[R] why does this simple example NOT work?

2012-07-20 Thread Martin Ivanov
Hello, I want to create and save objects in a loop, but this is precluded by the following obstacle: this part of the script fails to work: assign(x=paste(a, 1, sep=), value=1); save(paste(a, 1, sep=), file=paste(paste(a, 1, sep=), .RData, sep=)) Do you know any workaround? I am already out

Re: [R] why does this simple example NOT work?

2012-07-20 Thread Berend Hasselman
Martin Ivanov wrote Hello, I want to create and save objects in a loop, but this is precluded by the following obstacle: this part of the script fails to work: assign(x=paste(a, 1, sep=), value=1); save(paste(a, 1, sep=), file=paste(paste(a, 1, sep=), .RData, sep=)) Do you know

Re: [R] convert deldir$delsgs to a X3D IndexedTriangleSet

2012-07-20 Thread Erdal Karaca
I have managed to use the tripack package which is a bit simpler to use (for me) and performs better (timely)... ## # inputFile format: x y z inputFile - d:\\inputfile.xyz.txt # output file will contain a x3d scene embedded in a html file to be

Re: [R] median comparison tests

2012-07-20 Thread Tal Galili
You can do a transformation on your Y, and than use the normal tools. Using something like a median test is not advisable due to low power, and a wilcox.test is considered a better choice (although the meaning is more complex when observations are not symmetrically distributed). If you wish to

[R] UTK mirror

2012-07-20 Thread Jason Curole
Hi all, The past couple of days I have been trying to update my R installation (Debian) and I am getting the following: Get:9 http://http.us.debian.org squeeze/main amd64 Packages [6,542 kB] Ign http://mirrors.nics.utk.edu squeeze-cran/ Release Ign http://mirrors.nics.utk.edu squeeze-cran/

Re: [R] Removing values from a string

2012-07-20 Thread arun
Hi, This should make much more sense onenew-data.frame(keyword=gsub((NA){0,1}\\|, ,one$keyword)) onenew1-data.frame(keyword=gsub((NA){0,1},,onenew$keyword)) onenew1    keyword 1 auto 2 auto insurance quote 3   auto insurance 4    insurance 5   auto

Re: [R] A graph with a positive y-axis intercept

2012-07-20 Thread arun
HI, I guess you wanted to change the scale of Y-axis:  plot(X,Y,ylim=c(0,25)) A.K. - Original Message - From: Lekgatlhamang, lexi Setlhare lexisetlh...@yahoo.com To: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Cc: Sent: Thursday, July 19, 2012 5:31 PM Subject: [R] A graph with

[R] generic functions question in building a new package

2012-07-20 Thread zgu9
Hi all, I'm trying to build a package 'Thiele', but run into problems with generic functions. I have a class Benefit, and defined the function print.Benefit. When I try R CMD check Thiele in X11, this warning came out --- Functions/methods with usage in documentation object 'Benefit' but

Re: [R] convert deldir$delsgs to a X3D IndexedTriangleSet

2012-07-20 Thread Rolf Turner
On 19/07/12 20:40, Erdal Karaca wrote: Oh, I dont want anyone to do anything for me. I am just asking for hints/infos to be able to do it myself... I was hoping that someone has already done this... But anyways, I will post my solution once I have succeeded... If you haven't already looked at

Re: [R] median comparison tests

2012-07-20 Thread arun
Hi, Check this link. http://r.789695.n4.nabble.com/help-comparing-two-median-with-R-td822998.html A.K. - Original Message - From: Data Analytics Corp. w...@dataanalyticscorp.com To: r-help@r-project.org Cc: Sent: Thursday, July 19, 2012 4:14 PM Subject: [R] median comparison tests

Re: [R] change file name from file0.1_data.RData to file1_data.Rdata

2012-07-20 Thread Yasir Kaheil
use function system in R for (x in 1:100){ system (paste(rename file0.,x,_data.RData file,x,_data.Rdata,sep=)) } - Yasir Kaheil -- View this message in context: http://r.789695.n4.nabble.com/change-file-name-from-file0-1-data-RData-to-file1-data-Rdata-tp4637135p4637136.html Sent from the R

[R] Creating Multiple Repeating samples and Cross Correlating them.

2012-07-20 Thread Rbc1356
I'm having a lot of trouble getting this done and nothing I've written has been remotely successful. Basically I have about 64 binary data sets stored as vectors, with 72900 entries in each. I am not very familiar with cross correlations, but I was advised that I should create 1000 randomized date

Re: [R] Truncating (rounding down) to nearest half hour.

