Re: [R] nested for loops too slow
Well, sort of...
aggregate() is basically a wrapper for lapply(), which ultimately must loop
over the function call at the R interpreter level, as opposed to vectorized
functions that loop at the C level and hence can be orders of magnitude
faster. As a result, there is often little difference in efficiency between
explicit and *smart* (in the sense that Pat Burns has already pointed out
of not growing structures at each iteration,among other things) for()
looping and apply-type calls. For some of us, the chief advantage of the
*apply idioms is that the code is more readable and maintainable, with R
handling fussy details of loop indexing, for example.lapply() is also more
in keeping with the functional programming paradigm.
Others
find both these "virtues" to be annoyances,
however, and prefer explicit *smart* looping. Chaque un á
son goû
t
.
None of which necessarily denies the wisdom of the approach you've
suggested, however. It may indeed be considerably faster,
but timing will have to tell. I am just trying to correct
(again)
the
widely held misperception
that yo
u
seem to
express
.
Cheers,
Bert
Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374
"Data is not information. Information is not knowledge. And knowledge is
certainly not wisdom."
Clifford Stoll
On Sun, Apr 12, 2015 at 1:48 PM, Thierry Onkelinx
wrote:
> You don't need loops at all.
>
> grw <- aggregate(gw ~ ts + ISEG + iter, data = dat, FUN = sum)
> GRW <- aggregate(gw ~ ts + ISEG, data = grw, FUN = function(x){max(x) -
> min(x)})
> DC <- aggregate(div ~ ts + ISEG, data = subset(dat, IRCH == 1), FUN =
> function(x){max(x) - min(x)})
> iter <- aggregate(iter ~ ts + ISEG, data = subset(dat, IRCH == 1), FUN
> = max)
> tmp <- merge(DC, iter)
> merge(tmp, GRW)
>
> another option is to use the plyr package
>
> library(plyr)
> merge(
> ddply(
> subset(dat, IRCH == 1),
> c("ts", "ISEG"),
> summarize,
> divChng = max(div) - min(div),
> max.iter = max(iter)
> ),
> ddply(
> dat,
> c("ts", "ISEG"),
> summarize,
> gwChng = diff(range(ave(gw, iter, FUN = sum)))
> )
> )
>
> Best regards,
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
> Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
>
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> 2015-04-12 15:47 GMT+02:00 Morway, Eric :
>
> > The small example below works lighting-fast; however, when I run the same
> > script on my real problem, a 1Gb text file, the for loops have been
> running
> > for over 24 hrs and I have no idea if the processing is 10% done or 90%
> > done. I have not been able to figure out a betteR way to code up the
> > material within the for loops at the end of the example below. The
> > contents of divChng, the final product, are exactly what I'm after, but I
> > need help formulating more efficient R script, I've got two more 1Gb
> files
> > to process after the current one finishes, whenever that is...
> >
> > I appreciate any insights/solutions, Eric
> >
> > dat <- read.table(textConnection("ISEG IRCH div gw
> > 1 1 265 229
> > 1 2 260 298
> > 1 3 234 196
> > 54 1 432 485
> > 54 39 467 485
> > 54 40 468 468
> > 54 41 460 381
> > 54 42 489 502
> > 1 1 265 317
> > 1 2 276 225
> > 1 3 217 164
> > 54 1 430 489
> > 54 39 456 495
> > 54 40 507 607
> > 54 41 483 424
> > 54 42 457 404
> > 1 1 265 278
> > 1 2 287 370
> > 1 3 224 274
> > 54 1 412 585
> > 54 39 473 532
> > 54 40 502 595
> > 54 41 497 441
> > 54 42 447 467
> > 1 1 230 258
> > 1 2 251 152
> > 1 3 199 179
> > 54 1 412 415
> > 54 39 439 538
> > 54 40 474 486
> > 54 41 477 484
> > 54 42 413 346
> > 1 1 230 171
> > 1 2 262 171
> > 1 3 217 263
> > 54 1 432 485
> > 54 39 455 482
> > 54 40 493 419
> > 54 41 489 536
> > 54 42 431 504
> > 1 1 1002 1090
> > 1 2 1222 1178
> > 1 3 1198 1177
> > 54 1 1432 1485
> > 54 39 1876 1975
> > 54 40 1565 1646
> > 54 41 1455 1451
> > 54 42 1427 1524
> > 1 1 1002 968
> > 1 2 1246 1306
> > 1 3 1153 1158
> > 54 1 1532 1585
> > 54 39 1790 1889
> > 54 40 1490 1461
> > 54 41 1518 1536
> > 54 42 1486 1585
> > 1 1 1002 1081
> > 1 2 1229 1262
> > 1 3 1142 1241
> > 54 1 1632 1659
> > 54 39 1797 1730
> > 54 40 1517 1466
> > 54 41 1527 1589
Re: [R] nested for loops too slow
You don't need loops at all.
grw <- aggregate(gw ~ ts + ISEG + iter, data = dat, FUN = sum)
GRW <- aggregate(gw ~ ts + ISEG, data = grw, FUN = function(x){max(x) -
min(x)})
DC <- aggregate(div ~ ts + ISEG, data = subset(dat, IRCH == 1), FUN =
function(x){max(x) - min(x)})
iter <- aggregate(iter ~ ts + ISEG, data = subset(dat, IRCH == 1), FUN
= max)
tmp <- merge(DC, iter)
merge(tmp, GRW)
another option is to use the plyr package
library(plyr)
merge(
ddply(
subset(dat, IRCH == 1),
c("ts", "ISEG"),
summarize,
divChng = max(div) - min(div),
max.iter = max(iter)
),
ddply(
dat,
c("ts", "ISEG"),
summarize,
gwChng = diff(range(ave(gw, iter, FUN = sum)))
)
)
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
2015-04-12 15:47 GMT+02:00 Morway, Eric :
> The small example below works lighting-fast; however, when I run the same
> script on my real problem, a 1Gb text file, the for loops have been running
> for over 24 hrs and I have no idea if the processing is 10% done or 90%
> done. I have not been able to figure out a betteR way to code up the
> material within the for loops at the end of the example below. The
> contents of divChng, the final product, are exactly what I'm after, but I
> need help formulating more efficient R script, I've got two more 1Gb files
> to process after the current one finishes, whenever that is...
