Re: [R] How to make a nomogam and Calibration plot
Dear Harrell, Many thanks for your quick response! However, after try and try, I still have difficulty to solve my questions. I post my questions again. I hope someone can help me run the data and draw the nomogram and calibration plot for me. I know that is not good but indeed I have no way to go. The problems almost drove me mad! Best regards! Ping Tang Dear R users, I am a new R user and something stops me when I try to write a academic article. I want to make a nomogram to predict the risk of prostate cancer (PCa) using several factors which have been selected from the Logistic regression run under the SPSS. Always, a calibration plot is needed to validate the prediction accuracy of the nomogram. However, I tried many times and read a lot of posts with respect to this topic but I still couldn't figure out how to draw the nomogram and the calibration plot. Attached file is the dataset for the research. It will be very grateful if someone can save his/her time to help for my questions. Warmest regards! Logistic Regression Classification Tablea,b ObservedPredicted Pca-YN Percentage Correct 0 1 Step 0 Pca-YN 0 295 0 100.0 1 218 0 .0 Overall Percentage 57.5 Variables in the Equation B S.E.Walddf Sig.Exp(B) 95.0% C.I.for EXP(B) Lower Upper Step 1a Age .031.0154.491 1 .0341.032 1.002 1.062 DRE 1.173 .26619.492 1 .0003.233 1.920 5.443 LogPV -2.857 .50931.532 1 .000.057.021.156 LogPSA 2.316 .24688.416 1 .00010.132 6.253 16.419 Constant-1.024 1.273 .6481 .421.359 The equation: Probability = e-1.024+0.31age+1.173DRE+-2.857LogPV+2.316LogPSA 1+e-1.024+0.31age+1.173DRE+-2.857LogPV+2.316LogPSA My questions are, 1.How to draw a nomogram (similar to the below figure 1) to predict the probability of cancer using R? 2. How to make the Calibration plot (similar to the below figure 2) which used to validate the prediction accuracy of the nomogram using R? And how to calculate the concordance index (C-index) ? http://r.789695.n4.nabble.com/file/n3714477/untitled.jpg http://r.789695.n4.nabble.com/file/n3714477/%E9%99%84%E4%BB%B62.jpg http://r.789695.n4.nabble.com/file/n3714477/Dataset.xls Dataset.xls -- View this message in context: http://r.789695.n4.nabble.com/How-to-make-a-nomogam-and-Calibration-plot-tp3710068p3714477.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] cdplot error
Fairly new at this. Trying to create a conditional density plot. cdplot(status~harvd.l,data=phy) Error in cdplot.formula(status~harvd.l,data=phy): dependent variable should be a factor What does this error mean? Status is a binary response of infestation (0/1) and harvd.l is the log of timber harvest density per catchment. Thanks. -- View this message in context: http://r.789695.n4.nabble.com/cdplot-error-tp3714454p3714454.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] AICcmodavg functions and 'mer' class models
What is teh reason some functions in the AICcmodavg package do not work with 'mer' class models? One such example would be the 'importance' function. Thanks Ronny -- View this message in context: http://r.789695.n4.nabble.com/AICcmodavg-functions-and-mer-class-models-tp3714534p3714534.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] create a list under constraints
Hi:
Here's one way; using the mdply() function in the plyr package:
k - c(1,2,3,4,5)
i - c(0,1,3,2,1)
# Takes two scalars k and i as input, outputs a data frame
ff - function(k, i) data.frame(k = rep(k, i+1), i = seq(0, i, by = 1))
library('plyr')
mdply(data.frame(k, i), ff) # returns a data frame
# -
Another way to do this is to use the mapply() function
This one returns a matrix.
# -
gg - function(k, i) cbind(k = rep(k, i+1), i = seq(0, i, by = 1))
do.call(rbind, mapply(gg, k, i))
HTH,
Dennis
On Tue, Aug 2, 2011 at 6:40 PM, Kathie kathryn.lord2...@gmail.com wrote:
Hi, R users,
Here is an example.
k - c(1,2,3,4,5)
i - c(0,1,3,2,1)
if k=1, then i=0
if k=2, then i=0, 1
if k=3, then i=0, 1, 2, 3
if k=4, then i=0, 1, 2
if k=5, then i=0, 1
so i'd like to create a list like below.
list
k i
1 1 0
2 2 0
3 2 1
4 3 0
5 3 1
6 3 2
7 3 3
8 4 0
9 4 1
10 4 2
11 5 0
12 5 1
I tried expand.grid, but I can't.
Any suggestion will be greatly appreciated.
Regards,
Kathryn Lord
--
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Re: [R] Error while trying to install a package
On Mon, 01-Aug-2011 at 02:55PM -0400, Sushil Amirisetty wrote:
|
| Hi Everyone,
|
| When i try to install a package using
|
| install.packages(agricolae)
| --- Please select a CRAN mirror for use in this session ---
| |
|
|
| The cursor keeps blinking i dont get a popup menu to choose a CRAN
| mirror? Is it due to my proxy server settings? I tried to echo
| $http_proxy , it doesnt carry any proxy , its blank. Please help
| me.
Look back in the archives. There was a discussion in the last month
or so on how you make those settings. I don't remember the details
because they were to do with Windows (which I'm guessing is what
you're using).
| Thanks,
| Sushil.
| [[alternative HTML version deleted]]
|
| __
| R-help@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-help
| PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
| and provide commented, minimal, self-contained, reproducible code.
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) . Eleanor Roosevelt
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Re: [R] convert a splus randomforest object to R
Hi Jimmy Years ago I think that Splus introduced an argument when dumping of old.style = T or something similar to dump it into a form that could be read into R. This may only be for data.frames etc not things like random forest objects Regards Duncan Duncan Mackay Department of Agronomy and Soil Science University of New England ARMIDALE NSW 2351 Email: home mac...@northnet.com.au At 10:10 03/08/2011, you wrote: Hi, I have a randomforest object cost.rf that was created in splus 8.0, now I need to use this trained RF model in R. So in Splus, I dump the RF file as below data.dump(cost.rf, file=cost.rf.txt, oldStyle=T) then in R, restore the dumped file, library(foreign) data.restore(cost.rf.txt) it works fine and able to restore the cost.rf object. But when I try to pass a new data through this randomforest object using predict() function, it gives me error message. in R: library(randomForest) set.seed(2211) pred - predict(cost.rf, InputData[ , ]) Error in object$forest$cutoff : $ operator is invalid for atomic vectors Looks like after restoring the dump file, the object is not compatible in R. Have anyone successfully converted a splus randomforest object to R? what will be the appropriate method to do this? Thanks in advance. Jimmy == This communication contains information that is confidential, and solely for the use of the intended recipient. It may contain information that is privileged and exempt from disclosure under applicable law. If you are not the intended recipient of this communication, please be advised that any disclosure, copying, distribution or use of this communication is strictly prohibited. Please also immediately notify SCAN Health Plan at 1-800-247-5091, x5263 and return the communication to the originating address. Thank You. == [[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. __ 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] cdplot error
On 03/08/11 05:52, wildernessness wrote: Fairly new at this. Trying to create a conditional density plot. cdplot(status~harvd.l,data=phy) Error in cdplot.formula(status~harvd.l,data=phy): dependent variable should be a factor What does this error mean? Status is a binary response of infestation (0/1) Probably status is a numerical variable rather than a factor**. Try print(is.factor(phy$status)) and if that is FALSE then phy$status - factor(phy$status, labels=c(N, Y)) cdplot(status~harvd.l,data=phy) Hope this helps a little. Allan and harvd.l is the log of timber harvest density per catchment. Thanks. -- View this message in context: http://r.789695.n4.nabble.com/cdplot-error-tp3714454p3714454.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] Finding dependancies?
Hi although the background is that it happened on an hpc cluster, this question does *not* concern hpc computing with R. I was using R on a cluster and had to install several packages in my home directory. Now the head node was migrated to new hardware (new install as well) and many dependencies for my in $HOME installed packages, which were present on the old head, are missing on the new head. Now I could simply try to run my script, wait for the error message, mail the administrator to install the package, try again, ... . But this is a tedious process - and I can not go to him directly, as I am sitting opn a different continent. So my question: is there an easy way (like ldd for programs), to identify the dependencies which are not met, and how could I use that on the packages? Thanks, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax (F): +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug [[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] lattice: index plot
Does xyplot(y ~ seq_along(y), xlab = Index) do what you want? Not exactly, because it does not work once multipanel conditioning comes into play: xyplot(y~seq_along(y)|factor(rep(1:2, each=5)), xlab = Index) The points in the right panel are plotted from 6:10 while the points in the left panel are plotted from 1:5. Of course I could do something like xyplot(y~rep(1:5, 2) |factor(rep(1:2, each=5)), xlab = Index) in this toy example, but as pointed out this becomes very cumbersome if the grouping variable does not follow a pattern. BTW: my toy example did not work with multipanel conditioning either, but one can work around that too using the subscripts argument in the panel function (I skipped that exercise for the sake of brevity, but I must admit that it obscured somehow my real intention, sorry for that). However, the more I think of it the more I believe that I have to provide the x's explicitly nevertheless and my solution would be: set.seed(123) y - rnorm(20) grp - index - sample(3, 20, TRUE) index[unlist(lapply(levels(as.factor(grp)), function(n) which(as.factor(grp)==n)))] - unlist(tapply(grp, grp, seq_along)) xyplot(y ~ index | factor(grp), xlab = Index) This should work, but it seems to be a rather elaborate solution, especially since an index plot is nothing too fancy. So maybe I'm not seeing the wood for trees, but does anybody know an easier way? Thanks. KR, -Thorn __ 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] cdplot error
On 2011-08-02 21:52, wildernessness wrote: Fairly new at this. Trying to create a conditional density plot. cdplot(status~harvd.l,data=phy) Error in cdplot.formula(status~harvd.l,data=phy): dependent variable should be a factor What does this error mean? Status is a binary response of infestation (0/1) and harvd.l is the log of timber harvest density per catchment. Your question suggests that have not looked at help(cdplot) which clearly says just what the error message says and/or you aren't aware that 'factor' has a specific meaning in R in which case a look at chapter 4 of 'An Introduction to R' likely would be profitable. Peter Ehlers Thanks. -- View this message in context: http://r.789695.n4.nabble.com/cdplot-error-tp3714454p3714454.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] Running R in a sandbox
Hello, The idea is to grant access of remote users to R running on Linux. Users must have ability to run their R scripts but avoid corrupting the operating system. How one can restrict/limit access of remote users to certain R functions? For example, dealing with IO (file system), graphical tools, etc. Thank you. -- Kind regards, Antonio Rodriges __ 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] fixInNamespace
Dear all, I would like to ask how one can access certain methods via fixInNamespace. Is there some option / way for selecting a certain methods for a defined signature. Thank you for your answer and efforts in advance! Best, Michael -- __ 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] conditional data replace (recode, change or whatsoever)
Hello, I have a big data.frame, a piece of it as follows. a b c d 1 58009 2010-11-02 0 NA 2 114761 NA 1 2008-11-05 3 184440 NA 1 2009-12-08 4 189372 NA 0 NA 5 105286 NA 0 NA 6 186717 NA 0 NA 7 189106 NA 0 NA 8 127306 NA 0 NA 9 157342 2011-04-25 0 NA I want to replace b[NA] values with 20011-07-28 where c==0. I use rstudio and i'm a novice. -- View this message in context: http://r.789695.n4.nabble.com/conditional-data-replace-recode-change-or-whatsoever-tp3714715p3714715.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] Odp: conditional data replace (recode, change or whatsoever)
Hi Hello, I have a big data.frame, a piece of it as follows. a b c d 1 58009 2010-11-02 0 NA 2 114761 NA 1 2008-11-05 3 184440 NA 1 2009-12-08 4 189372 NA 0 NA 5 105286 NA 0 NA 6 186717 NA 0 NA 7 189106 NA 0 NA 8 127306 NA 0 NA 9 157342 2011-04-25 0 NA I want to replace b[NA] values with 20011-07-28 where c==0. I use rstudio and i'm a novice. I believe there are better solutions but I would use two steps select rows where c==0 (see also FAQ 7.31) sel-which(big.data.frame$c==0) change NA values in b column based on sel big.data.frame$b[sel][is.na(big.data.frame$b[sel])]-20011-07-28 Beware of data types AFAIK R can not accept 20011-07-28 as a date. Regards Petr -- View this message in context: http://r.789695.n4.nabble.com/conditional- data-replace-recode-change-or-whatsoever-tp3714715p3714715.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] conditional data replace (recode, change or whatsoever)
Please do your homework before asking the list: An introduction to R, chapter 7 Am 03.08.2011 10:05, schrieb zcatav: Hello, I have a big data.frame, a piece of it as follows. a b c d 1 58009 2010-11-02 0 NA 2 114761 NA 1 2008-11-05 3 184440 NA 1 2009-12-08 4 189372 NA 0 NA 5 105286 NA 0 NA 6 186717 NA 0 NA 7 189106 NA 0 NA 8 127306 NA 0 NA 9 157342 2011-04-25 0 NA I want to replace b[NA] values with 20011-07-28 where c==0. I use rstudio and i'm a novice. -- View this message in context: http://r.789695.n4.nabble.com/conditional-data-replace-recode-change-or-whatsoever-tp3714715p3714715.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] R-help Digest, Vol 102, Issue 3
Wir sind bis am 20. August in den Ferien und werden keine e-mails beantworten. Bei dringenden Fällen melden Sie sich bei Stefanie von Felten steffi.vonfel...@oikostat.ch We are on vacation until 20. August. In urgent cases, please contact Stefanie von Felten steffi.vonfel...@oikostat.ch __ 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] syntax with do.call and `[`
Dear List, i would like to mimic the behaviour or the following indexing with a do.call construct to be able to supply the arguments to `[` as a list: test = matrix[1:4,2] result = test[2,] My try, however, did not work: result = do.call(`[`,list(test,2,NULL)) result = do.call(`[`,list(test,2,)) result = do.call(`[`,list(test,2,'')) How can I use the do.call in that way with leaving the second indexing vector blanc? Cheers Jannis __ 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] Need to compute density as done by panel.histogram
On 2011-08-02 11:51, Sébastien Bihorel wrote: Hi, This might be a simple problem but I don't know how to calculate a random variable density the way panel.histogram does it before it creates the actual density rectangles. The documentation says that it uses the density function but the actual code suggests that the hist.constructor function (which does not seem to be easily accessible). The documentation in ?histogram is misleading. I think that the intent is that density() is used in panel.densityplot but panel.histogram uses hist(), as is clear in ?panel.histogram. So you'll find the code for the density rectangles in hist.default where 'counts' is computed and followed with dens - counts/(n * diff(breaks)) You might find the code for truehist() in the MASS package easy to follow. To see how hist.constructor calls hist(): lattice:::hist.constructor Peter Ehlers Any suggestion for computing the density values of foo$x in the following example will be welcome. require(lattice) set.seed(12345) foo1- data.frame(x=rnorm(100,0,0.1),grp=1,by=rep(1:2,each=50),by2=rep(1:2,times=50)) foo2- data.frame(x=rnorm(100,2,1),grp=2,by=rep(1:2,each=50),by2=rep(1:2,times=50)) foo- rbind(foo1,foo2) xplot- histogram(~x,data=foo, type='density') PS: the present question relates to a workaround for another problem previously submitted to the list ( https://stat.ethz.ch/pipermail/r-help/attachments/20110727/5f0a8853/attachment.pl). [[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. __ 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] conditional data replace (recode, change or whatsoever)
As others have noted, this is discussed in many free R tutorials, but if you want to do it in one line I think this should do it: X[is.NA(X[,b])(X[,c]==0),b]-2011-07-28 #where X is the name of the data frame. It's a somewhat convoluted line of code but if you read it inside out the logic is clear: Find those rows where column b is NA and c is 1 by searching all rows of the relevant column (the X[,something] syntax): select those rows and the b column. Put the desired date in those slots. let me know of I can further clarify this. I changed the date assuming a typo on your end. Welcome and good luck getting started with R, Michael Weylandt On Aug 3, 2011, at 4:05 AM, zcatav zca...@gmail.com wrote: Hello, I have a big data.frame, a piece of it as follows. abcd 1580092010-11-020NA 2114761NA12008-11-05 3184440NA12009-12-08 4189372NA0NA 5105286NA0NA 6186717NA0NA 7189106NA0NA 8127306NA0NA 91573422011-04-250NA I want to replace b[NA] values with 20011-07-28 where c==0. I use rstudio and i'm a novice. -- View this message in context: http://r.789695.n4.nabble.com/conditional-data-replace-recode-change-or-whatsoever-tp3714715p3714715.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] Odp: conditional data replace (recode, change or whatsoever)
Petr Pikal wrote: Hi I believe there are better solutions but I would use two steps select rows where c==0 (see also FAQ 7.31) sel-which(big.data.frame$c==0) change NA values in b column based on sel big.data.frame$b[sel][is.na(big.data.frame$b[sel])]-20011-07-28 Beware of data types AFAIK R can not accept 20011-07-28 as a date. Regards Petr Thanks, it runs like a charm. Replaced date format just a typo. -- View this message in context: http://r.789695.n4.nabble.com/conditional-data-replace-recode-change-or-whatsoever-tp3714715p3715080.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] conditional data replace (recode, change or whatsoever)
Your suggestion works perfect as i pointed previous message. Now have another question about data editing. I try this code: X[X[,c]==1,b]-X[,d] and results with error: `[-.data.frame`(`*tmp*`, X[, c] == 1, b, value = c(NA, : replacement has 9 rows, data has 2 Logically i selected 2 rows with X[,c]==1. Than i want to replace in that rows its own data from d to b with X[,b]-X[,d]. What is wrong? -- View this message in context: http://r.789695.n4.nabble.com/conditional-data-replace-recode-change-or-whatsoever-tp3714715p3715218.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] Coefficient names when using lm() with contrasts
Dear R Users,
Am using lm() with contrasts as below. If I skip the contrasts()
statement, I get the coefficient names to be
names(results$coef)
[1] (Intercept) VarAcat VarArat VarB
which are much more meaningful than ones based on integers.