2012-07-20 Thread arun
Hi, Just a variant of creating rounded down minutes vector: minutes-ifelse(ceiling(as.numeric(substr(t[,1],15,16))30),30,00) #or minutes1-ifelse(floor(as.numeric(substr(dat1[,1],15,16))30),30,00) identical(minutes,minutes1) #[1] TRUE minutes3-floor( as.numeric( substr( t[,1], 15, 16 ) ) / 30

Re: [R] A graph with a positive y-axis intercept

2012-07-20 Thread Lekgatlhamang, lexi Setlhare
Dear Sarah and A.K., Yes, both your suggestions give me exactly what I wanted. Thank you kindly.   Lexi From: Sarah Goslee sarah.gos...@gmail.com Cc: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Sent: Thursday, July 19, 2012 11:36 PM Subject: Re: [R] A

Re: [R] Subsetting problem data, 2

2012-07-20 Thread Lib Gray
I'm getting this error message: nms-names(data)[grep(vars,names(data))] Warning message: In grep(vars, names(data)) : argument 'pattern' has length 1 and only the first element will be used Is there a way around this? On Thu, Jul 19, 2012 at 6:17 PM, Rui Barradas ruipbarra...@sapo.pt wrote:

Re: [R] R code for to check outliers

2012-07-20 Thread Angus Wallace
Really appreciate the discussion on outliers. I come from an engineering signal processing background, and my thinking has generally been that an outlier is outside a threshold of - distance from the mean - rarity that we don't need/want to capture in whatever model we're building. In my

Re: [R] Subsetting problem data, 2

2012-07-20 Thread Lib Gray
I'm still getting the message (if this is what you were suggesting I try). The data set I'm using has many more columns other than these variables; could that be a problem? I didn't think it would affect it. pattern - L[1-8][12] nms-names(data)[grep(vars,names(data))] Warning message: In

Re: [R] Changing ungrouped cases to grouped cases

2012-07-20 Thread arun
Hi, Try this: dat1-read.table(text= y    A  B  C 0    1    1  2 0    1    2  1 1    1    1  2 0    1    1  2 1    1    1  2 1    1    2  1 0    1    2  2 ,sep=,header=TRUE)  dat2-aggregate(y~A+B+C,data=dat1,sum)  dat2-dat2[,c(4,1:3)] dat3-dat2[with(dat2,rev(order(y,A,B,C))),]  dat3   y A B C 2 2

[R] (no subject)

2012-07-20 Thread Suman Pramanik
Dear Sir, I am using timereg package for analysing competing risk data. There are two options in method: proportional and additive. How to choose among the methods for analysis and how to check which of the methods are appropiate for the specific data. Tanks a lot. Dr Suman Kumar

Re: [R] Last answer

2012-07-20 Thread arun
Hi, Try this:  ans-function(){.Last.value}  2+3 [1] 5  ans() [1] 5 A.K. - Original Message - From: darnold dwarnol...@suddenlink.net To: r-help@r-project.org Cc: Sent: Friday, July 20, 2012 1:12 AM Subject: [R] Last answer Hi, In Matlab, I can access the last computation as

Re: [R] Subsetting problem data, 2

2012-07-20 Thread Chris Campbell
Hi! # toy data toyData - data.frame(x = 1:4, y = 5:8, xy = 9:12, z = 13:16) vars - c(x, z) # pattern is an argument of grep args(grep) # pattern must only consist of a single element # otherwise only the first element is used grep(pattern =

Re: [R] generic functions question in building a new package

2012-07-20 Thread Uwe Ligges
On 19.07.2012 22:44, zgu9 wrote: Hi all, I'm trying to build a package 'Thiele', but run into problems with generic functions. I have a class Benefit, and defined the function print.Benefit. When I try R CMD check Thiele in X11, this warning came out --- Functions/methods with usage in

[R] function for inverse normal transformation

2012-07-20 Thread carol white
Hi, What is the function for inverse normal transformation? Thanks, Carol [[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

[R] Creating a pdf with layers?

2012-07-20 Thread Christoph Scherber
Dear all, Is it possible to create a pdf file with layers using the pdf() device in R? Many thanks for your help! Christoph (using R 2.15.1 on Windows 7 64-Bit) -- PD Dr Christoph Scherber Georg-August University Goettingen Department of Crop Science Agroecology Grisebachstrasse 6 D-37077

Re: [R] why does this simple example NOT work?

