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# file nnet/nnet.R
# copyright (C) 1994-2013 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/
#
nnet <- function(x, ...) UseMethod("nnet")
nnet.formula <- function(formula, data, weights, ...,
subset, na.action, contrasts=NULL)
{
class.ind <- function(cl)
{
n <- length(cl)
x <- matrix(0, n, length(levels(cl)))
x[(1L:n) + n * (as.vector(unclass(cl)) - 1L)] <- 1
dimnames(x) <- list(names(cl), levels(cl))
x
}
m <- match.call(expand.dots = FALSE)
if(is.matrix(eval.parent(m$data)))
m$data <- as.data.frame(data)
m$... <- m$contrasts <- NULL
m[[1L]] <- quote(stats::model.frame)
m <- eval.parent(m)
Terms <- attr(m, "terms")
x <- model.matrix(Terms, m, contrasts)
cons <- attr(x, "contrast")
xint <- match("(Intercept)", colnames(x), nomatch=0L)
if(xint > 0L) x <- x[, -xint, drop=FALSE] # Bias term is used for intercepts
w <- model.weights(m)
if(length(w) == 0L) w <- rep(1, nrow(x))
y <- model.response(m)
if(is.factor(y)) {
lev <- levels(y)
counts <- table(y)
if(any(counts == 0L)) {
empty <- lev[counts == 0L]
warning(sprintf(ngettext(length(empty),
"group %s is empty",
"groups %s are empty"),
paste(sQuote(empty), collapse=" ")), domain = NA)
y <- factor(y, levels=lev[counts > 0L])
}
if(length(lev) == 2L) {
y <- as.vector(unclass(y)) - 1
res <- nnet.default(x, y, w, entropy=TRUE, ...)
res$lev <- lev
} else {
y <- class.ind(y)
res <- nnet.default(x, y, w, softmax=TRUE, ...)
res$lev <- lev
}
} else res <- nnet.default(x, y, w, ...)
res$terms <- Terms
res$coefnames <- colnames(x)
res$call <- match.call()
res$na.action <- attr(m, "na.action")
res$contrasts <- cons
res$xlevels <- .getXlevels(Terms, m)
class(res) <- c("nnet.formula", "nnet")
res
}
nnet.default <-
function(x, y, weights, size, Wts, mask=rep(TRUE, length(wts)),
linout=FALSE, entropy=FALSE, softmax=FALSE, censored=FALSE, skip=FALSE,
rang=0.7, decay=0, maxit=100, Hess=FALSE, trace=TRUE,
MaxNWts=1000, abstol=1.0e-4, reltol=1.0e-8, ...)
{
net <- NULL
x <- as.matrix(x)
y <- as.matrix(y)
if(any(is.na(x))) stop("missing values in 'x'")
if(any(is.na(y))) stop("missing values in 'y'")
if(dim(x)[1L] != dim(y)[1L]) stop("nrows of 'x' and 'y' must match")
if(linout && entropy) stop("entropy fit only for logistic units")
if(softmax) {
linout <- TRUE
entropy <- FALSE
}
if(censored) {
linout <- TRUE
entropy <- FALSE
softmax <- TRUE
}
net$n <- c(dim(x)[2L], size, dim(y)[2L])
net$nunits <- as.integer(1L + sum(net$n))
net$nconn <- rep(0, net$nunits+1L)
net$conn <- numeric(0L)
net <- norm.net(net)
if(skip) net <- add.net(net, seq(1L,net$n[1L]),
seq(1L+net$n[1L]+net$n[2L], net$nunits-1L))
if((nwts <- length(net$conn))==0) stop("no weights to fit")
if(nwts > MaxNWts)
stop(gettextf("too many (%d) weights", nwts), domain=NA)
nsunits <- net$nunits
if(linout) nsunits <- net$nunits - net$n[3L]
net$nsunits <- nsunits
net$decay <- decay
net$entropy <- entropy
if(softmax && NCOL(y) < 2L)
stop("'softmax = TRUE' requires at least two response categories")
net$softmax <- softmax
net$censored <- censored
if(missing(Wts))
if(rang > 0) wts <- runif(nwts, -rang, rang)
else wts <- rep(0, nwts)
else wts <- Wts
if(length(wts) != nwts) stop("weights vector of incorrect length")
if(length(mask) != length(wts)) stop("incorrect length of 'mask'")
if(trace) {
cat("# weights: ", length(wts)) #
nw <- sum(mask != 0)