>
> I appreciate any insights/solutions, Eric
>
> dat <- read.table(textConnection("ISEG IRCH div gw
> 1 1 265 229
> 1 2 260 298
> 1 3 234 196
> 54 1 432 485
> 54 39 467 485
> 54 40 468 468
> 54 41 460 381
> 54 42 489 502
> 1 1 265 317
> 1 2 276 225
> 1 3 217 164
> 54 1 430 489
> 54 39 456 495
> 54 40 507 607
> 54 41 483 424
> 54 42 457 404
> 1 1 265 278
> 1 2 287 370
> 1 3 224 274
> 54 1 412 585
> 54 39 473 532
> 54 40 502 595
> 54 41 497 441
> 54 42 447 467
> 1 1 230 258
> 1 2 251 152
> 1 3 199 179
> 54 1 412 415
> 54 39 439 538
> 54 40 474 486
> 54 41 477 484
> 54 42 413 346
> 1 1 230 171
> 1 2 262 171
> 1 3 217 263
> 54 1 432 485
> 54 39 455 482
> 54 40 493 419
> 54 41 489 536
> 54 42 431 504
> 1 1 1002 1090
> 1 2 1222 1178
> 1 3 1198 1177
> 54 1 1432 1485
> 54 39 1876 1975
> 54 40 1565 1646
> 54 41 1455 1451
> 54 42 1427 1524
> 1 1 1002 968
> 1 2 1246 1306
> 1 3 1153 1158
> 54 1 1532 1585
> 54 39 1790 1889
> 54 40 1490 1461
> 54 41 1518 1536
> 54 42 1486 1585
> 1 1 1002 1081
> 1 2 1229 1262
> 1 3 1142 1241
> 54 1 1632 1659
> 54 39 1797 1730
> 54 40 1517 1466
> 54 41 1527 1589
> 54 42 1514 1612"),header=TRUE)
>
> dat$seq <- ifelse(dat$ISEG==1 & dat$IRCH==1, 1, 0)
> tmp <- diff(dat[dat$seq==1,]$div)!=0
> dat$idx <- 0
> dat[dat$seq==1,][c(TRUE,tmp),]$idx <- 1
> dat$ts <- cumsum(dat$idx)
> dat$iter <- ave(dat$seq, dat$ts,FUN=cumsum)
> dat$ct <- seq(1:length(dat[,1]))
>
> timeStep <- unique(dat$ts)
> SEG <- unique(dat$ISEG)
> divChng <- data.frame(ts=NA, ISEG=NA, divChng=NA, gwChng=NA, iter=NA)
>
> #Can the following be rescripted for better harnessing R's processing
> power?
>
> for (i in 1:length(timeStep)){
> for (j in 1:length(SEG)){
> datTS <- subset(dat,ts==timeStep[i] & ISEG==SEG[j] & IRCH==1)
> datGW <- subset(dat,ts==timeStep[i] & ISEG==SEG[j])
> grw <- aggregate(gw ~ iter, datGW, sum)
>
> DC <- max(datTS$div)-min(datTS$div)
> GRW <- max(grw$gw) - min(grw$gw)
> divChng <- rbind(divChng,c(datTS$ts[1], SEG[j], DC, GRW,
> max(datTS$iter)))
> }
> }
> divChng <- divChng[!is.na(divChng$ISEG),]
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented
Re: [R] nested for loops too slow
You are certainly in Circle 2 of 'The R Inferno',
which I suspect is where almost all of the
computation time is coming from.
Instead of doing:
divChng <- rbind(divChng,c(datTS$ts[1], SEG[j], DC, GRW,
max(datTS$iter)))
it would be much better to create 'divChng' to
be the final length and then in the loop do:
divChng[count,] <- c(datTS$ts[1], SEG[j], DC, GRW,
max(datTS$iter))
count <- count + 1
You may also want to explore 'tapply'.
If this is something you will be doing
a lot of, then you should probably learn
the 'data.table' package.
http://www.burns-stat.com/documents/books/the-r-inferno/
Pat
On 12/04/2015 14:47, Morway, Eric wrote:
The small example below works lighting-fast; however, when I run the same
script on my real problem, a 1Gb text file, the for loops have been running
for over 24 hrs and I have no idea if the processing is 10% done or 90%
done. I have not been able to figure out a betteR way to code up the
material within the for loops at the end of the example below. The
contents of divChng, the final product, are exactly what I'm after, but I
need help formulating more efficient R script, I've got two more 1Gb files
to process after the current one finishes, whenever that is...