2012-07-20 Thread Duncan Murdoch
On 12-07-20 2:50 AM, Martin Ivanov wrote: Hello, I want to create and save objects in a loop, but this is precluded by the following obstacle: this part of the script fails to work: assign(x=paste(a, 1, sep=), value=1); save(paste(a, 1, sep=), file=paste(paste(a, 1, sep=), .RData, sep=))

Re: [R] function for inverse normal transformation

2012-07-20 Thread Duncan Murdoch
On 12-07-20 6:21 AM, carol white wrote: Hi, What is the function for inverse normal transformation? qnorm Duncan Murdoch Thanks, Carol [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] function for inverse normal transformation

2012-07-20 Thread carol white
Thanks for your reply. So to derive it from a given data set, is the following correct to do? my_data.p =2*pnorm(abs(my_data),lower.tail=FALSE) my_data.q = qnorm(my_data.p) Cheers, From: Duncan Murdoch murdoch.dun...@gmail.com Cc: r-h...@stat.math.ethz.ch

[R] conditional subset and reorder dataframe rows

2012-07-20 Thread Iain Gallagher
Hi List I have a dataframe (~1,200,000 rows deep) and I'd like to conditionally reorder groups of rows in this dataframe. I would like to reorder any rows where the Chr.Strand column contains a '-' but reorder within subsets delineated by the Probe.Set.Name column. # toy example

Re: [R] function for inverse normal transformation

2012-07-20 Thread Duncan Murdoch
On 12-07-20 7:36 AM, carol white wrote: Thanks for your reply. So to derive it from a given data set, is the following correct to do? my_data.p =2*pnorm(abs(my_data),lower.tail=FALSE) my_data.q = qnorm(my_data.p) I don't know what you're trying to do, but that doesn't look like it does

Re: [R] rcspline.problem

2012-07-20 Thread Bart Ferket
Dear Peter, This indeed resolves the problem. Many thanks. My apologies for not starting a new thread. I am a new R user and not yet fully integrated into the R community. Kind regards, Bart Ferket -- View this message in context:

Re: [R] Forced inclusion of varaibles in validate command as well as step

2012-07-20 Thread D. Lofaro
Dear prof. Harrell, I'm not able to use the force option with fastbw, here an example of the error I've got (dataset stagec rpart package): fitstc - cph(Surv(stagec$pgtime,stagec$pgstat) ~ age + eet + g2 + grade + gleason + ploidy, data=stagec) fbwstc -

[R] Execute a function

2012-07-20 Thread carla moreira
Hi, I would like to evaluate a function, with 3 arguments, for instance, myfunc-function(a,b,c) { sqrt(a)-exp(b)+4*c } How to execute myfunc(x,y,z), for all x, all y and all z, where x,y,z are vectors? Thank you very much in advance -- View

Re: [R] Creating a pdf with layers?

2012-07-20 Thread Prof Brian Ripley
On 20/07/12 12:07, Christoph Scherber wrote: Dear all, Is it possible to create a pdf file with layers using the pdf() device in R? No. Is it possible to specify layers in the R graphics language or any device? (From what I understand by 'layers', no.) The author of pdf() Many thanks

Re: [R] Line chart with a double matrix

2012-07-20 Thread ramonovelar
Thanks David for the solution, I paste here the code with a few changes: par(xpd = NA, oma = c(5, 0, 0, 0)) matplot(t(buffersump[,1:6]), type=l, xaxt=n, lwd=3, ylab=Porcentajes de respuestas afirmativas) axis(1, 1:6, colnames(buffersump2)) legend(bottomright, legend=rownames(buffersump2),

[R] TukeyHSD not working

2012-07-20 Thread Michael Eisenring
Dear r-help members. I would like to compare species numbers of moths between eight different forests (each sampled for six nights). I would like to do a nested anova to compare species numbers between forests and nights. For more site specific details I wanted to do a Tukey test (TukeyHSD).

[R] Crosstab with Average and Count

2012-07-20 Thread vioravis
I have the following data: x - as.factor(c(1,1,1,2,2,2,3,3,3)) y - as.factor(c(10,10,10,20,20,20,30,30,30)) z - c(100,100,NA,200,200,200,300,300,300) I could create the cross tab of x and y with Sum of z as its elements using the xtabs function as follows: # X Vs. Y with Sum Z xtabs(z ~ x + y)

[R] qplot/ggplot

2012-07-20 Thread Anamika K
Hello, I have a file like this (just a snapshot) where I have numerical values for various genes, I want a line plot with shading (may be using smooth ?) using qplot or ggplot : Gene1 10 14 12 23 11 11 33 1 ..(multiple columns) Gene2 4 2 1 1 3 4 1 2 . Gene3 2 5 7 5 6 89 7 3 .. Gene4 1

Re: [R] function for inverse normal transformation

2012-07-20 Thread arun
HI, Probably this might be helpful for you. http://rgm2.lab.nig.ac.jp/RGM2/func.php?rd_id=fBasics:dist-nigFit A.K. - Original Message - From: carol white wht_...@yahoo.com To: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Cc: Sent: Friday, July 20, 2012 6:21 AM Subject: [R]

