Re: [R] Ploting gradient

2011-07-27 Thread Alexander Engelhardt
Am 28.07.2011 03:25, schrieb Fernando Andreacci: I have a simple bar chart with annual precipitation (jan to dez). I want to plot, above each bar (on a line), a square wich is color based on a scale (0-100%). With 0 being white and 100 black, like a gradient. Is it possible? How to? Thanks He

[R] plotting matrix into 2D color plots with rainbow colors

2011-07-27 Thread hitendra padalia
Dear all, Can you pl. help me in plotting a matrix into 2D plot with more color options. I tried to plot with myImagePlot with RGB color ramp but it shows limited variation in color. There is a rainbow plot option also. Can anyone help me. Regards, Hitendra -- Hitendra Padalia, PhD Scientist/Eng

Re: [R] Correlated Multivariate Distribution Generator

2011-07-27 Thread Enrico Schumann
Just a pointer, not a solution: if you use the method I described, it all comes down to the initial correlation matrix that you specify for the Gaussian case. If you had the "correct" initial correlation matrix, it would lead to the desired linear correlation in your binomials. (But it is not guar

[R] Ordinary Least Products regression in R

2011-07-27 Thread Christopher Tong
Dear Bill, For bivariate data, ordinary least product regression is equivalent to geometric mean regression, or what Freedman/Pisani/Purves call the “SD Line” (line passing through the centroid of the data, whose slope's magnitude is the ratio of the standard deviations of the variables, and s

[R] Ploting gradient

2011-07-27 Thread Fernando Andreacci
I have a simple bar chart with annual precipitation (jan to dez). I want to plot, above each bar (on a line), a square wich is color based on a scale (0-100%). With 0 being white and 100 black, like a gradient. Is it possible? How to? Thanks -- Fernando Andreacci [[alternative HTML vers

Re: [R] Is R the right choice for simulating first passage times of random walks?

2011-07-27 Thread R. Michael Weylandt
Some more skilled folks can help with the curve fitting, but the general answer is yes -- R will handle this quite ably. Consider the following code: <<-->> n = 1e5 length = 1e5 R = matrix(sample(c(-1,1),length*n,replace=T),nrow=n) R = apply(R,1,cumsum) ## thi

Re: [R] Writing a summary file in R

2011-07-27 Thread a217
Thank you both very much! The codes are pretty slick and should greatly help me in my task. -- View this message in context: http://r.789695.n4.nabble.com/Writing-a-summary-file-in-R-tp3700031p3700382.html Sent from the R help mailing list archive at Nabble.com. _

Re: [R] apply is making me crazy...

2011-07-27 Thread Dennis Murphy
Hi: Try this: exampGood = lapply(2:4, function(x) matrix(rnorm(10 * x), ncol = x)) exampBad = lapply(1:3, function(x) matrix(rnorm(10 * x), ncol = x)) csfun <- function(m) { if(ncol(m) == 1L) {return(m)} else { t(as.matrix(apply(m, 1, cumsum))) } } lapply(exampGood, csfun) lapply(e

Re: [R] Writing a summary file in R

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 9:42 PM, Dennis Murphy wrote: Hi: Is this more or less what you're after? ## Note: This is the preferred way to send your data by e-mail. ## I used dput(data-frame-name) to produce this, ## where data-frame-name = 'df' on my end. df <- structure(list(V1 = c("chr1", "chr1",

Re: [R] a question about glht function

2011-07-27 Thread Lao Meng
Here's another question: What's kind of difference does glht tests? In other words, If I get 4 intercepts and 4 slopes for all levels of GROUP,then glht tests for the difference of the 4 intercepts or 4 slopes,or something else? Thanks. 2011/7/27 Lao Meng > Yes. > According to your suggestio

Re: [R] Is R the right choice for simulating first passage times of random walks?

2011-07-27 Thread William Dunlap
You can replace the inner loop for (i in 1:length) { if (s[i] < 0 && s[i + 1] >= 0) { z[i] = z[i] + 1 } } with the faster z <- z + (diff(s>=0)==1) (Using the latter forces you fix up the length of z to be one less than you declared -- your loop never touched the last entry in it

Re: [R] Writing a summary file in R

2011-07-27 Thread Dennis Murphy
Hi: Is this more or less what you're after? ## Note: This is the preferred way to send your data by e-mail. ## I used dput(data-frame-name) to produce this, ## where data-frame-name = 'df' on my end. df <- structure(list(V1 = c("chr1", "chr1", "chr1", "chr1", "chr3", "chr4", "chr4", "chr7", "chr7

Re: [R] apply is making me crazy...