I appreciate any insights/solutions, Eric
dat <- read.table(textConnection("ISEG IRCH div gw
1 1 265 229
1 2 260 298
1 3 234 196
54 1 432 485
54 39 467 485
54 40 468 468
54 41 460 381
54 42 489 502
1 1 265 317
1 2 276 225
1 3 217 164
54 1 430 489
54 39 456 495
54 40 507 607
54 41 483 424
54 42 457 404
1 1 265 278
1 2 287 370
1 3 224 274
54 1 412 585
54 39 473 532
54 40 502 595
54 41 497 441
54 42 447 467
1 1 230 258
1 2 251 152
1 3 199 179
54 1 412 415
54 39 439 538
54 40 474 486
54 41 477 484
54 42 413 346
1 1 230 171
1 2 262 171
1 3 217 263
54 1 432 485
54 39 455 482
54 40 493 419
54 41 489 536
54 42 431 504
1 1 1002 1090
1 2 1222 1178
1 3 1198 1177
54 1 1432 1485
54 39 1876 1975
54 40 1565 1646
54 41 1455 1451
54 42 1427 1524
1 1 1002 968
1 2 1246 1306
1 3 1153 1158
54 1 1532 1585
54 39 1790 1889
54 40 1490 1461
54 41 1518 1536
54 42 1486 1585
1 1 1002 1081
1 2 1229 1262
1 3 1142 1241
54 1 1632 1659
54 39 1797 1730
54 40 1517 1466
54 41 1527 1589
54 42 1514 1612"),header=TRUE)
dat$seq <- ifelse(dat$ISEG==1 & dat$IRCH==1, 1, 0)
tmp <- diff(dat[dat$seq==1,]$div)!=0
dat$idx <- 0
dat[dat$seq==1,][c(TRUE,tmp),]$idx <- 1
dat$ts <- cumsum(dat$idx)
dat$iter <- ave(dat$seq, dat$ts,FUN=cumsum)
dat$ct <- seq(1:length(dat[,1]))
timeStep <- unique(dat$ts)
SEG <- unique(dat$ISEG)
divChng <- data.frame(ts=NA, ISEG=NA, divChng=NA, gwChng=NA, iter=NA)
#Can the following be rescripted for better harnessing R's processing power?
for (i in 1:length(timeStep)){
for (j in 1:length(SEG)){
datTS <- subset(dat,ts==timeStep[i] & ISEG==SEG[j] & IRCH==1)
datGW <- subset(dat,ts==timeStep[i] & ISEG==SEG[j])
grw <- aggregate(gw ~ iter, datGW, sum)
DC <- max(datTS$div)-min(datTS$div)
GRW <- max(grw$gw) - min(grw$gw)
divChng <- rbind(divChng,c(datTS$ts[1], SEG[j], DC, GRW,
max(datTS$iter)))
}
}
divChng <- divChng[!is.na(divChng$ISEG),]
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] nested for loops too slow
The small example below works lighting-fast; however, when I run the same
script on my real problem, a 1Gb text file, the for loops have been running
for over 24 hrs and I have no idea if the processing is 10% done or 90%
done. I have not been able to figure out a betteR way to code up the
material within the for loops at the end of the example below. The
contents of divChng, the final product, are exactly what I'm after, but I
need help formulating more efficient R script, I've got two more 1Gb files
to process after the current one finishes, whenever that is...
I appreciate any insights/solutions, Eric
dat <- read.table(textConnection("ISEG IRCH div gw
1 1 265 229
1 2 260 298
1 3 234 196
54 1 432 485
54 39 467 485
54 40 468 468
54 41 460 381
54 42 489 502
1 1 265 317
1 2 276 225
1 3 217 164
54 1 430 489
54 39 456 495
54 40 507 607
54 41 483 424
54 42 457 404
1 1 265 278
1 2 287 370
1 3 224 274
54 1 412 585
54 39 473 532
54 40 502 595
54 41 497 441
54 42 447 467
1 1 230 258
1 2 251 152
1 3 199 179
54 1 412 415
54 39 439 538
54 40 474 486
54 41 477 484
54 42 413 346
1 1 230 171
1 2 262 171
1 3 217 263
54 1 432 485
54 39 455 482
54 40 493 419
54 41 489 536
54 42 431 504
1 1 1002 1090
1 2 1222 1178
1 3 1198 1177
54 1 1432 1485
54 39 1876 1975
54 40 1565 1646
54 41 1455 1451
54 42 1427 1524
1 1 1002 968
1 2 1246 1306
1 3 1153 1158
54 1 1532 1585
54 39 1790 1889
54 40 1490 1461
54 41 1518 1536
54 42 1486 1585
1 1 1002 1081
1 2 1229 1262
1 3 1142 1241
54 1 1632 1659
54 39 1797 1730
54 40 1517 1466
54 41 1527 1589
54 42 1514 1612"),header=TRUE)
dat$seq <- ifelse(dat$ISEG==1 & dat$IRCH==1, 1, 0)
tmp <- diff(dat[dat$seq==1,]$div)!=0
dat$idx <- 0
dat[dat$seq==1,][c(TRUE,tmp),]$idx <- 1
dat$ts <- cumsum(dat$idx)
dat$iter <- ave(dat$seq, dat$ts,FUN=cumsum)
dat$ct <- seq(1:length(dat[,1]))
timeStep <- unique(dat$ts)
SEG <- unique(dat$ISEG)
divChng <- data.frame(ts=NA, ISEG=NA, divChng=NA, gwChng=NA, iter=NA)
#Can the following be rescripted for better harnessing R's processing power?
