Re: [R] extract required data from already read data

On Thu, May 6, 2010 at 10:47 PM, Mohan L wrote: > > > > I am using source() to run program, like > >> source (sample.R) > > I want to know how to pass the argument to my sample.R, some this like > >> source(sample.R, xxx,FeMale) > >  Is it possible? any link will greatly appreciated. I do not be

Re: [R] Plotting Help

On 05/09/2010 07:10 AM, Ravi Ramaswamy wrote: Hi - Wondering if someone could help me with a plotting problem. I looked through the postings for this error message but the explanations are hard to follow. Basically I have matrix of 80 rows and 101 columns. I would like to generated a line grap

Re: [R] Count cases in a list

Elegant Henrique, thanks ! Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) ---

[R] lattice: customising panel.segments using groups

Hi, I want to customise the segments on an xyplot. Below is a simple example of what I'm trying to do... #Example dataset x <- c(-0.25, 0.25, 0.8) y <- c(-0.5, 0, 0.75) gp <- c("A", "I", "C") my.data <- cbind.data.frame(x,y,gp) #setting up the parameters to customise the lines w

Re: [R] Is it possible to rearrange the facets in ggplot while keeping everything else the same?

Hi: I'm not sure this is what you're looking for, but it sounds to me that you want to group subjects with the same Ab value together. If that's the case, then try this; your test data is called df ... df$Subject <- factor(df$Subject) p2 <- ggplot(df, aes(x = Day, y = Value, colour = Subject)) p2

Re: [R] P values

Dear R-Users, This list is observed by many great statisticians and non-statisticians. I just want to add this valuable link to this great discussion. http://www.stat.duke.edu/~berger/p-values.html Thanks and Best Regards, S. On Sat, May 8, 2010 a

[R] Panel data with binary dependent variable

Is it possible to do regressions in R using a panel data set with a binary dependent variable? I am familiar with using glm for logit and probit and plm for panel data, but am not sure how to combine the two. Are there any existing code examples? Thank you. Abiel

Re: [R] Evaluating matrices without using loops

z[y>z] <- y[y>z] [[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

[R] Evaluating matrices without using loops

Hi R users, I am trying to set the values of elements of one matrix based on the values of elements of another matrix. Say I have 2 matrices, y and z. y = matrix(rnorm(35), ncol=5) z = matrix(rep(0,35), ncol=5) I want z[i,j] to take a value of y[i,j] when y[i,j] is greater than 0, and zero o

Re: [R] P values

On May 8, 2010, at 9:38 PM, Duncan Murdoch wrote: On 08/05/2010 9:14 PM, Joris Meys wrote: On Sat, May 8, 2010 at 7:02 PM, Bak Kuss wrote: Just wondering. The smallest the p-value, the closer to 'reality' (the more accurate) the model is supposed to (not) be (?). How realistic is it

[R] Is it possible to rearrange the facets in ggplot while keeping everything else the same?

Hello, First, ggplot2 is great! Second, sorry for the basic nature of my question. I have data in the form of a melt table like this: Subject Day Ab VariableValue 1 1 Yes A 3 1 3 Yes A 5 1 5 Yes A 7 2 1

Re: [R] P values

On 08/05/2010 9:14 PM, Joris Meys wrote: On Sat, May 8, 2010 at 7:02 PM, Bak Kuss wrote: Just wondering. The smallest the p-value, the closer to 'reality' (the more accurate) the model is supposed to (not) be (?). How realistic is it to be that (un-) real? That's a common miscon

Re: [R] inquiry about Version 2.11.0

Maria Clara Soto Velez wrote: > > Hello, > > I am trying to download the newest versión of R (R version 2.11.0), but I > haven´t been able, because it seems that the file is not working properly. > > Could you help me? > No. You have not provided enough information for us to even take a gue

Re: [R] trellis/lattice: How to plot 4 panels with the same x-scale but different y-scales?

If you need the x axes to be aligned then I assume they must represent the same variable, in which case it should be enough to have one x axis label for each column of panels. The trellis/lattice way is to use strip labels to distinguish the panels in other ways. Regards, -Felix On 7 May 2010 18

Re: [R] P values

On Sat, May 8, 2010 at 7:02 PM, Bak Kuss wrote: > > Just wondering. > > The smallest the p-value, the closer to 'reality' (the more accurate) > the model is supposed to (not) be (?). > > How realistic is it to be that (un-) real? > That's a common misconception. A p-value expresses no more tha