Can anyone tell me how to get R to keep the coefficient names based on the
factor levels whilst using contrasts rather than labelling them with
integers?
Many thanks in advance,
Pete
Cardiff, UK
dt=read.table(testreg.txt,sep=,,header=T)
dt
ID VarA VarB VarC
1 1 cat2 23
2 2 dog3 56
3 3 rat5 35
4 4 cat2 43
5 5 cat7 51
6 6 dog3 31
7 7 dog4 65
8 8 rat1 18
9 9 rat6 49
10 10 dog3 28
dt$VarA=relevel(dt$VarA,ref=dog)
treat3=matrix(-1/3,ncol=2,nrow=3); for (i in 1:2) {treat3[i+1,i]=2/3}
contrasts(dt$VarA)=treat3
levels(dt$VarA)
[1] dog cat rat
results=lm(formula=VarC~VarA+VarB, data=dt)
names(results$coef)
[1] (Intercept) VarA1 VarA2 VarB
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Re: [R] conditional data replace (recode, change or whatsoever)
As R notes, the problem is that you are trying to fit 9 rows into two: specifically, note that on the left hand side you select only those rows such that X[,c]==1 (which is 2 for your data) while on the right hand you select all 9rows of column d so they simply don't fit. If you change the code to X[X[,c]==1,b]-X[X[,c]==1,d] it will move the column d rows corresponding to the ones you've selected on the LHS. Hopefully that makes sense. Michael Weylandt On Wed, Aug 3, 2011 at 8:09 AM, zcatav zca...@gmail.com wrote: Your suggestion works perfect as i pointed previous message. Now have another question about data editing. I try this code: X[X[,c]==1,b]-X[,d] and results with error: `[-.data.frame`(`*tmp*`, X[, c] == 1, b, value = c(NA, : replacement has 9 rows, data has 2 Logically i selected 2 rows with X[,c]==1. Than i want to replace in that rows its own data from d to b with X[,b]-X[,d]. What is wrong? -- View this message in context: http://r.789695.n4.nabble.com/conditional-data-replace-recode-change-or-whatsoever-tp3714715p3715218.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. [[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] conditional data replace (recode, change or whatsoever)
On Wed, Aug 3, 2011 at 8:09 AM, zcatav zca...@gmail.com wrote: Your suggestion works perfect as i pointed previous message. Now have another question about data editing. I try this code: X[X[,c]==1,b]-X[,d] and results with error: `[-.data.frame`(`*tmp*`, X[, c] == 1, b, value = c(NA, : replacement has 9 rows, data has 2 Logically i selected 2 rows with X[,c]==1. Than i want to replace in that rows its own data from d to b with X[,b]-X[,d]. What is wrong? Also check out transform and ifelse, e.g. transform(X, b = ifelse(is.na(b) c == 0, 2011-07-28, b)) transform(X, b = ifelse(c == 1, d, c)) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.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] syntax with do.call and `[`
Good question, Jannis. I couldn't figure out how to specify the j argument in the [ function as empty or missing either. One work around is to specify ALL the columns as the j argument: test - matrix(1:4, 2) # I think this is what you meant in your original post, not matrix[1:4, 2] result1 - test[2, ] result2 - do.call([, list(test, 2, seq(dim(test)[2]))) test result1 result2 Jean `·.,, (((º `·.,, (((º `·.,, (((º Jean V. Adams Statistician U.S. Geological Survey Great Lakes Science Center 223 East Steinfest Road Antigo, WI 54409 USA From: Jannis bt_jan...@yahoo.de To: r-help@r-project.org Date: 08/03/2011 05:35 AM Subject: [R] syntax with do.call and `[` Sent by: r-help-boun...@r-project.org Dear List, i would like to mimic the behaviour or the following indexing with a do.call construct to be able to supply the arguments to `[` as a list: test = matrix[1:4,2] result = test[2,] My try, however, did not work: result = do.call(`[`,list(test,2,NULL)) result = do.call(`[`,list(test,2,)) result = do.call(`[`,list(test,2,'')) How can I use the do.call in that way with leaving the second indexing vector blanc? Cheers Jannis __ 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] How to make a nomogam and Calibration plot
The nomogram you included was produced by the Design package, the precursor to the rms package. You will have to take the time to intensively read the rms package documentation. Note that how you developed the model (e.g., allowing for non-linearity in log PSA, not using stepwise regression which invalidates the results, making sure all clinically relevant predictors are in the model, ...) is the most important step. The process you are going through generally requires an M.S. in biostatistics. Frank sytangping wrote: Dear Harrell, Many thanks for your quick response! However, after try and try, I still have difficulty to solve my questions. I post my questions again. I hope someone can help me run the data and draw the nomogram and calibration plot for me. I know that is not good but indeed I have no way to go. The problems almost drove me mad! Best regards! Ping Tang Dear R users, I am a new R user and something stops me when I try to write a academic article. I want to make a nomogram to predict the risk of prostate cancer (PCa) using several factors which have been selected from the Logistic regression run under the SPSS. Always, a calibration plot is needed to validate the prediction accuracy of the nomogram. However, I tried many times and read a lot of posts with respect to this topic but I still couldn't figure out how to draw the nomogram and the calibration plot. Attached file is the dataset for the research. It will be very grateful if someone can save his/her time to help for my questions. Warmest regards! Logistic Regression Classification Tablea,b ObservedPredicted Pca-YN Percentage Correct 0 1 Step 0Pca-YN 0 295 0 100.0 1 218 0 .0 Overall Percentage 57.5 Variables in the Equation B S.E.Walddf Sig.Exp(B) 95.0% C.I.for EXP(B) Lower Upper Step 1a Age .031.0154.491 1 .0341.032 1.002 1.062 DRE 1.173 .26619.492 1 .0003.233 1.920 5.443 LogPV -2.857 .50931.532 1 .000.057.021.156 LogPSA 2.316 .24688.416 1 .00010.132 6.253 16.419 Constant-1.024 1.273 .6481 .421.359 The equation: Probability = e-1.024+0.31age+1.173DRE+-2.857LogPV+2.316LogPSA 1+e-1.024+0.31age+1.173DRE+-2.857LogPV+2.316LogPSA My questions are, 1.How to draw a nomogram (similar to the below figure 1) to predict the probability of cancer using R? 2. How to make the Calibration plot (similar to the below figure 2) which used to validate the prediction accuracy of the nomogram using R? And how to calculate the concordance index (C-index) ? http://r.789695.n4.nabble.com/file/n3714477/untitled.jpg http://r.789695.n4.nabble.com/file/n3714477/%E9%99%84%E4%BB%B62.jpg http://r.789695.n4.nabble.com/file/n3714477/Dataset.xls Dataset.xls - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/How-to-make-a-nomogam-and-Calibration-plot-tp3710068p3715336.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] Running R in a sandbox
Antonio Rodriges wrote: The idea is to grant access of remote users to R running on Linux. Users must have ability to run their R scripts but avoid corrupting the operating system. Check RStudio.org Dieter -- View this message in context: http://r.789695.n4.nabble.com/Running-R-in-a-sandbox-tp3714716p3715351.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] xlsx error
Andrew Winterman wrote: I'm trying to use the xlsx package to read a series of excel spreadsheets into R, but my code is failing at the first step. I setwd into my the directory with the spreadsheets, and, as a test ask for the first one: read.xlsx(file = Argentina Final.xls, sheetIndex = 1) I promptly get an error message: Error in .jcall(row[[ir]], Lorg/apache/poi/xssf/usermodel/XSSFCell;, : Check if your Java installation is ok. Try to access an rJava function directly for a test Dieter -- View this message in context: http://r.789695.n4.nabble.com/xlsx-error-tp3714057p3715367.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] 3D Bar Graphs in ggplot2?
So I take it 3D pie charts are out? P.S. It is not about hiding anything. It is about consulting and being told by your client to make 3D pie charts and change this font or that color to make the graphs more apealing. Given that I am the one trying to open the door to using R where I work it would be much easier if I could simply use a 2D graph. -- View this message in context: http://r.789695.n4.nabble.com/3D-Bar-Graphs-in-ggplot2-tp3713305p3715382.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] conditional data replace (recode, change or whatsoever)
On Aug 3, 2011, at 8:09 AM, zcatav wrote: Your suggestion works perfect as i pointed previous message. Now have another question about data editing. I try this code: X[X[,c]==1,b]-X[,d] and results with error: `[-.data.frame`(`*tmp*`, X[, c] == 1, b, value = c(NA, : replacement has 9 rows, data has 2 Logically i selected 2 rows with X[,c]==1. Than i want to replace in that rows its own data from d to b with X[,b]-X[,d]. What is wrong? You need to apply the same logical test/selection on the rows of the RHS as you are doing on the LHS. Possibly: X[ X[,c]==1, b] - X[ X[,c]==1, d] (No data, not tested code.) -- David Winsemius, MD 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] Running R in a sandbox
On Wed, Aug 3, 2011 at 9:04 AM, Antonio Rodriges antonio@gmail.com wrote: Hello, The idea is to grant access of remote users to R running on Linux. Users must have ability to run their R scripts but avoid corrupting the operating system. Ordinary users can't corrupt the operating system on Linux[1]. The worst they can do is run CPU- and memory-intensive tasks that can slow things down for everyone and conceivably bring the system to a halt, but there are ways of limiting CPU and memory usage per user session. What don't you want them to do? Barry [1] Security holes excepted. But those will be present in any sandbox solution. __ 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] Error Installing or Updating Packages (Maybe because of a proxy)
Hello David, I encountered the same problem of yours. What did you do to resolve it? Thanks for your reply Mohammad -- View this message in context: http://r.789695.n4.nabble.com/Error-Installing-or-Updating-Packages-Maybe-because-of-a-proxy-tp3462312p3715332.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] slow computation of functions over large datasets
Hello there,
Im computing the total value of an order from the price of the order items
using a for loop and the ifelse function. I do this on a large dataframe
(close to 1m lines). The computation of this function is painfully slow: in
1min only about 90 rows are calculated.
The computation time taken for a given number of rows increases with the
size of the dataset, see the example with my function below:
# small dataset: function performs well
exampledata-data.frame(orderID=c(1,1,1,2,2,3,3,3,4),itemPrice=c(10,17,9,12,25,10,1,9,7))
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
{exampledata[i,orderAmount]-ifelse(exampledata[i,orderID]==exampledata[i-1,orderID],exampledata[i-1,orderAmount]+exampledata[i,itemPrice],exampledata[i,itemPrice])})
# large dataset: the very same computational task takes much longer
exampledata2-data.frame(orderID=c(1,1,1,2,2,3,3,3,4,5:200),itemPrice=c(10,17,9,12,25,10,1,9,7,25:220))
exampledata2[1,orderAmount]-exampledata2[1,itemPrice]
system.time(for (i in 2:9)
{exampledata2[i,orderAmount]-ifelse(exampledata2[i,orderID]==exampledata2[i-1,orderID],exampledata2[i-1,orderAmount]+exampledata2[i,itemPrice],exampledata2[i,itemPrice])})
Does someone know a way to increase the speed?
Thank you very much!
Caroline
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[R] equivalent of var.test(x,y) for skew and kurtosis
Dear R-users, I am comparing differences in variance, skew, and kurtosis between two groups. For variance the comparison is easy: just var.test(group1, group2) I am using agostino.test() for skew, and anscombe.test() for kurtosis. However, I can't find an equivalent of the F.test or Mood.test for comparing kurtosis or skewness between two samples. Would the test just be a 1 df test on the difference in Z or F scores returned by the agostino or anscombe? How are the differences distributed: chi2? Any guidance greatly appreciated. google and wikipedia return hits for measuring the third and fourth standardized moments, but none I can see for comparing differences on these parameters. best, tim __ 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] slow computation of functions over large datasets
Dear Caroline,
Here is a faster and more elegant solution.
n - 1
exampledata - data.frame(orderID = sample(floor(n / 5), n, replace = TRUE),
itemPrice = rpois(n, 10))
library(plyr)
system.time({
+ ddply(exampledata, .(orderID), function(x){
+ data.frame(itemPrice = x$itemPrice, orderAmount =
cumsum(x$itemPrice))
+ })
+ })
user system elapsed
1.670.001.69
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
+
{exampledata[i,orderAmount]-ifelse(exampledata[i,orderID]==exampledata[i-1,orderID],exampledata[i-1,orderAmount]+exampledata[i,itemPrice],exampledata[i,itemPrice])})
user system elapsed
11.940.02 11.97
Best regards,
Thierry
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
Namens Caroline Faisst
Verzonden: woensdag 3 augustus 2011 15:26
Aan: r-help@r-project.org
Onderwerp: [R] slow computation of functions over large datasets
Hello there,
I'm computing the total value of an order from the price of the order items
using
a for loop and the ifelse function. I do this on a large dataframe (close
to
1m lines). The computation of this function is painfully slow: in 1min only
about
90 rows are calculated.
The computation time taken for a given number of rows increases with the size
of the dataset, see the example with my function below:
# small dataset: function performs well
exampledata-
data.frame(orderID=c(1,1,1,2,2,3,3,3,4),itemPrice=c(10,17,9,12,25,10,1,9,7))
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
{exampledata[i,orderAmount]-
ifelse(exampledata[i,orderID]==exampledata[i-1,orderID],exampledata[i-
1,orderAmount]+exampledata[i,itemPrice],exampledata[i,itemPrice])})
# large dataset: the very same computational task takes much longer
exampledata2-
data.frame(orderID=c(1,1,1,2,2,3,3,3,4,5:200),itemPrice=c(10,17,9,12,25,1
0,1,9,7,25:220))
exampledata2[1,orderAmount]-exampledata2[1,itemPrice]
system.time(for (i in 2:9)
{exampledata2[i,orderAmount]-
ifelse(exampledata2[i,orderID]==exampledata2[i-
1,orderID],exampledata2[i-
1,orderAmount]+exampledata2[i,itemPrice],exampledata2[i,itemPrice])})
Does someone know a way to increase the speed?
Thank you very much!