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 7:44 PM, Gene Leynes wrote: > David, > > Thanks for the suggestion, but I think your answer only works > because I was printing the wrong thing (because apply with margin=1 > transposes the results, And if you want to change that, then the t() function is readily at ha

Re: [R] Is R the right choice for simulating first passage times of random walks?

2011-07-27 Thread Mike Marchywka
Top posting cuz hotmail decided not to highlight... Personally I would tend to use java or c++ for the inner loops but you could of course later make an R package out of that. This is especially true if your code will be used elsewhere in a performance critical system. For example, I wrote som

Re: [R] Is R the right choice for simulating first passage times of random walks?

2011-07-27 Thread Paul Menzel
Dear R folks, Am Donnerstag, den 28.07.2011, 01:36 +0200 schrieb Paul Menzel: > I need to simulate first passage times for iterated partial sums. The > related papers are for example [1][2]. > > As a start I want to simulate how long a simple random walk stays > negative, which should result th

Re: [R] apply is making me crazy...

2011-07-27 Thread Gene Leynes
David, Thanks for the suggestion, but I think your answer only works because I was printing the wrong thing (because apply with margin=1 transposes the results, something I always forget). Check this to see what I mean: str(answerGood) str(answerBad) Adding "as.matrix" is interesting and

Re: [R] Executing for loop by grouping variable within dataframe

2011-07-27 Thread Dennis Murphy
Hi: I don't get exactly the same results as you did in the second group (how does temp.t[1] = -2.0 instead of -2.2?) but try this: locality=c("USC00020958", "USC00020958", "USC00020958", "USC00020958", "USC00020958", "USC00021001","USC00021001", "USC00021001", "USC00021001", "USC00021001", "USC00

[R] Is R the right choice for simulating first passage times of random walks?

2011-07-27 Thread Paul Menzel
Dear R folks, I need to simulate first passage times for iterated partial sums. The related papers are for example [1][2]. As a start I want to simulate how long a simple random walk stays negative, which should result that it behaves like n^(-½). My code looks like this. 8< c

Re: [R] Writing a summary file in R

2011-07-27 Thread a217
Yes, that is the general objective. I'll look-into aggregates in R and see if anything helps. Thanks, a217 -- View this message in context: http://r.789695.n4.nabble.com/Writing-a-summary-file-in-R-tp3700031p3700071.html Sent from the R help mailing list archive at Nabble.com. _

Re: [R] Writing a summary file in R

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 7:02 PM, a217 wrote: Hello, I have an input file: http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt where col 1 is chromosome, column2 is start of region, column 3 is end of region, column 4 and 5 is base position, column 6 is total reads, column 7 i

Re: [R] fitting sine wave

2011-07-27 Thread Dennis Murphy
Hi: This is a linear model since you have no nonlinear term *in the parameters*. The model you postulated is as far as you can go since you have 1 df for error (unless you remove the intercept term). As the plot below shows, a linear model does not fit the data well - basically, it provides a quad

[R] Writing a summary file in R

2011-07-27 Thread a217
Hello, I have an input file: http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt where col 1 is chromosome, column2 is start of region, column 3 is end of region, column 4 and 5 is base position, column 6 is total reads, column 7 is methylation data, and column 8 is the strand.

Re: [R] for loop help

2011-07-27 Thread Gene Leynes
I'm not sure what you're doing... but here are some tips about the parts I can understand. 1) you don't need to use "which" as much. This works fine: stnID <- stnid[!duplicated(stnid)] 2) "which" works within a for loop 3) Do you realize that "stnID" is shorter after you removed duplicates

[R] Using identify() through Rterm

2011-07-27 Thread Joana
Hello. I am using R via PHP by making a system call, like this $cmd = "echo source(\"$maindir\") | \"$Rterm\" --vanilla --slave --ess --args ... and I would like to know if there is any way of showing the identify() interactivity in the browser on my website, save the selected points, close

Re: [R] Big data and column correspondence problem

2011-07-27 Thread murilofm
Daniel, thanks for the help. I finally made it, doing the merging separately. Daniel Malter wrote: > > On a different note: how are you matching if AA has multiple matches in > BB? > About that, all I have to do is check whether, for any of the BB which matches with AA, the indicator equals 1.

Re: [R] apply is making me crazy...

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 6:22 PM, Gene Leynes wrote: I have tried a lot of ways around this, but I can't find a way to make apply work in a generalized way because it causes a failure whenever reduces the dimensions of its output. The following example is easier to understand than the question.