Re: [R] Increasing the font size on axes in trellis

Thanks a million, David. I addded: scales=list(x=list(cex=1.3),y=list(cex=1.3)), in the dotplot call and it totally worked. Thank you! Dimitri On Sat, May 8, 2010 at 5:25 PM, David Winsemius wrote: > > On May 8, 2010, at 3:43 PM, Dimitri Liakhovitski wrote: > >> Hello, >> >> the code below gives

Re: [R] apply a function on elements of a list two by two

Thx, works like a charm. And indeed, I didn't realize combn could be that powerful. Thx for pointing that out. @ Patrick : thanks for the tip. It was just a fast coded toy example, but it never hurts to get reminded about the more efficient way, even with toy examples. Cheers Joris On Sat, May 8

Re: [R] Machine Learning and R

good question! if there is such a book, i'd also like to read as well. On Sun, May 9, 2010 at 7:41 AM, Ralf B wrote: > Hi all, > > I am looking for a good book that covers Machine Learning as a whole > and provides examples in R while not over focusing on the math (such > as in 'Elements of Stati

Re: [R] Machine Learning and R

Hi Ralf, May be this?http://cran.r-project.org/web/views/MachineLearning.html HTH, Jorge On Sat, May 8, 2010 at 7:41 PM, Ralf B <> wrote: > Hi all, > > I am looking for a good book that covers Machine Learning as a whole > and provides examples in R while not over focusing on the math (suc

[R] Machine Learning and R

Hi all, I am looking for a good book that covers Machine Learning as a whole and provides examples in R while not over focusing on the math (such as in 'Elements of Statistical Learning') but rather on descriptions and examples. I am relatively new to R and ML and, while solving problems with R, I

Re: [R] Using R with screenreading software

Rainer Scheuchenpflug wrote: Dear R-Experts, a student of mine tries to use the Windows-Rconsole with screen reading software (she is blind), and cannot access the command line (Menus are ok). The company which produces her screen reader tells her that this is due to the cursor used in Rconsole,

Re: [R] Adding NAs to data.frame

That seems to be a suitable situation for a loop although you might wish to write it like this: for ( nm in names(df) ) df[ v[[nm]], nm ] <- NA Note that R does not require semicolons at the end of each statement. On Sat, May 8, 2010 at 11:12 AM, wrote: > Hello, after the creation of a data.f

Re: [R] Adding NAs to data.frame

Try this: df <- as.data.frame(mapply(`[<-`, x = df, i = v, NA)) On Sat, May 8, 2010 at 12:12 PM, wrote: > Hello, after the creation of a data.frame I like to add NAs as follows: > > n <- 743; > x <- runif(n, 1, 7); > Y <- runif(n, 1, 7); > Ag6 <- runif(n, 1, 7); > df <- data.frame(x, Y, Ag6);

Re: [R] Count cases in a list

Try this also: colSums(sapply(nombreC, grepl, nombreL)) On Sat, May 8, 2010 at 5:22 AM, Sebastian Kruk wrote: > 2010/5/8 Tal Galili : > > Hi Sebastian, > > Please check if this does what you want: > > > > nombreL <- c("Alvaro Perez", "Sebastián García", "Luis Gomez", "Jorge > Rial", > > "Ronald

Re: [R] matrix cross product in R different from cross product in Matlab

Susanne Schmidt wrote: Hi all, I have been searching all sorts of documentation, reference cards, cheat sheets but can't find why R's crossprod(A, B) which is identical to A%*%B If you read the help page ?crossprod, you'll see it is supposed to be identical to t(A) %*% B. does not produ

Re: [R] Increasing the font size on axes in trellis

On May 8, 2010, at 3:43 PM, Dimitri Liakhovitski wrote: Hello, the code below gives me the picture I need - but there is on small thing I can't figure out. The plot has very small tick mark labels for both axes. I don't mean the axis labels - they are both good, but what is shown near the tick

[R] matrix cross product in R different from cross product in Matlab

Hi all, I have been searching all sorts of documentation, reference cards, cheat sheets but can't find why R's crossprod(A, B) which is identical to A%*%B does not produce the same as Matlabs cross(A, B) Supposedly both calculate the cross product, and say so, or where do I go wrong? R is on

[R] Plotting Help

Hi - Wondering if someone could help me with a plotting problem. I looked through the postings for this error message but the explanations are hard to follow. Basically I have matrix of 80 rows and 101 columns. I would like to generated a line graph that has 80 plots, one for each row, with the

[R] Increasing the font size on axes in trellis

Hello, the code below gives me the picture I need - but there is on small thing I can't figure out. The plot has very small tick mark labels for both axes. I don't mean the axis labels - they are both good, but what is shown near the tick marks. Please help me figure out what parameter I should ad