Caroline
[[alternative HTML version deleted]]
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[R] Combining multiple dependent variables for machine learning
Hi, I apologize for posting this here, I am also trying to post this on machine learning emailing lists. I have a set (18K) of sequences (22 nt long) and I have their counts at 4 different stages. The difference in counts from one stage to the next represents how well the sequence performed in the transition. The total counts remain about the same in each stage. So if a 1 sequence loses some counts in 1 stage, another sequence gains those counts in that stage. I am trying to build a predictor that combines these 4 stages. I have already tried to build an SVM using just the counts in the final stage but its not that great (0.3 correlation with test set). The problem I am facing now is how to combine these 4 stages into 1 dependent variable or something like that. The 4 stages are the dependent variables and the sequence is my independent variable. The aim is to use the count information in each stage to select how well the sequence performs across all 4 stages. I appreciate any suggestions for this problem. Sincerely, Vishal [[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] Need to compute density as done by panel.histogram
Thank you very much Peter, I'm going to dig deeper into the code of the functions you've listed. On Wed, Aug 3, 2011 at 6:57 AM, Peter Ehlers ehl...@ucalgary.ca wrote: On 2011-08-02 11:51, Sébastien Bihorel wrote: Hi, This might be a simple problem but I don't know how to calculate a random variable density the way panel.histogram does it before it creates the actual density rectangles. The documentation says that it uses the density function but the actual code suggests that the hist.constructor function (which does not seem to be easily accessible). The documentation in ?histogram is misleading. I think that the intent is that density() is used in panel.densityplot but panel.histogram uses hist(), as is clear in ?panel.histogram. So you'll find the code for the density rectangles in hist.default where 'counts' is computed and followed with dens - counts/(n * diff(breaks)) You might find the code for truehist() in the MASS package easy to follow. To see how hist.constructor calls hist(): lattice:::hist.constructor Peter Ehlers Any suggestion for computing the density values of foo$x in the following example will be welcome. require(lattice) set.seed(12345) foo1- data.frame(x=rnorm(100,0,0.1),**grp=1,by=rep(1:2,each=50),by2=** rep(1:2,times=50)) foo2- data.frame(x=rnorm(100,2,1),**grp=2,by=rep(1:2,each=50),by2=** rep(1:2,times=50)) foo- rbind(foo1,foo2) xplot- histogram(~x,data=foo, type='density') PS: the present question relates to a workaround for another problem previously submitted to the list ( https://stat.ethz.ch/**pipermail/r-help/attachments/** 20110727/5f0a8853/attachment.**plhttps://stat.ethz.ch/pipermail/r-help/attachments/20110727/5f0a8853/attachment.pl ). [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html 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] Combining multiple dependent variables for machine learning
Hi, On Wed, Aug 3, 2011 at 10:06 AM, Vishal Thapar vishaltha...@gmail.com wrote: Hi, I apologize for posting this here, I am also trying to post this on machine learning emailing lists. I have a set (18K) of sequences (22 nt long) and I have their counts at 4 different stages. The difference in counts from one stage to the next represents how well the sequence performed in the transition. The total counts remain about the same in each stage. So if a 1 sequence loses some counts in 1 stage, another sequence gains those counts in that stage. I am trying to build a predictor that combines these 4 stages. I have already tried to build an SVM using just the counts in the final stage but its not that great (0.3 correlation with test set). The problem I am facing now is how to combine these 4 stages into 1 dependent variable or something like that. The 4 stages are the dependent variables and the sequence is my independent variable. The aim is to use the count information in each stage to select how well the sequence performs across all 4 stages. I appreciate any suggestions for this problem. Suggestions? Yes. Read the posting guide and follow it. It isn't clear that this is even an R question, since you don't tell us anything about the packages or functions you are using, or about your data. There aren't any actual questions in your message, and your problem statement is exceedingly vague. You might find more help on the Bioconductor list, if in fact you are using R for your problem. Sarah -- Sarah Goslee http://www.functionaldiversity.org __ 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] lattice: index plot
On 2011-08-03 00:24, Thaler,Thorn,LAUSANNE,Applied Mathematics wrote:
Does
xyplot(y ~ seq_along(y), xlab = Index)
do what you want?
Not exactly, because it does not work once multipanel conditioning comes
into play:
xyplot(y~seq_along(y)|factor(rep(1:2, each=5)), xlab = Index)
The points in the right panel are plotted from 6:10 while the points in
the left panel are plotted from 1:5. Of course I could do something like
xyplot(y~rep(1:5, 2) |factor(rep(1:2, each=5)), xlab = Index)
in this toy example, but as pointed out this becomes very cumbersome if
the grouping variable does not follow a pattern.
BTW: my toy example did not work with multipanel conditioning either,
but one can work around that too using the subscripts argument in the
panel function (I skipped that exercise for the sake of brevity, but I
must admit that it obscured somehow my real intention, sorry for that).
However, the more I think of it the more I believe that I have to
provide the x's explicitly nevertheless and my solution would be:
set.seed(123)
y- rnorm(20)
grp- index- sample(3, 20, TRUE)
index[unlist(lapply(levels(as.factor(grp)), function(n)
which(as.factor(grp)==n)))]- unlist(tapply(grp, grp, seq_along))
xyplot(y ~ index | factor(grp), xlab = Index)
This should work, but it seems to be a rather elaborate solution,
especially since an index plot is nothing too fancy.
So maybe I'm not seeing the wood for trees, but does anybody know an
easier way?
Here's a way to use 'subscripts' in the xyplot.
The main problem is to determine the xlims to use.
dat - data.frame(y, grp)
## xlims
xL - function(groups){
tbl - table(groups)
xlim - c(0, max(tbl) + 1)
xlim
}
xyplot(y ~ seq_along(y) | factor(grp), data = dat,
xlim = xL(dat$grp),
panel = function(y, subscripts){
x - seq_along(subscripts)
panel.xyplot(x, y)
}
)
Peter Ehlers
Thanks.
KR,
-Thorn
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[R] confint() in stats4 package
Hi there,
I had a problem when I hoped to get confidence intervals for the
parameters I got using mle() of stats4 package. This problem would not
appear if ``fixed'' option was not used. The following mini-example will
demo the problem:
x - c(100, 56, 32, 18, 10, 1)
r - c(18, 17, 10, 6, 4, 3)
n - c(18, 22, 17, 21, 23, 20)
loglik.1 - function(alpha, beta, c) {
x - log10(x)
P - c + (1-c) * pnorm(alpha + beta * x)
control - which(x == -Inf)
if (length(control) != 0) P[control] - c
P - pmax(pmin(P,1),0)
-(sum(r * log(P)) + sum((n - r)* log(1-P)))
}
loglik.2 - function(alpha, beta) {
x - log10(x)
P - pnorm(alpha + beta * x)
P - pmax(pmin(P,1),0)
-(sum(r * log(P)) + sum((n - r)* log(1-P)))
}
library(stats4)
fit.1 - mle(loglik.1, start = list(alpha = 0, beta = 0, c = 0), method
= BFGS, fixed = list(c=0))
fit.2 - mle(loglik.2, start = list(alpha = 0, beta = 0), method =
BFGS, fixed = list())
confint(fit.1)
Profiling...
Error in approx(sp$y, sp$x, xout = cutoff) :
need at least two non-NA values to interpolate
In addition: Warning message:
In approx(sp$y, sp$x, xout = cutoff) : collapsing to unique 'x' values
confint(fit.2)
Profiling...
2.5 %97.5 %
alpha -2.5187909 -1.144600
beta 0.9052395 1.876322
The version I test the above code is 2.11.1 and 2.13.1.
I hope to know what's the matter? and how to avoid the error, and get
the correct confidence intervals for the parameters? Any suggestions
will be really appreciated.
P.S.: I noticed that there was a file named mle.R.rej in the source
directory of stats4. A broken patch? Thanks!
Regards,
Jinsong
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Re: [R] syntax with do.call and `[`
On Aug 3, 2011, at 12:30 , Jannis wrote: Dear List, i would like to mimic the behaviour or the following indexing with a do.call construct to be able to supply the arguments to `[` as a list: test = matrix[1:4,2] result = test[2,] My try, however, did not work: result = do.call(`[`,list(test,2,NULL)) result = do.call(`[`,list(test,2,)) result = do.call(`[`,list(test,2,'')) How can I use the do.call in that way with leaving the second indexing vector blanc? alist() actually allows this, although probably more by coincidence than by design. Watch: do.call(`[`, alist(test, 2, )) [1] 2 4 If you want to turn this into a programming idiom, be aware that there are subtle differences because alist() does not evaluate its arguments. E.g., the two plots below are not quite the same. x - 1:10 y - rnorm(10) do.call(plot, list(x, y)) do.call(plot, alist(x, y)) -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com Døden skal tape! --- Nordahl Grieg __ 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] slow computation of functions over large datasets
On Aug 3, 2011, at 9:25 AM, Caroline Faisst wrote:
Hello there,
Im computing the total value of an order from the price of the
order items
using a for loop and the ifelse function.
Ouch. Schools really should stop teaching SAS and BASIC as a first
language.
I do this on a large dataframe
(close to 1m lines). The computation of this function is painfully
slow: in
1min only about 90 rows are calculated.
The computation time taken for a given number of rows increases with
the
size of the dataset, see the example with my function below:
# small dataset: function performs well
exampledata-
data
.frame
(orderID=c(1,1,1,2,2,3,3,3,4),itemPrice=c(10,17,9,12,25,10,1,9,7))
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
{exampledata[i,orderAmount]-
ifelse
(exampledata
[i
,orderID
]==exampledata[i-1,orderID],exampledata[i-1,orderAmount]
+exampledata[i,itemPrice],exampledata[i,itemPrice])})
Try instead using 'ave' to calculate a cumulative 'sum' within
orderID:
exampledata$orderAmt - with(exampledata, ave(itemPrice, orderID,
FUN=cumsum) )
I assure you this will be more reproducible, faster, and
understandable.
# large dataset:
medium dataset really. Barely nudges the RAM dial on my machine.
the very same computational task takes much longer
exampledata2-
data
.frame
(orderID
=
c
(1,1,1,2,2,3,3,3,4,5
:200),itemPrice=c(10,17,9,12,25,10,1,9,7,25:220))
exampledata2[1,orderAmount]-exampledata2[1,itemPrice]
system.time(for (i in 2:9)
{exampledata2[i,orderAmount]-
ifelse
(exampledata2
[i
,orderID
]==exampledata2[i-1,orderID],exampledata2[i-1,orderAmount]
+exampledata2[i,itemPrice],exampledata2[i,itemPrice])})
system.time( exampledata2$orderAmt - with(exampledata2,
ave(itemPrice, orderID, FUN=cumsum) ) )
user system elapsed
35.106 0.811 35.822
On a three year-old machine. Not as fast as I expected, but not long
enough to require refilling the coffee cup either.
--
David.
Does someone know a way to increase the speed?
--
David Winsemius, MD
West Hartford, CT
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Re: [R] syntax with do.call and `[`
On Wed, 3 Aug 2011, peter dalgaard wrote: On Aug 3, 2011, at 12:30 , Jannis wrote: Dear List, i would like to mimic the behaviour or the following indexing with a do.call construct to be able to supply the arguments to `[` as a list: test = matrix[1:4,2] result = test[2,] My try, however, did not work: result = do.call(`[`,list(test,2,NULL)) result = do.call(`[`,list(test,2,)) result = do.call(`[`,list(test,2,'')) How can I use the do.call in that way with leaving the second indexing vector blanc? alist() actually allows this, although probably more by coincidence than by design. Watch: do.call(`[`, alist(test, 2, )) [1] 2 4 If you want to turn this into a programming idiom, be aware that there are subtle differences because alist() does not evaluate its arguments. E.g., the two plots below are not quite the same. x - 1:10 y - rnorm(10) do.call(plot, list(x, y)) do.call(plot, alist(x, y)) I decided to forbear suggesting that, not least as someone who writes test = matrix[1:4,2] appears to know very little R and test even less. But for indexing the answer could be something like do.call(`[`, list(test, 2, TRUE)) as in almost all cases (including here) an empty index is equivalent to TRUE (which is recycled to the required length). -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] step
Hello I am using the step function in order to do backward selection for a linear model of more than 200 variables but it doesn't work correctly. I think, there is a problem, if the matrix has same or more columns than rows. And if the matrix has too much columns the step-function doesn't work because the function will work with all columns together and I think, this is the problem. Is there a solution or a bug fixing of this problem? Thanks a lot -- View this message in context: http://r.789695.n4.nabble.com/step-tp3715681p3715681.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] conditional data replace (recode, change or whatsoever)
Gabor Grothendieck wrote: On Wed, Aug 3, 2011 at 8:09 AM, zcatav lt;zca...@gmail.comgt; wrote: Your suggestion works perfect as i pointed previous message. Now have another question about data editing. I try this code: X[X[,c]==1,b]-X[,d] and results with error: `[-.data.frame`(`*tmp*`, X[, c] == 1, b, value = c(NA, : replacement has 9 rows, data has 2 Logically i selected 2 rows with X[,c]==1. Than i want to replace in that rows its own data from d to b with X[,b]-X[,d]. What is wrong? Also check out transform and ifelse, e.g. transform(X, b = ifelse(is.na(b) c == 0, 2011-07-28, b)) transform(X, b = ifelse(c == 1, d, c)) transform(X, b = ifelse(is.na(b) c == 0, 2011-07-28, b)) This code results as follows. Data at [1,b] and [9,b] not managed as Date. a b c d 1 58009 14915 0 NA 2 114761 NA 1 2008-11-05 3 184440 NA 1 2009-12-08 4 189372 2011-07-28 0 NA 5 105286 2011-07-28 0 NA 6 186717 2011-07-28 0 NA 7 189106 2011-07-28 0 NA 8 127306 2011-07-28 0 NA 9 157342 15089 0 NA And the second code transform(X, b = ifelse(c == 1, d, c)) results as follows. Data at [,b] are completly lost. a b c d 1 58009 1 0 NA 2 114761 14188 1 2008-11-05 3 184440 14586 1 2009-12-08 4 189372 1 0 NA 5 105286 1 0 NA 6 186717 1 0 NA 7 189106 1 0 NA 8 127306 1 0 NA 9 157342 1 0 NA I think this solution not proper for me. -- View this message in context: http://r.789695.n4.nabble.com/conditional-data-replace-recode-change-or-whatsoever-tp3714715p3715525.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] conditional data replace (recode, change or whatsoever)
David Winsemius wrote: On Aug 3, 2011, at 8:09 AM, zcatav wrote: You need to apply the same logical test/selection on the rows of the RHS as you are doing on the LHS. Possibly: X[ X[,c]==1, b] - X[ X[,c]==1, d] This solution was suggested by R. Michael Weylandt and it works great. -- View this message in context: http://r.789695.n4.nabble.com/conditional-data-replace-recode-change-or-whatsoever-tp3714715p3715544.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] Memory limit in Aggregate()
Hi Peter,
Thanks for these information.
I used a column concatenating the listBy data to do this aggregation : (I
don't know if it's the best solution, but it seems to work).
aggregateMultiBy - function(x, by, FUN){
tableBy = data.frame(by)
tableBy$byKey =
for(colBy in names(by))
tableBy$byKey = paste(tableBy$byKey,
as.character(tableBy[,colBy]),)
tableOut - aggregate( x = x
, by = list(byKey = tableBy$byKey)
, FUN = FUN)
tableOut - merge( x = tableOut
, y = tableBy
, by = byKey)
tableOut$byKey - NULL
return(tableOut)
}
Thanks again,
Guillaume
--
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[R] lme4 help pls!
Hi, I have some difficulties to work with the function lmer from lme4. My responses are binary form and i want to use forward selection to my 12 covariates but i dont know how can I choose them based on deviance. Can someone pls give me a example so i can apply. For example my covariates are gestation,smoking ...and my response baby b1=lmer(baby~ (1|id), data, binomial) Thanks. -- View this message in context: http://r.789695.n4.nabble.com/lme4-help-pls-tp3715628p3715628.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] Rattle loading String to Vector file from WEKA
Hi all,
I have been using WEKA to do some text classification work and I want to try
out R.
The problem is I cannot load the String to Vector ARFF files created by
WEKA's string parser into Rattle .