Re: [R] ?plot: Add an example on how to plot functions to the help of `plot`.

2011-07-27 Thread Gene Leynes
Paul, I agree completely. I didn't come at this with a programming background, and I never noticed the other plot links, or understood their importance. The "plot" help page was one of the first help pages I ever looked at and I remember that It was totally confusing. In fact, help pages like th

Re: [R] ?plot: Add an example on how to plot functions to the help of `plot`.

2011-07-27 Thread Paul Menzel
Am Mittwoch, den 27.07.2011, 18:04 -0400 schrieb David Winsemius: > On Jul 27, 2011, at 5:53 PM, Paul Menzel wrote: > > as `plot.function` is not explicitly mentioned in `?plot`. > > Right, but the fact that it _is_ described as a "generic" function > will tell the clueful that other methods ot

[R] apply is making me crazy...

2011-07-27 Thread Gene Leynes
I have tried a lot of ways around this, but I can't find a way to make apply work in a generalized way because it causes a failure whenever reduces the dimensions of its output. The following example is easier to understand than the question. I wish it had a "drop=TRUE/FALSE" option like the "["

[R] Ordinary Least Products regression in R

2011-07-27 Thread Bill Hyman
Dear all, Does any one know if any R package or function can do Ordinary Least Products regression? Many thanks! Bill __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-proj

Re: [R] ?plot: Add an example on how to plot functions to the help of `plot`.

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 5:53 PM, Paul Menzel wrote: as `plot.function` is not explicitly mentioned in `?plot`. Right, but the fact that it _is_ described as a "generic" function will tell the clueful that other methods other than the default method may exist, and that their availability may

Re: [R] ?plot: Add an example on how to plot functions to the help of `plot`.

2011-07-27 Thread Paul Menzel
Am Mittwoch, den 27.07.2011, 17:21 -0400 schrieb David Winsemius: > On Jul 27, 2011, at 4:53 PM, Paul Menzel wrote: > > Am Mittwoch, den 27.07.2011, 13:26 -0700 schrieb Bert Gunter: > >> Paul: > >> No such change is needed. > > > > Well the fact is, that I as a beginner was looking for who I could

Re: [R] for loop help

2011-07-27 Thread Steven Kennedy
Hi Cassie, I'm not sure exactly what you are trying to get: i assume that each station will have a different ppt value for each year-month combination, but it looks like you're trying to get one ppt value for each station. Steve On Thu, Jul 28, 2011 at 1:30 AM, Wilson, Cassandra J wrote: > I a

Re: [R] create a index.date column

2011-07-27 Thread Dennis Murphy
Hi: I prefer to use one of the summarization packages for this sort of thing, but aggregate() works, too. Here are two versions of the same idea: # Uses ddply() in the plyr package: index.date <- function(d) { require('plyr') out1 <- ddply(d, .(id, rcat), summarise, index = max(tdiff))

Re: [R] ?plot: Add an example on how to plot functions to the help of `plot`.

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 4:53 PM, Paul Menzel wrote: Dear Bert, Am Mittwoch, den 27.07.2011, 13:26 -0700 schrieb Bert Gunter: Paul: No such change is needed. Well the fact is, that I as a beginner was looking for who I could plot normal functions, so one more example would have helped me.

Re: [R] To Merge or to use Indicator Variables?

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 8:40 AM, oaxacamatt wrote: Greetings all, I have two sets of data that I would like to investigate. The first is gene/genome related data given different 'cell-states'. The second set of data is relates the genes to a biological pathway. /(I think in pictures so here go

Re: [R] ?plot: Add an example on how to plot functions to the help of `plot`.

2011-07-27 Thread Paul Menzel
Dear Bert, Am Mittwoch, den 27.07.2011, 13:26 -0700 schrieb Bert Gunter: > Paul: > No such change is needed. Well the fact is, that I as a beginner was looking for who I could plot normal functions, so one more example would have helped me. > You do not understand S3 methods. That is probably

[R] Fitting binary regression models with asymmetric link

2011-07-27 Thread Caio Azevedo
Hi all, Is there any R package that fits binary regression models with power (generalized) logistic link function? Thanks a lot in advance, Best, Caio [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.eth

[R] Conditional Autoregressive Value at Risk (CAViaR)

2011-07-27 Thread shanepower1...@gmail.com
Hi, I am trying to replicate Engle and Manganelli's paper Conditional Autoregressive Value at Risk (CAViaR) by Regression Quantiles. I have the Matlab code which I cannot get to work as I have never used Matlab before, does anyone know if there is the same code available to estimate the CAViaR mod

Re: [R] Correlated Multivariate Distribution Generator

2011-07-27 Thread Yue Yu
Thanks, Enrico and Harold. I have searched the archives for this topic, but all I can find is about the multivariate normal or uniform generator, which doesn't help in my case. Harold's transformation is good for getting the correlation, but the negative binomial distribution will be changed afte

Re: [R] Extend my code to run several data at once.