Re: [R] function for inverse normal transformation

2012-07-20 Thread carol white
I have a continuous data. So to calculate the inverse normal transformation, I thought that I should first calculate the Z-score normalized data and then, calculate the p-value et the quantile transformation. Does this seem to be more sensible my_data.p

Re: [R] function for inverse normal transformation

2012-07-20 Thread Rui Barradas
Hello, No it's not correct, you are computing a what seems to be a two-tailed probabiity, so the inverse should account for it. Look closely: you take the absolute value, then the upper tail probability, then multiply 2 into it. Reverse these steps to get the correct value. # Helper function

Re: [R] Execute a function

2012-07-20 Thread Jessica Streicher
You mean executing the function for all combinations of values? For example, if you have a-b-c-1:2 you would get back the values of myfunc(1,1,1) myfunc(1,1,2) myfunc(1,2,1) myfunc(1,2,2) myfunc(2,1,1) myfunc(2,1,2) myfunc(2,2,1) myfunc(2,2,2) ? On 20.07.2012, at 13:05, carla moreira wrote:

Re: [R] Execute a function

2012-07-20 Thread Benno Pütz
Not quite sure what you are aiming at, but looking at ?mapply or ?expand.grid could be helpful Benno On Jul 20, 2012, at 1:05 PM, carla moreira wrote: Hi, I would like to evaluate a function, with 3 arguments, for instance, myfunc-function(a,b,c) { sqrt(a)-exp(b)+4*c

Re: [R] Defining a variable outside of optim or differential equation solver.

2012-07-20 Thread Thomas Petzoldt
Hi Tjun Kat, you can define variables outside the ode function, but normally NOT state variables, because their values need to be updated by the solver during the simulation process. But, if you want to block this for any debugging purposes and want to e.g. fix a derivative to a certain

Re: [R] complexity of operations in R

2012-07-20 Thread Jan van der Laan
See below for the complete mail to which I reply which was not sent to rhelp. == emptyexpandlist2-list(ne=0,l=array(NA, dim=c(1, 1000L)),len=1000L) addexpandlist2-function(x,prev){ if(prev$len==prev$ne){ n2-prev$len*2 prev - list(ne=prev$ne, l=array(prev$l, dim=c(1, n2)),

Re: [R] function for inverse normal transformation

2012-07-20 Thread carol white
Thanks Rui. I changed my scripts to the followings and I think that it still is not correct. See also the attached file. Thanks for your help,  tmp  [1]  2.502519  1.828576  3.755778 17.415000  3.779296  2.956850  2.379663  [8]  1.103559  8.920316  2.744500  2.938480  7.522174 10.629200 

[R] Speeding up a loop

2012-07-20 Thread wwreith
General problem: I have 20 projects that can be invested in and I need to decide which combinations meet a certain set of standards. The total possible combinations comes out to 2^20. However I know for a fact that the number of projects must be greater than 5 and less than 13. So far the the code

Re: [R] Execute a function

2012-07-20 Thread Carla Moreira
Yes, I do. But I need to control how the permutations are done. Thank you. 2012/7/20 Jessica Streicher j.streic...@micromata.de You mean executing the function for all combinations of values? For example, if you have a-b-c-1:2 you would get back the values of myfunc(1,1,1) myfunc(1,1,2)

Re: [R] qplot/ggplot

2012-07-20 Thread John Kane
I think we need some raw data. Have a look at ?dput for a way to supply it. It might help if you supplied some sample code of what you have tried. I want a line plot is not particularly helpful. John Kane Kingston ON Canada -Original Message- From: anamika...@gmail.com Sent:

Re: [R] Execute a function

2012-07-20 Thread Jessica Streicher
Well, what do you want to control there? Need a subset? Need an ordering? On 20.07.2012, at 15:00, Carla Moreira wrote: Yes, I do. But I need to control how the permutations are done. Thank you. 2012/7/20 Jessica Streicher j.streic...@micromata.de You mean executing the function

Re: [R] Crosstab with Average and Count

2012-07-20 Thread John Kane
Not quite what you asked for but would this do? library(plyr) x - as.factor(c(1,1,1,2,2,2,3,3,3)) y - as.factor(c(10,10,10,20,20,20,30,30,30)) z - c(100,100,NA,200,200,200,300,300,300) df1 - data.frame(x, y, z) (dsum - ddply(df1, .(x, y), summarise, sum = sum(z, na.rm = TRUE),

[R] overlay contourplot with labels over spplot with color regions?