Looking at the logs I get something like:
/Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
:
scan() expected 'a real', got '2281}'/
*My ARFF data file looks a bit like this:*
/@relation 'reviewData'
@attribute polarity {0,2}
.
@attribute $$ numeric
@attribute we numeric
@attribute wer numeric
@attribute win numeric
@attribute work numeric
@data
{0 2,63 1,71 1,100 1,112 1,140 1,186 1,228 1}
{14 1,40 1,48 1,52 1,61 1,146 1}
{2 1,41 1,43 1,57 1,71 1,79 1,106 1,108 1,133 1,146 1,149 1,158 1,201 1}
{0 2,6 1,25 1,29 1,42 1,49 1,69 1,82 1,108 1,116 1,138 1,140 1,155 1}
/
Any ideas how I can convert this into an R readable format?
Cheers!
--
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[R] How to map current Europe?
Hello All, I was trying to generate a map of Europe with the following codes: europe-map(database=world, fill=FALSE, plot=TRUE,xlim=c(-25,70),ylim=c(35,71)) However, the world database is too old to have right European country names. Could anyone help? Thanks, Tianchan -- View this message in context: http://r.789695.n4.nabble.com/How-to-map-current-Europe-tp3715709p3715709.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] Combining multiple dependent variables for machine learning -- fortunes candidate?
I thought Sarah's reply was great and, alas, should probably be templated for this list. Not sure it fits as a fortunes package entry, but I thought it at least worthy of consideration. Cheers, Bert ... I appreciate any suggestions for this problem. Sarah Goslee replied: Suggestions? Yes. Read the posting guide and follow it. It isn't clear that this is even an R question, since you don't tell us anything about the packages or functions you are using, or about your data. There aren't any actual questions in your message, and your problem statement is exceedingly vague. Sarah -- Sarah Goslee http://www.functionaldiversity.org -- Men by nature long to get on to the ultimate truths, and will often be impatient with elementary studies or fight shy of them. If it were possible to reach the ultimate truths without the elementary studies usually prefixed to them, these would not be preparatory studies but superfluous diversions. -- Maimonides (1135-1204) Bert Gunter Genentech Nonclinical Biostatistics __ 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] Running R in a sandbox
On Wed, 2011-08-03 at 11:04 +0300, Antonio Rodriges wrote: Hello, The idea is to grant access of remote users to R running on Linux. Users must have ability to run their R scripts but avoid corrupting the operating system. How one can restrict/limit access of remote users to certain R functions? For example, dealing with IO (file system), graphical tools, etc. We've been here before, IIRC. But I'm too lazy to check the archives - that's your job ;-) Try a search on http://finzi.psych.upenn.edu/search.html for relevant terms and make sure you turn on the email lists and off the functions/vignettes. Thank you. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] How to calculate the number of time a given string can be displayed in the width of a grid viewport
Dear R users,
I am trying to determine how many characters can be displayed within the
width of an open grid viewport. Unfortunately, the arithmetic operation that
seems obvious in this case is be permitted with unit objects (see example
below). Although it isa brut force way to get this number (using a while
loop where the string would be modified by appending the original string to
itseft until its width is bigger than the width of the viewport), this
solution seems a bit overworked. Any suggestion would be welcome.
Sebastien
require(grid)
dev.off()
dev.new()
nstr - ''
str - 'O'
nInWidth - floor(unit(1,'npc')/unit(1,'strwidth',str)) # Does not work
nInWidth - 0
convertWidth(unit(1,'strwidth',nstr),'npc')
while
(unclass(convertWidth(unit(1,'strwidth',paste(nstr,str,sep='')),'npc'))[1] -
1 =.Machine$double.eps){
nInWidth - nInWidth +1
nstr - paste(nstr,str,sep='')
}
nInWidth
grid.text(paste(rep(str,nInWidth),collapse=''),
x = unit(0.5, npc), y = unit(0.5, npc),
draw = TRUE)
[[alternative HTML version deleted]]
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Re: [R] slow computation of functions over large datasets
On Aug 3, 2011, at 9:59 AM, ONKELINX, Thierry wrote:
Dear Caroline,
Here is a faster and more elegant solution.
n - 1
exampledata - data.frame(orderID = sample(floor(n / 5), n, replace
= TRUE), itemPrice = rpois(n, 10))
library(plyr)
system.time({
+ ddply(exampledata, .(orderID), function(x){
+ data.frame(itemPrice = x$itemPrice, orderAmount = cumsum(x
$itemPrice))
+ })
+ })
user system elapsed
1.670.001.69
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
+ {exampledata[i,orderAmount]-
ifelse
(exampledata
[i
,orderID
]==exampledata[i-1,orderID],exampledata[i-1,orderAmount]
+exampledata[i,itemPrice],exampledata[i,itemPrice])})
user system elapsed
11.940.02 11.97
I tried running this method on the large dataset (2MM row) the OP
offered, and needed to eventually interrupt it so I could get my
console back:
system.time({
+ ddply(exampledata2, .(orderID), function(x){
+ data.frame(itemPrice = x$itemPrice, orderAmount = cumsum(x
$itemPrice))
+ })
+ })
Timing stopped at: 808.473 1013.749 1816.125
The same task with ave() took 35 seconds.
--
david.
Best regards,
Thierry
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org
]
Namens Caroline Faisst
Verzonden: woensdag 3 augustus 2011 15:26
Aan: r-help@r-project.org
Onderwerp: [R] slow computation of functions over large datasets
Hello there,
I'm computing the total value of an order from the price of the
order items using
a for loop and the ifelse function. I do this on a large
dataframe (close to
1m lines). The computation of this function is painfully slow: in
1min only about
90 rows are calculated.
The computation time taken for a given number of rows increases
with the size
of the dataset, see the example with my function below:
# small dataset: function performs well
exampledata-
data
.frame
(orderID=c(1,1,1,2,2,3,3,3,4),itemPrice=c(10,17,9,12,25,10,1,9,7))
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
{exampledata[i,orderAmount]-
ifelse
(exampledata[i,orderID]==exampledata[i-1,orderID],exampledata[i-
1,orderAmount]
+exampledata[i,itemPrice],exampledata[i,itemPrice])})
# large dataset: the very same computational task takes much longer
exampledata2-
data
.frame
(orderID=c(1,1,1,2,2,3,3,3,4,5:200),itemPrice=c(10,17,9,12,25,1
0,1,9,7,25:220))
exampledata2[1,orderAmount]-exampledata2[1,itemPrice]
system.time(for (i in 2:9)
{exampledata2[i,orderAmount]-
ifelse(exampledata2[i,orderID]==exampledata2[i-
1,orderID],exampledata2[i-
1,orderAmount]
+exampledata2[i,itemPrice],exampledata2[i,itemPrice])})
Does someone know a way to increase the speed?
Thank you very much!
Caroline
David Winsemius, MD
West Hartford, CT
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Re: [R] conditional data replace (recode, change or whatsoever)
zcatav zcatav at gmail.com writes: Your suggestion works perfect as i pointed previous message. Now have another question about data editing. I try this code: X[X[,c]==1,b]-X[,d] and results with error: `[-.data.frame`(`*tmp*`, X[, c] == 1, b, value = c(NA, : replacement has 9 rows, data has 2 is this equivalent and/or preferred to: X$b[X$c==1]-X$d[X$c==1] ?? I assume this goes back to the various indexing methods for a dataframe, an object vector that is a column of a data frame vs. an object data frame that happens to be one column of a larger data frame. on a very large data set is one preferable for speed? one for memory use? I tend to index using $ operators often and if I should quit let me know!! Thanks, Justin Logically i selected 2 rows with X[,c]==1. Than i want to replace in that rows its own data from d to b with X[,b]-X[,d]. What is wrong? -- View this message in context: http://r.789695.n4.nabble.com/conditional-data-replace-recode-change-or-whatsoever-tp3714715p3715218.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] 3D Bar Graphs in ggplot2?
On 8/3/2011 6:07 AM, wwreith wrote: So I take it 3D pie charts are out? At least with ggplot, yes. 2D pie charts are somewhat tricky with ggplot, even. They can be gone with stacked, normalized bar charts projected into polar coordinates, if I recall properly. Not limited to ggplot, there is pie() in the graphics package, and pie3D() in the plotrix package. I couldn't find anything that would do bar plots with a 3D effect; the closest was the scatterplot3d package, but that is more a way to do a two dimensional array of bars, rather than a 3D effect. P.S. It is not about hiding anything. It is about consulting and being told by your client to make 3D pie charts and change this font or that color to make the graphs more apealing. Given that I am the one trying to open the door to using R where I work it would be much easier if I could simply use a 2D graph. External requirements can make us make choices we otherwise might not have. If the client is amenable to education, you could slowly try to persuade (say, using side-by-side examples), but some are not. Good luck. -- View this message in context: http://r.789695.n4.nabble.com/3D-Bar-Graphs-in-ggplot2-tp3713305p3715382.html Sent from the R help mailing list archive at Nabble.com. -- Brian S. Diggs, PhD Senior Research Associate, Department of Surgery Oregon Health Science University __ 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] How to calculate the number of times a given string can be displayed in the width of a grid viewport
There was too many spelling mistakes in my original post so I have
decided to re-submit it. So here is it
Dear R users,
I am trying to determine how many characters can be displayed within
the width of an open grid viewport. Unfortunately, the arithmetic
operation that seems obvious in this case is not permitted with unit
objects (see example below). Although there is a brute force way to
get this number (using a while loop where the string would be modified
by appending the original string to itseft until its width is larger
than the width of the viewport), this solution seems a bit overworked.
Any suggestion would be welcome.
Sebastien
require(grid)
dev.off()
dev.new()
nstr - ''
str - 'O'
nInWidth - floor(unit(1,'npc')/unit(1,'strwidth',str)) # Does not work
nInWidth - 0
convertWidth(unit(1,'strwidth',nstr),'npc')
while
(unclass(convertWidth(unit(1,'strwidth',paste(nstr,str,sep='')),'npc'))[1]
- 1 =.Machine$double.eps){
nInWidth - nInWidth +1
nstr - paste(nstr,str,sep='')
}
nInWidth
grid.text(paste(rep(str,nInWidth),collapse=''),
x = unit(0.5, npc), y = unit(0.5, npc),
draw = TRUE)
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Re: [R] Error Installing or Updating Packages (Maybe because of a proxy)
1. you wrote to the mailing list rather than to the original poster. 2. you forgot to cite the original post, hence we do not know what you are referring to. PLease do read the posting guide to this list! Uwe Ligges On 03.08.2011 14:53, mohammad...@gmail.com wrote: Hello David, I encountered the same problem of yours. What did you do to resolve it? Thanks for your reply Mohammad -- View this message in context: http://r.789695.n4.nabble.com/Error-Installing-or-Updating-Packages-Maybe-because-of-a-proxy-tp3462312p3715332.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extract p value from coxme object
You can look at the code coxme:::print.coxme There you will see that the global test is a chisquare chi1 - 2*diff(x$loglik[1:2]) with x$df[1] degrees of freedom. The fixed effects coefficients are found in x$coefficients$fixed, and the variances are diag(x$var)[-(1:nfrail)]. (The variances for the random coefficients are first, and then those for the fixed effects). If there are 5 fixed coefficients, their variance/covariance matrix is the lower right 5x5 corner of x$var. Terry Therneau __ 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] slow computation of functions over large datasets
This takes about 2 secs for 1M rows:
n - 100
exampledata - data.frame(orderID = sample(floor(n / 5), n, replace = TRUE),
itemPrice = rpois(n, 10))
require(data.table)
# convert to data.table
ed.dt - data.table(exampledata)
system.time(result - ed.dt[
+ , list(total = sum(itemPrice))
+ , by = orderID
+ ]
+)
user system elapsed
1.300.051.34
str(result)
Classes ‘data.table’ and 'data.frame': 198708 obs. of 2 variables:
$ orderID: int 1 2 3 4 5 6 8 9 10 11 ...
$ total : num 49 37 72 92 50 76 34 22 65 39 ...
head(result)
orderID total
[1,] 149
[2,] 237
[3,] 372
[4,] 492
[5,] 550
[6,] 676
On Wed, Aug 3, 2011 at 9:25 AM, Caroline Faisst
caroline.fai...@gmail.com wrote:
Hello there,
I’m computing the total value of an order from the price of the order items
using a “for” loop and the “ifelse” function. I do this on a large dataframe
(close to 1m lines). The computation of this function is painfully slow: in
1min only about 90 rows are calculated.
The computation time taken for a given number of rows increases with the
size of the dataset, see the example with my function below:
# small dataset: function performs well
exampledata-data.frame(orderID=c(1,1,1,2,2,3,3,3,4),itemPrice=c(10,17,9,12,25,10,1,9,7))
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
{exampledata[i,orderAmount]-ifelse(exampledata[i,orderID]==exampledata[i-1,orderID],exampledata[i-1,orderAmount]+exampledata[i,itemPrice],exampledata[i,itemPrice])})
# large dataset: the very same computational task takes much longer
exampledata2-data.frame(orderID=c(1,1,1,2,2,3,3,3,4,5:200),itemPrice=c(10,17,9,12,25,10,1,9,7,25:220))
exampledata2[1,orderAmount]-exampledata2[1,itemPrice]
system.time(for (i in 2:9)
{exampledata2[i,orderAmount]-ifelse(exampledata2[i,orderID]==exampledata2[i-1,orderID],exampledata2[i-1,orderAmount]+exampledata2[i,itemPrice],exampledata2[i,itemPrice])})
Does someone know a way to increase the speed?
Thank you very much!