2011-07-27 Thread EdBo
Hi Daniel, I am still failing to do that? May you look at my look. It is calculating the estimates for one row. How do I incorporate the other data that has all other columns? Thanks Ed Sent from BlackBerry® wireless device -Original Message- From: "Daniel Malter [via R]" Date: Sat,

Re: [R] ?plot: Add an example on how to plot functions to the help of `plot`.

2011-07-27 Thread Bert Gunter
Paul: No such change is needed. You do not understand S3 methods. See ?plot.default and read about S3 methods (e.g. in the tutorial Introduction to R or the Language manual). -- Bert On Wed, Jul 27, 2011 at 12:30 PM, Paul Menzel wrote: > Dear R folks, > > > currently the section Examples contain

[R] problems with predict in fGarch

2011-07-27 Thread Luis Felipe Parra
Hello I am trying to use predict from an arma-Garch model (arma(2, 2) + garch(1, 1)) and I am getting the following error: Error en arima(x = object@data, order = c(max(u, 1), 0, max(v, 1)), init = c(ar, : non-stationary AR part from CSS Does anybody know what can be the reason of this error?

[R] ?plot: Add an example on how to plot functions to the help of `plot`.

2011-07-27 Thread Paul Menzel
Dear R folks, currently the section Examples contains the following as an example on how to plot a “normal” function. plot(sin, -pi, 2*pi) Since it does not contain the argument for the function it would be helpful to add for example the following. ## plots the graph of f(x) =

Re: [R] [solved] How to search for R related topics in search engines?

2011-07-27 Thread Paul Menzel
Am Mittwoch, den 27.07.2011, 14:36 -0400 schrieb David Winsemius: > On Jul 27, 2011, at 10:12 AM, Paul Menzel wrote: > > I am having problems getting good results when searching for R related > > topics, that means I have not found out yet what keywords I should use > > to get only relevant result

Re: [R] How to search for R related topics in search engines?

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 10:12 AM, Paul Menzel wrote: Dear R folks, I am having problems getting good results when searching for R related topics, that means I have not found out yet what keywords I should use to get only relevant results. Most of the time I get also MATLAB related things and n

[R] Hidden Markov Models in R

2011-07-27 Thread Edward Patzelt
R Community - I am attempting to fit a model as described in Hampton, Bossaerts, and O'doherty (J. Neuroscience) 2006. They use a bayesian hidden markov model to model the Reversal Learning data. I have tried using HMM and depmixS4 with no success. My data is a Reversal Learning Task in which t

Re: [R] Placing brackets around the values in a data frame

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 2:00 PM, Abraham Mathew wrote: Lets say I have the following data frame. df = data.frame(word = c("David", "James", "Sara", "Jamie", "Jon")) df I was trying to place brackets , [ ] , around each string. I'll be exporting it with write.table and quotes=FALSE, so it will ev

Re: [R] How to search for R related topics in search engines?

2011-07-27 Thread Duncan Murdoch
On 27/07/2011 10:12 AM, Paul Menzel wrote: Dear R folks, I am having problems getting good results when searching for R related topics, that means I have not found out yet what keywords I should use to get only relevant results. Most of the time I get also MATLAB related things and nothing rela

Re: [R] Placing brackets around the values in a data frame

2011-07-27 Thread Uwe Ligges
On 27.07.2011 20:00, Abraham Mathew wrote: Lets say I have the following data frame. df = data.frame(word = c("David", "James", "Sara", "Jamie", "Jon")) df I was trying to place brackets , [ ] , around each string. I'll be exporting it with write.table and quotes=FALSE, so it will eventually

Re: [R] Installing CAIC

2011-07-27 Thread Uwe Ligges
On 25.07.2011 19:42, eilunedpearce wrote: Hi, I'm trying to install CAIC directly into the newest version of R using the code on the R-Forge CAIC website and I get an error message: install.packages("CAIC", repos="http://R-Forge.R-project.org";) Warning message: In getDependencies(pkgs, depen

Re: [R] How to search for R related topics in search engines?