if(nw < length(wts)) cat(" (", nw, " variable)\n",sep="")
else cat("\n")
flush.console()
}
if(length(decay) == 1L) decay <- rep(decay, length(wts))
.C(VR_set_net,
as.integer(net$n),
as.integer(net$nconn),
as.integer(net$conn),
as.double(decay),
as.integer(nsunits),
as.integer(entropy),
as.integer(softmax),
as.integer(censored)
)
ntr <- dim(x)[1L]
nout <- dim(y)[2L]
if(missing(weights)) weights <- rep(1, ntr)
if(length(weights) != ntr || any(weights < 0))
stop("invalid weights vector")
Z <- as.double(cbind(x,y))
storage.mode(weights) <- "double"
tmp <- .C(VR_dovm,
as.integer(ntr), Z, weights,
as.integer(length(wts)),
wts=as.double(wts),
val=double(1),
as.integer(maxit),
as.logical(trace),
as.integer(mask),
as.double(abstol), as.double(reltol),
ifail = integer(1L)
)
net$value <- tmp$val
net$wts <- tmp$wts
net$convergence <- tmp$ifail
tmp <- matrix(.C(VR_nntest,
as.integer(ntr), Z, tclass = double(ntr*nout),
as.double(net$wts))$tclass, ntr, nout)
dimnames(tmp) <- list(rownames(x), colnames(y))
net$fitted.values <- tmp
tmp <- y - tmp
dimnames(tmp) <- list(rownames(x), colnames(y))
net$residuals <- tmp
.C(VR_unset_net)
if(entropy) net$lev <- c("0","1")
if(softmax) net$lev <- colnames(y)
net$call <- match.call()
if(Hess) net$Hessian <- nnetHess(net, x, y, weights)
class(net) <- "nnet"
net
}
predict.nnet <- function(object, newdata, type=c("raw","class"), ...)
{
if(!inherits(object, "nnet")) stop("object not of class \"nnet\"")
type <- match.arg(type)
if(missing(newdata)) z <- fitted(object)
else {
if(inherits(object, "nnet.formula")) { #
## formula fit
newdata <- as.data.frame(newdata)
rn <- row.names(newdata)
## work hard to predict NA for rows with missing data
Terms <- delete.response(object$terms)
m <- model.frame(Terms, newdata, na.action = na.omit,
xlev = object$xlevels)
if (!is.null(cl <- attr(Terms, "dataClasses")))
.checkMFClasses(cl, m)
keep <- match(row.names(m), rn)
x <- model.matrix(Terms, m, contrasts.arg = object$contrasts)
xint <- match("(Intercept)", colnames(x), nomatch=0L)
if(xint > 0L) x <- x[, -xint, drop=FALSE] # Bias term is used for intercepts
} else {
## matrix ... fit
if(is.null(dim(newdata)))
dim(newdata) <- c(1L, length(newdata)) # a row vector
x <- as.matrix(newdata) # to cope with dataframes
if(any(is.na(x))) stop("missing values in 'x'")
keep <- 1L:nrow(x)
rn <- rownames(x)
}
ntr <- nrow(x)
nout <- object$n[3L]
.C(VR_set_net,
as.integer(object$n), as.integer(object$nconn),
as.integer(object$conn), rep(0.0, length(object$wts)),
as.integer(object$nsunits), as.integer(0L),
as.integer(object$softmax), as.integer(object$censored))
z <- matrix(NA, nrow(newdata), nout,
dimnames = list(rn, dimnames(object$fitted.values)[[2L]]))
z[keep, ] <- matrix(.C(VR_nntest,
as.integer(ntr),
as.double(x),
tclass = double(ntr*nout),
as.double(object$wts)
)$tclass, ntr, nout)
.C(VR_unset_net)
}
switch(type, raw = z,
class = {
if(is.null(object$lev)) stop("inappropriate fit for class")
if(ncol(z) > 1L) object$lev[max.col(z)]
else object$lev[1L + (z > 0.5)]
})
}
eval.nn <- function(wts)
{
z <- .C(VR_dfunc,
as.double(wts), df = double(length(wts)), fp = as.double(1))
fp <- z$fp
attr(fp, "gradient") <- z$df
fp
}
add.net <- function(net, from, to)
{
nconn <- net$nconn
conn <- net$conn
for(i in to){
ns <- nconn[i+2L]
cadd <- from
if(nconn[i+1] == ns) cadd <- c(0,from)
con <- NULL
if(ns > 1L) con <- conn[1L:ns]