2012-07-20 Thread Martin Ivanov
Dear R users, I have the following problem. I plot a SpatialPixelsDataFrame object with spplot and I need to add a contourplot of another spatial variable. To be more precise, I plot the SpatialPixelsDataFrame of the mean precipitation over Germany with coloured regions and I want to overlay

Re: [R] Crosstab with Average and Count

2012-07-20 Thread Marc Schwartz
On Jul 20, 2012, at 5:30 AM, vioravis wrote: I have the following data: x - as.factor(c(1,1,1,2,2,2,3,3,3)) y - as.factor(c(10,10,10,20,20,20,30,30,30)) z - c(100,100,NA,200,200,200,300,300,300) I could create the cross tab of x and y with Sum of z as its elements using the xtabs

Re: [R] Crosstab with Average and Count

2012-07-20 Thread David L Carlson
There are lots of possibilities. Here's one using only xtabs(): dframe - na.omit(data.frame(x, y, z)) zsum - xtabs(z~x+y, dframe) zcount - xtabs(~x+y, dframe) zmean - ifelse(is.nan(zsum/zcount), 0, zsum/zcount) -- David L Carlson Associate Professor of

Re: [R] Creating Multiple Repeating samples and Cross Correlating them.

2012-07-20 Thread John Kane
It would help if you supplied some code for us to see what you have tried. However something like this would presumably give you the sample data sets --note only n=100 in the example. mymat - matrix(NA, ncol= 100, nrow= 100) for (n in 1: 100) { mymat[,n] - sample(c(0,1), 100, replace =

Re: [R] Execute a function

2012-07-20 Thread Peter Ehlers
On 2012-07-20 04:05, carla moreira wrote: Hi, I would like to evaluate a function, with 3 arguments, for instance, myfunc-function(a,b,c) { sqrt(a)-exp(b)+4*c } How to execute myfunc(x,y,z), for all x, all y and all z, where x,y,z are

Re: [R] Speeding up a loop

2012-07-20 Thread Jean V Adams
I've had to do something similar, so I wrote a small function to help. This runs in about 1/4 the time of your code on my machine. Others may have a more efficient approach. all.combs - function(num, from=0, to=num) { # create a matrix of all possible combinations of num items #

Re: [R] Execute a function

2012-07-20 Thread Bert Gunter
Inline. -- Bert On Fri, Jul 20, 2012 at 6:59 AM, Peter Ehlers ehl...@ucalgary.ca wrote: On 2012-07-20 04:05, carla moreira wrote: Hi, I would like to evaluate a function, with 3 arguments, for instance, myfunc-function(a,b,c) { sqrt(a)-exp(b)+4*c

Re: [R] function for inverse normal transformation

2012-07-20 Thread David L Carlson
Rui's example included z-score data (drawn from rnorm). You converted your data to z-scores so you need to compare your results to the z-scores not the original data. Change these lines: tmp.qnorm = qnorm(tmp.p/2,lower.tail=FALSE)*sign(scale(tmp)) # sign is of scale(tmp) not tmp

Re: [R] function for inverse normal transformation

2012-07-20 Thread Duncan Murdoch
On 20/07/2012 8:28 AM, carol white wrote: Thanks Rui. I changed my scripts to the followings and I think that it still is not correct. You haven't told us clearly what you are trying to achieve, and you don't tell us what is wrong with what you have. How do you expect anyone to help?

Re: [R] TukeyHSD not working

2012-07-20 Thread Jean V Adams
Michael, Use dput() to output your data (or perhaps a small subset). Then paste the result of that call and your R code (just those lines of code that are needed to reproduce the problem) right in your message to R-help. That makes it easier for the R-help list readers to help you

Re: [R] Speeding up a loop

2012-07-20 Thread Petr Savicky
On Fri, Jul 20, 2012 at 05:45:30AM -0700, wwreith wrote: General problem: I have 20 projects that can be invested in and I need to decide which combinations meet a certain set of standards. The total possible combinations comes out to 2^20. However I know for a fact that the number of projects

Re: [R] Creating a pdf with layers?

2012-07-20 Thread Christoph Scherber
Dear Prof Ripley, Many thanks for your response. In fact, latticeExtra and ggplot2 both state they work with layers, but essentially this is nothing more than sequentially adding graphical output to an existing device. But given that PDF can include layers since version 1.5 it would be

[R] convert date to a factor

2012-07-20 Thread Yolande Tra
Hello, I would like to convert date as a factor to represent time in a repeated measure situation in the following code. How would I do that? d - read.csv(file.path(dataDir,data.csv), as.is=T,stringsAsFactors = FALSE) d[1:2,] id date ab c y 1 1

Re: [R] Speeding up a loop

2012-07-20 Thread Jean V Adams
Petr, This is great. MUCH faster than the code I provided. And much more elegant code. Thanks for posting! Jean Petr Savicky savi...@cs.cas.cz wrote on 07/20/2012 09:26:34 AM: On Fri, Jul 20, 2012 at 05:45:30AM -0700, wwreith wrote: General problem: I have 20 projects that can be invested