Caroline
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] strsplit and forward slash '/'
Hi All, is there a way of using strsplit with a forward slash '/' as the splitting point? For data such as: 1 T/TC/C 16/33 2 T/TC/C 33/36 3 T/TC/C 16/34 4 T/TC/C 16/31 5 C/CC/C 28/29 6 T/TC/C 16/34 strsplit(my.data[1,1], /) # and any variation thereof Error in strsplit(apoe[1, 1], /) : non-character argument Any advice will be gratefully received. Best wishes, Federico -- Federico C. F. Calboli Department of Epidemiology and Biostatistics Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.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] gstat error
Hello. I am running the examples provided in the gstat help menus. When I try to run the following in predict.gstat: data(meuse) coordinates(meuse)= ~x+y v-variogram(log(zinc)~1, meuse) I get the following error message: Error in vector(double, length) : invalid 'length' argument What's the problem? Gilbert __ 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] strsplit and forward slash '/'
On 03/08/2011 12:37 PM, Federico Calboli wrote: Hi All, is there a way of using strsplit with a forward slash '/' as the splitting point? For data such as: 1 T/TC/C 16/33 2 T/TC/C 33/36 3 T/TC/C 16/34 4 T/TC/C 16/31 5 C/CC/C 28/29 6 T/TC/C 16/34 strsplit(my.data[1,1], /) # and any variation thereof Error in strsplit(apoe[1, 1], /) : non-character argument It looks as though your my.data[1,1] value is a factor, not a character value. strsplit(as.character(my.data[1,1]), /) would work, or you could avoid getting factors in the first place, using the stringsAsFactors argument when you create the dataframe. Duncan Murdoch Any advice will be gratefully received. Best wishes, Federico -- Federico C. F. Calboli Department of Epidemiology and Biostatistics Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.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] strsplit and forward slash '/'
Hi Federico, A forward slash isn't a special character: strsplit(T/T, /) [[1]] [1] T T so there's some other problem. Are you sure that your first column contains strings and not factors? What does str(my.data) tell you? Does strsplit(as.character(my.data[1,1]), /) work? If you used read.table() to get your data in, you might want the as.is=TRUE or the stringsAsFactors=FALSE argument. Sarah On Wed, Aug 3, 2011 at 12:37 PM, Federico Calboli f.calb...@imperial.ac.uk wrote: Hi All, is there a way of using strsplit with a forward slash '/' as the splitting point? For data such as: 1 T/T C/C 16/33 2 T/T C/C 33/36 3 T/T C/C 16/34 4 T/T C/C 16/31 5 C/C C/C 28/29 6 T/T C/C 16/34 strsplit(my.data[1,1], /) # and any variation thereof Error in strsplit(apoe[1, 1], /) : non-character argument Any advice will be gratefully received. Best wishes, Federico -- Sarah Goslee http://www.sarahgoslee.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] strsplit and forward slash '/'
On 3 Aug 2011, at 17:41, Duncan Murdoch wrote: It looks as though your my.data[1,1] value is a factor, not a character value. strsplit(as.character(my.data[1,1]), /) Thanks Duncan, this solved it. Best Federico would work, or you could avoid getting factors in the first place, using the stringsAsFactors argument when you create the dataframe. Duncan Murdoch Any advice will be gratefully received. Best wishes, Federico -- Federico C. F. Calboli Department of Epidemiology and Biostatistics Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.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. -- Federico C. F. Calboli Department of Epidemiology and Biostatistics Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.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] strsplit and forward slash '/'
On 3 Aug 2011, at 17:46, Sarah Goslee wrote: Hi Federico, A forward slash isn't a special character: strsplit(T/T, /) [[1]] [1] T T so there's some other problem. Are you sure that your first column contains strings and not factors? What does str(my.data) tell you? Does strsplit(as.character(my.data[1,1]), /) work? yes! Thanks Federico If you used read.table() to get your data in, you might want the as.is=TRUE or the stringsAsFactors=FALSE argument. Sarah On Wed, Aug 3, 2011 at 12:37 PM, Federico Calboli f.calb...@imperial.ac.uk wrote: Hi All, is there a way of using strsplit with a forward slash '/' as the splitting point? For data such as: 1 T/TC/C 16/33 2 T/TC/C 33/36 3 T/TC/C 16/34 4 T/TC/C 16/31 5 C/CC/C 28/29 6 T/TC/C 16/34 strsplit(my.data[1,1], /) # and any variation thereof Error in strsplit(apoe[1, 1], /) : non-character argument Any advice will be gratefully received. Best wishes, Federico -- Sarah Goslee http://www.sarahgoslee.com -- Federico C. F. Calboli Department of Epidemiology and Biostatistics Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.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] R CMD check problem
On 03/08/2011 12:47 PM, Baidya Nath Mandal wrote: Dear Murdoch, After setting CYGWIN=nodosfilewarning, i re-ran the R CMD check and got following message: * installing *source* package 'mypackage' ... ** libs ERROR: compilation failed for package 'mypackage' * removing 'C:/Rpackages/mypackage.Rcheck/mypackage' The log file contained following. * using log directory 'C:/Rpackages/mypackage.Rcheck' * using R version 2.13.0 (2011-04-13) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'mypackage/DESCRIPTION' ... OK * this is package 'mypackage' version '1.1' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking for executable files ... OK * checking whether package 'mypackage' can be installed ... ERROR Installation failed. See 'C:/Rpackages/mypackage.Rcheck/00install.out' for details. The src directory contains nothing since all my codes are in R and are in the R directory. I have checked that the code works fine in R console. My DESCRIPTION file is like this: Package: mypackage Version: 1.1 Date: 2011-07-14 Title: abcd Author: B N Mandalmandal.s...@gmail.com Maintainer: B N Mandalmandal.s...@gmail.com Depends: R(= 2.13.0) Description: xyz License: GPL (=2) and NAMESPACE file contains export(fun1) I have checked Rd files are fine. Can you suggest what may be wrong now? You should delete your src directory if you don't need it. Duncan Murdoch regards, BN Mandal On Tue, Aug 2, 2011 at 4:17 PM, Duncan Murdochmurdoch.dun...@gmail.comwrote: On 11-08-02 5:26 AM, Baidya Nath Mandal wrote: Dear friends, I am building an R package called *mypackage*. I followed every possible steps (to my understanding) for the same. I got following problem while doing *R CMD check mypackage*. * installing *source* package 'mypackage' ... ** libs cygwin warning: MS-DOS style path detected: C:/PROGRA~1/R/R-213~1.0/etc/**i386/Makeconf Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-213~**1.0/etc/i386/Makeconf CYGWIN environment variable option nodosfilewarning turns off this warning. Consult the user's guide for more details about POSIX paths: http://cygwin.com/cygwin-ug-**net/using.html#using-pathnameshttp://cygwin.com/cygwin-ug-net/using.html#using-pathnames I believe that warning is ignorable, but you can turn it off using set CYGWIN=nodosfilewarning It probably didn't cause the error below. ERROR: compilation failed for package 'mypackage' I don't know what did cause that error, but it's likely something in your src directory of the package. What do you have there? Duncan Murdoch * removing 'C:/Rpackages/mypackage.**Rcheck/mypackage'. What I understood from above is that it is something with PATH variable. I had set the following PATH variable: C:\Rtools\bin;C:\Rtools\MinGW\**bin;C:\Program Files\R\R-2.13.0\bin;C:\**Program Files\MiKTeX 2.9\miktex\bin;%SystemRoot%\**system32;%SystemRoot%;%** SystemRoot%\System32\Wbem;%**SYSTEMROOT%\System32\** WindowsPowerShell\v1.0\;C:\**Program Files\HTML Help Workshop Can anybody suggest what possibly could have gone wrong? Thanks, BN Mandal [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.htmlhttp://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] slow computation of functions over large datasets
On Aug 3, 2011, at 12:20 PM, jim holtman wrote:
This takes about 2 secs for 1M rows:
n - 100
exampledata - data.frame(orderID = sample(floor(n / 5), n, replace
= TRUE), itemPrice = rpois(n, 10))
require(data.table)
# convert to data.table
ed.dt - data.table(exampledata)
system.time(result - ed.dt[
+ , list(total = sum(itemPrice))
+ , by = orderID
+ ]
+)
user system elapsed
1.300.051.34
Interesting. Impressive. And I noted that the OP wanted what cumsum
would provide and for some reason creating that longer result is even
faster on my machine than the shorter result using sum.
--
David.
str(result)
Classes ‘data.table’ and 'data.frame': 198708 obs. of 2 variables:
$ orderID: int 1 2 3 4 5 6 8 9 10 11 ...
$ total : num 49 37 72 92 50 76 34 22 65 39 ...
head(result)
orderID total
[1,] 149
[2,] 237
[3,] 372
[4,] 492
[5,] 550
[6,] 676
On Wed, Aug 3, 2011 at 9:25 AM, Caroline Faisst
caroline.fai...@gmail.com wrote:
Hello there,
I’m computing the total value of an order from the price of the
order items
using a “for” loop and the “ifelse” function. I do this on a large
dataframe
(close to 1m lines). The computation of this function is painfully
slow: in
1min only about 90 rows are calculated.
The computation time taken for a given number of rows increases
with the
size of the dataset, see the example with my function below:
# small dataset: function performs well
exampledata-
data
.frame
(orderID=c(1,1,1,2,2,3,3,3,4),itemPrice=c(10,17,9,12,25,10,1,9,7))
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
{exampledata[i,orderAmount]-
ifelse
(exampledata
[i
,orderID
]==exampledata[i-1,orderID],exampledata[i-1,orderAmount]
+exampledata[i,itemPrice],exampledata[i,itemPrice])})
# large dataset: the very same computational task takes much longer
exampledata2-
data
.frame
(orderID
=
c
(1,1,1,2,2,3,3,3,4,5
:200),itemPrice=c(10,17,9,12,25,10,1,9,7,25:220))
exampledata2[1,orderAmount]-exampledata2[1,itemPrice]
system.time(for (i in 2:9)
{exampledata2[i,orderAmount]-
ifelse
(exampledata2
[i
,orderID
]==exampledata2[i-1,orderID],exampledata2[i-1,orderAmount]
+exampledata2[i,itemPrice],exampledata2[i,itemPrice])})
Does someone know a way to increase the speed?
Thank you very much!
Caroline
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Data Munger Guru
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.
David Winsemius, MD
West Hartford, CT
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] gstat error
On 2011-08-03 09:40, gbre...@ssc.wisc.edu wrote: Hello. I am running the examples provided in the gstat help menus. When I try to run the following in predict.gstat: data(meuse) coordinates(meuse)= ~x+y v-variogram(log(zinc)~1, meuse) I get the following error message: Error in vector(double, length) : invalid 'length' argument What's the problem? You should at the very least provide your sessionInfo(). Peter Ehlers Gilbert __ 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] Coefficient names when using lm() with contrasts
If you add column names to your contrast matrix (treat3) then those names will
be used in the coefficient names.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Peter Morgan
Sent: Wednesday, August 03, 2011 6:12 AM
To: r-help@r-project.org
Subject: [R] Coefficient names when using lm() with contrasts
Dear R Users,
Am using lm() with contrasts as below. If I skip the contrasts()
statement, I get the coefficient names to be
names(results$coef)
[1] (Intercept) VarAcat VarArat VarB
which are much more meaningful than ones based on integers.
Can anyone tell me how to get R to keep the coefficient names based on
the
factor levels whilst using contrasts rather than labelling them with
integers?
Many thanks in advance,
Pete
Cardiff, UK
dt=read.table(testreg.txt,sep=,,header=T)
dt
ID VarA VarB VarC
1 1 cat2 23
2 2 dog3 56
3 3 rat5 35
4 4 cat2 43
5 5 cat7 51
6 6 dog3 31
7 7 dog4 65
8 8 rat1 18
9 9 rat6 49
10 10 dog3 28
dt$VarA=relevel(dt$VarA,ref=dog)
treat3=matrix(-1/3,ncol=2,nrow=3); for (i in 1:2) {treat3[i+1,i]=2/3}
contrasts(dt$VarA)=treat3
levels(dt$VarA)
[1] dog cat rat
results=lm(formula=VarC~VarA+VarB, data=dt)
names(results$coef)
[1] (Intercept) VarA1 VarA2 VarB
[[alternative HTML version deleted]]
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guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] slow computation of functions over large datasets
On Aug 3, 2011, at 2:01 PM, Ken wrote:
Hello,
Perhaps transpose the table attach(as.data.frame(t(data))) and use
ColSums() function with order id as header.
-Ken Hutchison
Got any code? The OP offered a reproducible example, after all.
--
David.
On Aug 3, 2554 BE, at 1:12 PM, David Winsemius
dwinsem...@comcast.net wrote:
On Aug 3, 2011, at 12:20 PM, jim holtman wrote:
This takes about 2 secs for 1M rows:
n - 100
exampledata - data.frame(orderID = sample(floor(n / 5), n,
replace = TRUE), itemPrice = rpois(n, 10))
require(data.table)
# convert to data.table
ed.dt - data.table(exampledata)
system.time(result - ed.dt[
+ , list(total = sum(itemPrice))
+ , by = orderID
+ ]
+)
user system elapsed
1.300.051.34
Interesting. Impressive. And I noted that the OP wanted what cumsum
would provide and for some reason creating that longer result is
even faster on my machine than the shorter result using sum.
--
David.
str(result)
Classes ‘data.table’ and 'data.frame': 198708 obs. of 2 variables:
$ orderID: int 1 2 3 4 5 6 8 9 10 11 ...
$ total : num 49 37 72 92 50 76 34 22 65 39 ...
head(result)
orderID total
[1,] 149
[2,] 237
[3,] 372
[4,] 492
[5,] 550
[6,] 676
On Wed, Aug 3, 2011 at 9:25 AM, Caroline Faisst
caroline.fai...@gmail.com wrote:
Hello there,
I’m computing the total value of an order from the price of the
order items
using a “for” loop and the “ifelse” function. I do this on a
large dataframe
(close to 1m lines). The computation of this function is
painfully slow: in
1min only about 90 rows are calculated.
The computation time taken for a given number of rows increases
with the
size of the dataset, see the example with my function below:
# small dataset: function performs well
exampledata-
data
.frame
(orderID=c(1,1,1,2,2,3,3,3,4),itemPrice=c(10,17,9,12,25,10,1,9,7))
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
{exampledata[i,orderAmount]-
ifelse
(exampledata
[i
,orderID
]==exampledata[i-1,orderID],exampledata[i-1,orderAmount]
+exampledata[i,itemPrice],exampledata[i,itemPrice])})
# large dataset: the very same computational task takes much longer
exampledata2-
data
.frame
(orderID
=
c
(1,1,1,2,2,3,3,3,4,5
:200),itemPrice=c(10,17,9,12,25,10,1,9,7,25:220))
exampledata2[1,orderAmount]-exampledata2[1,itemPrice]
system.time(for (i in 2:9)
{exampledata2[i,orderAmount]-
ifelse
(exampledata2
[i
,orderID
]==exampledata2[i-1,orderID],exampledata2[i-1,orderAmount]
+exampledata2[i,itemPrice],exampledata2[i,itemPrice])})
Does someone know a way to increase the speed?
Thank you very much!
Caroline
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--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
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Re: [R] gstat error
Here is my sessionInfo() sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines grid stats graphics grDevices utils datasets methods [9] base other attached packages: [1] spsurvey_2.1-2 lmtest_0.9-27 zoo_1.6-5 [4] car_2.0-9 survival_2.36-5 nnet_7.3-1 [7] spgwr_0.6-10spatialCovariance_0.6-4 spatial_7.3-2 [10] spatgraphs_2.44 sgeostat_1.0-23 rworldmap_0.1211 [13] fields_6.3 spam_0.23-0 RPyGeo_0.9-2 [16] RSAGA_0.91-1shapefiles_0.6 RgoogleMaps_1.1.9.7 [19] raster_1.8-22 RArcInfo_0.4-10 RColorBrewer_1.0-2 [22] PBSmodelling_2.61.210 PBSmapping_2.61.9 mapproj_1.1-8.3 [25] mapdata_2.1-4 intamap_1.3-8 evd_2.2-4 [28] mvtnorm_0.9-96 automap_1.0-9 rgdal_0.6-33 [31] gmaps_0.2 maps_2.1-6 glmmBUGS_1.9 [34] spdep_0.5-32coda_0.14-2 deldir_0.0-13 [37] maptools_0.8-7 foreign_0.8-42 Matrix_0.999375-46 [40] lattice_0.19-17 boot_1.2-43 abind_1.3-0 [43] MASS_7.3-11 geosphere_1.2-19geonames_0.8 [46] rjson_0.2.3 ctv_0.7-2 GEOmap_1.5-13 [49] akima_0.5-4 RPMG_2.0-5 splancs_2.01-27 [52] geomapdata_1.0-4geoRglm_0.8-33 geoR_1.6-34 [55] gstat_0.9-81sp_0.9-81 nlme_3.1-98 loaded via a namespace (and not attached): [1] tcltk_2.12.2 tools_2.12.2 On 2011-08-03 09:40, gbre...@ssc.wisc.edu wrote: Hello. I am running the examples provided in the gstat help menus. When I try to run the following in predict.gstat: data(meuse) coordinates(meuse)= ~x+y v-variogram(log(zinc)~1, meuse) I get the following error message: Error in vector(double, length) : invalid 'length' argument What's the problem? You should at the very least provide your sessionInfo(). Peter Ehlers Gilbert __ 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] Convert matrix to numeric
I have a matrix that looks like this: structure(c(0.0376673981759913, 0.111066500741386, 1, 1103, 18, OPEN, DEPR, 0.0404073656092023, 0.115186044704599, 1, 719, 18, OPEN, DEPR, 0.0665342096693433, 0.197570061769498, 1, 1103, 18, OPEN, DEPR, 0.119287147905722, 0.356427096010845, 1, 1103, 18, OPEN, DEPR), .Dim = c(7L, 4L), .Dimnames = list( c(Sn, SlnC, housenum, date, hour, flue, pressurization ), c(10019.BLO, 1002.BLO, 10020.BLO, 10021.BLO))) How do I convert rows 1-5 to numeric? I tried mode() - numeric but that doesn't change anything. I also tried converting this to a table then converting to numeric, but I got: (list) object cannot be coerced to type 'double' Jeff __ 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] limits on liniar model
Can I put limits on the lm() command? I only know that you can choose a liniar model with or without an intercept, but can I put other limits on the coefficients (for example- the intercept must be bigger than 1) ? _ Walla! Mail - [1]Get your free unlimited mail today References 1. http://www.walla.co.il/ __ 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] Case-by-case tolerance needed for successful integrate()
Hello,
We are trying to use R to simulate a model based on parameters 'a' and 'b'.