Re: [R] memisc output to latex

The correct spelling is forLaTeX with a capital T. On Sat, May 8, 2010 at 2:10 PM, michele wrote: > Hi, > I am trying to output a table in a Latex format with write.mtable. > This is my code: > > h.summary <- mtable("linear" = hlm, "quadratic" = hqd, > summary.stats=c("R-squared","adj. R-squared"

Re: [R] memisc output to latex

On May 8, 2010, at 2:10 PM, michele wrote: Hi, I am trying to output a table in a Latex format with write.mtable. This is my code: h.summary <- mtable("linear" = hlm, "quadratic" = hqd, summary.stats=c("R-squared","adj. R-squared", "p")) h.summary <- relabel(h.summary, "J" = "J", "I(J^2)" = "J

Re: [R] How to insert angular brackets in plot text?

On May 8, 2010, at 10:46 AM, manojit wrote: I am somewhat of a newbie, and trying to insert angular brackets in my axis label, something like expression(group("(",italic(N),")")) that seems to work fine, but returns "invalid delimiter" error when I replace the "(",")" pair with "<",">".

[R] memisc output to latex

Hi, I am trying to output a table in a Latex format with write.mtable. This is my code: h.summary <- mtable("linear" = hlm, "quadratic" = hqd, summary.stats=c("R-squared","adj. R-squared", "p")) h.summary <- relabel(h.summary, "J" = "J", "I(J^2)" = "J^2") write.mtable(h.summary, forLatex=TRUE, fil

Re: [R] help on hmisc

Thanks very much it was Hmisc that I was looking for. Originally I would get a message saying that Hmisc was not available for 64bit when I tried downloading it through R. Thanks very much, Natalie 2010/5/8 Uwe Ligges > > > On 08.05.2010 15:04, Frank E Harrell Jr wrote: > >> On 05/07/2010 10:1

Re: [R] Count cases in a list

func2 <- function(x) which(grepl(x, noquote(nombreL))) lapply(noquote(nombreC), func2) Side note: if you wanted the object a in Tal's solution to be a vector, you could use sapply() rather than lapply(). For this problem, the solution has to be a list because the position matches are unequal in nu

[R] How to insert angular brackets in plot text?

I am somewhat of a newbie, and trying to insert angular brackets in my axis label, something like expression(group("(",italic(N),")")) that seems to work fine, but returns "invalid delimiter" error when I replace the "(",")" pair with "<",">". The alternative expression(paste("<",italic(N),">")) d

Re: [R] memory limit

On 05/08/2010 10:00 AM, Uwe Ligges wrote: > > > On 08.05.2010 18:52, Zoppoli, Gabriele (NIH/NCI) [G] wrote: >> >> Hi, >> >> when I try to import a microarray CEL batch, I get this error message: >> >>> myAB<- ReadAffy () > > This seems to be more related to the BioC mailing list. yes http://

Re: [R] P values

Robert A LaBudde wrote: > At 01:40 PM 5/6/2010, Joris Meys wrote: > >> On Thu, May 6, 2010 at 6:09 PM, Greg Snow wrote: >> >> >>> Because if you use the sample standard deviation then it is a t test not a >>> z test. >>> >>> >> I'm doubting that seriously... >> >> You calculate normalized Z-values

Re: [R] memory limit

On 08.05.2010 18:52, Zoppoli, Gabriele (NIH/NCI) [G] wrote: Hi, when I try to import a microarray CEL batch, I get this error message: myAB<- ReadAffy () This seems to be more related to the BioC mailing list. Error in .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra, :

[R] memory limit

Hi, when I try to import a microarray CEL batch, I get this error message: > myAB <- ReadAffy () Error in .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra, : cannot allocate vector of length 1287151200 which, assuming the value is in bites, is below my RAM values (3 Gb recogni

Re: [R] Source.R file from cmd line

Look at the documentation of Rscript, e.g. ?Rscript at the R prompt. On Sat, 8 May 2010, Robin Jeffries wrote: I want to set up a windows system task that will run a .R script at pre-specified times. Can someone please help with the command line syntax that I would assign to the task? I know

[R] Source.R file from cmd line

I want to set up a windows system task that will run a .R script at pre-specified times. Can someone please help with the command line syntax that I would assign to the task? I know that i can open a command prompt, type R, and then source the file, but I don't know how to pass multiple line argu

[R] Adding NAs to data.frame

Hello, after the creation of a data.frame I like to add NAs as follows: n <- 743; x <- runif(n, 1, 7); Y <- runif(n, 1, 7); Ag6 <- runif(n, 1, 7); df <- data.frame(x, Y, Ag6); # a list with positions: v <- apply(df, 2, function(x) sample(n, sample(1:ceiling(5*n/100), 1), repl=F)); # a loop too muc

