Re: [R] Binary Search

?findInterval On 8/8/07, Matthew Walker [EMAIL PROTECTED] wrote: Hi! R is an amazing piece of software and with so many libraries it can do almost anything... but I was very surprised that a standard binary search function seems not to exist. I can find other much more highly-complex

Re: [R] XL files

Hi Animesh, Can you send an example of an Excel file you need to process (and the result you wish to get)? Regards, Moshe. --- Acharjee, Animesh [EMAIL PROTECTED] wrote: Dear All, I am new to R. I need to read XLs files, parse the data and convert them into txt format for

Re: [R] how to include bar values in a barplot?

On Wednesday 08 August 2007 00:40:56 Donatas G. wrote: On Tuesday 07 August 2007 22:09:52 Donatas G. wrote: How do I include bar values in a barplot (or other R graphics, where this could be applicable)? To make sure I am clear I am attaching a barplot created with OpenOffice.org which

[R] Creating netcdf from table

Hi! I have a table with 3 columns, 2 for long/lat coordinates and 1 for values (radon concentration). I have Tables for every week of the year 2006, always same coordinates but other values, i.e. time series. Now I want to create a NetCDF file for, which is much easier to handle than 52 tables. I

Re: [R] how to include bar values in a barplot?

Please see ?format ?round Note that text() is said to expect a character vector, so why did you supply a numeric vector? labels: a character vector or expression specifying the _text_ to be written. An attempt is made to coerce other language objects (names and calls)

[R] Reading data from a string

Hi, I'am looking for ways in R to read in data from a character string in my wiki. Currently I see two possibilities: 1.) write my own routine 2.) using read.table(textConnection(mydata)) Of course, I want to avoid writing my own routine and textConnection is a forbidden command by the R-PHP

[R] Find out the workspace name

R-help, Sometimes there might be several R sessions open at the same time. In Windows no name appears in the R main bar (just R Console) Is it possible to know the name of the workspace. I ussually write it on the script I am working on but I wish to know without having to search in a text file.

[R] Odp: Error in as.double.default(x) : (list) object cannot be coerced to 'double'

Hi Far from beeing an expert I can decide from your post that you probably mix R objects matrix x data frame x list. All of them have specific features and you sometimes cannot convert one to another easily. See what your objects are and how they look like by e.g. str(X1) or mode or typeof I

[R] simulation-binomial

hello, i want to do a binomial simulation, by taking 200 var. from one group (x) and 300 from another (y). the prob. for disease=.6 in both groups. x - rbinom(200, 1, .6) y - rbinom(300, 1, .6) if the person is from group x - the probability to find the disease, assuming the person is sick, is

[R] test for contingency table when there are many zeros

Here is my table tt A B 1 297 398 2 470 376 3 30 23 4 3 3 5 0 0 b/c two cells are zero, I can't use chisq.test() in R which gives the following output; chisq.test(tt) Pearson's Chi-squared test data: tt X-squared = NaN, df = 4, p-value = NA Warning message:

Re: [R] Find out the workspace name

?getwd() ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance

Re: [R] Find out the workspace name

On Wed, 8 Aug 2007, ONKELINX, Thierry wrote: ?getwd() and ?setWindowTitle, which even has this as the first example. help.search(window title) gets you there. [mailto:[EMAIL PROTECTED] Namens Luis Ridao Cruz Sometimes there might be several R sessions open at the same time. In Windows no

[R] Namespace problem

Hi All, I have some questions about making a R-package. I would like to use a namespace. The package contains analysis functions and also a graphical user interface. I would like to allow user to use only the analysis function and not the GUI functions which are mainly bindings to graphical

Re: [R] saving output

Lynn Disney wrote: I have a question about how to save the output of a logistic regression model in some format (delimited, preferably) so that I can manipulate it to make nice tables in excel. I have tried print, save, write, none seem to do what I want them to. Does anyone have any ideas?