2011-07-27 Thread Jeremy Miles
Use rseek.org. Jeremy On 27 July 2011 07:12, Paul Menzel wrote: > Dear R folks, > > > I am having problems getting good results when searching for R related > topics, that means I have not found out yet what keywords I should use > to get only relevant results. Most of the time I get also MATLAB

Re: [R] Plotting a function that includes logical operators

2011-07-27 Thread Duncan Murdoch
On 27/07/2011 9:21 AM, dean123 wrote: Hi David, I am trying to define t as a single numeric value and not as a vector.. I want the function to realise that if I call test(t) and t is less than equal 10 return zero, if t greater than 10 return 2*t. Am i missing some code in which to define t a nu

Re: [R] RODBC sqlSave problem with bigint numbers

2011-07-27 Thread PtitBleu
I spent all the day on this problem and I've just finally found a solution: with options(digits=13), it now works. If I hadn't found this, I would have used the solution of Renaud (but not very convenient to me). Nice end of day, (Happy) Ptit Bleu. -- View this message in context: http://r.789

[R] Executing for loop by grouping variable within dataframe

2011-07-27 Thread ssobek
Dear list, I have a large dataset which is structured as follows: locality=c("USC00020958", "USC00020958", "USC00020958", "USC00020958", "USC00020958", "USC00021001","USC00021001", "USC00021001", "USC00021001", "USC00021001", "USC00021001") temp.a=c(-1.2, -1.2, -1.2, -1.2, -1.1, -2.2, -2.4, -2.6

[R] fitting sine wave

2011-07-27 Thread Tonja Krueger
Dear R-helpers   I have 7 data points that I want to fit a continuous curve to, that should look similar to a sine wave My data points would mark the local minima and maxima respectively. This is what I’ve got so far. And I would keep doing so, but sadly nls() then says that it has reached the ma

Re: [R] Accessing the index of factor in by() function

2011-07-27 Thread Merik Nanish
On Tue, Jul 26, 2011 at 10:12 AM, Ista Zahn wrote: > OK, easy enough: > > dat.tmp <- data.frame(id, month, value) > my.plot <- function(dat) {print(dat[, c("id", "value")])} > by(dat.tmp, id, my.plot) Excellent. The output of that last line is: * id value 1 110 2 112 3 111 4 1

[R] How to search for R related topics in search engines?

2011-07-27 Thread Paul Menzel
Dear R folks, I am having problems getting good results when searching for R related topics, that means I have not found out yet what keywords I should use to get only relevant results. Most of the time I get also MATLAB related things and nothing related at all. The nature of this is of course t

[R] Placing brackets around the values in a data frame

2011-07-27 Thread Abraham Mathew
Lets say I have the following data frame. df = data.frame(word = c("David", "James", "Sara", "Jamie", "Jon")) df I was trying to place brackets , [ ] , around each string. I'll be exporting it with write.table and quotes=FALSE, so it will eventually look like: [David] [James] [Sara] Can

Re: [R] RODBC sqlSave problem with bigint numbers

2011-07-27 Thread Jason Becker
In fact, I always use a string for ID variables because you can get some funky matching errors due to mismatches in precision. Bill Gould at Stata Corp said this well in a recent blog post "1. Use theory to check IDs if they are numeric One way the id variable can become corrupted is if it is not

[R] create a index.date column

2011-07-27 Thread jose Bartolomei
Dear R users, I created a matrix that tells me the first day of use of a category by id. #Calculate time difference test$tdiff<-as.numeric(difftime(as.Date("2002-09-01"), test$ftime, units = "days")) # obtain the index date per person and dcategory

[R] Rationale for different Cooks distances in cooks.distance and plot.lm

2011-07-27 Thread S Ellison
Is anyone able to offer a reason that, when using weights in an lm fit, the Cook's distances shown in plot.lm(x, which=4) differ from those calculated by cooks.distance(x) ? I can see that they _are_ different and the code tells me _how_ they differ (essentially, one is using the weights and

Re: [R] Creating a flat legend 'grob' for lattice xyplot

2011-07-27 Thread Mark
Hi Marcus, That's almost it! So ncol and column do the same thing in different functions... gah! Because my real use of xyplot I override the default plotting colors and character, autokey doesn't 'know' this, so they don't match. So the addition of the par.settings element is needed (from anot

[R] for loop help

2011-07-27 Thread Wilson, Cassandra J
I am having a hard time putting the below into a loop, where it pulls out ppt from all he stations I have versus having to go through and hard code the data to the specific stations. I tried stnID <- stnid[which(duplicated(stnid)==FALSE)] for(i in 1:length(stnID)) { ppt[i] <- ppt[which(stnid==[i]

Re: [R] Help with boxplot

2011-07-27 Thread oaxacamatt
Jz, guys lay off. I think you are being a little to hard on the poor soul. The manuals are written in computer-eez and some of the tutorials are no better. /If you can't help then don't answer./ In the meantime, Tia, I apologize. But I suggest you try and try a good book or website that c

[R] To Merge or to use Indicator Variables?