Re: [R] Speeding up a loop

2012-07-20 Thread Petr Savicky
On Fri, Jul 20, 2012 at 04:26:34PM +0200, Petr Savicky wrote: On Fri, Jul 20, 2012 at 05:45:30AM -0700, wwreith wrote: General problem: I have 20 projects that can be invested in and I need to decide which combinations meet a certain set of standards. The total possible combinations comes

Re: [R] Execute a function

2012-07-20 Thread Peter Ehlers
Bert, The only thing wrong is that I'm still 75% asleep! Yikes!! Thanks for the heads-up. Carla: See Bert's solution. Peter Ehlers On 2012-07-20 07:10, Bert Gunter wrote: Inline. -- Bert On Fri, Jul 20, 2012 at 6:59 AM, Peter Ehlers ehl...@ucalgary.ca wrote: On 2012-07-20 04:05, carla

Re: [R] [RsR] How does rlm in R decide its w weights for each IRLS iteration?

2012-07-20 Thread S Ellison
-Original Message- Subject: [RsR] How does rlm in R decide its w weights for each IRLS iteration? I am also confused about the manual: a. The input arguments: wt.method are the weights case weights (giving the relative importance of case, so a weight of 2 means

Re: [R] why does this simple example NOT work?

2012-07-20 Thread Berend Hasselman
Duncan Murdoch-2 wrote On 12-07-20 2:50 AM, Martin Ivanov wrote: Hello, I want to create and save objects in a loop, but this is precluded by the following obstacle: this part of the script fails to work: assign(x=paste(a, 1, sep=), value=1); save(paste(a, 1, sep=),

Re: [R] TukeyHSD not working

2012-07-20 Thread Jean V Adams
Michael Eisenring eimic...@ethz.ch wrote on 07/20/2012 09:35:03 AM: Dear Jean, thanks for this email. I'm grateful for this instruction Just to make sure that I understood you properly: something like this?: Michael, Yes, this is perfect. Very helpful. My data:

Re: [R] [External] Re: Speeding up a loop

2012-07-20 Thread Jean V Adams
Reith, William [USA] reith_will...@bah.com wrote on 07/20/2012 09:52:02 AM: Would this matrix eat up memory making the rest of my program slower? Each x needs to be multiplied by a matrix and the results checked against a set of thresholds. Doing them one at a time takes at least 24 hours

Re: [R] Speeding up a loop

2012-07-20 Thread Jean V Adams
Reith, William [USA] reith_will...@bah.com wrote on 07/20/2012 09:52:02 AM: Would this matrix eat up memory making the rest of my program slower? Each x needs to be multiplied by a matrix and the results checked against a set of thresholds. Doing them one at a time takes at least 24 hours

Re: [R] Changing ungrouped cases to grouped cases

2012-07-20 Thread Christopher Desjardins
Thanks the aggregate() command is what I was looking for. Chris On Thu, Jul 19, 2012 at 9:03 PM, David L Carlson dcarl...@tamu.edu wrote: dtf - read.table(text=y A B C + 0 11 2 + 0 12 1 + 1 11 2 + 0 11 2 + 1 11 2 + 1 12

Re: [R] convert date to a factor

2012-07-20 Thread R. Michael Weylandt
d$date - factor(d$date) Best, Michael On Fri, Jul 20, 2012 at 9:44 AM, Yolande Tra yolande@gmail.com wrote: Hello, I would like to convert date as a factor to represent time in a repeated measure situation in the following code. How would I do that? d -

[R] Extracting standard errors for adjusted fixed effect sizes in lmer

2012-07-20 Thread Matthew Ouellette
Dear R help list, I have done a lot of searching but have not been able to find an answer to my problem. I apologize in advance if this has been asked before. I am applying a mixed model to my data using lmer. I will use sample data to illustrate my question: library(lme4) library(arm)

[R] Dissolve polygon

2012-07-20 Thread Celine
Hi, I am working with a SpatialPolygonsDataFrame of many islands. There are a lot of polygons (islands) composing my SpatialPolygonsDataFrame. I want to extract the elevation of each island. I need to separate the different polygons (like dissolve function in arcgis), to have the elevation of

Re: [R] Subsetting problem data, 2

2012-07-20 Thread arun
Hi, Just a doubt regarding the dataset. Suppose, I include two more patients F and G with different missing values as in this new dataset and run the code. dat1-read.table(text= Patient  Cycle  V1  V2  V3  V4  V5 A  1  0.4  0.1  0.5  1.5  NA A  2  0.3  0.2  0.5  1.6  NA A  3  0.3  NA  0.6  1.7 