Re: [R] Interaction factor and numeric variable versus separate

Thanks to all for the very helpful replies the reference to a chapter in MASS! Sven On Tue, 2007-08-07 at 12:07 -0400, Gabor Grothendieck wrote: Also check this post https://stat.ethz.ch/pipermail/r-help/2007-May/132866.html for a number of formulations. On 8/7/07, Ted Harding [EMAIL

[R] tapply grand mean

Hi R-users, I have a data.frame like this (modificated from https://stat.ethz.ch/pipermail/r-help/2007-August/138124.html). y1 - rnorm(20) + 6.8 y2 - rnorm(20) + (1:20*1.7 + 1) y3 - rnorm(20) + (1:20*6.7 + 3.7) y - c(y1,y2,y3) x - rep(1:5,12) f - gl(3,20, labels=paste(lev, 1:3, sep=)) d -

Re: [R] tapply grand mean

Lauri Nikkinen wrote: Hi R-users, I have a data.frame like this (modificated from https://stat.ethz.ch/pipermail/r-help/2007-August/138124.html). y1 - rnorm(20) + 6.8 y2 - rnorm(20) + (1:20*1.7 + 1) y3 - rnorm(20) + (1:20*6.7 + 3.7) y - c(y1,y2,y3) x - rep(1:5,12) f - gl(3,20,

Re: [R] tapply grand mean

Thanks Chuck but I would fancy the output made by tapply because the idea is to make a barplot based on those values. -Lauri 2007/8/8, Chuck Cleland [EMAIL PROTECTED]: Lauri Nikkinen wrote: Hi R-users, I have a data.frame like this (modificated from

Re: [R] tapply grand mean

Lauri Nikkinen wrote: Thanks Chuck but I would fancy the output made by tapply because the idea is to make a barplot based on those values. -Lauri sum1 - summary(y ~ x + f, data = d, fun=mean, method=cross, overall=TRUE) df - data.frame(x = sum1$x, f = sum1$f, y = sum1$S)

Re: [R] Changing font in boxplots

I don't know if boxplot will accept a font argument.m From ?boxplot it is not clear. You may need to set the par() command before the boxplot Example: par(font.lab=4) boxplot(mass ~ family, data=mydata, ylab=mass %, xlab=family,las=1, cex.axis=1) --- G Iossa, School Biological Sciences [EMAIL

Re: [R] Mixture of Normals with Large Data

BertG == Bert Gunter [EMAIL PROTECTED] on Tue, 7 Aug 2007 16:18:18 -0700 writes: TV Have you considered the situation of wanting to TV characterize probability densities of prevalence TV estimates based on a complex random sample of some TV large population.

[R] Changing font in boxplots

Hi all, I am very new to R and this might be a simple question but I have looked everywhere you suggest before writing to you. I am trying to change font type from san-serif to a serif (Times New Romans) on all labels and axis of my boxplot. I have used this function in other plots before,

Re: [R] Changing font in boxplots

Hi John, Thanks so much for such a quick reply. I have tried to set all to Times font running par(font.lab=6) (not 4, maybe this is a local setting on my machine?) but now the boxplot shown has the x and y labels in Times New Roman and the x and y axis still in Arial. Any idea why R is not

[R] Successively eliminating most frequent elemets

Dear experts, I have a 10x2 matrix T containing random integers. I would like to delete pairs (rows) iteratively, which contain the most frequent element either in the first or second column: T - matrix(trunc(runif(20)*10), nrow=10, ncol=2) G - matrix(0, nrow=6, ncol=2) for (i in

Re: [R] Changing font in boxplots

On Wed, 8 Aug 2007, G Iossa, School Biological Sciences wrote: Hi John, Thanks so much for such a quick reply. I have tried to set all to Times font running par(font.lab=6) (not 4, maybe this is a local setting on my machine?) '6' is a setting specific to certain devices on Windows. You

Re: [R] Changing font in boxplots

Hi John, Thanks so much for such a quick reply. I have tried to set all to Times font running par(font.lab=6) (not 4, maybe this is a local setting on my machine?) but now the boxplot shown has the x and y labels in Times New Roman and the x and y axis still in Arial. Any idea why R is