2011-07-27 Thread oaxacamatt
Greetings all, I have two sets of data that I would like to investigate. The first is gene/genome related data given different 'cell-states'. The second set of data is relates the genes to a biological pathway. /(I think in pictures so here goes.)/ *dataframe1* gene, cell-state1, cell-state2 gene1,

Re: [R] plotting the ending point in a for loop

2011-07-27 Thread Jean V Adams
Add this line of code to the end of your function, after the plot() function. points(B1[N], B2[N], pch=16, col=10) Jean `·.,, ><(((º> `·.,, ><(((º> `·.,, ><(((º> Jean V. Adams Statistician U.S. Geological Survey Great Lakes Science Center 223 East Steinfest Road Antigo, WI 54409 USA

Re: [R] Plotting a function that includes logical operators

2011-07-27 Thread dean123
Hi David, I am trying to define t as a single numeric value and not as a vector.. I want the function to realise that if I call test(t) and t is less than equal 10 return zero, if t greater than 10 return 2*t. Am i missing some code in which to define t a numeric value instead of a vector? Also,

Re: [R] Creating a flat legend 'grob' for lattice xyplot

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 1:31 PM, Mark wrote: Hi, I want my xyplot legend to be flat, not tall, and there seems to be no way for xyplot's auto.key and key elements to do this: I tried many, many permutations of what I could find in the archives and reading the documentation. If there there's a

Re: [R] plotting the ending point in a for loop

2011-07-27 Thread Uwe Ligges
Don't really undertsand, are you looking for points(B2[N], B1[N]) ? Uwe Ligges On 27.07.2011 11:59, Rebecca Gray wrote: Hello, I would appreciate if someone could help me with this query. I would like to plot a line chart of all of the points in a "for" loop. I would also like to plot th

Re: [R] Plotting problems directional or rose plots

2011-07-27 Thread alanm (Alan Mitchell)
I ran the code I sent earlier and there were a few bugs. That's what I get for using my phone to write code. This works a little better. #direction angle<-seq(0,350,10) #distance factor extends to dist = sample.int(9000,size=length(angle)) #list of colors, order corrisponds to associated

Re: [R] scripting qqplot and qqnorm

2011-07-27 Thread Uwe Ligges
On 25.07.2011 07:11, Vihan Pandey wrote: Hi all, I am an R newbie, and I have a question about scripting. I have the following lines which I want to put int\ o a script which I can call from the shell of a Mac/Linux machine : myrns<- read.csv(file="/Users/vihan/test.csv",sep="",header=FALSE)

Re: [R] R on Multicore for Linux

2011-07-27 Thread Uwe Ligges
On 24.07.2011 20:15, Madana_Babu wrote: Hi Lei, Thanks for your solution. It worked. Now I have another query. After creating multiple DF[[i]]'s how do I aggregate them into one data frame say DF (I want to bind all the data frames into one data frame). I have more than 1000 DF[[i]]'s how ca

Re: [R] Creating a flat legend 'grob' for lattice xyplot

2011-07-27 Thread Gesmann, Markus
Hi Mark, I believe the argument you are looking for is column not ncol. Try the following: library(lattice) xyplot(1~1, auto.key=list( bty='n', pch=rep(c(15,17),2), col=c('brown','green','blue','red'), columns=4, text=c('How','to make','this into', 'a grob?'), space="top" )) Regards Mar

Re: [R] Message for R-help mailing list

2011-07-27 Thread Uwe Ligges
On 27.07.2011 02:17, Jeremy Miles wrote: This is clearly a message for the R-help mailing list, since it was sent to the R help mailing list. fisher.test(x)[1] Since the test object is actually a list, your probably want fisher.test(x)[[1]] or more obvious fisher.test(x)[["p.value"]] Uwe

[R] Creating a flat legend 'grob' for lattice xyplot

2011-07-27 Thread Mark
Hi, I want my xyplot legend to be flat, not tall, and there seems to be no way for xyplot's auto.key and key elements to do this: I tried many, many permutations of what I could find in the archives and reading the documentation. If there there's a way to make it flat, please tell me what the mag