Re: [R] TukeyHSD not working

2012-07-20 Thread arun
Hi, Check this link. http://stackoverflow.com/questions/5904513/tukeyhsd-after-within-factors-anova A.K. - Original Message - From: Michael Eisenring eimic...@ethz.ch To: r-help@r-project.org Cc: Sent: Friday, July 20, 2012 6:15 AM Subject: [R] TukeyHSD not working Dear r-help

[R] r-h...@stat.math.ethz.ch

2012-07-20 Thread Norman....
Contact me with your full names, phone numbers and residential address if you own this email r-h...@stat.math.ethz.ch. I have a proposal for you [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] Crosstab with Average and Count

2012-07-20 Thread arun
Hi, Try this: dat1-data.frame(x,y,z)  xtabs(z~x+y,aggregate(z~x+y,dat1,mean))    y x    10  20  30   1 100   0   0   2   0 200   0   3   0   0 300 table(dat1$z,dat1$y)   10 20 30   100  2  0  0   200  0  3  0   300  0  0  3 or, table(dat1$x,dat1$z)        100 200 300   1   2   0   0

Re: [R] TukeyHSD not working

2012-07-20 Thread arun
HI, I don't have much experience with laercio package.  If it works for you, it is good. A.K. - Original Message - From: Michael Eisenring eimic...@ethz.ch To: arun smartpink...@yahoo.com Cc: Sent: Friday, July 20, 2012 8:38 AM Subject: Re: [R] TukeyHSD not working Hi Thanks for

Re: [R] Execute a function

2012-07-20 Thread carla moreira
Yes, that's this. Thank you very much. 2012/7/20 Peter Ehlers [via R] ml-node+s789695n463721...@n4.nabble.com On 2012-07-20 04:05, carla moreira wrote: Hi, I would like to evaluate a function, with 3 arguments, for instance, myfunc-function(a,b,c) { sqrt(a)-exp(b)+4*c

Re: [R] cenbox(): Changing Default x-axis Group Labels

2012-07-20 Thread MacQueen, Don
Hi Rich, I don't have a cenbox() function that I can find, but your solution will (probably? hopefully?) be along the lines of: foo - boxplot( y ~ x, data=sdf, plot=FALSE) foo$names - ifelse(foo$names, Label for TRUE, Label for FALSE) bxp(foo) where sdf is a dataframe containing your data

Re: [R] convert date to a factor

2012-07-20 Thread Yolande Tra
Thanks, Y On Fri, Jul 20, 2012 at 11:47 AM, R. Michael Weylandt michael.weyla...@gmail.com wrote: d$date - factor(d$date) Best, Michael On Fri, Jul 20, 2012 at 9:44 AM, Yolande Tra yolande@gmail.com wrote: Hello, I would like to convert date as a factor to represent time in a

Re: [R] cenbox(): Changing Default x-axis Group Labels

2012-07-20 Thread Rich Shepard
On Fri, 20 Jul 2012, MacQueen, Don wrote: I don't have a cenbox() function that I can find, but your solution will (probably? hopefully?) be along the lines of: Don, Well, I must have mis-typed that although I'm sure I read about it in the NADA.pdf or Dennis' book. I'll look again. I don't

Re: [R] convert date to a factor

2012-07-20 Thread Yolande Tra
Thanks, Y On Fri, Jul 20, 2012 at 1:02 PM, arun smartpink...@yahoo.com wrote: Hi, Try this: dat1-read.table(text= iddateab cy 1 1 8/6/2008Red15B 22 2 1 8/6/2008 Green 15B 22 ,sep=,header=TRUE)

[R] any package available to calculate systematic root mean square error (RMSEs)?

2012-07-20 Thread Peng Zhao
Hi. Is there any package available to calculate the systematic root mean square error (RMSEs) and unsystematic RMSE (RMSEu)? I could not find such a package. I am too lazy to calculate them step by step. The calculation could be found in equation 3 and 4 in the Appendix A of the following link:

Re: [R] convert date to a factor

2012-07-20 Thread arun
Hi, Try this: dat1-read.table(text=    id    date    a    b  c    y 1  1 8/6/2008    Red    15    B  22 2  1 8/6/2008  Green  15    B  22 ,sep=,header=TRUE)  dat1$date-with(dat1,as.factor(date))  dat1   id date a  b c  y 1  1 8/6/2008   Red 15 B

Re: [R] findAssocs()

2012-07-20 Thread rtw30606
Hi Here is some code to illustrate how the correlations are calculated. data - c(word1, word1 word2,word1 word2 word3,word1 word2 word3 word4,word1 word2 word3 word4 word5) frame - data.frame(data) frame data 1 word1 2