[R] Error: Cannot Coerce POSIXt to POSIXct when building package

A newbie here - please forgive me if this is a basic question. We have an in house package built in R 2.2.1 (yes we're a little behind the times at our firm)and would like to rebuild it using R 2.5.1. However, when I try and build the package from source, I keep getting this error: Error in

Re: [R] Changing font in boxplots

Thanks everyone for your replies. And sorry if I have not been clear enough in my query (although I did say that I run R on Windows). Typing either par(family=serif) or par(font.axis=6) solved the problem. Much obliged, Graziella --On 08 August 2007 14:58 +0100 Prof Brian Ripley [EMAIL

[R] Error: Cannot Coerce POSIXt to POSIXct when building package

A newbie here - please forgive me if this is a basic question. We have an in house package built in R 2.2.1 (yes we're a little behind the times at our firm)and would like to rebuild it using R 2.5.1. However, when I try and build the package from source, I keep getting this error: Error in

Re: [R] Changing font in boxplots

--- Prof Brian Ripley [EMAIL PROTECTED] wrote: On Wed, 8 Aug 2007, G Iossa, School Biological Sciences wrote: Hi John, Thanks so much for such a quick reply. I have tried to set all to Times font running par(font.lab=6) (not 4, maybe this is a local setting on my machine?)

Re: [R] Error: Cannot Coerce POSIXt to POSIXct when building package

On Wed, 8 Aug 2007, Praveen Kanakamedala wrote: A newbie here - please forgive me if this is a basic question. We have an in house package built in R 2.2.1 (yes we're a little behind the times at our firm)and would like to rebuild it using R 2.5.1. However, when I try and build the package

Re: [R] small sample techniques

Indeed, I understand what you say. The df of freedom for the dummy example is n1+n2-2 = 8. But when I run the t.test I get it as 5.08, am I missing something? -Original Message- From: Moshe Olshansky [mailto:[EMAIL PROTECTED] Sent: Tuesday, August 07, 2007 9:05 PM To: Nair,

[R] Problems with nls-function

Dear all I have got some problems with a least-squares regression using the function nls. I want to estimate h, k and X of the following formula by using nls : exp(2*200*(q^2-4*h/k-0.25+(2/k-0.5+4*h^2/k^2)*log(abs((k*q^2+2*h*q-1)/(0.25*k-h-1)/((-k*q^2-2*h*q+1)*X) y as defined by c(0.009747

Re: [R] Error: Cannot Coerce POSIXt to POSIXct when building package

Thank you very much for your response. I think I found the offending code. It's somewhere in here. setClass(timeSeries, representation( Data = matrix, positions = character, format = character, FinCenter = character, units = character, recordIDs = data.frame, title = character, documentation

[R] fit.contrast - contrast testing with lme

I need some help on contrast testing with lme. It seems fit.contrast in 'gmodels' package works fine for simple contrasting among levels of a factor such as fit.contrast(fit.lme, Trust, c(1,-1)) Estimate Std. Error t-value Pr(|t|) Trust c=( 1 -1 ) -0.001442638

Re: [R] Mixture of Normals with Large Data

On Wed, 8 Aug 2007, Martin Maechler wrote: BertG == Bert Gunter [EMAIL PROTECTED] on Tue, 7 Aug 2007 16:18:18 -0700 writes: TV Have you considered the situation of wanting to TV characterize probability densities of prevalence TV estimates based on a complex random sample

Re: [R] small sample techniques

On Wed, 8 Aug 2007, Nair, Murlidharan T wrote: Indeed, I understand what you say. The df of freedom for the dummy example is n1+n2-2 = 8. But when I run the t.test I get it as 5.08, am I missing something? Yes. You are probably looking for the version of the t.test that assumes equal