con <- c(con, cadd)
if(length(conn) > ns) con <- c(con, conn[(ns+1L):length(conn)])
for(j in (i+1L):net$nunits) nconn[j+1L] <- nconn[j+1L]+length(cadd)
conn <- con
}
net$nconn <- nconn
net$conn <- con
net
}
norm.net <- function(net)
{
n <- net$n; n0 <- n[1L]; n1 <- n0+n[2L]; n2 <- n1+n[3L];
if(n[2L] <= 0) return(net)
net <- add.net(net, 1L:n0,(n0+1L):n1)
add.net(net, (n0+1L):n1, (n1+1L):n2)
}
which.is.max <- function(x)
{
y <- seq_along(x)[x == max(x)]
if(length(y) > 1L) sample(y, 1L) else y
}
nnetHess <- function(net, x, y, weights)
{
x <- as.matrix(x)
y <- as.matrix(y)
if(dim(x)[1L] != dim(y)[1L]) stop("dims of 'x' and 'y' must match")
nw <- length(net$wts)
decay <- net$decay
if(length(decay) == 1) decay <- rep(decay, nw)
.C(VR_set_net,
as.integer(net$n),
as.integer(net$nconn),
as.integer(net$conn),
as.double(decay),
as.integer(net$nsunits),
as.integer(net$entropy),
as.integer(net$softmax),
as.integer(net$censored)
)
ntr <- dim(x)[1L]
if(missing(weights)) weights <- rep(1, ntr)
if(length(weights) != ntr || any(weights < 0))
stop("invalid weights vector")
Z <- as.double(cbind(x,y))
storage.mode(weights) <- "double"
z <- matrix(.C(VR_nnHessian, as.integer(ntr), Z, weights,
as.double(net$wts), H = double(nw*nw))$H,
nw, nw)
.C(VR_unset_net)
z
}
class.ind <- function(cl)
{
n <- length(cl)
cl <- as.factor(cl)
x <- matrix(0, n, length(levels(cl)) )
x[(1L:n) + n*(unclass(cl)-1L)] <- 1
dimnames(x) <- list(names(cl), levels(cl))
x
}
print.nnet <- function(x, ...)
{
if(!inherits(x, "nnet")) stop("not a legitimate neural net fit")
cat("a ",x$n[1L],"-",x$n[2L],"-",x$n[3L]," network", sep="")
cat(" with", length(x$wts),"weights\n")
if(length(x$coefnames)) cat("inputs:", x$coefnames, "\noutput(s):",
deparse(formula(x)[[2L]], backtick=TRUE), "\n")
cat("options were -")
tconn <- diff(x$nconn)
if(tconn[length(tconn)] > x$n[2L]+1L) cat(" skip-layer connections ")
if(x$nunits > x$nsunits && !x$softmax) cat(" linear output units ")
if(x$entropy) cat(" entropy fitting ")
if(x$softmax) cat(" softmax modelling ")
if(x$decay[1L] > 0) cat(" decay=", x$decay[1L], sep="")
cat("\n")
invisible(x)
}
coef.nnet <- function(object, ...)
{
wts <- object$wts
wm <- c("b", paste("i", seq_len(object$n[1L]), sep=""))
if(object$n[2L] > 0L)
wm <- c(wm, paste("h", seq_len(object$n[2L]), sep=""))
if(object$n[3L] > 1L) wm <- c(wm,
paste("o", seq_len(object$n[3L]), sep=""))
else wm <- c(wm, "o")
names(wts) <- apply(cbind(wm[1+object$conn],
wm[1L+rep(1L:object$nunits - 1L,
diff(object$nconn))]),
1L, function(x) paste(x, collapse = "->"))
wts
}
summary.nnet <- function(object, ...)
{
class(object) <- c("summary.nnet", class(object))
object
}
print.summary.nnet <- function(x, ...)
{
cat("a ",x$n[1L],"-",x$n[2L],"-",x$n[3L]," network", sep="")
cat(" with", length(x$wts),"weights\n")
cat("options were -")
tconn <- diff(x$nconn)
if(tconn[length(tconn)] > x$n[2L]+1L) cat(" skip-layer connections ")
if(x$nunits > x$nsunits && !x$softmax) cat(" linear output units ")
if(x$entropy) cat(" entropy fitting ")
if(x$softmax) cat(" softmax modelling ")
if(x$decay[1L] > 0) cat(" decay=", x$decay[1L], sep="")
cat("\n")
wts <- format(round(coef.nnet(x),2))
lapply(split(wts, rep(1L:x$nunits, tconn)),
function(x) print(x, quote=FALSE))
invisible(x)
}
# residuals.nnet <- function(object, ...) object$residuals
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