#' @param infovar A two-column matrix containing variable identification numbers and the number of elements of the variable. Generated if omitted.
#' @param varnames The name of the variable. Generated if omitted.
#' @param valuenames A list of the names of the variables with the name of the elements of their frame of discernment.
#' @param inforel Not used here. Defined within function \code{\link{bcaRel}}.
#' @return y An object of class \code{bcaspec} called a bca for "basic chance assignment": \itemize{
#' \item tt The table of focal elements. Rownames of the matrix of focal elements are generated from the column names of the elements of the frame. See \code{\link{nameRows}} for details.
#' \item qq Commonality functions from the frame of discernment to \eqn{[0,1]}
#' \item spec A two column matrix. First column contains numbers given to the subsets, 1 to \code{nrow(tt)}. Second column contains the mass values of the subsets.
#' \item con The measure of conflict.
#' \item infovar The number of the variable and the size of the frame of discernment.
#' \item varnames The name of the variable.
#' \item valuenames A list of length 1 consisting of the name of the variable with the names of the elements of the frame of discernment (the column names of the \code{tt} matrix).
#' \item ssnames A list of subsets names done from the column names of the tt matrix.
#' \item inforel Set at 0. used in function \code{\link{bcaRel}}.
#' }
#' @author Claude Boivin
#' @export
#' @examples
#' tt<- t(matrix(c(1,0,1,1),ncol = 2))
#' m<- c(.9,.1)
#' cnames <- c("yes","no")
#' bca(tt, m)
#' bca(tt, m, cnames)
#' tt1<- t(matrix(c(1,0,1,1),ncol = 2))
#' colnames(tt1) <- c("yes", "no")
#' m <- c(.9, .1)
#' bca(tt=tt1, m, idvar = 1)
#' x <- bca(tt=matrix(c(0,1,1,1,1,0,1,1,1),nrow = 3,
#' byrow = TRUE), m = c(0.2,0.5, 0.3), include_all = TRUE,
#' cnames = c("a", "b", "c"), idvar = 1)
#' y <- bca(tt=matrix(c(1,0,0,1,1,1),nrow = 2,
#' byrow = TRUE), m = c(0.6,0.4),
#' cnames = c("a", "b", "c"),varnames = "y", idvar = 1)
#' vacuous <- bca(matrix(c(1,1,1), nrow = 1), m = 1, cnames = c("a","b","c"), ssnames = c("a","b","c"))
#' @references \itemize{
#' \item Shafer, G., (1976). A Mathematical Theory of Evidence. Princeton University Press, Princeton, New Jersey, p. 38: Basic probability assignment.
#' \item Guan, J. W. and Bell, D. A., (1991). Evidence Theory and its Applications. Elsevier Science Publishing company inc., New York, N.Y., p. 29: Mass functions and belief functions
#' }
bca<-function(tt = NULL, m, qq = NULL, W2c = NULL, method = NULL, include_all = FALSE, cnames = NULL, con = NULL, ssnames = NULL, idvar = NULL, infovar = NULL, varnames = NULL, valuenames = NULL, inforel=NULL) {
#
# Local variables: ztable, zdup, zframe, znames, str1, str2, tt_all, m_all
# Functions calls: nameRows, DoSSnames
#
# 1, Empty section
#
# 2. Determine names of columns of tt matrix and fix some parameters
#
# 2 Check inputs: bca constructed with a (0,1) description matrix
# Check on tt
if (is.null(tt)) {
stop("Error in input arguments: description matrix tt is missing.")
}
#
# Check column names
if (is.null(cnames)) {
cnames <- colnames(tt, do.NULL = FALSE, prefix = "col")
}
#
# Check for duplicates column names
ztable <- outer(cnames, cnames, "==")
zdup <- apply(ztable, 2, sum)
if (sum(zdup) != ncol(tt)) {
stop("Error in input arguments: Duplicate names in column names of tt matrix or in column names supplied.")
}
#
# Check mass vector
#
if((abs(sum(m)-1)>0.000001) | (length(tt[,1])!=length(m)) ) {
stop("Error in input arguments: check your input data.")
}
else {
colnames(tt) <- cnames # for the case where tt matrix had no column names
rownames(tt) <- nameRows(tt)
if (is.null(con)) { con <- 0 }
if (is.null(idvar)) { idvar <- 0 }
#
# including all elements of the frame in the bca
# encode the complete tt matrix
#
if (include_all == TRUE) {
n_frame <- ncol(tt)
tt_all <- t(sapply(1:2^n_frame,FUN = function(x) {encode(rep(2,n_frame), x-1)}) )
colnames(tt_all) <- colnames(tt)
rownames(tt_all) <- nameRows(tt_all)
}
#
# 3. Build infovar parameter
#
if (is.null(infovar)) {
infovar <- matrix(c(idvar, ncol(tt)), ncol = 2)
}
colnames(infovar) <- c("varnb", "size")
idvar <- infovar[,1]
#
# 4. Build varnames and valuenames (former = infovaluenames)
#
# check and use varnames if provided
if (include_all == TRUE) {
if (is.null(valuenames) | missing(valuenames)) {
valuenames <- split(colnames(tt_all), rep(paste(rep("v",length(idvar)),c(1:length(idvar)),sep=""), infovar[,2]))
}
}
else {
if (is.null(valuenames) | missing(valuenames)) {
valuenames <- split(colnames(tt), rep(paste(rep("v",length(idvar)),c(1:length(idvar)),sep=""), infovar[,2]))
}
}
if (!is.null(varnames)) {
if (is.numeric(varnames)) {
stop("Names of variables must start with a letter.")
}
if (length(varnames) != (nrow(infovar)) ) {
stop("number of variable names not equal to number of variables") }
names(valuenames) <- varnames
}
if (is.null(varnames)) {
varnames <- names(valuenames)
}
#
# 5. Build specification matrix spec
#
spec <- cbind((1:nrow(tt)), m)
colnames(spec) <- c("specnb", "mass")
rownames(spec) <- rownames(tt)
#
# mass vector and spec matrix of all elements of the frame
if (include_all == TRUE) {
# 2. add elements with 0 mass to the bca
# masses
m_mat <- matrix(spec[,2])
rownames(m_mat) <- rownames(tt)
# compute expanded vector of masses
str1 <- rownames(tt_all)
str2 <-rownames(m_mat)
m_mat_pos <- outer(str1, str2, "==")
m_all <- m_mat_pos %*% m_mat
m <- m_all
spec <- cbind((1:nrow(tt_all)), m)
colnames(spec) <- c("specnb", "mass")
rownames(spec) <- rownames(tt_all)
}
#
# Update tt
#
if (include_all == TRUE) {
tt <- tt_all
}
#
# 6. inforel parameter
#
if (missing(inforel) | is.null(inforel)) {
inforel <- matrix(c(0, 0), ncol = 2)
}
colnames(inforel) <- c("relnb", "depth")
#
# 7 build subsets names
#
if (is.null(ssnames) == TRUE ) {
znames <- DoSSnames(tt)
}
else {
znames <- ssnames
}
# 7.1 build qq
if (is.null(qq) == TRUE ) {
qq <- commonality(tt,m,method,W2c)
}
#
# 8. Construction of the result
#
y<-list(con = con, tt = tt, qq=qq, spec = spec , infovar = infovar, varnames = varnames, valuenames = valuenames, ssnames = znames, inforel = inforel)
# end test
#
class(y) <- append(class(y), "bcaspec")
return(y)
}
}
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