Re: [R] simulation-binomial

That depends on what you meant by writing the conditional probability. Bayes rule says that the probability of testing positive when one has the disease is calculated as follows: Pr(T+ | D+)=(Pr(D+ | T+)*Pr(T+))/Pr(D+) is that what you mean? Kyle H. Ambert Department of Behavioral

[R] prediction using gam

I am fitting a two dimensional smoother in gam, say junk = gam(y~s(x1,x2)), to a response variable y that is always positive and pretty well behaved, both x1 and x2 are contained within [0,1]. I then create a new dataset for prediction with values of (x1,x2) within the range of the original

Re: [R] Problems with nls-function

On 8/8/07, Michael Petram [EMAIL PROTECTED] wrote: Dear all I have got some problems with a least-squares regression using the function nls. I want to estimate h, k and X of the following formula by using nls :

Re: [R] R2WinBUGS results not different with different runs

Gregor Gorjanc wrote: toby909 at gmail.com writes: Is this a specialty with R2WinBUGS? Does it have something to do with the seed value? Isnt the seed value reset everytime I restart winbugs? I always have the same seed if I start WinBUGS multiple times. So you get exactly the same

[R] Help using gPath

Hi everyone,I'm trying to figure out how to use gPath and the documentation is not very helpful :( I have the following plot object: plot-surrounds:: background plot.gTree.378:: background guide.gTree.355:: (background.rect.345, minor-horizontal.segments.347, minor-vertical.segments.349,

[R] Logistic Models, Cross Validation, error tables , Monte Carlo Simulation?

Thanks Mr. Ellison, Your remark helped solve my error table problem. However, I found a new one. Now that I have my error tables, i realised that it is no good statistical practise to validate a model, based one one error table. So i should use a tool like K-fold CV. ex: binary_model -

[R] rational or float?

Hi All, I am using the function fractions() and cognates from MASS. I would like to be able to tell if some calculations I am doing on some rationals are transformed into floats and then retransformed into rationals. For instance I suspect that as.fractions(1/8) + as.fractions(1/4) does

[R] Change in R**2 for block entry regression

Hi all, I'm demonstrating a block entry regression using R for my regression class. For each block, I get the R**2 and the associated F. I do this with separate regressions adding the next block in and then get the results by writing separate summary() statements for each regression. Is

[R] Rcmdr window border lost

Dear all, I have recently lost my Rcmdr window borders (all my other programs have borders)! I am unsure of what I have done, although I have recently update.packages() in R... How can I reclaim them? I am using: Ubuntu Linux (Feisty) R version 2.5.1 R Commander Version 1.3-5 I have deleted

Re: [R] test for contingency table when there are many zeros

fisher.test(tt) Francisco gallon li wrote: Here is my table tt A B 1 297 398 2 470 376 3 30 23 4 3 3 5 0 0 b/c two cells are zero, I can't use chisq.test() in R which gives the following output; chisq.test(tt) Pearson's Chi-squared test data: tt

Re: [R] prediction using gam

Without seeing the data and results it's hard to say. mgcv::predict.gam is already `safe' so that's not the issue. It's also pretty heavily tested, so a problem with that function wouldn't be the first place I'd look. How `large positive' are the predictions relative to the observed response?

[R] cointegration analysis

Hello, I tried to use urca package (R) for cointegration analysis. The data matrix to be investigated for cointegration contains 8 columns (variables). Both procedures, Phillips Ouliaris test and Johansen's procedures give errors (error in evaluating the argument 'object' in selecting a method

[R] Relocating Axis Label/Title --2

Apologies for the previous mail (I sent it off too early by mistake). This is the correct example: rm(list=ls()) D_mean-seq(-5,5,length=100) y-exp(-D_mean^2/5) pdf(my.pdf) plot(D_mean,y,type=l,yaxt=n,lty=2,lwd=2,col=black, ylab = list(expression(paste(dN/dlogD[agg], [*cm^-3*]))), xlab =