Re: [R] color of error bars in Dotplot (Hmisc)

2011-07-27 Thread Peter Ehlers
On 2011-07-27 05:35, Dieter Menne wrote: Irene Prix wrote: In a grouped Dotplot, is there any way to set the color of error bars to be the same as the corresponding symbols? ... require(lattice) require(Hmisc) data(barley) Dotplot(variety~Cbind(yield, yield+2, yield-2)|year, groups=site, dat

Re: [R] Suppressing messages while executing function

2011-07-27 Thread Duncan Murdoch
On 27/07/2011 12:50 PM, Megh Dal wrote: Dear all, while executing some function, there are some custom messages popping up onto the R console and I do not want to see them. While looking into the corresponding codes of those function, I see that those are coming from message() function. Is th

[R] Suppressing messages while executing function

2011-07-27 Thread Megh Dal
Dear all, while executing some function, there are some custom messages popping up onto the R console and I do not want to see them. While looking into the corresponding codes of those function, I see that those are coming from message() function. Is there any way to stop those messages coming

Re: [R] Correlated Multivariate Distribution Generator

2011-07-27 Thread Doran, Harold
Do you mean something like this? > cors <- matrix(c(1, .9, .8, .8, .9, 1, .8, .8, .8, .8, 1, .9, .8, .8, .9, 1), > 4) > L <- chol(cors) > N <- 1000 > dat <- cbind(rnbinom(N, mu = 4, size = 1), rnbinom(N, mu = 4, size = 1), > rnbinom(N, mu = 4, size = 1), rnbinom(N, mu = 4, size = 1)) > result <-

[R] R Remote Procedure Call

2011-07-27 Thread xiagao1982
Hi all, I have written some functionalities in C# and want to call them in R, maybe from another machine. I have found the following methods: 1. wrapper the C# code as Web Service: I noticed that there is a package named SSOAP, but it seems not yet finished and might be not fully compatible wit

Re: [R] replacing elements of vector through elements of another vector

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 10:52 AM, Marcus Mund wrote: Hello everybody, I hope this question is not too silly but I'm almost going crazy about that and could not find a solution. I have two variables, say A and B and I would like to combine them in C. In particular I want a C-value of B when B is

Re: [R] Referencing a column using a function argument

2011-07-27 Thread Eik Vettorazzi
Hi, use tableName[["columnName"]] without quotes, e.g. tableName[[columnName]] # see ?"[[" and indexing is done via x<-length(tableName[[columnName]][tableName[[columnName]] > 6] ) but you may consider x<-sum(tableName[[columnName]]>6) which saves some time and typing Hth. Am 27.07.2011 17:2

Re: [R] How to adjust y-axis when using panel.densityplot within histogram function

2011-07-27 Thread Sébastien Bihorel
Thanks David, Unfortunately, that is an option that I cannot use. The code that I provided was a simplification of a more complex workflow that accommodates various types of histograms (count, density or percentage). The actual panel function of my histogram call contains several switches that all

Re: [R] replacing elements of vector through elements of another vector

2011-07-27 Thread Marc Schwartz
On Jul 27, 2011, at 9:52 AM, Marcus Mund wrote: > Hello everybody, > > I hope this question is not too silly but I'm almost going crazy about > that and could not find a solution. > > I have two variables, say A and B and I would like to combine them in C. > In particular I want a C-value of B w

[R] tsDyn package (TVAR usage)‏

2011-07-27 Thread francesca.brusa
Hi, I'm using the tsDyn package to estimate a multivariate threshold VAR. Currently, I'm in trouble with the selection of an external transition variable. I cannot select it properly. My xls spreadsheet (rates3) contains 3 variables: I want to use the first and the second one as "data" and the thir

[R] Referencing a column using a function argument

2011-07-27 Thread Lin, YunHui
Hi all, I've been having trouble with something that seems like it should be fairly straight forward. Any help at all from more experienced users is appreciated! I'd like to write a function that uses a column name as an argument. However, I run into problems when I try to reference this colum

[R] replacing elements of vector through elements of another vector

2011-07-27 Thread Marcus Mund
Hello everybody, I hope this question is not too silly but I'm almost going crazy about that and could not find a solution. I have two variables, say A and B and I would like to combine them in C. In particular I want a C-value of B when B is not NA and the A value in case that B is NA: A B

[R] Inversions in hierarchical clustering were they shouldn't be

2011-07-27 Thread Jonas Dehairs
Hi, I'm using heatmap.2 to cluster my data, using the centroid method for clustering and the maximum method for calculating the distance matrix: library("gplots") library("RColorBrewer") test <- matrix(c(0.96, 0.07, 0.97, 0.98, 0.50, 0.28, 0.29, 0.77, 0.08, 0.96, 0.51, 0.51, 0.