for (i in 1:length(timeStep)){
for (j in 1:length(SEG)){
datTS <- subset(dat,ts==timeStep[i] & ISEG==SEG[j] & IRCH==1)
datGW <- subset(dat,ts==timeStep[i] & ISEG==SEG[j])
grw <- aggregate(gw ~ iter, datGW, sum)
DC <- max(datTS$div)-min(datTS$div)
GRW <- max(grw$gw) - min(grw$gw)
divChng <- rbind(divChng,c(datTS$ts[1], SEG[j], DC, GRW,
max(datTS$iter)))
}
}
divChng <- divChng[!is.na(divChng$ISEG),]
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested "for" loops
I sent a post yesterday that I found out why my function didn't work. It's ok now it works. Thank you all. -- View this message in context: http://r.789695.n4.nabble.com/nested-for-loops-tp3992089p3994996.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested "for" loops
No idea how this relates to what you said originally but glad you got it all worked out. And let us all reiterate: really, don't use nested for loops...there's a better way: promise! Michael On Sat, Nov 5, 2011 at 2:20 PM, nick_pan wrote: > I found the way out - it was because the borders of the vectors was close > enough thats why I had the same result while I was adding points to the > sequence. The example I gave was irrelevant but I made in order to find out > that the problem was. > Thank you all for your answers. > > > -- > View this message in context: > http://r.789695.n4.nabble.com/nested-for-loops-tp3992089p3993917.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested "for" loops
Bert, this is not helpful. Since for loops and apply functions are not vectorized, why are you admonishing Carl that vectorizing doesn't always speed up algorithms? He didn't reference apply functions as being vectorized. But you seem to be doing so. I would assert that vectorizing DOES always speed up algorithms, but things people sometimes think are vectorizing are not really. --- Jeff Newmiller The . . Go Live... DCN: Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Bert Gunter wrote: Carl: "Almost anything you can do in a for() loop can be done easier and faster with vectorization.-- " That is false: while this is certainly true for a great many basic vectorized operations, it is certainly false for most other things -- simulations are a typical example. Note that __ply type operations in base R, plyr , and other packages are (generally) _not_vectorized; they are "disguised" loops. Explicit for() loops are often just as fast or even a bit faster, though many of us prefer what we consider the more transparent functional style code of the __ply's. Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[alternative HTML version deleted]] _ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested "for" loops
I found the way out - it was because the borders of the vectors was close enough thats why I had the same result while I was adding points to the sequence. The example I gave was irrelevant but I made in order to find out that the problem was. Thank you all for your answers. -- View this message in context: http://r.789695.n4.nabble.com/nested-for-loops-tp3992089p3993917.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested "for" loops
Carl: "Almost anything you can do in a for() loop can be done easier and faster with vectorization.-- " That is false: while this is certainly true for a great many basic vectorized operations, it is certainly false for most other things -- simulations are a typical example. Note that __ply type operations in base R, plyr , and other packages are (generally) _not_vectorized; they are "disguised" loops. Explicit for() loops are often just as fast or even a bit faster, though many of us prefer what we consider the more transparent functional style code of the __ply's. Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested "for" loops
You need to define "l" as a dimensioned object , either a vector or an array,
and then assign the value of your calculation to the correctly indexed
"location" in that object. Otherwise you are just overwriting the value each
time through the loop. Use these help pages (and review "Introduction to R"
?array
?vector
?"["
On Nov 4, 2011, at 7:49 PM, nick_pan wrote:
> Hi all , I have written a code with nested "for" loops .
> The aim is to estimate the maximum likelihood by creating 3 vectors with the
> same length( sequence )
> and then to utilize 3 "for" loops to make combinations among the 3 vectors ,
> which are (length)^3 in number , and find the one that maximize the
> likelihood ( maximum likelihood estimator).
>
>
> The code I created, runs but I think something goes wrong...because when I
> change the length of the vectors but not the bounds the result is the
> same!!!
>
> I will give a simple example(irrelevant but proportional to the above) to
> make it more clear...
>
> Lets say we want to find the combination that maximize the multiplication of
> the entries of some vectors.
>
> V1<-c(1,2,3)
> V2<-c(5, 2 , 4)
> V3<-c( 4, 3, 6)
>
> The combination we look for is ( 3 , 5 , 6) that give us 3*5*6 = 90
>
> If I apply the following in R , I won't take this result
>
> V1<-c(1,2,3)
> V2<-c(5, 2 , 4)
> V3<-c( 4, 3, 6)
>
> for( i in V1){
> for( j in V2) {
> for( k in V3){
>
> l<- i*j*k
>
> }
> }
> }
> l
>
> Then " l<- i*j*k " is number and not vector(of all multiplications of all
> the combinations) , and is 3*4*6 = 72.
>
> How can I fix the code?
>
>
>
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/nested-for-loops-tp3992089p3992089.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested "for" loops
If in fact this is homework, you will do yourself, your classmates, and possibly your teacher if you let them know that, at least in R, almost anything you can do in a for() loop can be done easier and faster with vectorization. If you teacher can't comprehend this, get him fired. a<-c(4,6,3) b<- c( 9,4,1) d <- c(4,7,2,8) winning.value <- max(outer(a,outer(b,d,"*"),"*")) From: R. Michael Weylandt Date: Sat, 05 Nov 2011 10:21:05 -0400 Why do you need to do it with nested for loops? It is of course possible - and I hinted how to do it in my first email - but there's no reason as far as I can see to do so, particularly as a means of MLE. Sounds suspiciously like homework... Michael On Nov 4, 2011, at 10:14 PM, nick_pan wrote: > Thank you , this works but I have to do it with nested for loops... > > Could you suggest me a way ? > -- Sent from my Cray XK6 "Pendeo-navem mei anguillae plena est." __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested "for" loops
Why do you need to do it with nested for loops? It is of course possible - and I hinted how to do it in my first email - but there's no reason as far as I can see to do so, particularly as a means of MLE. Sounds suspiciously like homework... Michael On Nov 4, 2011, at 10:14 PM, nick_pan wrote: > Thank you , this works but I have to do it with nested for loops... > > Could you suggest me a way ? > > > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/nested-for-loops-tp3992089p3992324.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested "for" loops
Thank you , this works but I have to do it with nested for loops... Could you suggest me a way ? -- View this message in context: http://r.789695.n4.nabble.com/nested-for-loops-tp3992089p3992324.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested "for" loops
Your problem is that you redefine l each time through the loops and
don't record old values; you could do so by using c() for
concatenation, but perhaps this is what you are looking for:
exp(rowSums(log(expand.grid(V1, V2, V3
Hope this helps,
Michael
On Fri, Nov 4, 2011 at 7:49 PM, nick_pan wrote:
> Hi all , I have written a code with nested "for" loops .