Re: [R] simulation-binomial

I have the probability: P(T+ / D+) i want to find P(T+,D+) which is: P(T+ / D+)*P(D+) and i have those probabilities. i dont know how to write this in R. something like this: (say p2 is the conditional prob. and p1 is the joint prob.) p2 - p1/.6 x - rbinom(200, 1, .6) y - rbinom(300, 1, .6) if

Re: [R] Relocating Axis Label/Title

Have a look at mar in ?par. You might want to try something like mar=c(5, 5, 4, 2) + 0.1 rather than the default of c(5, 4, 4, 2) + 0.1 . --- Lorenzo Isella [EMAIL PROTECTED] wrote: Dear All, I am experiencing some problems with relocating an axis title. I visited the following link before

Re: [R] how to include bar values in a barplot?

Do you mean like this? my.values=10:15 x - barplot(my.values, ylim=c(0,11)) text(x, my.values, labels=my.values, pos=3) It is very bad practice and OOo should have its fingers slapped for perpetuating such a form. --- Donatas G. [EMAIL PROTECTED] wrote: How do I include bar

[R] Regsubsets statistics

Dear R-help, I have used the regsubsets function from the leaps package to do subset selection of a logistic regression model with 6 independent variables and all possible ^2 interactions. As I want to get information about the statistics behind the selection output, I´ve intensively searched

Re: [R] small sample techniques

About using t tests and confidence intervals for large samples - large may need to be very large. The old pre-computer-age rule of n = 30 is inadequate. For example, for an exponential distribution, the actual size of a nominal 2.5% one-sided t-test is not accurate to within 10% (i.e. between

[R] converting character string to an expression

Hi Everyone, I would simply like to coerce a character string into an expression: something like: as.expression(paste(letters[1:3], collapse=+)) but I can't seem to get rid of the quotes. The only way I can get it to work is using as.formula: as.expression(as.formula(paste(~,

[R] mice package

Hi all, I am trying to run the mice package (for multiple imputation) on a data frame that is 5174 x 100. When I run mice(frame), I get the following response: Error in solve.default(t(xobs) %*% xobs) : Lapack routine dgesv: system is exactly singular and execution

Re: [R] simulation-binomial

Does this do what you want? x2 - rbinom( 200, 1, ifelse(x, .95, p1/.6) ) y2 - rbinom( 300, 1, ifelse(y, .8, p1/.6) ) Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From:

Re: [R] S4 methods: unable to find an inherited method

Hi Paul, H. Paul Benton [EMAIL PROTECTED] writes: I consider myself pretty new to the whole OO based programming so I'm sorry if I'm doing something stupid. These sorts of questions might be better sent to the R-devel list... xml-read.metlin(url) Error in function (classes, fdef,

Re: [R] simulation-binomial

i will use that, thank you. sigalit. On 8/8/07, Greg Snow [EMAIL PROTECTED] wrote: Does this do what you want? x2 - rbinom( 200, 1, ifelse(x, .95, p1/.6) ) y2 - rbinom( 300, 1, ifelse(y, .8, p1/.6) ) Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center

Re: [R] Namespace problem

Dimitri Mahieux wrote: Hi All, I have some questions about making a R-package. I would like to use a namespace. The package contains analysis functions and also a graphical user interface. I would like to allow user to use only the analysis function and not the GUI functions which are

[R] Test (please ignore)

Please excuse this -- I need to test whether I can get through to R-help! (Have failed repeatedly today). Ted. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] converting character string to an expression

I think you're looking for parse(text=paste(letters[1:3], collapse=+)) --- Jarrod Hadfield [EMAIL PROTECTED] wrote: Hi Everyone, I would simply like to coerce a character string into an expression: something like: as.expression(paste(letters[1:3], collapse=+)) but I can't seem to

[R] ksvm-kernel

HI I am new to R. I have one problem in the predict function of the kernlab. I want to use ksvm and predict with kernelmatrix (S4 method for signature 'kernelMatrix') #executing the following sentences library(kernlab) # identity kernel k - function(x,y) { n-length(x) cont-0 for(i in