This involves the following integration:
model-function(s,x,a,b)(exp(-s*x*10^-5.5)*(s^(a-1)*(1-s)^(b-1)))
g- function(x,a,b){
out-c()
for (i in 1:length(x)){
out[i]-1- (integrate(model,0,1,x[i],a,b)$value / beta(a,b))
}
out
}
x- 10^seq(0,10,by=0.01)
y- g(x,a=0.8,b=0.5)
This gives the error
Error in integrate(model, 0, 1, x[i], a, b) : the integral is
probably divergent
Changing the relative or absolute tolerance solves this issue, but a certain
tolerance only works with a certain set of 'a' and 'b'.
For example, and abs.tol=10^-9 will make it work with a=0.8 and b=0.5 but
fail with a=0.3 and b=0.9.
We need this code to work for any reasonable value of 'a' and 'b' - as
seen by the shape of the distribution Beta(a,b).
We have tried using a different number of subdivisions without any luck.
The same integration in MATLAB works without any problem (using quad).
Anyone has an idea of why these problems occur and how to avoid them?
Many thanks.
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Re: [R] R CMD check problem
Dear Murdoch, After setting CYGWIN=nodosfilewarning, i re-ran the R CMD check and got following message: * installing *source* package 'mypackage' ... ** libs ERROR: compilation failed for package 'mypackage' * removing 'C:/Rpackages/mypackage.Rcheck/mypackage' The log file contained following. * using log directory 'C:/Rpackages/mypackage.Rcheck' * using R version 2.13.0 (2011-04-13) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'mypackage/DESCRIPTION' ... OK * this is package 'mypackage' version '1.1' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking for executable files ... OK * checking whether package 'mypackage' can be installed ... ERROR Installation failed. See 'C:/Rpackages/mypackage.Rcheck/00install.out' for details. The src directory contains nothing since all my codes are in R and are in the R directory. I have checked that the code works fine in R console. My DESCRIPTION file is like this: Package: mypackage Version: 1.1 Date: 2011-07-14 Title: abcd Author: B N Mandal mandal.s...@gmail.com Maintainer: B N Mandal mandal.s...@gmail.com Depends: R(= 2.13.0) Description: xyz License: GPL (=2) and NAMESPACE file contains export(fun1) I have checked Rd files are fine. Can you suggest what may be wrong now? regards, BN Mandal On Tue, Aug 2, 2011 at 4:17 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 11-08-02 5:26 AM, Baidya Nath Mandal wrote: Dear friends, I am building an R package called *mypackage*. I followed every possible steps (to my understanding) for the same. I got following problem while doing *R CMD check mypackage*. * installing *source* package 'mypackage' ... ** libs cygwin warning: MS-DOS style path detected: C:/PROGRA~1/R/R-213~1.0/etc/**i386/Makeconf Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-213~**1.0/etc/i386/Makeconf CYGWIN environment variable option nodosfilewarning turns off this warning. Consult the user's guide for more details about POSIX paths: http://cygwin.com/cygwin-ug-**net/using.html#using-pathnameshttp://cygwin.com/cygwin-ug-net/using.html#using-pathnames I believe that warning is ignorable, but you can turn it off using set CYGWIN=nodosfilewarning It probably didn't cause the error below. ERROR: compilation failed for package 'mypackage' I don't know what did cause that error, but it's likely something in your src directory of the package. What do you have there? Duncan Murdoch * removing 'C:/Rpackages/mypackage.**Rcheck/mypackage'. What I understood from above is that it is something with PATH variable. I had set the following PATH variable: C:\Rtools\bin;C:\Rtools\MinGW\**bin;C:\Program Files\R\R-2.13.0\bin;C:\**Program Files\MiKTeX 2.9\miktex\bin;%SystemRoot%\**system32;%SystemRoot%;%** SystemRoot%\System32\Wbem;%**SYSTEMROOT%\System32\** WindowsPowerShell\v1.0\;C:\**Program Files\HTML Help Workshop Can anybody suggest what possibly could have gone wrong? Thanks, BN Mandal [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html 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.
[R] r-help
Hey, Is there any function plotting several implicit functions (F(x,y)=0) on the same fig. Is there anyone who has an example code of how to do this? The contour3d function in the misc3d package only work with the functions with three dimensions. Thanks a lot. Many thanks for your help. KnifeBoot [[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] R CMD check problem
Many many thanks, working now. Best, BN Mandal On Wed, Aug 3, 2011 at 10:34 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 03/08/2011 12:47 PM, Baidya Nath Mandal wrote: Dear Murdoch, After setting CYGWIN=nodosfilewarning, i re-ran the R CMD check and got following message: * installing *source* package 'mypackage' ... ** libs ERROR: compilation failed for package 'mypackage' * removing 'C:/Rpackages/mypackage.**Rcheck/mypackage' The log file contained following. * using log directory 'C:/Rpackages/mypackage.**Rcheck' * using R version 2.13.0 (2011-04-13) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * checking for file 'mypackage/DESCRIPTION' ... OK * this is package 'mypackage' version '1.1' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking for executable files ... OK * checking whether package 'mypackage' can be installed ... ERROR Installation failed. See 'C:/Rpackages/mypackage.**Rcheck/00install.out' for details. The src directory contains nothing since all my codes are in R and are in the R directory. I have checked that the code works fine in R console. My DESCRIPTION file is like this: Package: mypackage Version: 1.1 Date: 2011-07-14 Title: abcd Author: B N Mandalmandal.s...@gmail.com Maintainer: B N Mandalmandal.s...@gmail.com Depends: R(= 2.13.0) Description: xyz License: GPL (=2) and NAMESPACE file contains export(fun1) I have checked Rd files are fine. Can you suggest what may be wrong now? You should delete your src directory if you don't need it. Duncan Murdoch regards, BN Mandal On Tue, Aug 2, 2011 at 4:17 PM, Duncan Murdochmurdoch.duncan@gmail.**commurdoch.dun...@gmail.com wrote: On 11-08-02 5:26 AM, Baidya Nath Mandal wrote: Dear friends, I am building an R package called *mypackage*. I followed every possible steps (to my understanding) for the same. I got following problem while doing *R CMD check mypackage*. * installing *source* package 'mypackage' ... ** libs cygwin warning: MS-DOS style path detected: C:/PROGRA~1/R/R-213~1.0/etc/ i386/Makeconf Preferred POSIX equivalent is: /cygdrive/c/PROGRA~1/R/R-213~1.0/etc/i386/Makeconf CYGWIN environment variable option nodosfilewarning turns off this warning. Consult the user's guide for more details about POSIX paths: http://cygwin.com/cygwin-ug-net/using.html#using-pathnameshttp://cygwin.com/cygwin-ug-**net/using.html#using-pathnames **http://cygwin.com/cygwin-ug-**net/using.html#using-pathnameshttp://cygwin.com/cygwin-ug-net/using.html#using-pathnames ** I believe that warning is ignorable, but you can turn it off using set CYGWIN=nodosfilewarning It probably didn't cause the error below. ERROR: compilation failed for package 'mypackage' I don't know what did cause that error, but it's likely something in your src directory of the package. What do you have there? Duncan Murdoch * removing 'C:/Rpackages/mypackage.Rcheck/mypackage'. What I understood from above is that it is something with PATH variable. I had set the following PATH variable: C:\Rtools\bin;C:\Rtools\MinGW\bin;C:\Program Files\R\R-2.13.0\bin;C:\Program Files\MiKTeX 2.9\miktex\bin;%SystemRoot%\system32;%SystemRoot%;%** SystemRoot%\System32\Wbem;%SYSTEMROOT%\System32\** WindowsPowerShell\v1.0\;C:\Program Files\HTML Help Workshop Can anybody suggest what possibly could have gone wrong? Thanks, BN Mandal [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-helphttps://stat.ethz.ch/mailman/**listinfo/r-help https://stat.**ethz.ch/mailman/listinfo/r-**helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.htmlhttp://www.**R-project.org/posting-guide.**htmlhttp://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] R-help Digest, Vol 102, Issue 3
Since we got this the x-th time now: Dear Fränzi Korner, please please please never ever add auto-replies to your account that also reply to mailing list messages! Thousands of readers of R-help get your auto reply everey day now! Best, Uwe Ligges On 03.08.2011 12:11, fraenzi.kor...@oikostat.ch wrote: Wir sind bis am 20. August in den Ferien und werden keine e-mails beantworten. Bei dringenden Fällen melden Sie sich bei Stefanie von Felten steffi.vonfel...@oikostat.ch We are on vacation until 20. August. In urgent cases, please contact Stefanie von Felten steffi.vonfel...@oikostat.ch __ 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] How to fit model in function using passed-in formula, then predict from another function
Hello R experts,
I am trying to fit an lme model within a function, using a formula that I
passed into the function, and then predict that model from a different
function. Could you please advise me on how to do this? The following code
illustrates the essence of what I'm trying to do. The actual scenario is
more complicated but this toy example illustrates the crux of the problem.
library(nlme)
Fit - function(f)
+ {
+ model - lme(f, BodyWeight, random = ~ Time) # BodyWeight is from
nlme package
+ return(model)
+ }
m1 - Fit(weight ~ Time * Diet)
Predict - function(m)
+ {
+ print(predict(m, m$data))
+ }
Predict(m1)
Error in eval(expr, envir, enclos) : object 'f' not found
traceback()
7: eval(expr, envir, enclos)
6: eval(mCall$fixed)
5: eval(eval(mCall$fixed)[-2])
4: predict.lme(m, m$data)
3: predict(m, m$data)
2: print(predict(m, m$data))
1: Predict(m1)
I have tried various things using parse(), eval(), force(), and so on and
could not figure it out. I suspect this all comes down to a basic ignorance
on my part regarding R's lazy evaluation mechanism, promises, and
environments. I've encountered similar problems elsewhere when passing other
things into functions. It seems like some packages, such as nlme here, have
this restriction and other packages do not. I would appreciate anything you
can do to enlighten me about how this is supposed to work.
Thanks very much,
Jason
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Re: [R] gstat error
I see a 'variogram' function in both spatial and gstat when I use ?? variogram on my machine that probably does not have even all of those packages installed. Are you sure they are the same (I looked they are not) or failing that that the one you expect is being chosen? And are you even sure that there is not a third or a fourth 'variogram' in one of those other packages? -- David. On Aug 3, 2011, at 2:45 PM, gbre...@ssc.wisc.edu wrote: Here is my sessionInfo() sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines grid stats graphics grDevices utils datasets methods [9] base other attached packages: [1] spsurvey_2.1-2 lmtest_0.9-27 zoo_1.6-5 [4] car_2.0-9 survival_2.36-5 nnet_7.3-1 [7] spgwr_0.6-10spatialCovariance_0.6-4 spatial_7.3-2 [10] spatgraphs_2.44 sgeostat_1.0-23 rworldmap_0.1211 [13] fields_6.3 spam_0.23-0 RPyGeo_0.9-2 [16] RSAGA_0.91-1shapefiles_0.6 RgoogleMaps_1.1.9.7 [19] raster_1.8-22 RArcInfo_0.4-10 RColorBrewer_1.0-2 [22] PBSmodelling_2.61.210 PBSmapping_2.61.9 mapproj_1.1-8.3 [25] mapdata_2.1-4 intamap_1.3-8 evd_2.2-4 [28] mvtnorm_0.9-96 automap_1.0-9 rgdal_0.6-33 [31] gmaps_0.2 maps_2.1-6 glmmBUGS_1.9 [34] spdep_0.5-32coda_0.14-2 deldir_0.0-13 [37] maptools_0.8-7 foreign_0.8-42 Matrix_0.999375-46 [40] lattice_0.19-17 boot_1.2-43 abind_1.3-0 [43] MASS_7.3-11 geosphere_1.2-19geonames_0.8 [46] rjson_0.2.3 ctv_0.7-2 GEOmap_1.5-13 [49] akima_0.5-4 RPMG_2.0-5 splancs_2.01-27 [52] geomapdata_1.0-4geoRglm_0.8-33 geoR_1.6-34 [55] gstat_0.9-81sp_0.9-81 nlme_3.1-98 loaded via a namespace (and not attached): [1] tcltk_2.12.2 tools_2.12.2 On 2011-08-03 09:40, gbre...@ssc.wisc.edu wrote: Hello. I am running the examples provided in the gstat help menus. When I try to run the following in predict.gstat: data(meuse) coordinates(meuse)= ~x+y v-variogram(log(zinc)~1, meuse) I get the following error message: Error in vector(double, length) : invalid 'length' argument What's the problem? You should at the very least provide your sessionInfo(). Peter Ehlers Gilbert __ 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. David Winsemius, MD 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.
[R] Help Needed in attempting to install 64-bit R!
Hello R Help,
I am attempting to install/build a 64-bit version of R to hopefully resolve
some memory.limit problems for a user who is running a simulation. The
'configure' runs fine and the compilation (make) runs fine until the very last
part (see below). I have libiconv in /usr/local/lib (no sure why I am getting
the referencing error). The config.site file is attached. ANY HELP YOU CAN
GIVE WOULD BE GREATLY APPRECIATED! :)
./configure --without-readline DYLIB_LDFLAGS=-xarch=v9 MAIN_LDFLAGS=-xarch=v9
Then I run /usr/ccs/bin/make
cc -xc99=all -xarch=v9 -xopenmp -L/usr/local/bin -o R.bin Rmain.o libR.a
-L../../lib -lRblas -R/usr/local/opt/SUNWspro/lib/v9:/opt/SUNWspro/lib/v9
-L/usr/local/opt/SUNWspro/lib/v9 -L/usr/local/opt/SUNWspro/prod/lib/v9
-L/usr/ccs/lib/sparcv9 -L/lib/sparcv9 -L/usr/lib/sparcv9 -lfui -lfai -lfai2
-lfsumai -lfprodai -lfminlai -lfmaxlai -lfminvai -lfmaxvai -lfsu -lsunmath
-lmtsk -lm -lnsl -lsocket -ldl -lm -licuuc -licui18n
cc: Warning: Specify a supported level of optimization when using -xopenmp,
-xopenmp will not set an optimization level in a future release. Optimization
level changed to 3 to support -xopenmp
Undefined first referenced
symbol in file
libiconv_close libR.a(sysutils.o)
libiconv_open libR.a(sysutils.o)
libiconvlibR.a(sysutils.o)
ld: fatal: Symbol referencing errors. No output written to R.bin
*** Error code 1
make: Fatal error: Command failed for target `R.bin'
Current working directory /usr/local/pkg/R-2.13.1/src/main
*** Error code 1
The following command caused the error:
/usr/ccs/bin/make install-bin-local
make: Fatal error: Command failed for target `R'
Current working directory /usr/local/pkg/R-2.13.1/src/main
*** Error code 1
The following command caused the error:
for d in scripts include extra appl nmath unix main modules library; do \
(cd ${d} /usr/ccs/bin/make R) || exit 1; \
done
make: Fatal error: Command failed for target `R'
Current working directory /usr/local/pkg/R-2.13.1/src
*** Error code 1
The following command caused the error:
for d in m4 tools doc etc share src tests po; do \
(cd ${d} /usr/ccs/bin/make R) || exit 1; \
done
make: Fatal error: Command failed for target `R'
Thanks,
Nynese
Nynese Tinsley, BSEE, MSCIS
UNIX Systems Analyst
Harvard School of Public Health
Center for Biostatistics in AIDS Research
651 Huntington Ave, FXB 614
Boston, MA 02115
617-432-3244 office#
617-432-2843 fax#
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[R] Model selection
Dear List, I have some difficulties to work with the function lmer from lme4. My responses are binary form and i want to use forward selection to my 12 covariates but i dont know how can I choose them based on deviance. Can someone pls give me a example so i can apply. For example my covariates are gestation,smoking ...and my response baby b1=lmer(baby~ (1|id), data, binomial) i will appreciate any help.thankss -- View this message in context: http://r.789695.n4.nabble.com/Model-selection-tp3716109p3716109.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] slow computation of functions over large datasets
Sorry about the lack of code, but using Davids example, would:
tapply(itemPrice, INDEX=orderID, FUN=sum)
work?
