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# file nnet/R/lvq.R
# copyright (C) 1994-9 W. N. Venables and B. D. Ripley
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 or 3 of the License
# (at your option).
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
#
#
lvqinit <- function(x, cl, size, prior, k=5)
{
x <- as.matrix(x)
n <- nrow(x)
p <- ncol(x)
if(length(cl) != n) stop("'x' and 'cl' have different lengths")
g <- as.factor(cl)
if(any(is.na(x)) || any(is.na(g)))
stop("no missing values are allowed")
counts <- tapply(rep(1, length(g)), g, sum)
prop <- counts/n
np <- length(prop)
# allow for supplied prior
if(missing(prior)) prior <- prop
else if(any(prior <0)||round(sum(prior), 5) != 1)
stop("invalid prior")
if(length(prior) != np) stop("'prior' is of incorrect length")
if(missing(size)) size <- min(round(0.4 * np * (np-1+p/2),0), n)
inside <- knn.cv(x, cl, k) == cl
selected <- numeric(0)
for(i in 1L:np){
set <- seq_along(g)[unclass(g)==i & inside]
if(length(set) > 1L)
set <- sample(set, min(length(set), round(size*prior[i])))
selected <- c(selected, set)
}
list(x = x[selected, , drop=FALSE], cl = cl[selected])
}
olvq1 <- function(x, cl, codebk, niter = 40*nrow(codebk$x), alpha = 0.3)
{
x <- as.matrix(x)
if(any(is.na(x)) || any(is.na(cl)))
stop("no missing values are allowed")
n <- nrow(x)
p <- ncol(x)
nc <- dim(codebk$x)[1L]
if(length(cl) != n) stop("'x' and 'cl' have different lengths")
iters <- sample(n, niter, TRUE)
z <- .C(VR_olvq,
as.double(alpha),
as.integer(n),
as.integer(p),
as.double(x),
as.integer(unclass(cl)),
as.integer(nc),
xc = as.double(codebk$x),
as.integer(codebk$cl),
as.integer(niter),
as.integer(iters-1L)
)
xc <- matrix(z$xc,nc,p)
dimnames(xc) <- dimnames(codebk$x)
list(x = xc, cl = codebk$cl)
}
lvq1 <- function(x, cl, codebk, niter = 100*nrow(codebk$x), alpha = 0.03)
{
x <- as.matrix(x)
if(any(is.na(x)) || any(is.na(cl)))
stop("no missing values are allowed")
n <- nrow(x)
p <- ncol(x)
nc <- dim(codebk$x)[1L]
if(length(cl) != n) stop("'x' and 'cl' have different lengths")
iters <- sample(n, niter, TRUE)
z <- .C(VR_lvq1,
as.double(alpha),
as.integer(n),
as.integer(p),
as.double(x),
as.integer(unclass(cl)),
as.integer(nc),
xc = as.double(codebk$x),
as.integer(codebk$cl),
as.integer(niter),
as.integer(iters-1L)
)
xc <- matrix(z$xc,nc,p)
dimnames(xc) <- dimnames(codebk$x)
list(x = xc, cl = codebk$cl)
}
lvq2 <- function(x, cl, codebk, niter = 100*nrow(codebk$x),
alpha = 0.03, win = 0.3)
{
x <- as.matrix(x)
if(any(is.na(x)) || any(is.na(cl)))
stop("no missing values are allowed")
n <- nrow(x)
p <- ncol(x)
nc <- dim(codebk$x)[1L]
if(length(cl) != n) stop("'x' and 'cl' have different lengths")
iters <- sample(n, niter, TRUE)
z <- .C(VR_lvq2,
as.double(alpha),
as.double(win),
as.integer(n),
as.integer(p),
as.double(x),
as.integer(unclass(cl)),
as.integer(nc),
xc = as.double(codebk$x),
as.integer(codebk$cl),
as.integer(niter),
as.integer(iters-1L)
)
xc <- matrix(z$xc,nc,p)
dimnames(xc) <- dimnames(codebk$x)
list(x = xc, cl = codebk$cl)
}
lvq3 <- function(x, cl, codebk, niter = 100*nrow(codebk$x),
alpha = 0.03, win = 0.3, epsilon = 0.1)
{
x <- as.matrix(x)
if(any(is.na(x)) || any(is.na(cl)))
stop("no missing values are allowed")
n <- nrow(x)
p <- ncol(x)
nc <- dim(codebk$x)[1L]
if(length(cl) != n) stop("'x' and 'cl' have different lengths")
iters <- sample(n, niter, TRUE)
z <- .C(VR_lvq3,
as.double(alpha),
as.double(win),
as.double(epsilon),
as.integer(n),
as.integer(p),
as.double(x),
as.integer(unclass(cl)),
as.integer(nc),
xc = as.double(codebk$x),
as.integer(codebk$cl),
as.integer(niter),
as.integer(iters-1L)
)
xc <- matrix(z$xc,nc,p)
dimnames(xc) <- dimnames(codebk$x)
list(x = xc, cl = codebk$cl)
}
lvqtest <- function(codebk, test) knn1(codebk$x, test, codebk$cl)
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