Re: [R] Help with boxplot

2011-07-27 Thread Bert Gunter
Tia: R is a statistical/data analysis/graphics programming language. There is a learning curve that you appear unwilling to climb. If I have misjudged you, please work through the "Introduction to R" tutorial. It will provide the information your need. If not, install R-Commander or another R GUI

Re: [R] Plotting problems directional or rose plots

2011-07-27 Thread alanm (Alan Mitchell)
I'm not sure if there are any packages that do this, but I've created similar plots in R. The easiest way I've found is to think in terms of a unit circle in polar coordinates for drawing the plot. I haven't tested the code below, but it will give you the idea. dist=dist/9000 t = seq(0,360

Re: [R] How to adjust y-axis when using panel.densityplot within histogram function

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 9:15 AM, Sébastien Bihorel wrote: Hi I would like to superimpose group-specific densityplots on top of an overall histogram using panel.histogram and panel.densityplot. Furthermore, I would like to automatically adjust the range of the y-axis to take into account the

Re: [R] Converting F-value from ANOVA to cohen's d in meta-analysis (metafor-package)

2011-07-27 Thread Viechtbauer Wolfgang (STAT)
Dear Jokel, Unfortunately, this won't work. The derivation of the equation given in the Handbook shows why this is so. First of all, note that d = (m1 - m2) / sp, where m1 and m2 are the means of the two groups and sp is the pooled SD. The two independent samples t-test (assuming homoscedastic

[R] Fixed: Expression: +/-sigma

2011-07-27 Thread ogbos okike
Hi Yves, Many thanks. Very straight forward, the way you put. Best regards Ogbos On 27 July 2011 15:13, Yves REECHT wrote: > ** > Hi, > > You may try something like: > > plot(rnorm(10), rnorm(10), main=expression("" %+-% 2*sigma)) > > HTH, > Yves > > Le 27/07/2011 14:57, ogbos okike a écrit : >

[R] How to adjust y-axis when using panel.densityplot within histogram function

2011-07-27 Thread Sébastien Bihorel
Hi I would like to superimpose group-specific densityplots on top of an overall histogram using panel.histogram and panel.densityplot. Furthermore, I would like to automatically adjust the range of the y-axis to take into account the ranges of both histogram and densityplot. This last part is wher

Re: [R] Expression: +/-sigma

2011-07-27 Thread David Winsemius
On Jul 27, 2011, at 8:57 AM, ogbos okike wrote: Dear List, I am trying to label a plot with the symbol +/- sigma. Using something like - expression (2*sigma) gives me the symbol 2ó. However, adding +/- to it beats me. The code I am using is: plot(x,y,type="l",main=" expression(paste("±"

Re: [R] Expression: +/-sigma

2011-07-27 Thread Yves REECHT
Hi, You may try something like: plot(rnorm(10), rnorm(10), main=expression("" %+-% 2*sigma)) HTH, Yves Le 27/07/2011 14:57, ogbos okike a écrit : > Dear List, > I am trying to label a plot with the symbol +/- sigma. Using something like > - expression (2*sigma) gives me the symbol 2ó. How

[R] Expression: +/-sigma

2011-07-27 Thread ogbos okike
Dear List, I am trying to label a plot with the symbol +/- sigma. Using something like - expression (2*sigma) gives me the symbol 2ó. However, adding +/- to it beats me. The code I am using is: plot(x,y,type="l",main=" expression(paste("±", plain(2*ó)),sep=""). Any suggestion will be appreciated.

Re: [R] nls - can't get published AICc and parameters

2011-07-27 Thread Ben Bolker
> summary(n1) Formula: LBM ~ c0 * time^gamma Parameters: Estimate Std. Error t value Pr(>|t|) c0 2.584780.36767 7.030 8.93e-06 *** gamma 0.292570.03781 7.738 3.21e-06 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 0.7124 on

Re: [R] lattice overlay

2011-07-27 Thread Dieter Menne
Ram H. Sharma wrote: > > I want to overlay lattice scatter plot: I do not know why the following > code > is not plotting subscripts ! Sorry if this question is too simple: > > Working example shortened: > > .panel.xyplot(x, y, pch=16, col = "green4", ylim = c(0, 10)) > > Because they ar

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