> The aim is to estimate the maximum likelihood by creating 3 vectors with the
> same length( sequence )
> and then to utilize 3 "for" loops to make combinations among the 3 vectors ,
> which are (length)^3 in number , and find the one that maximize the
> likelihood ( maximum likelihood estimator).
>
>
> The code I created, runs but I think something goes wrong...because when I
> change the length of the vectors but not the bounds the result is the
> same!!!
>
> I will give a simple example(irrelevant but proportional to the above) to
> make it more clear...
>
> Lets say we want to find the combination that maximize the multiplication of
> the entries of some vectors.
>
> V1<-c(1,2,3)
> V2<-c(5, 2 , 4)
> V3<-c( 4, 3, 6)
>
> The combination we look for is ( 3 , 5 , 6) that give us 3*5*6 = 90
>
> If I apply the following in R , I won't take this result
>
> V1<-c(1,2,3)
> V2<-c(5, 2 , 4)
> V3<-c( 4, 3, 6)
>
> for( i in V1){
> for( j in V2) {
> for( k in V3){
>
> l<- i*j*k
>
> }
> }
> }
> l
>
> Then " l<- i*j*k " is number and not vector(of all multiplications of all
> the combinations) , and is 3*4*6 = 72.
>
> How can I fix the code?
>
>
>
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/nested-for-loops-tp3992089p3992089.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] nested "for" loops
Hi all , I have written a code with nested "for" loops .
The aim is to estimate the maximum likelihood by creating 3 vectors with the
same length( sequence )
and then to utilize 3 "for" loops to make combinations among the 3 vectors ,
which are (length)^3 in number , and find the one that maximize the
likelihood ( maximum likelihood estimator).
The code I created, runs but I think something goes wrong...because when I
change the length of the vectors but not the bounds the result is the
same!!!
I will give a simple example(irrelevant but proportional to the above) to
make it more clear...
Lets say we want to find the combination that maximize the multiplication of
the entries of some vectors.
V1<-c(1,2,3)
V2<-c(5, 2 , 4)
V3<-c( 4, 3, 6)
The combination we look for is ( 3 , 5 , 6) that give us 3*5*6 = 90
If I apply the following in R , I won't take this result
V1<-c(1,2,3)
V2<-c(5, 2 , 4)
V3<-c( 4, 3, 6)
for( i in V1){
for( j in V2) {
for( k in V3){
l<- i*j*k
}
}
}
l
Then " l<- i*j*k " is number and not vector(of all multiplications of all
the combinations) , and is 3*4*6 = 72.
How can I fix the code?
--
View this message in context:
http://r.789695.n4.nabble.com/nested-for-loops-tp3992089p3992089.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested for loops
What do you want to do with the data being genereated? In the loop
you have, it will just return the last value generated. Let me ask my
favorite question: "What is the problem you are trying to solve". If
you get a memory problem with expand.grid, then if you are trying to
store the values in the 'for' loop, you will have the same problem.
How big is 'n'? If it is 3, you will have this many values:
> 3^20
[1] 3486784401
What are you going to do with them?
On Mon, Jul 5, 2010 at 5:06 PM, Senay ASMA wrote:
> Dear Admin,
> I will appreciate if you advise me an effective way to write the following R
> code including nested for loops. I cannot do it by using expand.grid
> function because it results with memory allocation problems.
> Thanks for your time and consideration.
>
> for(d1 in 0:n){
> for(d2 in 0:n){
> for(d3 in 0:n){
> for(d4 in 0:n){
> for(d5 in 0:n){
> for(d6 in 0:n){
> for(d7 in 0:n){
> for(d8 in 0:n){
> for(d9 in 0:n){
> for(d10 in 0:n){
> for(d11 in 0:n){
> for(d12 in 0:n){
> for(d13 in 0:n){
> for(d14 in 0:n){
> for(d15 in 0:n){
> for(d16 in 0:n){
> for(d17 in 0:n){
> for(d18 in 0:n){
> for(d19 in 0:n){
> for(d20 in 0:n){
>
> list=c(d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20)
>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] nested for loops
Le 05/07/10 23:06, Senay ASMA a écrit :
Dear Admin,
I will appreciate if you advise me an effective way to write the following R
code including nested for loops. I cannot do it by using expand.grid
function because it results with memory allocation problems.
Thanks for your time and consideration.
for(d1 in 0:n){
for(d2 in 0:n){
for(d3 in 0:n){
for(d4 in 0:n){
for(d5 in 0:n){
for(d6 in 0:n){
for(d7 in 0:n){
for(d8 in 0:n){
for(d9 in 0:n){
for(d10 in 0:n){
for(d11 in 0:n){
for(d12 in 0:n){
for(d13 in 0:n){
for(d14 in 0:n){
for(d15 in 0:n){
for(d16 in 0:n){
for(d17 in 0:n){
for(d18 in 0:n){
for(d19 in 0:n){
for(d20 in 0:n){
list=c(d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20)
Probably not what you want, but this should replicate the same effect as
the code you posted:
list <- rep( n, 20 )
Romain
--
Romain Francois
Professional R Enthusiast
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
|- http://bit.ly/98Uf7u : Rcpp 0.8.1
|- http://bit.ly/c6YnCi : graph gallery collage
`- http://bit.ly/bZ7ltC : inline 0.3.5
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] nested for loops
Dear Admin,
I will appreciate if you advise me an effective way to write the following R
code including nested for loops. I cannot do it by using expand.grid
function because it results with memory allocation problems.
Thanks for your time and consideration.
for(d1 in 0:n){
for(d2 in 0:n){
for(d3 in 0:n){
for(d4 in 0:n){
for(d5 in 0:n){
for(d6 in 0:n){
for(d7 in 0:n){
for(d8 in 0:n){
for(d9 in 0:n){
for(d10 in 0:n){
for(d11 in 0:n){
for(d12 in 0:n){
for(d13 in 0:n){
for(d14 in 0:n){
for(d15 in 0:n){
for(d16 in 0:n){
for(d17 in 0:n){
for(d18 in 0:n){
for(d19 in 0:n){
for(d20 in 0:n){
list=c(d1,d2,d3,d4,d5,d6,d7,d8,d9,d10,d11,d12,d13,d14,d15,d16,d17,d18,d19,d20)
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested For loops
Wouldn't the best approach be to adapt the acf function already
available in R and change it only to suit your needs?
cheers,
Paul
baloo mia wrote:
In the ACF(nlme) the normalization of the numerator has been done by N and I
want to normalize it by N-k, where N is the observations and k is the lag.
Baloo
--- On Tue, 12/22/09, ONKELINX, Thierry wrote:
From: ONKELINX, Thierry
Subject: RE: [R] Nested For loops
To: "baloo mia" , r-help@r-project.org
Date: Tuesday, December 22, 2009, 1:00 AM
Baloo,
Why don't you use the built-in acf function?
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens
baloo mia
Verzonden: dinsdag 22 december 2009 2:07
Aan: r-help@r-project.org
Onderwerp: [R] Nested For loops
Dear R experts,
Might be very simple question to ask but would be insightful. As the same story of nested
"for loops". following is the code that I am using to get the autocorrelation
function of the sample data. I have tried to get rid of for loops but since I am touching
R after such a long time that I need to practice more but I need help to revive my
skills. I know that apply() or sapply() would be beneficial. I need help...
Best Wishes,
Baloo
R code
--
acf_wal <- function (infile) {
data<-read.table(infile)
data_value <- data[,-1]
data_value_mean <- mean(data_value)
data_value_square <- (data_value - data_value_mean) ^ 2
square_sum<-sum(data_value_square)
entry<-NROW(data_value)
deno<-square_sum/entry
tab1<-c()
tab2<-c()
ps_value <- seq(0,(floor(entry/2)),1)
for(k in 0:(floor(entry/2))){
for (i in 1:(entry-k)) {
mult<-(data_value[i] - data_value_mean) * (data_value [i+k] -
data_value_mean)
tab1 <- c(tab1,mult)
}
auto_avg<-mean(tab1)
tab1<-c()
auto_corr<-auto_avg/deno
tab2<-c(tab2,auto_corr)
}
table_value <- cbind (ps_value, tab2)
colnames(table_value) <- c("#ps", "acf")
outfile<-unlist(strsplit(infile, split=".", fixed=TRUE))[1]
write.table(table_value,file=paste(outfile,"acf.dat",sep="-"),row.names=FALSE,sep="\t",quote=F)
}
--
Sample data
--
1 16.0071
2 16.7966
3 17.575
4 18.1614
5 15.982
6 16.8515
7 15.6828
8 14.9652
9 14.8623
10 14.7079
Help in this regard would be highly appreciated.
[[alternative HTML version deleted]]
Druk dit bericht a.u.b. niet onnodig af.
Please do not print this message unnecessarily.
Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in this message
and any annex are purely those of the writer and may not be regarded as stating
an official position of INBO, as long as the message is not confirmed by a duly
signed document.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone: +3130 274 3113 Mon-Tue
Phone: +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested For loops
In the ACF(nlme) the normalization of the numerator has been done by N and I
want to normalize it by N-k, where N is the observations and k is the lag.
Baloo
--- On Tue, 12/22/09, ONKELINX, Thierry wrote:
From: ONKELINX, Thierry
Subject: RE: [R] Nested For loops
To: "baloo mia" , r-help@r-project.org
Date: Tuesday, December 22, 2009, 1:00 AM
Baloo,
Why don't you use the built-in acf function?
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens
baloo mia
Verzonden: dinsdag 22 december 2009 2:07
Aan: r-help@r-project.org
Onderwerp: [R] Nested For loops
Dear R experts,
Might be very simple question to ask but would be insightful. As the same story
of nested "for loops". following is the code that I am using to get the
autocorrelation function of the sample data. I have tried to get rid of for
loops but since I am touching R after such a long time that I need to practice
more but I need help to revive my skills. I know that apply() or sapply() would
be beneficial. I need help...
Best Wishes,
Baloo
R code
--
acf_wal <- function (infile) {
data<-read.table(infile)
data_value <- data[,-1]
data_value_mean <- mean(data_value)
data_value_square <- (data_value - data_value_mean) ^ 2
square_sum<-sum(data_value_square)
entry<-NROW(data_value)
deno<-square_sum/entry
tab1<-c()
tab2<-c()
ps_value <- seq(0,(floor(entry/2)),1)
for(k in 0:(floor(entry/2))){
for (i in 1:(entry-k)) {
mult<-(data_value[i] - data_value_mean) * (data_value [i+k] -
data_value_mean)
tab1 <- c(tab1,mult)
}
auto_avg<-mean(tab1)
tab1<-c()
auto_corr<-auto_avg/deno
tab2<-c(tab2,auto_corr)
}
table_value <- cbind (ps_value, tab2)
colnames(table_value) <- c("#ps", "acf")
outfile<-unlist(strsplit(infile, split=".", fixed=TRUE))[1]
write.table(table_value,file=paste(outfile,"acf.dat",sep="-"),row.names=FALSE,sep="\t",quote=F)
}
--
Sample data
--
1 16.0071
2 16.7966
3 17.575
4 18.1614
5 15.982
6 16.8515
7 15.6828
8 14.9652
9 14.8623
10 14.7079
Help in this regard would be highly appreciated.
