Merry Xmas to all,
I am writing a function and curiously this runs sometimes on one data set
and fails on another and i cannot figure out why.
Any help much appreciated.
If i run the code below with
data <- iris[ ,1:4]
The code runs fine, but if i run on a large dataset i get the following
error (showing data structures as matrix is large)
> str(cluster.data)
num [1:9985, 1:811] 0 0 0 0 0 0 0 0 0 0 ...
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:811] "1073949105" "1073930585" "1073843224" "1073792624" ...
#(This is intended to be chr)
> str(iris)
'data.frame': 150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
$ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
$ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
$ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
$ Species : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 1 1 1
1 1 1 ...
> str(as.matrix(iris[,1:4]))
num [1:150, 1:4] 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:4] "Sepal.Length" "Sepal.Width" "Petal.Length" "Petal.Width"
n.cols <- ncol(data)
n.rows <- nrow(data)
X <- as.matrix(data)
stepsize <- 0.05
c1 <- (2 * pi) ** (n.cols / 2)
c2 <- n.rows * (smoothing ** (n.cols + 2))
c3 <- n.rows * (smoothing ** n.cols)
Kexp <- function(sqs){
return (exp((-1 * sqs) / (2 * smoothing ** 2)))
}
FindGradient <- function(x){
XmY <- t(x - t(X))
sqsum <- rowSums(XmY * XmY)
K <- sapply(sqsum, Kexp)
dens <- ((c1 * c3) ** -1) * sum(K)
grad <- -1 * ((c1 * c2) ** -1) * colSums(K * XmY)
return (list(gradient = grad,
density = dens))
}
attractors <- matrix(0, n.rows, n.cols)
densities <- matrix(0, n.rows)
> density.attractors <-
sapply(rep(1:n.rows), function(i) {
notconverged <- TRUE
# For each row loop through and find the attractor and density value.
x <- (X[i, ])
iters <- as.integer(1)
# Run gradient ascent for each point to obtain x*
while(notconverged == TRUE) {
find.gradient <- FindGradient(x)
next.x <- x + stepsize * find.gradient$gradient
change <- sqrt(sum((next.x - x) * (next.x - x)))
notconverged <- ifelse(change > tol, TRUE, FALSE)
x <- next.x
iters <- iters + 1
}
# store the attractor and density value
return(c(densities[i, ] <- find.gradient$density,
attractors[i, ] <- x))
})
Error in while (notconverged == TRUE) { :
missing value where TRUE/FALSE needed
>
Any help would be great
Mike
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