[R] Systematically biased count data regression model

Dear all, I am attempting to explain patterns of arthropod family richness (count data) using a regression model. It seems to be able to do a pretty good job as an explanatory model (i.e. demonstrating relationships between dependent and independent variables), but it has systematic problems as

[R] R memory usage

Hi All, I have two questions in terms of the memory usage in R (sorry if the questions are naive, I am not familiar with this at all). 1) I am running R in a linux cluster. By reading the R helps, it seems there are no default upper limits for vsize or nsize. Is this right? Is there an upper

Re: [R] Relocating Axis Label/Title --2

You don't need to move anything. Just allocate more room for what you have already. Try this: rm(list=ls()) D_mean-seq(-5,5,length=100) y-exp(-D_mean^2/5) pdf(my.pdf) ### par(mar = c(4.5, 4.5, 1, 1) + 0.1)# ###

Re: [R] Relocating Axis Label/Title --2 (Second try.)

I hate it when the line feeds get lost and the message becomes unintelligible. I'm sorry. You don't need to move anything. Just allocate more room for what you have already. Try this: rm(list=ls()) D_mean-seq(-5,5,length=100) y-exp(-D_mean^2/5) pdf(my.pdf) ### par(mar =

Re: [R] small sample techniques

As Thomas Lumley noted, there exist several versions of t-test. If you use t1 - t.test(x,y) then no assumption is made of x and y having equal variance and of the two sample sizes being equal and then an approximate t-test is used with an approximate number of degrees of freedom (and this is what

Re: [R] small sample techniques

On 9/08/2007, at 2:57 PM, Moshe Olshansky wrote: As Thomas Lumley noted, there exist several versions of t-test. snip If you use t3 - t.test(x,y,paired=TRUE) then equal sample sizes are assumed and the number of degrees of freedom is 4 (5-1). This is seriously misleading.

Re: [R] small sample techniques

Well, this an explanation of what is done in the paired t-test (and why the number of df is as it is). I was too lazy to write all this. It is nice that some list members are less lazy! --- Rolf Turner [EMAIL PROTECTED] wrote: On 9/08/2007, at 2:57 PM, Moshe Olshansky wrote: As Thomas

[R] passing variables

Hi am new to jmeter... hear am explaining what my problem is? i have recorded the fallowing operations in my application by using proxy server...i login to the application by using username and password...after getting the home page i have created a new brand by giving brandname and description

[R] Reading time/date string

Hello everyone, Can anyone tell me what function I should use to read time/date strings and turn them into a form such that I can easily calculate the difference of two? The strings I've got look like 10:17:07 02 Aug 2007. If I could calculate the number of seconds between them I'd be very

[R] tcltk error on Linux

I am having trouble getting tcltk package to load on openSuse 10.2 running R-devel. I have specifically put my /usr/share/tcl directory in my PATH, but R doesn't seem to see it. I also have installed tk on my system. Any ideas on what the problem is? Also, note that I have some warning

[R] plot table with sapply - labeling problems

Hi List, I am trying to label a barplot group with variable names when using sapply unsucessfully. I can't seem to extract the names for the indiviual plots: test-as.data.frame(cbind(round(runif(50,0,5)),round(runif(50,0,3)),roun d(runif(50,0,4 sapply(test, table)-vardist sapply(test,

Re: [R] Reading time/date string

Look at some of these functions... DateTimeClasses(base) Date-Time Classes as.POSIXct(base)Date-time Conversion Functions cut.POSIXt(base)Convert a Date or Date-Time Object to a Factor format.Date(base) Date Conversion Functions to and from Character Mark --- Mark W.

Re: [R] R2WinBUGS results not different with different runs

toby909 at gmail.com writes: Gregor Gorjanc wrote: toby909 at gmail.com writes: Is this a specialty with R2WinBUGS? Does it have something to do with the seed value? Isnt the seed value reset everytime I restart winbugs? I always have the same seed if I start WinBUGS multiple