Re: [R] help on hmisc

On 08.05.2010 15:04, Frank E Harrell Jr wrote: On 05/07/2010 10:12 AM, nvanzuy...@gmail.com wrote: Hi, I thought I would just jump in on this as I am running an i7 as well. I use hmisc for the doBy functions and it would make a huge difference particularly with large data sets to run this on

Re: [R] String manipulation

On May 8, 2010, at 10:05 AM, Webby wrote: Dear community, I have a problem with a string conversion: text [1] "" "and""\xc1d\xe1m" [4] "graphical" "interface" "MLP" [7] "Nagy" "networks" "Networks" [10] "neural"

Re: [R] String manipulation

See ?Encoding and ?iconv: iconv("\xc1d\xe1m", from = '', to = 'latin1') On Sat, May 8, 2010 at 11:05 AM, Webby wrote: > > Dear community, > > I have a problem with a string conversion: > > > text > [1] "" "and""\xc1d\xe1m" > [4] "graphical" "interf

Re: [R] apply a function on elements of a list two by two

Am 08.05.2010 15:43, schrieb Joris Meys: Dear all, I want to apply a function to list elements, two by two. I hoped that combn would help me out, but I can't get it to work. A nested for-loop works, but seems highly inefficient when you have large lists. Is there a more efficient way of approach

[R] String manipulation

Dear community, I have a problem with a string conversion: > text [1] "" "and""\xc1d\xe1m" [4] "graphical" "interface" "MLP" [7] "Nagy" "networks" "Networks" [10] "neural" "Neural" "RBF" [13] "

Re: [R] apply a function on elements of a list two by two

On May 8, 2010, at 9:43 AM, Joris Meys wrote: Dear all, I want to apply a function to list elements, two by two. I hoped that combn would help me out, but I can't get it to work. A nested for-loop works, but seems highly inefficient when you have large lists. Is there a more efficient way

[R] apply a function on elements of a list two by two

Dear all, I want to apply a function to list elements, two by two. I hoped that combn would help me out, but I can't get it to work. A nested for-loop works, but seems highly inefficient when you have large lists. Is there a more efficient way of approaching this? # Make some toy data data(iris)

Re: [R] How to add separate labels to the axes of each panel plot?

Dear all, I finally solved my problem. Here is a solution: library(lattice) library(grid) x=c(1,2,1,2,1,2,1,2) y=c(1,2,2,1,1,-1,-2000,2000) z=c("z1","z1","z2","z2","z3","z3","z4","z4") xlabs=c("x_1","x_2","x_3","x_4") xyplot(y~x|z,type="l",aspect=1,layout=c(2,2),as.table=TRUE, scales=lis

Re: [R] Latex and Stangle()

sorry for my late reply, Am 06.05.2010 13:16, schrieb Silvano: > It worked very well. > > Thanks Frank and Ruihong, both solutions were great. you might also want to try out package SweaveListingsUtils from CRAN, which provides some extra features interfacing the 'listings' package a

Re: [R] Latex and Stangle()

sorry for my late reply, Am 06.05.2010 13:16, schrieb Silvano: > It worked very well. > > Thanks Frank and Ruihong, both solutions were great. you might also want to try out package SweaveListingsUtils from CRAN, which provides some extra features interfacing the 'listings' package a

Re: [R] help on hmisc

On 05/07/2010 10:12 AM, nvanzuy...@gmail.com wrote: Hi, I thought I would just jump in on this as I am running an i7 as well. I use hmisc for the doBy functions and it would make a huge difference particularly with large data sets to run this on 64bit windows. I'm not sure how to compile from so

Re: [R] meaning of "<<-"

You might want to look at the answers to that question on stackoverflow.com: http://stackoverflow.com/questions/2628621 Hadley On Sat, May 8, 2010 at 1:59 AM, Ruihong Huang wrote: > Hi, > > In my memory, "<<-" means assigning via a pointer or alias. But this is not > officially defined in "R Lan

Re: [R] problem in using optim

That was great! I tried as what you said, not as many warnings as before, and it seems that it converges. Thank you Berend. and thank you all! Carol On Sat, May 8, 2010 at 5:00 PM, Berend Hasselman wrote: > > > Carol Gao wrote: > > > > I have generated some random variable from generalised gam

Re: [R] double-indexed list

Here is an example list of data. You would access it by: x[[day]][[hour]] instead of how you mentioned in your email. > # create a list of 3 days and 3 hours to show how the list would look > set.seed(1) > x <- vector('list', 3) # top level is day > for (day in 1:3){ + for (hour in 1:3){