[[alternative HTML version deleted]]
Druk dit bericht a.u.b. niet onnodig af.
Please do not print this message unnecessarily.
Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in this message
and any annex are purely those of the writer and may not be regarded as stating
an official position of INBO, as long as the message is not confirmed by a duly
signed document.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested For loops
Baloo,
Why don't you use the built-in acf function?
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens
baloo mia
Verzonden: dinsdag 22 december 2009 2:07
Aan: r-help@r-project.org
Onderwerp: [R] Nested For loops
Dear R experts,
Might be very simple question to ask but would be insightful. As the same story
of nested "for loops". following is the code that I am using to get the
autocorrelation function of the sample data. I have tried to get rid of for
loops but since I am touching R after such a long time that I need to practice
more but I need help to revive my skills. I know that apply() or sapply() would
be beneficial. I need help...
Best Wishes,
Baloo
R code
--
acf_wal <- function (infile) {
data<-read.table(infile)
data_value <- data[,-1]
data_value_mean <- mean(data_value)
data_value_square <- (data_value - data_value_mean) ^ 2
square_sum<-sum(data_value_square)
entry<-NROW(data_value)
deno<-square_sum/entry
tab1<-c()
tab2<-c()
ps_value <- seq(0,(floor(entry/2)),1)
for(k in 0:(floor(entry/2))){
for (i in 1:(entry-k)) {
mult<-(data_value[i] - data_value_mean) * (data_value [i+k] -
data_value_mean)
tab1 <- c(tab1,mult)
}
auto_avg<-mean(tab1)
tab1<-c()
auto_corr<-auto_avg/deno
tab2<-c(tab2,auto_corr)
}
table_value <- cbind (ps_value, tab2)
colnames(table_value) <- c("#ps", "acf")
outfile<-unlist(strsplit(infile, split=".", fixed=TRUE))[1]
write.table(table_value,file=paste(outfile,"acf.dat",sep="-"),row.names=FALSE,sep="\t",quote=F)
}
--
Sample data
--
1 16.0071
2 16.7966
3 17.575
4 18.1614
5 15.982
6 16.8515
7 15.6828
8 14.9652
9 14.8623
10 14.7079
Help in this regard would be highly appreciated.
[[alternative HTML version deleted]]
Druk dit bericht a.u.b. niet onnodig af.
Please do not print this message unnecessarily.
Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in this message
and any annex are purely those of the writer and may not be regarded as stating
an official position of INBO, as long as the message is not confirmed by a duly
signed document.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Nested For loops
Dear R experts,
Might be very simple question to ask but would be insightful. As the same story
of nested "for loops". following is the code that I am using to get the
autocorrelation function of the sample data. I have tried to get rid of for
loops but since I am touching R after such a long time that I need to practice
more but I need help to revive my skills. I know that apply() or sapply() would
be beneficial. I need help...
Best Wishes,
Baloo
R code
--
acf_wal <- function (infile) {
data<-read.table(infile)
data_value <- data[,-1]
data_value_mean <- mean(data_value)
data_value_square <- (data_value - data_value_mean) ^ 2
square_sum<-sum(data_value_square)
entry<-NROW(data_value)
deno<-square_sum/entry
tab1<-c()
tab2<-c()
ps_value <- seq(0,(floor(entry/2)),1)
for(k in 0:(floor(entry/2))){
for (i in 1:(entry-k)) {
mult<-(data_value[i] - data_value_mean) * (data_value [i+k] -
data_value_mean)
tab1 <- c(tab1,mult)
}
auto_avg<-mean(tab1)
tab1<-c()
auto_corr<-auto_avg/deno
tab2<-c(tab2,auto_corr)
}
table_value <- cbind (ps_value, tab2)
colnames(table_value) <- c("#ps", "acf")
outfile<-unlist(strsplit(infile, split=".", fixed=TRUE))[1]
write.table(table_value,file=paste(outfile,"acf.dat",sep="-"),row.names=FALSE,sep="\t",quote=F)
}
--
Sample data
--
1 16.0071
2 16.7966
3 17.575
4 18.1614
5 15.982
6 16.8515
7 15.6828
8 14.9652
9 14.8623
10 14.7079
Help in this regard would be highly appreciated.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested for loops
On Tue, Jul 14, 2009 at 2:29 PM, Gabor Grothendieck wrote: > seq. <- function(from, to) seq(from = from, length = max(0, to - from + 1)) Really nice! Thank you! -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested for loops
On Tue, Jul 14, 2009 at 1:56 PM, David Winsemius wrote: >> temp[ upper.tri(temp) ] > [1] 7 13 14 19 20 21 25 26 27 28 31 32 33 34 35 Thanks! I didn't know about that function; it certainly makes things a lot easier. For example, until now I have used the following, homemade expression (1:N^2)[which((1:N^2)!=seq(0,(N-1)*N,by=N)+(1:N))] to get the indices of the non-diagonal entries of a matrix :-) -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested for loops
Try this:
seq. <- function(from, to) seq(from = from, length = max(0, to - from + 1))
seq.(11, 10)
On Tue, Jul 14, 2009 at 1:38 AM, Michael Knudsen wrote:
> Hi,
>
> I have spent some time locating a quite subtle (at least in my
> opinion) bug in my code. I want two nested for loops traversing the
> above-diagonal part of a square matrix. In pseudo code it would
> something like
>
> for i = 1 to 10
> {
> for j = i+1 to 10
> {
> // do something
> }
> }
>
> However, trying to do the same in R, my first try was
>
> for (i in 1:10)
> {
> for (j in (i+1):10)
> {
> // do something
> }
> }
>
> but there's a problem here. For i=10, the last for loop is over 11:10.
> Usually programming laguages would regard what corresponds to 11:10 as
> empty, but A:B with A bigger than B is in R interpreted as the numbers
> from B to A in reverse order.