-Ken Hutchison
On Aug 3, 2554 BE, at 2:09 PM, David Winsemius dwinsem...@comcast.net wrote:
On Aug 3, 2011, at 2:01 PM, Ken wrote:
Hello,
Perhaps transpose the table attach(as.data.frame(t(data))) and use ColSums()
function with order id as header.
-Ken Hutchison
Got any code? The OP offered a reproducible example, after all.
--
David.
On Aug 3, 2554 BE, at 1:12 PM, David Winsemius dwinsem...@comcast.net
wrote:
On Aug 3, 2011, at 12:20 PM, jim holtman wrote:
This takes about 2 secs for 1M rows:
n - 100
exampledata - data.frame(orderID = sample(floor(n / 5), n, replace =
TRUE), itemPrice = rpois(n, 10))
require(data.table)
# convert to data.table
ed.dt - data.table(exampledata)
system.time(result - ed.dt[
+ , list(total = sum(itemPrice))
+ , by = orderID
+ ]
+)
user system elapsed
1.300.051.34
Interesting. Impressive. And I noted that the OP wanted what cumsum would
provide and for some reason creating that longer result is even faster on
my machine than the shorter result using sum.
--
David.
str(result)
Classes ‘data.table’ and 'data.frame': 198708 obs. of 2 variables:
$ orderID: int 1 2 3 4 5 6 8 9 10 11 ...
$ total : num 49 37 72 92 50 76 34 22 65 39 ...
head(result)
orderID total
[1,] 149
[2,] 237
[3,] 372
[4,] 492
[5,] 550
[6,] 676
On Wed, Aug 3, 2011 at 9:25 AM, Caroline Faisst
caroline.fai...@gmail.com wrote:
Hello there,
I’m computing the total value of an order from the price of the order
items
using a “for” loop and the “ifelse” function. I do this on a large
dataframe
(close to 1m lines). The computation of this function is painfully slow:
in
1min only about 90 rows are calculated.
The computation time taken for a given number of rows increases with the
size of the dataset, see the example with my function below:
# small dataset: function performs well
exampledata-data.frame(orderID=c(1,1,1,2,2,3,3,3,4),itemPrice=c(10,17,9,12,25,10,1,9,7))
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
{exampledata[i,orderAmount]-ifelse(exampledata[i,orderID]==exampledata[i-1,orderID],exampledata[i-1,orderAmount]+exampledata[i,itemPrice],exampledata[i,itemPrice])})
# large dataset: the very same computational task takes much longer
exampledata2-data.frame(orderID=c(1,1,1,2,2,3,3,3,4,5:200),itemPrice=c(10,17,9,12,25,10,1,9,7,25:220))
exampledata2[1,orderAmount]-exampledata2[1,itemPrice]
system.time(for (i in 2:9)
{exampledata2[i,orderAmount]-ifelse(exampledata2[i,orderID]==exampledata2[i-1,orderID],exampledata2[i-1,orderAmount]+exampledata2[i,itemPrice],exampledata2[i,itemPrice])})
Does someone know a way to increase the speed?
Thank you very much!
Caroline
[[alternative HTML version deleted]]
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--
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Data Munger Guru
What is the problem that you are trying to solve?
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PLEASE do read the posting guide
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David Winsemius, MD
West Hartford, CT
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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West Hartford, CT
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[R] R.app installer probs on Snow Leopard
Have tried to install R.app several times (6, in fact: versions 2.12, 13 14, both 32 and 64 bit versions), using packages freshly downloaded from the official project page, and failed every time, given exception reports such as the following (appended below, the 2 reports arising out of my 1st 6th attempts). Machine software version specifics are all contained therein. What am i missing, i wonder? Any clues would be most appreciated -thanx! /w 8(snip)---8 Process: R [15997] Path:/Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: ??? (???) Code Type: X86-64 (Native) Parent Process: launchd [179] Date/Time: 2011-08-03 16:13:36.857 +0100 OS Version: Mac OS X 10.6.8 (10K540) Report Version: 6 Interval Since Last Report: 23665 sec Crashes Since Last Report: 5 Per-App Crashes Since Last Report: 3 Anonymous UUID: A3B4FAD8-70A5-420F-A0E1-E02624B493A5 Exception Type: EXC_BREAKPOINT (SIGTRAP) Exception Codes: 0x0002, 0x Crashed Thread: 0 Dyld Error Message: Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib Referenced from: /Applications/R.app/Contents/MacOS/R Reason: image not found Binary Images: 0x7fff5fc0 - 0x7fff5fc3bdef dyld 132.1 (???) 69130DA3-7CB3-54C8-ABC5-423DECDD2AF7 /usr/lib/dyld Model: MacBookPro5,5, BootROM MBP55.00AC.B03, 2 processors, Intel Core 2 Duo, 2.53 GHz, 4 GB, SMC 1.47f2 Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB Memory Module: global_name AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8D), Broadcom BCM43xx 1.0 (5.10.131.42.4) Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial ports Network Service: AirPort, AirPort, en1 Serial ATA Device: ST9250315ASG, 232.89 GB Serial ATA Device: HL-DT-ST DVDRW GS23N USB Device: Internal Memory Card Reader, 0x05ac (Apple Inc.), 0x8403, 0x2650 / 2 USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8507, 0x2440 / 2 USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x0610 / 2 USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8213, 0x0611 / 4 USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x0237, 0x0460 / 3 USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0x0450 / 2 8(snip)---8 Process: R [16330] Path:/Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: ??? (???) Code Type: X86 (Native) Parent Process: launchd [179] Date/Time: 2011-08-03 17:18:06.587 +0100 OS Version: Mac OS X 10.6.8 (10K540) Report Version: 6 Interval Since Last Report: 27534 sec Crashes Since Last Report: 9 Per-App Crashes Since Last Report: 7 Anonymous UUID: A3B4FAD8-70A5-420F-A0E1-E02624B493A5 Exception Type: EXC_BREAKPOINT (SIGTRAP) Exception Codes: 0x0002, 0x Crashed Thread: 0 Dyld Error Message: Library not loaded: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib Referenced from: /Applications/R.app/Contents/MacOS/R Reason: image not found Binary Images: 0x8fe0 - 0x8fe4162b dyld 132.1 (???) 1C06ECD9-A2D7-BB10-AF50-0F2B598A7DEC /usr/lib/dyld Model: MacBookPro5,5, BootROM MBP55.00AC.B03, 2 processors, Intel Core 2 Duo, 2.53 GHz, 4 GB, SMC 1.47f2 Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB Memory Module: global_name AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8D), Broadcom BCM43xx 1.0 (5.10.131.42.4) Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial ports Network Service: AirPort, AirPort, en1 Serial ATA Device: ST9250315ASG, 232.89 GB Serial ATA Device: HL-DT-ST DVDRW GS23N USB Device: Internal Memory Card Reader, 0x05ac (Apple Inc.), 0x8403, 0x2650 / 2 USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8507, 0x2440 / 2 USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x0610 / 2 USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8213, 0x0611 / 4 USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x0237, 0x0460 / 3 USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0x0450 / 2 8(snip)---8 __ 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] Convert matrix to numeric
On 03/08/2011 3:04 PM, Jeffrey Joh wrote: I have a matrix that looks like this: structure(c(0.0376673981759913, 0.111066500741386, 1, 1103, 18, OPEN, DEPR, 0.0404073656092023, 0.115186044704599, 1, 719, 18, OPEN, DEPR, 0.0665342096693433, 0.197570061769498, 1, 1103, 18, OPEN, DEPR, 0.119287147905722, 0.356427096010845, 1, 1103, 18, OPEN, DEPR), .Dim = c(7L, 4L), .Dimnames = list( c(Sn, SlnC, housenum, date, hour, flue, pressurization ), c(10019.BLO, 1002.BLO, 10020.BLO, 10021.BLO))) How do I convert rows 1-5 to numeric? I tried mode()- numeric but that doesn't change anything. Every entry in a matrix has the same type, so you can't change just those rows other than by extracting them into a separate matrix and changing that. Duncan Murdoch I also tried converting this to a table then converting to numeric, but I got: (list) object cannot be coerced to type 'double' Jeff __ 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] slow computation of functions over large datasets
Hello,
Perhaps transpose the table attach(as.data.frame(t(data))) and use ColSums()
function with order id as header.
-Ken Hutchison
On Aug 3, 2554 BE, at 1:12 PM, David Winsemius dwinsem...@comcast.net wrote:
On Aug 3, 2011, at 12:20 PM, jim holtman wrote:
This takes about 2 secs for 1M rows:
n - 100
exampledata - data.frame(orderID = sample(floor(n / 5), n, replace =
TRUE), itemPrice = rpois(n, 10))
require(data.table)
# convert to data.table
ed.dt - data.table(exampledata)
system.time(result - ed.dt[
+ , list(total = sum(itemPrice))
+ , by = orderID
+ ]
+)
user system elapsed
1.300.051.34
Interesting. Impressive. And I noted that the OP wanted what cumsum would
provide and for some reason creating that longer result is even faster on my
machine than the shorter result using sum.
--
David.
str(result)
Classes ‘data.table’ and 'data.frame': 198708 obs. of 2 variables:
$ orderID: int 1 2 3 4 5 6 8 9 10 11 ...
$ total : num 49 37 72 92 50 76 34 22 65 39 ...
head(result)
orderID total
[1,] 149
[2,] 237
[3,] 372
[4,] 492
[5,] 550
[6,] 676
On Wed, Aug 3, 2011 at 9:25 AM, Caroline Faisst
caroline.fai...@gmail.com wrote:
Hello there,
I’m computing the total value of an order from the price of the order items
using a “for” loop and the “ifelse” function. I do this on a large dataframe
(close to 1m lines). The computation of this function is painfully slow: in
1min only about 90 rows are calculated.
The computation time taken for a given number of rows increases with the
size of the dataset, see the example with my function below:
# small dataset: function performs well
exampledata-data.frame(orderID=c(1,1,1,2,2,3,3,3,4),itemPrice=c(10,17,9,12,25,10,1,9,7))
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
{exampledata[i,orderAmount]-ifelse(exampledata[i,orderID]==exampledata[i-1,orderID],exampledata[i-1,orderAmount]+exampledata[i,itemPrice],exampledata[i,itemPrice])})
# large dataset: the very same computational task takes much longer
exampledata2-data.frame(orderID=c(1,1,1,2,2,3,3,3,4,5:200),itemPrice=c(10,17,9,12,25,10,1,9,7,25:220))
exampledata2[1,orderAmount]-exampledata2[1,itemPrice]
system.time(for (i in 2:9)
{exampledata2[i,orderAmount]-ifelse(exampledata2[i,orderID]==exampledata2[i-1,orderID],exampledata2[i-1,orderAmount]+exampledata2[i,itemPrice],exampledata2[i,itemPrice])})
Does someone know a way to increase the speed?
Thank you very much!
Caroline
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Data Munger Guru
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.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Convert matrix to numeric
How about Matrix[1:5,]=as.numeric(Matrix[1:5,]) -Ken Hutchison On Aug 3, 2554 BE, at 3:04 PM, Jeffrey Joh johjeff...@hotmail.com wrote: I have a matrix that looks like this: structure(c(0.0376673981759913, 0.111066500741386, 1, 1103, 18, OPEN, DEPR, 0.0404073656092023, 0.115186044704599, 1, 719, 18, OPEN, DEPR, 0.0665342096693433, 0.197570061769498, 1, 1103, 18, OPEN, DEPR, 0.119287147905722, 0.356427096010845, 1, 1103, 18, OPEN, DEPR), .Dim = c(7L, 4L), .Dimnames = list( c(Sn, SlnC, housenum, date, hour, flue, pressurization ), c(10019.BLO, 1002.BLO, 10020.BLO, 10021.BLO))) How do I convert rows 1-5 to numeric? I tried mode() - numeric but that doesn't change anything. I also tried converting this to a table then converting to numeric, but I got: (list) object cannot be coerced to type 'double' Jeff __ 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] implicit functions (was r-help)
On 03/08/2011 11:21 AM, KnifeBoot wrote: Hey, Is there any function plotting several implicit functions (F(x,y)=0) on the same fig. Is there anyone who has an example code of how to do this? The contour3d function in the misc3d package only work with the functions with three dimensions. Thanks a lot. contour() will do it. Use add=TRUE to add extra functions. Duncan Murdoch P.S. Please use a more informative subject line! __ 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] limits on liniar model
Please use R's search capabilities before posting. RSiteSearch(Linear Model with Constraints) appears to give you what you're looking for. Incidentally, with constraints, the model is no longer linear, I believe. -- Bert 2011/8/3 ראובן אברמוביץ gantk...@walla.com: Can I put limits on the lm() command? I only know that you can choose a liniar model with or without an intercept, but can I put other limits on the coefficients (for example- the intercept must be bigger than 1) ? _ Walla! Mail - [1]Get your free unlimited mail today References 1. http://www.walla.co.il/ __ 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. -- Men by nature long to get on to the ultimate truths, and will often be impatient with elementary studies or fight shy of them. If it were possible to reach the ultimate truths without the elementary studies usually prefixed to them, these would not be preparatory studies but superfluous diversions. -- Maimonides (1135-1204) Bert Gunter Genentech Nonclinical Biostatistics __ 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] Convert matrix to numeric
Hi Jeffrey, On Wed, Aug 3, 2011 at 3:04 PM, Jeffrey Joh johjeff...@hotmail.com wrote: I have a matrix that looks like this: structure(c(0.0376673981759913, 0.111066500741386, 1, 1103, 18, OPEN, DEPR, 0.0404073656092023, 0.115186044704599, 1, 719, 18, OPEN, DEPR, 0.0665342096693433, 0.197570061769498, 1, 1103, 18, OPEN, DEPR, 0.119287147905722, 0.356427096010845, 1, 1103, 18, OPEN, DEPR), .Dim = c(7L, 4L), .Dimnames = list( c(Sn, SlnC, housenum, date, hour, flue, pressurization ), c(10019.BLO, 1002.BLO, 10020.BLO, 10021.BLO))) Thank you for providing a small working example. How do I convert rows 1-5 to numeric? I tried mode() - numeric but that doesn't change anything. Two things are going on here. First, a matrix can only contain one kind of data. For this example, since there are strings the whole thing has to be character. A data frame is intended to hold different kinds of data, but each column has to be a single type. So if you want those values to be numeric instead of character, you'll need to transpose your matrix and convert it to a data frame. tempdata - structure(c(0.0376673981759913, 0.111066500741386, 1, 1103, 18, OPEN, DEPR, 0.0404073656092023, 0.115186044704599, 1, 719, 18, OPEN, DEPR, 0.0665342096693433, 0.197570061769498, 1, 1103, 18, OPEN, DEPR, 0.119287147905722, 0.356427096010845, 1, 1103, 18, OPEN, DEPR), .Dim = c(7L, 4L), .Dimnames = list( c(Sn, SlnC, housenum, date, hour, flue, pressurization ), c(10019.BLO, 1002.BLO, 10020.BLO, 10021.BLO))) tempdata - data.frame(t(tempdata), stringsAsFactors=FALSE) Once you have the right kind of object, you can convert the five columns of interest to numeric. This needs to be done a column at a time, I think: tempdata[, 1:5] - apply(tempdata[,1:5], 2, as.numeric) Sarah -- Sarah Goslee http://www.functionaldiversity.org __ 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] Convert matrix to numeric
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Ken Sent: Wednesday, August 03, 2011 12:13 PM To: Jeffrey Joh Cc: r-help@r-project.org Subject: Re: [R] Convert matrix to numeric How about Matrix[1:5,]=as.numeric(Matrix[1:5,]) -Ken Hutchison On Aug 3, 2554 BE, at 3:04 PM, Jeffrey Joh johjeff...@hotmail.com wrote: I have a matrix that looks like this: structure(c(0.0376673981759913, 0.111066500741386, 1, 1103, 18, OPEN, DEPR, 0.0404073656092023, 0.115186044704599, 1, 719, 18, OPEN, DEPR, 0.0665342096693433, 0.197570061769498, 1, 1103, 18, OPEN, DEPR, 0.119287147905722, 0.356427096010845, 1, 1103, 18, OPEN, DEPR), .Dim = c(7L, 4L), .Dimnames = list( c(Sn, SlnC, housenum, date, hour, flue, pressurization ), c(10019.BLO, 1002.BLO, 10020.BLO, 10021.BLO))) How do I convert rows 1-5 to numeric? I tried mode() - numeric but that doesn't change anything. Ken, You can't store the numeric values back in the matrix, because rows 6 and 7 contain character values. Everything will just be converted back to character. You need to create a new matrix for the numeric values. Hope this is helpful, Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 __ 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] slow computation of functions over large datasets
On Aug 3, 2011, at 3:05 PM, Ken wrote:
Sorry about the lack of code, but using Davids example, would:
tapply(itemPrice, INDEX=orderID, FUN=sum)
work?