Re: [R] Count cases in a list

One last thing, i want to know in which position was founded every name. 2010/5/8 Tal Galili : > There you go: > > nombreL <- c("Alvaro Perez", "Sebastian García","Sebastian 2", "Luis Gomez", > "Jorge Rial", "Ronaldo Apud", "Ana María Bianco") > nombreC <- c("Alvaro", "Ana","Jorge","Ronaldo", "Seb

Re: [R] Count cases in a list

There you go: nombreL <- c("Alvaro Perez", "Sebastian García","Sebastian 2", "Luis Gomez", "Jorge Rial", "Ronaldo Apud", "Ana María Bianco") nombreC <- c("Alvaro", "Ana","Jorge","Ronaldo", "Sebastian") func1 <- function(x) { length(grep(x, noquote(nombreL))) } a <- lapply(noquote(nombreC), func1

Re: [R] Error in RImageJ

This is a known issue. You can: - ask apple to fix it - use R embedded into a java application, e.g. JGR Romain Le 08/05/10 03:49, Fredy Mejía a écrit : Hello everybody, I'm running R under Mac OS 10.6.3 on a MacBook 2.16 GHz Intel Core 2 Duo. I've recently installed R 2.11.0 and the RImag

Re: [R] Count cases in a list

2010/5/8 Tal Galili : > Hi Sebastian, > Please check if this does what you want: > > nombreL <- c("Alvaro Perez", "Sebastián García", "Luis Gomez", "Jorge Rial", > "Ronaldo Apud", "Ana María Bianco") > nombreC <- c("Alvaro", "Ana","Jorge","Ronaldo", "Sebastian") > func1 <- function(x) > { > grep(x,

Re: [R] glm binomial loglog (NOT cloglog) link

can you please say specifically how to modify the make.link function -- View this message in context: http://r.789695.n4.nabble.com/glm-binomial-loglog-NOT-cloglog-link-tp849370p2135909.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] meaning of "<<-"

try: ?"<<-" This is used for assigning to an object that exists in a parent environment from which you made the assigning (thus allows some playing with R's lexical scoping). Contact Details:--- Contact me: tal.gal...@gmail.com

[R] modify the make.link function GLM

can someone please tell me how modify the make.link function i want to update the function with this code but every time i save it R never keeps my new version. i have tried to unbind first and then assign. i also tried the fixInNamespace but that doesnt work either. can someone please tell me ho

Re: [R] Count cases in a list

Hi Sebastian, Please check if this does what you want: nombreL <- c("Alvaro Perez", "Sebastián García", "Luis Gomez", "Jorge Rial", "Ronaldo Apud", "Ana María Bianco") nombreC <- c("Alvaro", "Ana","Jorge","Ronaldo", "Sebastian") func1 <- function(x) { grep(x, noquote(nombreL)) } lapply(noquote(n

Re: [R] Count cases in a list

Hi, for example I have two list: nombreL <- c("Alvaro Perez", "Sebastián García", "Luis Gomez", "Jorge Rial", "Ronaldo Apud",..., "Ana María Bianco") nombreC <- c("Alvaro",..., "Ana",...,"Jorge",...,"Ronaldo", "Sebastian",...) and my code is: cuenta <- 0 topL <- length(nombreL) topC <- length(no

Re: [R] Count cases in a list

Hi Sebastian, Please add an example to the code you made, so to make it easier to help you. p.s: it seems possible to make it faster using lapply Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read

[R] Count cases in a list

Hi everybody, I would like to count how many times names in list L, nombreL, apear in list C, nombreC. Can I improve the next program? cuenta <- 0 topL <- length(nombreL) topC <- length(nombreC) for (i in 1:topL) { for (j in 1:topC) {

Re: [R] overlap dot plots with box plots

Looks like you're just missing the 'add=TRUE' argument; see below. On 2010-05-07 11:07, ADM wrote: Hi, I am new in R and would like to dot plot my real data points from different categories and put box plot overlapping. To give a feeling of the distribution of my data and the real values. I ma

Re: [R] problem in using optim

Carol Gao wrote: > > I have generated some random variable from generalised gamma distribution, > and now I need to use them to test on my optim function. Please see below: > > *##Need to install package VGAM first before calling rggamma function > library(VGAM) > x <- rggamma(500,scale=gamma(1

[R] meaning of "<<-"

Hi, In my memory, "<<-" means assigning via a pointer or alias. But this is not officially defined in "R Language Definition". Could anybody help for the clarification? Thank you very much! Bests, Ruihong __ R-help@r-project.org mailing list https: