[R] Automated figure production

Hello, everybody Two questions: 1) I am new to maillists, and particularly to r-help maillist. Where specifically do I go online to see my question and answers to it??? If I use the searchable archives, or archives by Robert King, I see my question but not the answers, though I know that at

Re: [R] how to fill between 2 stair plots

Williams Scott wrote: Hi all, I want to create a simple plot with 2 type='s' lines on it: plot(a, b, type='s') lines(x, y, type='s') I wish to then fill the area between the curves with a colour to accentuate the differences eg col=gray(0.95). I cant seem to come up with a simple method

Re: [R] how to fill between 2 stair plots

Williams Scott napsal(a): Hi all, I want to create a simple plot with 2 type='s' lines on it: plot(a, b, type='s') lines(x, y, type='s') I wish to then fill the area between the curves with a colour to accentuate the differences eg col=gray(0.95). I cant seem to come up with a simple

Re: [R] Automated figure production

On 26 Feb 2007 at 9:14, Sergey Goriatchev wrote: Date sent: Mon, 26 Feb 2007 09:14:17 +0100 From: Sergey Goriatchev [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Subject:[R] Automated figure production Hello, everybody Two

[R] Chi Square with two tab-delimited text files

Hi, I want to do a chi square test and I have two tab delimited text files with Expected and Observed values to compare. Each file contains only the values and are 48 rows by 116 columns. I have managed to do something with them, but I don't think it is right as I got a p value of 1. In this

Re: [R] Double-banger function names: preferences and suggestions

hadley wickham wrote: What do you prefer/recommend for double-banger function names: 1 scale.colour 2 scale_colour 3 scaleColour 1 is more R-like, but conflicts with S3. 2 is a modern version of number 1, but not many packages use it. Number 3 is more java-like. (I like number 2

Re: [R] some caracter dont work with JGR

Den Fr, 2007-02-23, 19:21 skrev Ronaldo Reis Junior: Hi, I testing JGR and I like, but my ~ caracter dont work. My keyboard is Brazilian ABNT2. The key is OK, only in JGR it dont work. Anybody have any idea about this? Yes, and it's known problem -- see e.g.

Re: [R] nested design in lme, need help with specifying model

Dear Radka I'm not sure I quite understand your design and quite where the nesting comes in. But a quick suggestion is why are you adding species as random as well as fixed? I don't think you can do this or indeed should do it. I think this is why you get problems with your fixed effects. If

[R] Add-up duplicates and merge

Hello, a have two matrices of data as below. I would like to add-up the duplicate in terms of pair of names in rows, and then merge the values in the second matrix to the pairs as two new variables x3 and x4. Input ,x1,x2 jane.mike,31,43 jane.steve,32,2 jane.steve,5,3 jim.mike,76,5

[R] PlotAffyRNAdeg on Estrogen Data

Hi everyone, I'm trying to generate an RNA degradation plot of the Estrogen example data plot, but seem to get an error. I've tried defining an ylim value, ylim=c(0,30) , but it doesn't seem to work either. My code is as follows: RNAdeg-AffyRNAdeg(Data) png(DegLoc, width=720,

Re: [R] Add-up duplicates and merge

Hello, for the first task change the names if they are character into a factor and have a look at ?by For the merge you will need strsplit() on character vectors (so be carefull to change the factor back to character) and merge() Regards, Winfried -Original Message- From: [EMAIL

Re: [R] Chi Square with two tab-delimited text files

Carina Brehony napsal(a): Hi, I want to do a chi square test and I have two tab delimited text files with Expected and Observed values to compare. Each file contains only the values snip There are a lot of chi^2 tests, most of them compare OE quantities and it is not clear which one you want

Re: [R] Chi Square with two tab-delimited text files

Yes, I would like to do a goodness-of-fit test. -Original Message- From: Petr Klasterecky [mailto:[EMAIL PROTECTED] Sent: 26 February 2007 11:50 To: Carina Brehony Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Chi Square with two tab-delimited text files Carina Brehony napsal(a): Hi,

Re: [R] Chi Square with two tab-delimited text files

It's a bit difficult to advise without knowing what the rows and columns represent, but why not just calculate the statistic yourself, given that you already have observed and expected values? For example: chi2 - sum((y-x)^2/x) On 26/02/07, Carina Brehony [EMAIL PROTECTED] wrote: Yes, I

Re: [R] If you had just one book on R to buy...

On 2/25/07, Julien Barnier [EMAIL PROTECTED] wrote: Hi, I am starting a new job as a study analyst for a social science research unit. I would really like to use R as my main tool for data manipulation and analysis. So I'd like to ask you, if you had just one book on R to buy (or to keep),

Re: [R] Chi Square with two tab-delimited text files

Hi, The files look like below and the rows and columns are numbers of genetic types e.g. row1 is type 4; column1 is type A. So for, row1:column1 cell there are 78 type 4/type A combinations. I hope this makes sense! 78 500 18 6 0 4 0 1 6 1

[R] Rdonlp2 0.2-1 released

Hello R-lists, I have released the new version of Rdonlp2 (an extension package to solve nonlinear constrained optimization problem). 0.2-1 improves stability and usability, and runs little faster. Windows, OSX binary, and source files are available from: http://arumat.net/Rdonlp2/ Any

Re: [R] Chi Square with two tab-delimited text files

In that case, you can just ignore the expected values and use the observed values in the chisq.test. The reason you got a p value of 1 before is because the second argument was ignored, and so you did a chi square test on the expected values alone. If you have loaded the obseved values into a

[R] PLotting R graphics/symbols without user x-y scaling

Is it possible to add lines or other user defined graphics to a plot in R that does not depend on the user scale for the plot? For example I have a plot plot(x,y) and I want to add some graphic that is scaled in inches or cm but I do not want the graphic to change when the x-y scales are changed

Re: [R] Chi Square with two tab-delimited text files

Hi, Thanks for the input. I have tried the test again just using the Observed values and the read.table() function and get this: data: y X-squared = NaN, df = 5405, p-value = NA Warning message: Chi-squared approximation may be incorrect in: chisq.test(y) So it doesn't seem to like it! I

Re: [R] PlotAffyRNAdeg on Estrogen Data

Hi Tony, This question concerns a Bioconductor package, so is best asked on the BioC mailing list instead of R-help. Best, Jim Brooks, Anthony B wrote: Hi everyone, I'm trying to generate an RNA degradation plot of the Estrogen example data plot, but seem to get an error. I've tried

[R] Test of Presence Matrix HOWTO?

Hello, Imagine 3 lists like so: a - list(A,B,C,D) b - list(A,B,E,F) c - list(A,C,E,G) What I need (vennDiagram) is a matrix characterizing with 1 or 0 whether any given member is present or not like so: x1 x2 x3 [1,] 1 1 1 [2,] 1 1 0 [3,] 1 0 1 [4,] 1 0 0 [5,] 0 1 1 [6,]

[R] someattributes

I'd like to use someattributes(), as described in documentation for R version 2.4.1 (windows build) help(attributes) however, someattributes() does not seem to exist. someattributes() Error: could not find function someattributes Is this true or am I doing something wrong? -John

Re: [R] Test of Presence Matrix HOWTO?

a - c(A,B,C,D) b - c(A,B,E,F) c - c(A,C,E,G) Df - cbind(a, b, c) apply(Df, 2, function(x)(LETTERS[1:7] %in% x)) a b c [1,] TRUE TRUE TRUE [2,] TRUE TRUE FALSE [3,] TRUE FALSE TRUE [4,] TRUE FALSE FALSE [5,] FALSE TRUE TRUE [6,] FALSE TRUE FALSE [7,] FALSE FALSE

Re: [R] Test of Presence Matrix HOWTO?

you can use something like the following: a - list(A,B,C,D) b - list(A,B,E,F) c - list(A,C,E,G) # abc - list(a, b, c) unq.abc - unique(unlist(abc)) out.lis - lapply(abc, %in%, x = unq.abc) out.lis lapply(out.lis, as.numeric) I hope it helps. Best, Dimitris Dimitris

[R] LD50 contrasts with lmer/lme4

Dear R-list, I have a data set from 20 pigs, each of which is tested at crossed 9 doses (logdose -4:4) and 3 skin treatment substances when exposed to a standard polluted environment. So there are 27 patches on each pig. The response is irritation=yes/no. I want to determine equally effective

Re: [R] someattributes

On Feb 26, 2007, at 10:35 AM, Thaden, John J wrote: I'd like to use someattributes(), as described in documentation for R version 2.4.1 (windows build) help(attributes) however, someattributes() does not seem to exist. someattributes() Error: could not find function someattributes Is

Re: [R] Double-banger function names: preferences and suggestions

Thanks to every one who contributed - there definitely isn't a consensus, but perhaps a slight preference towards number 3 (camelCase). I'm not sure yet if this beats out my personal preference for number 2. Hadley On 2/25/07, hadley wickham [EMAIL PROTECTED] wrote: What do you

[R] Barplot Graph

Hello everyone: I want to draw a Par plot but I don't know how to choose different pattern of of colors for different bars to be able to distinguish them in a black and white print. I want some kinds of patterns on the bars such as '///' or '\\\' or … Suppose I have the following data in the

[R] Adding duplicates by rows

Hi, I am trying to add duplicates of matrix mat by row. Commands subset(mat,duplicated(rownames(mat))) or mat[which(duplicated(rownames(mat))),] return only half of the required indices. How can I find the remaining ones, ie the matches, so that I can add them up? Thanks, Serguei

[R] survival analysis using rpart

Hello, I use rpart to predict survival time and have a problem in interpreting the output of “estimated rate”. Here is an example of what I do: stagec - read.table(http://www.stanford.edu/class/stats202/DATA/stagec.data;, col.names=c(pgtime, pgstat, age,eet, g2, grade, gleason, ploidy))

[R] Partial whitening of time series?

I have a time series with a one year lag, ar=0.5. The series has some interesting events that disappear when the series is whitened (i.e., fitting an AR process and looking at the residuals). I'd like to remove the autocorrelation in stages to see the effect on the time series. Is there a way to

Re: [R] Adding duplicates by rows

Serguei Kaniovski wrote: Hi, I am trying to add duplicates of matrix mat by row. Commands subset(mat,duplicated(rownames(mat))) or mat[which(duplicated(rownames(mat))),] return only half of the required indices. How can I find the remaining ones, ie the matches, so that I can add

Re: [R] Partial whitening of time series?

andy, if your model is Xt = 0.5 * Xt-1 + e, then it should have Xt = 0.1 * Xt-1 + 0.4 * Xt-1 + e (Xt - 0.1*Xt-1) = 0.4 * Xt-1 + e so what you need to do is to substract part of lag from your series. it is just my $0.02. On 2/26/07, Andy Bunn [EMAIL PROTECTED] wrote: I have a time series with a

[R] eigenvalue ordering

Hi all, Is it possible to get unordered eigenvalues and eigenvectors of a symmetric matrix in R? Any help appreciated. Regards, Kaustubh - [[alternative HTML version deleted]] __

Re: [R] eigenvalue ordering

Kaustubh Patil wrote: Is it possible to get unordered eigenvalues and eigenvectors of a symmetric matrix in R? Yes, see help(eigen). If you are strict about the unordered part, do a sample(set, size) to randomize the eigenvalues. Alberto Monteiro

Re: [R] eigenvalue ordering

Alberto Monteiro wrote: Kaustubh Patil wrote: Is it possible to get unordered eigenvalues and eigenvectors of a symmetric matrix in R? Yes, see help(eigen). Er, where do you see anything about (un)order? As far as I know, there's no natural ordering of eigenvalues and eigenvalue

Re: [R] Macros in R

If I understand the question correctly, I would do this: for (i in 1:54) assign( paste('input',i,sep='') , matrix( dataset$variable, nrow=1) ) You now have 54 matrices, named input1, input2, ... input54, each having 1 row and as many columns as dataset$variable is long. (also, they're

Re: [R] eigenvalue ordering

Peter Dalgaard wrote: Is it possible to get unordered eigenvalues and eigenvectors of a symmetric matrix in R? Yes, see help(eigen). Er, where do you see anything about (un)order? As far as I know, there's no natural ordering of eigenvalues and eigenvalue algorithms generally find

[R] 2 data frames - list in one out put , matrix in another ??

I have two more or less parallel dataframes that are giving me different results on one subset of variables. I know that I assembled the 2 dataframes slightly differently but I don't see why I am getting this result because one set of variables are labelled and the other is not. Variable names

Re: [R] someattributes

I had written ...someattributes() does not seem to exist. And Haris Skiadas replied My help shows it as moreattributes, not someattributes. (MacOSX), though doesn't sound like it should be platform-specific). Thanks for correcting me. Actually, my windows R documentation says

[R] returns from dnorm and dmvnorm

Hi All, Why would calls to dnorm and dmvnorm return values that are above 1? For example, dnorm(0.3,mean=0, sd=0.1) [1] 3.989423 This is happening on two different installations of R that I have. Thank you. Hailu [[alternative HTML version deleted]]

[R] hierarchical clustering using cutree

Hi Everyone, I am doing hierarchical clustering analysis and have a question regarding cutree. I am doing things like this: hc - hclust(dist(X)) a - cutree(hc, k=2) Basically a is a vector containing the assignments of 1 or 2 for each sample. May I know how cutree decides to assign 1 and 2's

Re: [R] returns from dnorm and dmvnorm

well, nobody said that the density must be smaller than 1, right? :-) it's just the value of the normal density function at the point you asked. you may try doing that by hand and, with the correct math, you'll get the same thing. b On Feb 26, 2007, at 3:03 PM, A Hailu wrote: Hi All, Why

Re: [R] someattributes

On Feb 26, 2007, at 3:00 PM, Thaden, John J wrote: Thanks for correcting me. Actually, my windows R documentation says mostattributes(), but it makes no difference -- none of the three show up as function names or R objects. That's because there is no mostattributes function, it only works

Re: [R] someattributes

On 2/26/07, Thaden, John J [EMAIL PROTECTED] wrote: I had written ...someattributes() does not seem to exist. And Haris Skiadas replied My help shows it as moreattributes, not someattributes. (MacOSX), though doesn't sound like it should be platform-specific). Thanks for correcting

Re: [R] returns from dnorm and dmvnorm

On Feb 26, 2007, at 3:03 PM, A Hailu wrote: Hi All, Why would calls to dnorm and dmvnorm return values that are above 1? For example, dnorm(0.3,mean=0, sd=0.1) [1] 3.989423 Because dnorm gives you the density function, whose integral is the distribution function, which is likely

Re: [R] returns from dnorm and dmvnorm

I guarantee that it would also happen on all future versions of R. Why would you expect density to be smaller than 1? The only constraints on density are that (a) it is non-negative and (b) it integrates to one. The smaller the variance, the greater the density is around its center. Density can

Re: [R] someattributes (actually, mostattributes)

Haris Skiadas replied Thanks for correcting me. Actually, my windows R documentation says mostattributes(), but it makes no difference -- none of the three show up as function names or R objects. That's because there is no mostattributes function, it only works as an assignment:

Re: [R] returns from dnorm and dmvnorm

Yes, you are right. Thanks. On 2/27/07, Benilton Carvalho [EMAIL PROTECTED] wrote: well, nobody said that the density must be smaller than 1, right? :-) it's just the value of the normal density function at the point you asked. you may try doing that by hand and, with the correct math,

Re: [R] Partial whitening of time series?

Thanks, I wasn't thinking real clearly when I pressed 'send'. All figured out now. -A -Original Message- From: Wensui Liu [mailto:[EMAIL PROTECTED] Sent: Monday, February 26, 2007 10:15 AM To: Andy Bunn Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Partial whitening of time series?

Re: [R] returns from dnorm and dmvnorm

Thanks everyone. I should have thought of dnorm as a straing return from the normal density formula. Hailu On 2/27/07, Charilaos Skiadas [EMAIL PROTECTED] wrote: On Feb 26, 2007, at 3:03 PM, A Hailu wrote: Hi All, Why would calls to dnorm and dmvnorm return values that are above 1? For

Re: [R] Double-banger function names: preferences and suggestions

The underscore versus left-arrow conundrum has its roots in the evolution of ASCII during the middle of the last century. Some Teletype machines in the 1970s (when the S language was being developed) still had a left arrow, and its ASCII code was used in S as a one keystroke convenience for

[R] training svm

Hello. I'm new to R and I'm trying to solve a classification problem. I have a training dataset of about 40,000 rows and 50 columns. When I try to train support vector machine, it gives me this error after a few seconds: Error in predict.svm(ret, xhold) : Model is empty! This is the code I

[R] match() function with a little enhancement

Dear R users, I was wondering if R has a built-in function doing the following : my_match(values_vector,lookup_vector) { for each value of values_vector : if value %in% lookup_vector, then value is unchanged else, value is changed the the closest element of lookup_vector, closest meaning the

Re: [R] match() function with a little enhancement

try this: values - c(Kiwis, Bananas, Ananas, Cherries, Peer) vector - c(Oranges, Bananas, Apples, Cherries, Lemons) vector - sort(vector) vector [1] Apples Bananas Cherries Lemons Oranges x - sapply(values, function(x)ifelse(x=vector, -1, 1)) x Kiwis Bananas Ananas Cherries Peer

Re: [R] PLotting R graphics/symbols without user x-y scaling

Hi Jonathan Lees wrote: Is it possible to add lines or other user defined graphics to a plot in R that does not depend on the user scale for the plot? For example I have a plot plot(x,y) and I want to add some graphic that is scaled in inches or cm but I do not want the graphic to

Re: [R] Crosstabbing multiple response data

Thanks to Charles, Gabor, and a private message from Frank E Harrell with some good ideas and help. This crossprod approach was very clever, I would never have thought of it. Best, Michael - Original Message From: Charles C. Berry [EMAIL PROTECTED] To: Michael Wexler [EMAIL

[R] looping

Greetings: I am looking for some help (probably really basic) with looping. What I want to do is repeatedly sample observations (about 100 per sample) from a large dataset (100,000 observations). I would like the samples labelled sample.1, sample.2, and so on (or some other suitably simple

[R] RDA and trend surface regression

Dear all, I'm performing RDA on plant presence/absence data, constrained by geographical locations. I'd like to constrain the RDA by the extended matrix of geographical coordinates -ie the matrix of geographical coordinates completed by adding all terms of a cubic trend surface regression- .

Re: [R] RDA and trend surface regression

Helene, You will have to give us more information, such as your system/versions and a small reproducible example. We try to stress that questions are more easily answered when there are a lot of specific details given and a reproducible case can be tested. Here are two comments though: 1. The

[R] prop.test or chisq.test ..?

Hi everyone, Suppose I have a count the occurrences of positive results, and the total number of occurrences: pos - 14 total - 15 testing that the proportion of positive occurrences is greater than 0.5 gives a p-value and confidence interval: prop.test( pos, total, p=0.5,

Re: [R] PLotting R graphics/symbols without user x-y scaling

You can use par(usr) to get the min/max coords of the plot and then use that. For example, this will plot a red dot in the middle of the plot area regardless of the coordinates: plot(1:10) # sample plot usr - par(usr) points(mean(usr[1:2]), mean(usr[3:4]), pch = 20, col = red) # red dot See

Re: [R] looping

You do not say -- and I am unable to divine -- whether you wish to sample with or without replacement: each time or as a whole. In general, when you want to do this sort of thing, the fastest way to do it is just to sample everything you need at once and then form it into a list or matrix or

Re: [R] Optimizing the loop for large data

Rusers: I am trying to apply a quadratic discriminant function to find the best classification outcomes. 1 is assigned to the values greater than a threshold value; and 0 otherwise. I would like to see how the apparent error rates and the optimal error rate change with increasing threshold

[R] exact matching of names in attr

In R 2.5.0 (r40806), one of the change is to allow partial matching of name in the attr function. However, how can I tell if I have an exact match or not? For example, checking to see if an object has a name attribute, then giving it one if it doesn't: dat - data.frame(x=1:10,y=rnorm(10))

[R] looping

Another way is to use an indexed list, which is far more tidier than your method. If you mean about 100 as in an irregular number, then a list is your friend (i.e., a ragged array, that can have sometimes 97 samples, sometime 105 samples, etc.). Similar to your example: dat -

[R] How to use bash command in R script?

Dear All: Maybe it is a too basic question, but I don't how to find the answer. Sorry for that. What I want to do is call a shell command, which will provide two numbers, and assign those numbers to a vector. For example: The following command: $mxresult.sh ABC.mx mxresult.sh is a script

Re: [R] How to use bash command in R script?

Guo Wei-Wei wrote: Dear All: Maybe it is a too basic question, but I don't how to find the answer. Sorry for that. What I want to do is call a shell command, which will provide two numbers, and assign those numbers to a vector. For example: The following command: $mxresult.sh ABC.mx

Re: [R] exact matching of names in attr

if (!name %in% names(attributes(dat))) { ... } /Henrik On 2/26/07, Michael Toews [EMAIL PROTECTED] wrote: In R 2.5.0 (r40806), one of the change is to allow partial matching of name in the attr function. However, how can I tell if I have an exact match or not? For example, checking to see

Re: [R] 2 data frames - list in one out put , matrix in another ??

Hi as I do not know what class is labelled and not knowing about your data I just try to give you some hints. What says str(adata) and str(bdata) about structure of your data? It can be possible that in second case the structure of resulting table can be formed into matrix and apply probably

Re: [R] How to use bash command in R script?

?system. Cheers, Andrew On Tue, Feb 27, 2007 at 02:05:09PM +0800, Guo Wei-Wei wrote: Dear All: Maybe it is a too basic question, but I don't how to find the answer. Sorry for that. What I want to do is call a shell command, which will provide two numbers, and assign those numbers to a

[R] RDA and trend surface regression

'm performing RDA on plant presence/absence data, constrained by geographical locations. I'd like to constrain the RDA by the extended matrix of geographical coordinates -ie the matrix of geographical coordinates completed by adding all terms of a cubic trend surface regression- . This

[R] fitting of all possible models

Hi, Fitting all possible models (GLM) with 10 predictors will result in loads of (2^10 - 1) models. I want to do that in order to get the importance of variables (having an unbalanced variable design) by summing the up the AIC-weights of models including the same variable, for every variable

Re: [R] How to use bash command in R script?

Thank you all! I solved my problem with your help. Best wishes, Wei-Wei __ R-help@stat.math.ethz.ch 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