Hi all,
Thanks for the suggestions. Updating the function as below to break the
problem into chunks seemed to do the trick - perhaps there is a relatively
small limit to the size of a vector that R can work with?
Best
rotate <- function(x,y,tilt,threshold){
df.main<-data.frame(x,y)
if(length(x)> threshold){
l <- round(length(x)/ threshold, 0)
dfchunk <- split(df.main, factor(sort(rank(row.names(df.main))%%l)))
n<-length(summary(dfchunk)[,1])
xy<-vector("list", n)
for (i in 1:n){
wk.df <- dfchunk[[i]]
x <- wk.df$x
y <- wk.df$y
d2 <- x^2+y^2
rotate.dis<-sqrt(d2)
or.rad <- atan(x/y)
or.deg <- Rad2Deg(or.rad)
or.deg[is.na(or.deg)] <- 0
tilt.in <- tilt + or.deg
xy[[i]]<-data.frame(Pol2Car(distance=rotate.dis, deg=tilt.in))
}
xy<-do.call("rbind", xy[1:n])
} else {
d2 <- x^2+y^2
rotate.dis<-sqrt(d2)
or.rad <- atan(x/y)
or.deg <- Rad2Deg(or.rad)
n <- length(or.deg)
for(i in 1:n){
if(is.na(or.deg[i])==TRUE) {or.deg[i] <- 0}
}
tilt.in <- tilt + or.deg
xy<-data.frame(Pol2Car (distance=rotate.dis, deg=tilt.in))
}
xy
}
*Ben Caldwell*
Graduate Fellow
University of California, Berkeley
130 Mulford Hall #3114
Berkeley, CA 94720
Office 223 Mulford Hall
(510)859-3358
On Tue, Mar 5, 2013 at 1:44 PM, Peter Alspach <
peter.alsp...@plantandfood.co.nz> wrote:
> Tena koe Benjamin
>
> I haven't looked at you code in detail, but in general ifelse is slow and
> can generally be avoided. For example,
>
> ben <- 1:10^7
> system.time(BEN <- ifelse(ben<10, NA, -ben))
> user system elapsed
> 1.31 0.24 1.56
> system.time({BEN1 <- -ben; BEN1[BEN1> -10] <- NA})
> user system elapsed
> 0.17 0.03 0.20
> all.equal(BEN, BEN1)
> [1] TRUE
>
> HTH ...
>
> Peter Alspach
>
> -----Original Message-----
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
> On Behalf Of Benjamin Caldwell
> Sent: Wednesday, 6 March 2013 10:18 a.m.
> To: r-help
> Subject: [R] Function completely locks up my computer if the input is too
> big
>
> Dear r-help,
>
>
> Somewhere in my innocuous function to rotate an object in Cartesian space
> I've created a monster that completely locks up my computer (requires a
> hard reset every time). I don't know if this is useful description to
> anyone - the mouse still responds, but not the keyboard and not windows
> explorer.
>
> The script only does this when the input matrix is large, and so my
> initial runs didn't catch it as I used a smaller matrix to speed up the
> test runs.
> When I tried an input matrix with a number of dimensions in the same order
> of magnitude as the data I want to read in, R and my computer choked. This
> was a surprise for me, as I've always been able to break execution in the
> past or do other tasks. So i tried it again, and still no dice.
>
> Now I need the function to work as subsequent functions/functionality are
> dependent, and I can't see anything on the face of it that would likely
> cause the issue.
>
> Any insight on why this happens in general or specifically in my case are
> appreciated. Running R 15.2, Platform: x86_64-w64-mingw32/x64 (64-bit) on a
> windows 7 machine with 4 mb RAM. In the meantime I suppose I'll write a
> loop to do this function piece-wise for larger data and see if that helps.
>
> Script is attached and appended below.
>
> Thanks
>
> Ben Caldwell
>
>
>
> #compass to polar coordinates
>
> compass2polar <- function(x) {-x+90}
>
>
>
> #degrees (polar) to radians
>
> Deg2Rad <- function(x) {(x*pi)/180}
>
>
>
> # radians to degrees
>
> Rad2Deg <- function (rad) (rad/pi)*180
>
>
>
> # polar to cartesian coordinates - assumes degrees those from a compass.
> output is a list, x & y of equal length
>
> Pol2Car <- function(distance,deg) {
>
>
> rad <- Deg2Rad(compass2polar(deg))
>
> rad <- rep(rad, length(distance))
>
>
> x <- ifelse(is.na(distance), NA, distance * cos(rad))
>
> y <- ifelse(is.na(distance), NA, distance * sin(rad))
>
>
> x<-round(x,2)
>
> y<-round(y,2)
>
>
> cartes<- list(x,y)
>
> name<-c('x','y')
>
> names(cartes)<-name
>
> cartes
>
> }
>
>
>
>
>
> #rotate an object, with assumed origin at 0,0, in any number of degrees
>
> rotate <- function(x,y,tilt){ 8
>
>
> d2 <- x^2+y^2
>
> rotate.dis<-sqrt(d2)
>
> or.rad <- atan(x/y)
>
> or.deg <- Rad2Deg(or.rad)
>
>
> n <- length(or.deg)
>
> for(i in 1:n){
>
> if(is.na(or.deg[i])==TRUE) {or.deg[i] <- 0}
>
> }
>
> # browser()
>
> tilt.in <- tilt + or.deg
>
>
> xy<-Pol2Car (distance=rotate.dis, deg=tilt.in)
>
> # if(abs(tilt) >= 0) {
>
> # shift.frame <- cbind(xy$x, xy$y)
>
> # shift.frame.val <- shift.frame[shift.frame[,2]==min(shift.frame[,2]),]
>
> # shift.x<- shift.frame.val[1] * -1
>
> # shift.y<- shift.frame.val[2] * -1
>
> # x<-xy$x + shift.x
>
> # y<-xy$y + shift.y
>
> # }
>
> # name <- c('x', 'y')
>
> # xy<-list(x,y)
>
> # names(xy)<-name
>
> xy
>
> }
>
>
> x <- seq(0,5, .5)
>
> y <- seq(0,5, .5)
>
> z <- seq(0,5, .5)
>
> dquad<-expand.grid(x,y,z)
>
> name<-c("y","x","z")
>
> names(dquad)<-name
>
>
> plot(dquad$x, dquad$y, xlim=c(-25,25), ylim=c(-25,25))
>
>
> #this works fine
>
> rotated<-rotate(dquad$x, dquad$y, 45)
>
>
>
> points(rotated$x, rotated$y, col='green')
>
>
> # profiling of both time and memory
>
> Rprof("myFunction.out", memory.profiling=T)
>
> y <- myFunction(x)
>
> Rprof(NULL)
>
> summaryRprof("myFunction.out", memory="both")
>
>
>
> #############
>
> x <- seq(0,5, .1)
>
> y <- seq(0,5, .1)
>
> z <- seq(0,5, .1)
>
> dquad<-expand.grid(x,y,z)
>
> name<-c("y","x","z")
>
> names(dquad)<-name
>
> # running the below locks up my machine (commented out to avoid accidental
> run)
>
> # rotated<-rotate(dquad$x, dquad$y, 45)
>
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