Re: [R] R packages installation error in Ubuntu

2012-07-20 Thread uday
hi , last time I did not mention the specific version of linux and it was problem with only syntax but with correction I got new error. I found that some people has faced this problem before and some of them have mentioned that it may be because of dependencies issue and

Re: [R] cenbox(): Changing Default x-axis Group Labels

2012-07-20 Thread Peter Ehlers
On 2012-07-20 09:41, Rich Shepard wrote: On Fri, 20 Jul 2012, MacQueen, Don wrote: I don't have a cenbox() function that I can find, but your solution will (probably? hopefully?) be along the lines of: Don, Well, I must have mis-typed that although I'm sure I read about it in the

Re: [R] Dissolve polygon

2012-07-20 Thread Barry Rowlingson
On Fri, Jul 20, 2012 at 4:51 PM, Celine bellard.cel...@gmail.com wrote: Hi, I am working with a SpatialPolygonsDataFrame of many islands. There are a lot of polygons (islands) composing my SpatialPolygonsDataFrame. I want to extract the elevation of each island. Is each island a row in

Re: [R] function for inverse normal transformation

2012-07-20 Thread Rui Barradas
Hello, Yes, Carol is comparing what can't be compared. Your code should do it, I hope. Rui Barradas Em 20-07-2012 15:12, David L Carlson escreveu: Rui's example included z-score data (drawn from rnorm). You converted your data to z-scores so you need to compare your results to the z-scores

Re: [R] Speeding up a loop

2012-07-20 Thread wwreith
That is faster than what I was doing and reducing 15% of my iterations it still very helpful. Next question. I need to multiply each row x[i,] of the matrix x by another matrix A. Specifically for(i in 1:n) { If (x[i,]%*%A[,1].5 || x[i,]%*%A[,2]42 || x[i,]%*%A[,3]150) { x-x[-i,] n-n-1 }. #In

Re: [R] Speeding up a loop

2012-07-20 Thread Richard M. Heiberger
This works to multiply the ith row of a by the ith value of b. It might be what you can use a - matrix(1:30, 6, 5) b - 1:6 a a*b To simplify your code, I think you can do this---one multiplication xA - x %*% A Now you can do the tests on xA and not have any matrix multiplications inside the

Re: [R] Changing ungrouped cases to grouped cases

2012-07-20 Thread Christopher Desjardins
As a follow up is there any way to also get the count for each combination? For example y A B C 0 11 2 0 12 1 1 11 2 0 11 2 1 11 2 1 12 1 0 12 2 Should become: y A B C count 2 1 1 24 1 1 2

Re: [R] [RsR] How does rlm in R decide its w weights for each IRLS iteration?

2012-07-20 Thread Valentin Todorov
Hi Michael, S Ellison, I do not actually understand what you want to achieve with the M estimates of rlm in MASS, but why you do not give a try of lmrob in 'robustbase'. Please have a llok in the references (?lmrob) about the advantages of MM estimators over the M estimators. Best regards,

Re: [R] Changing ungrouped cases to grouped cases

2012-07-20 Thread Rui Barradas
Hello, Still with aggregate, use length() not sum(). dtagroup - aggregate(y ~ A + B + C, data=dtf, sum) dtalength - aggregate(y ~ A + B + C, data=dtf, length) # Now merge the two names(dtalength)[4] - count mm - merge(dtagroup, dtalength) # And make it pretty mm - mm[, c(y, A, B, C, count)]

Re: [R] Changing ungrouped cases to grouped cases

2012-07-20 Thread Peter Ehlers
On 2012-07-20 12:09, Rui Barradas wrote: Hello, Still with aggregate, use length() not sum(). dtagroup - aggregate(y ~ A + B + C, data=dtf, sum) dtalength - aggregate(y ~ A + B + C, data=dtf, length) # Now merge the two names(dtalength)[4] - count mm - merge(dtagroup, dtalength) # And make

Re: [R] cenbox(): Changing Default x-axis Group Labels

2012-07-20 Thread Rich Shepard
On Fri, 20 Jul 2012, Peter Ehlers wrote: Well, You didn't say (in your original request) that you were using the NADA package. The function is cenboxplot() and it's just a wrapper for boxplot() and hence passes arguments to boxplot(). Thus the solution to your problem is just to add the

Re: [R] function for inverse normal transformation

2012-07-20 Thread John Fox
Dear Carol, -Original Message- From: carol white [mailto:wht_...@yahoo.com] Sent: July-20-12 2:45 PM To: John Fox Subject: Re: inverse normal transformation Thanks John for your quick reply. The purpose of applying inverse normal transformation is to reduce the impact of

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