Doesn't do the cumulative sums or the assignment into column of the
same data.frame. That's why I used ave, because it keeps the sequence
correct.
--
David.
-Ken Hutchison
On Aug 3, 2554 BE, at 2:09 PM, David Winsemius
dwinsem...@comcast.net wrote:
On Aug 3, 2011, at 2:01 PM, Ken wrote:
Hello,
Perhaps transpose the table attach(as.data.frame(t(data))) and use
ColSums() function with order id as header.
-Ken Hutchison
Got any code? The OP offered a reproducible example, after all.
--
David.
On Aug 3, 2554 BE, at 1:12 PM, David Winsemius dwinsem...@comcast.net
wrote:
On Aug 3, 2011, at 12:20 PM, jim holtman wrote:
This takes about 2 secs for 1M rows:
n - 100
exampledata - data.frame(orderID = sample(floor(n / 5), n,
replace = TRUE), itemPrice = rpois(n, 10))
require(data.table)
# convert to data.table
ed.dt - data.table(exampledata)
system.time(result - ed.dt[
+ , list(total = sum(itemPrice))
+ , by = orderID
+ ]
+)
user system elapsed
1.300.051.34
Interesting. Impressive. And I noted that the OP wanted what
cumsum would provide and for some reason creating that longer
result is even faster on my machine than the shorter result using
sum.
--
David.
str(result)
Classes ‘data.table’ and 'data.frame': 198708 obs. of 2
variables:
$ orderID: int 1 2 3 4 5 6 8 9 10 11 ...
$ total : num 49 37 72 92 50 76 34 22 65 39 ...
head(result)
orderID total
[1,] 149
[2,] 237
[3,] 372
[4,] 492
[5,] 550
[6,] 676
On Wed, Aug 3, 2011 at 9:25 AM, Caroline Faisst
caroline.fai...@gmail.com wrote:
Hello there,
I’m computing the total value of an order from the price of the
order items
using a “for” loop and the “ifelse” function. I do this on a
large dataframe
(close to 1m lines). The computation of this function is
painfully slow: in
1min only about 90 rows are calculated.
The computation time taken for a given number of rows increases
with the
size of the dataset, see the example with my function below:
# small dataset: function performs well
exampledata-
data
.frame
(orderID
=c(1,1,1,2,2,3,3,3,4),itemPrice=c(10,17,9,12,25,10,1,9,7))
exampledata[1,orderAmount]-exampledata[1,itemPrice]
system.time(for (i in 2:length(exampledata[,1]))
{exampledata[i,orderAmount]-
ifelse
(exampledata
[i
,orderID
]==exampledata[i-1,orderID],exampledata[i-1,orderAmount]
+exampledata[i,itemPrice],exampledata[i,itemPrice])})
# large dataset: the very same computational task takes much
longer
exampledata2-
data
.frame
(orderID
=
c
(1,1,1,2,2,3,3,3,4,5
:200),itemPrice=c(10,17,9,12,25,10,1,9,7,25:220))
exampledata2[1,orderAmount]-exampledata2[1,itemPrice]
system.time(for (i in 2:9)
{exampledata2[i,orderAmount]-
ifelse
(exampledata2
[i
,orderID
]==exampledata2[i-1,orderID],exampledata2[i-1,orderAmount]
+exampledata2[i,itemPrice],exampledata2[i,itemPrice])})
Does someone know a way to increase the speed?
Thank you very much!
Caroline
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What is the problem that you are trying to solve?
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David Winsemius, MD
West Hartford, CT
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Re: [R] the significance of BEKK estimation
Here is one more question, How could I input an asymmetry in volatility speci cation in the BEKK function? As far as I know, the BEKK estimation function is mvBEKK.est(eps, order = c(1,1), params = NULL, fixed = NULL, method = BFGS, verbose = F) I totally have no idea to exert an asymmetry into. Many thanks! Sincere, Zoe -- View this message in context: http://r.789695.n4.nabble.com/the-significance-of-BEKK-estimation-tp3716586p3716597.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] the significance of BEKK estimation
Dear ALL, I use BEKK package to estimate Bivariate GARCH model. But when the results come out, there's no t-stat or p-value of the estimated coeffients. Does anyone know how to get the significance? Followings are the codes I input, P1=data.frame(x,y) y1=mvBEKK.est(P1) mvBEKK.diag(y1) Anyhelp would be appreciated! Sincere, Zoe -- View this message in context: http://r.789695.n4.nabble.com/the-significance-of-BEKK-estimation-tp3716586p3716586.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] gstat error
To add to David's comments (nice catch, BTW), I found three variogram() functions as a result of ??variogram. The one that gets used is from the package that is highest in the search path (notice that gstat is 55th (!!)) - that would be the one from the spatial package. [The other is in the SpatialExtremes package, which is not loaded, so the one in spatial is masking the one in gstat.] To use the variogram() function in gstat, call gstat::variogram (...). Dennis On Wed, Aug 3, 2011 at 12:04 PM, David Winsemius dwinsem...@comcast.net wrote: I see a 'variogram' function in both spatial and gstat when I use ??variogram on my machine that probably does not have even all of those packages installed. Are you sure they are the same (I looked they are not) or failing that that the one you expect is being chosen? And are you even sure that there is not a third or a fourth 'variogram' in one of those other packages? -- David. On Aug 3, 2011, at 2:45 PM, gbre...@ssc.wisc.edu wrote: Here is my sessionInfo() sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines grid stats graphics grDevices utils datasets methods [9] base other attached packages: [1] spsurvey_2.1-2 lmtest_0.9-27 zoo_1.6-5 [4] car_2.0-9 survival_2.36-5 nnet_7.3-1 [7] spgwr_0.6-10 spatialCovariance_0.6-4 spatial_7.3-2 [10] spatgraphs_2.44 sgeostat_1.0-23 rworldmap_0.1211 [13] fields_6.3 spam_0.23-0 RPyGeo_0.9-2 [16] RSAGA_0.91-1 shapefiles_0.6 RgoogleMaps_1.1.9.7 [19] raster_1.8-22 RArcInfo_0.4-10 RColorBrewer_1.0-2 [22] PBSmodelling_2.61.210 PBSmapping_2.61.9 mapproj_1.1-8.3 [25] mapdata_2.1-4 intamap_1.3-8 evd_2.2-4 [28] mvtnorm_0.9-96 automap_1.0-9 rgdal_0.6-33 [31] gmaps_0.2 maps_2.1-6 glmmBUGS_1.9 [34] spdep_0.5-32 coda_0.14-2 deldir_0.0-13 [37] maptools_0.8-7 foreign_0.8-42 Matrix_0.999375-46 [40] lattice_0.19-17 boot_1.2-43 abind_1.3-0 [43] MASS_7.3-11 geosphere_1.2-19 geonames_0.8 [46] rjson_0.2.3 ctv_0.7-2 GEOmap_1.5-13 [49] akima_0.5-4 RPMG_2.0-5 splancs_2.01-27 [52] geomapdata_1.0-4 geoRglm_0.8-33 geoR_1.6-34 [55] gstat_0.9-81 sp_0.9-81 nlme_3.1-98 loaded via a namespace (and not attached): [1] tcltk_2.12.2 tools_2.12.2 On 2011-08-03 09:40, gbre...@ssc.wisc.edu wrote: Hello. I am running the examples provided in the gstat help menus. When I try to run the following in predict.gstat: data(meuse) coordinates(meuse)= ~x+y v-variogram(log(zinc)~1, meuse) I get the following error message: Error in vector(double, length) : invalid 'length' argument What's the problem? You should at the very least provide your sessionInfo(). Peter Ehlers Gilbert __ 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. David Winsemius, MD 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. __ 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] Convert matrix to numeric
Here's what you _should_ do 1) transpose 2a) as.data.frame 3a) fix the stupid default stringsAsFactor behavior 4a) convert the first 5 columns to numeric dfrm - as.data.frame( t( structure(.) ) ) dfrm[, 1:5] -lapply(dfrm[, 1:5], as.character) dfrm[, 1:5] -lapply(dfrm[, 1:5], as.numeric) Or: 1) transpose 2b) as.data.frame with stringsAsFactors= FALSE 3b) convert to numeric On Aug 3, 2011, at 3:04 PM, Jeffrey Joh wrote: I have a matrix that looks like this: structure(c(0.0376673981759913, 0.111066500741386, 1, 1103, 18, OPEN, DEPR, 0.0404073656092023, 0.115186044704599, 1, 719, 18, OPEN, DEPR, 0.0665342096693433, 0.197570061769498, 1, 1103, 18, OPEN, DEPR, 0.119287147905722, 0.356427096010845, 1, 1103, 18, OPEN, DEPR), .Dim = c(7L, 4L), .Dimnames = list( c(Sn, SlnC, housenum, date, hour, flue, pressurization ), c(10019.BLO, 1002.BLO, 10020.BLO, 10021.BLO))) How do I convert rows 1-5 to numeric? I tried mode() - numeric but that doesn't change anything. I also tried converting this to a table then converting to numeric, but I got: (list) object cannot be coerced to type 'double' Jeff __ 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. David Winsemius, MD 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] limits on liniar model
It is hard to prove a negative, but to the best of my knowledge lm will not do
what you want. This does not mean there is not a function that will perform
your analyses; the sort of thing you want to do is often accomplished using
non-linear methods.
John
ראובן אברמוביץgantk...@walla.com 8/3/2011 12:00:04 PM
Can I put limits on the lm() command? I only know that you can choose a
liniar model with or without an intercept, but can I put other limits on
the coefficients (for example- the intercept must be bigger than 1) ?
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Re: [R] R.app installer probs on Snow Leopard
On Aug 3, 2011, at 18:35 , Walter Ludwick wrote: Have tried to install R.app several times (6, in fact: versions 2.12, 13 14, both 32 and 64 bit versions), using packages freshly downloaded from the official project page, and failed every time, given exception reports such as the following (appended below, the 2 reports arising out of my 1st 6th attempts). Machine software version specifics are all contained therein. What am i missing, i wonder? Any clues would be most appreciated -thanx! /w What did you do to install? For a plain install, just get http://cran.r-project.org/bin/macosx/R-2.13.1.pkg open it and follow the instructions. If you tried to install the http://cran.r-project.org/bin/macosx/Mac-GUI-1.41.tar.gz then I suspect that you missed the point, that R.app is something you install _on_ _top_ _of_ an installation of R itself. 8(snip)---8 Process: R [15997] Path:/Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: ??? (???) Code Type: X86-64 (Native) Parent Process: launchd [179] Date/Time: 2011-08-03 16:13:36.857 +0100 OS Version: Mac OS X 10.6.8 (10K540) Report Version: 6 Interval Since Last Report: 23665 sec Crashes Since Last Report: 5 Per-App Crashes Since Last Report: 3 Anonymous UUID: A3B4FAD8-70A5-420F-A0E1-E02624B493A5 Exception Type: EXC_BREAKPOINT (SIGTRAP) Exception Codes: 0x0002, 0x Crashed Thread: 0 Dyld Error Message: Library not loaded: /Library/Frameworks/R.framework/Versions/2.14/Resources/lib/libR.dylib Referenced from: /Applications/R.app/Contents/MacOS/R Reason: image not found Binary Images: 0x7fff5fc0 - 0x7fff5fc3bdef dyld 132.1 (???) 69130DA3-7CB3-54C8-ABC5-423DECDD2AF7 /usr/lib/dyld Model: MacBookPro5,5, BootROM MBP55.00AC.B03, 2 processors, Intel Core 2 Duo, 2.53 GHz, 4 GB, SMC 1.47f2 Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB Memory Module: global_name AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8D), Broadcom BCM43xx 1.0 (5.10.131.42.4) Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial ports Network Service: AirPort, AirPort, en1 Serial ATA Device: ST9250315ASG, 232.89 GB Serial ATA Device: HL-DT-ST DVDRW GS23N USB Device: Internal Memory Card Reader, 0x05ac (Apple Inc.), 0x8403, 0x2650 / 2 USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8507, 0x2440 / 2 USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x0610 / 2 USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8213, 0x0611 / 4 USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x0237, 0x0460 / 3 USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0x0450 / 2 8(snip)---8 Process: R [16330] Path:/Applications/R.app/Contents/MacOS/R Identifier: org.R-project.R Version: ??? (???) Code Type: X86 (Native) Parent Process: launchd [179] Date/Time: 2011-08-03 17:18:06.587 +0100 OS Version: Mac OS X 10.6.8 (10K540) Report Version: 6 Interval Since Last Report: 27534 sec Crashes Since Last Report: 9 Per-App Crashes Since Last Report: 7 Anonymous UUID: A3B4FAD8-70A5-420F-A0E1-E02624B493A5 Exception Type: EXC_BREAKPOINT (SIGTRAP) Exception Codes: 0x0002, 0x Crashed Thread: 0 Dyld Error Message: Library not loaded: /Library/Frameworks/R.framework/Versions/2.12/Resources/lib/libR.dylib Referenced from: /Applications/R.app/Contents/MacOS/R Reason: image not found Binary Images: 0x8fe0 - 0x8fe4162b dyld 132.1 (???) 1C06ECD9-A2D7-BB10-AF50-0F2B598A7DEC /usr/lib/dyld Model: MacBookPro5,5, BootROM MBP55.00AC.B03, 2 processors, Intel Core 2 Duo, 2.53 GHz, 4 GB, SMC 1.47f2 Graphics: NVIDIA GeForce 9400M, NVIDIA GeForce 9400M, PCI, 256 MB Memory Module: global_name AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x8D), Broadcom BCM43xx 1.0 (5.10.131.42.4) Bluetooth: Version 2.4.5f3, 2 service, 19 devices, 1 incoming serial ports Network Service: AirPort, AirPort, en1 Serial ATA Device: ST9250315ASG, 232.89 GB Serial ATA Device: HL-DT-ST DVDRW GS23N USB Device: Internal Memory Card Reader, 0x05ac (Apple Inc.), 0x8403, 0x2650 / 2 USB Device: Built-in iSight, 0x05ac (Apple Inc.), 0x8507, 0x2440 / 2 USB Device: BRCM2046 Hub, 0x0a5c (Broadcom Corp.), 0x4500, 0x0610 / 2 USB Device: Bluetooth USB Host Controller, 0x05ac (Apple Inc.), 0x8213, 0x0611 / 4 USB Device: Apple Internal Keyboard / Trackpad, 0x05ac (Apple Inc.), 0x0237, 0x0460 / 3 USB Device: IR Receiver, 0x05ac (Apple Inc.), 0x8242, 0x0450 / 2 8(snip)---8 __
Re: [R] R.app installer probs on Snow Leopard
Did you install R first? R.app is just a GUI around the actual R code that could run without any assistance in a terminal session. Generally one installs both R and R.app from the super-bundle. Since you provided no details of which .pkg files were chosen we are left guessing. (And this is really supposed to be posted to the MAC-SIG list, anyway.) -- David. On Aug 3, 2011, at 12:35 PM, Walter Ludwick wrote: Have tried to install R.app several times (6, in fact: versions 2.12, 13 14, both 32 and 64 bit versions), using packages Names? Links? freshly downloaded from the official project page, And that means what? The ATT page? or the CRAN page? and failed every time, given exception reports such as the following (appended below, the 2 reports arising out of my 1st 6th attempts). Machine software version specifics are all contained therein. What am i missing, i wonder? We don't know because so many details are still, missing. Any clues would be most appreciated -thanx! /w (Running R 2.13.1 on OSX 10.5.8) -- David Winsemius, MD 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.
