Hello,
Em 18-07-2012 09:06, Patrick Burns escreveu:
It looks to me like the following
should do what you want:
f2 <- function(dotot) array(FALSE, c(dotot, 1))
What am I missing?
That matrix is even faster?
f2 <- function(dotot) array(FALSE, c(dotot, 1))
f3 <- function(dotot) matrix(FALSE, dotot, 1)
t2 <- system.time(replicate(1e4, f2(1000)))
t3 <- system.time(replicate(1e4, f3(1000)))
rbind(t2, t3, t2/t3)
Rui Barradas
Pat
On 17/07/2012 21:58, Johan Henriksson wrote:
thanks for the link! I should read it through. that said, I didn't find
any good general solution to the problem so here I post some attempts
for general input. maybe someone knows how to speed this up. both my
solutions are theoretically O(n) for creating a list of n elements. The
function to improve is O(n^2) which should suck tremendously - but the
slow execution of R probably blows up the constant factor of the smarter
solutions.
Array doubling comes close in speed for large lists but it would be
great if it could be comparable for smaller lists. One hidden cost I see
directly is that allocating a list in R is O(n), not O(1) (or close),
since it always fills it with values. Is there a way around this? I
guess by using C, one could just malloc() and leave the content
undefined - but is there no better way?
thanks,
/Johan
################################
# the function we wish to improve
f<-function(dotot){
v<-matrix(ncol=1,nrow=0)
for(i in 1:dotot){
v<-rbind(v,FALSE)
}
return(v)
}
##########################
# first attempt: linked lists
emptylist <- NA
addtolist <- function(x,prev){
return(list(x,prev))
}
g<-function(dotot){
v<-emptylist
for(i in 1:dotot){
v<-addtolist(FALSE,v)
}
return(v)
}
####################################
# second attempt: array doubling
emptyexpandlist<-list(nelem=0,l=matrix(ncol=1,nrow=0))
addexpandlist<-function(x,prev){
if(nrow(prev$l)==prev$nelem){
nextsize<-max(nrow(prev$l),1)
prev$l<-rbind(prev$l,matrix(ncol=1,nrow=nextsize))
}
prev$nelem<-prev$nelem+1
prev$l[prev$nelem]<-x
return(prev)
}
compressexpandlist<-function(prev){
return(as.vector(prev$l[1:prev$nelem]))
}
h<-function(dotot){
v<-emptyexpandlist
for(i in 1:dotot){
v<-addexpandlist(FALSE,v)
}
return(compressexpandlist(v))
}
#########################################
dotot=100000
system.time(f(dotot))
#system.time(g(dotot))
system.time(h(dotot))
On Tue, Jul 17, 2012 at 8:42 PM, Patrick Burns <pbu...@pburns.seanet.com
<mailto:pbu...@pburns.seanet.com>> wrote:
Johan,
If you don't know 'The R Inferno', it might
help a little. Circle 2 has an example of
how to efficiently (relatively speaking) grow
an object if you don't know the final length.
http://www.burns-stat.com/__pages/Tutor/R_inferno.pdf
<http://www.burns-stat.com/pages/Tutor/R_inferno.pdf>
If you gave a simple example of how your code
looks now and what you want it to do, then you
might get some ideas of how to improve it.
Pat
On 17/07/2012 12:47, Johan Henriksson wrote:
Hello!
I am optimizing my code in R and for this I need to know a bit
more about
the internals. It would help tremendously if someone could link
me to a
page with O()-complexities of all the operations.
In this particular case, I need something like a linked list
with O(1)
insertLast/First ability. I can't preallocate a vector since I
do not know
the final size of the list ahead of time.
The classic array-doubling trick would give me O(1) amortized
time but it's
a bit messy. The other alternative I see would be to recursively
store
lists (elem, (elem, (elem, (...)))), which I take also would
work? But I'd
rather go for a standard R solution if there is one!
cheers,
/Johan
--
Patrick Burns
pbu...@pburns.seanet.com <mailto:pbu...@pburns.seanet.com>
twitter: @portfolioprobe
http://www.portfolioprobe.com/__blog
<http://www.portfolioprobe.com/blog>
http://www.burns-stat.com
(home of 'Some hints for the R beginner'
and 'The R Inferno')
--
--
-----------------------------------------------------------
Johan Henriksson, PhD
Karolinska Institutet
Ecobima AB - Custom solutions for life sciences
http://www.ecobima.se <http://www.ecobima.com> http://mahogny.areta.org
http://www.endrov.net
<http://www.endrov.net>
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