>
> Is there a clever way to make nested loops like the one above in R?
>
> --
> Michael Knudsen
> micknud...@gmail.com
> http://lifeofknudsen.blogspot.com/
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested for loops
On Jul 14, 2009, at 2:25 AM, Michael Knudsen wrote: On Tue, Jul 14, 2009 at 8:20 AM, Michael Knudsen wrote: What do you mean? It looks a like a very general solution to me. Just got an email suggesting using the functions col and row. For example temp = matrix(c(1:36),nrow=6) which(col(temp)>row(temp)) This gives the indices (in the matrix viewed as a vector) of the above-diagonal entries. If you want the entries it would then be: temp[ col(temp) > row(temp) ] But more simply: > temp[ upper.tri(temp) ] [1] 7 13 14 19 20 21 25 26 27 28 31 32 33 34 35 > If you want the row and column numbers then: > row(temp)[ col(temp) > row(temp)] [1] 1 1 2 1 2 3 1 2 3 4 1 2 3 4 5 > col(temp)[ col(temp) > row(temp) ] [1] 2 3 3 4 4 4 5 5 5 5 6 6 6 6 6 Any solution that uses col and row will create two additional matrices of the same size as the original at least for the duration of the operation. For the sub-and super-diagonals: http://finzi.psych.upenn.edu/Rhelp08/2009-March/191379.html -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested for loops
On Tue, Jul 14, 2009 at 8:20 AM, Michael Knudsen wrote: > What do you mean? It looks a like a very general solution to me. Just got an email suggesting using the functions col and row. For example temp = matrix(c(1:36),nrow=6) which(col(temp)>row(temp)) This gives the indices (in the matrix viewed as a vector) of the above-diagonal entries. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested for loops
On Tue, Jul 14, 2009 at 8:03 AM, Moshe Olshansky wrote: > Make it > for (i in 1:9) Thanks. That's also how I solved the problem myself. I just somehow think it makes my code look rather clumsy and opaque. Maybe I just have to get used to this kind of nasty tricks. > This is not the general solution, (...) What do you mean? It looks a like a very general solution to me. -- Michael Knudsen micknud...@gmail.com http://lifeofknudsen.blogspot.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested for loops
Make it
for (i in 1:9)
This is not the general solution, but in your case when i=10 you do not want to
do anything.
--- On Tue, 14/7/09, Michael Knudsen wrote:
> From: Michael Knudsen
> Subject: [R] Nested for loops
> To: r-help@r-project.org
> Received: Tuesday, 14 July, 2009, 3:38 PM
> Hi,
>
> I have spent some time locating a quite subtle (at least in
> my
> opinion) bug in my code. I want two nested for loops
> traversing the
> above-diagonal part of a square matrix. In pseudo code it
> would
> something like
>
> for i = 1 to 10
> {
> for j = i+1 to 10
> {
> // do something
> }
> }
>
> However, trying to do the same in R, my first try was
>
> for (i in 1:10)
> {
> for (j in (i+1):10)
> {
> // do something
> }
> }
>
> but there's a problem here. For i=10, the last for loop is
> over 11:10.
> Usually programming laguages would regard what corresponds
> to 11:10 as
> empty, but A:B with A bigger than B is in R interpreted as
> the numbers
> from B to A in reverse order.
>
> Is there a clever way to make nested loops like the one
> above in R?
>
> --
> Michael Knudsen
> micknud...@gmail.com
> http://lifeofknudsen.blogspot.com/
>
> __
> R-help@r-project.org
> mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained,
> reproducible code.
>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Nested for loops
> -Original Message-
> From: r-help-boun...@r-project.org
> [mailto:r-help-boun...@r-project.org] On Behalf Of Michael Knudsen
> Sent: Monday, July 13, 2009 10:39 PM
> To: r-help@r-project.org
> Subject: [R] Nested for loops
>
> Hi,
>
> I have spent some time locating a quite subtle (at least in my
> opinion) bug in my code. I want two nested for loops traversing the
> above-diagonal part of a square matrix. In pseudo code it would
> something like
>
> for i = 1 to 10
> {
>for j = i+1 to 10
>{
> // do something
>}
> }
>
> However, trying to do the same in R, my first try was
>
> for (i in 1:10)
> {
>for (j in (i+1):10)
>{
>// do something
>}
> }
>
> but there's a problem here. For i=10, the last for loop is over 11:10.
> Usually programming laguages would regard what corresponds to 11:10 as
> empty, but A:B with A bigger than B is in R interpreted as the numbers
> from B to A in reverse order.
>
> Is there a clever way to make nested loops like the one above in R?
>
Michael,
If you are tryuly interested in the ABOVE diagonal elements (i.e. not
including diagonal element temselves), the your loop should be
for (i in 1:9)
{
for (j in (i+1):10)
{
// do something
}
}
And you avoid your current problem.
Hope this is helpful,
Dan
Daniel Nordlund
Bothell, WA USA
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Nested for loops
Hi,
I have spent some time locating a quite subtle (at least in my
opinion) bug in my code. I want two nested for loops traversing the
above-diagonal part of a square matrix. In pseudo code it would
something like
for i = 1 to 10
{
for j = i+1 to 10
{
// do something
}
}
However, trying to do the same in R, my first try was
for (i in 1:10)
{
for (j in (i+1):10)
{
// do something
}
}
but there's a problem here. For i=10, the last for loop is over 11:10.
Usually programming laguages would regard what corresponds to 11:10 as
empty, but A:B with A bigger than B is in R interpreted as the numbers
from B to A in reverse order.
Is there a clever way to make nested loops like the one above in R?
--
Michael Knudsen
micknud...@gmail.com
http://lifeofknudsen.blogspot.com/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
