similar to: checker/chequer board pattern as a colour

Dear All, just a quick example: > x = 1:25 > x[12] = NA > x [1] 1 2 3 4 5 6 7 8 9 10 11 NA 13 14 15 16 17 18 19 20 21 22 23 24 25 > y = x[x<10] > y [1] 1 2 3 4 5 6 7 8 9 NA Is there any way of NOT getting NA for y = x[x<10]? Similarly > y = x[x<15] > y [1] 1 2 3 4 5 6 7 8 9 10 11 NA 13 14 How do I get rid of the NA (not post

Hi All, I'm having a problem with barplot: mydata [1,] 2 108 0 0 0 1 3 0 0 0 0 0 7 18 3 4 8 20 26 20 19 7 1 1 mycol = c(rep('yellow', 2), rep('white', 3), rep('orange',2), rep('white', 5), rep('orange',3), rep('red',9)) barplot(mydata, col = mycol) gives me an uniformly yellow barplot. How do I solve this? bw Federico

Hi All, I am writing a function that reads a file in myfile = file('myfile.raw', 'rb') . . . . . close(myfile) No matter what, I get the warning Warning message: closing unused connection 3 (myfile.raw) Since the whole thing is in a function, I'd like to avoid unecessary noise for the user, and I'd like to kill the warning -- without having to mess with global options.

Hi, I am subsetting a matrix thus: test [,1] [,2] [,3] [1,] 1 7 13 [2,] 2 8 14 [3,] 3 9 15 [4,] 4 10 16 [5,] 5 11 17 [6,] 6 12 18 test[cbind(c(1,3,5), c(2,1,3))] [1] 7 3 17 This works fine, and is the equivalent of c(test[1,2], test[3,1], test[5,3]). cbind(c(1,3,5), c(2,1,3)) would obviously look like: [,1] [,2] [1,] 1 2 [2,]

Hi, according to the help file rtags does not support VI(M) yet. Is there any known hack to ctags to get tags for R in VI(M)? BW F -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com

Hi All, I have the following command: cat(rbind(table(gen$sex, gen$ddn2)[1,],round(table(gen$sex, gen$ddn2)[1,]/apply(table(gen$sex, gen$ddn2),2,sum) * 100)), sep = c(' (','%)\n'), file = '') 3 (20%) 17 (30%) 15 (31 i.e. it does NOT print the last separator, which is something that bugs me a bit, given that fact I'm trying to have some copy-paste ready stuff to put

Hi All, I have a parameter that is bimodal, and I want to get some sort of linear model done with it results = some.linear.function(bimodal.param ~ factor1 + some other stuff, mydata) I want to see if factor 1 matters (it has 3 levels, of of which can be taken as baseline), i.e: summary(results) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -2.108522

Hi All, I have a left truncated, right censored cox model: coxph(Surv(start, stop, censor) ~ x + y, mydata) I would like to know how much of the observed variance (as a number between 0 and 1) is explained by each variable. How could I do that? Adding terms sequentially and then using anova(mod1, mod2) tells me whether I get a significant improvement of the fit, but does not tell me how much

Hi, I have a coxph model like coxph(Surv(start, stop, censor) ~ x + y, mydata) I would like to calculate the Schoenfeld residuals for the null, i.e the same model where the beta hat vector (in practical terms, the coeff vector spat out by summary()) is constrained to be all 0s --all lese stays the same. I could calculate it by hand, but I was wondering if there is a way of doing it with

Dear All, a new version of MultiPhen (0.3) is available on CRAN, and will be available to a mirror near you soon. *Please upgrade* because this release is a bug fix release. A new version, with improvements in the output and more useful error messages is basically ready, but I will wait to release it until next week to add other possible improvements. For all asking for the related paper, Paul

dear all, I'm totally new to R and want to install the RQDA package. It fails because of a dependency with gWidgetsRGtk2, which doesn't install because of the following: > * installing *source* package ?gWidgetsRGtk2? ... ** R ** inst ** preparing package for lazy loading Error in eval(expr, envir, enclos) : konnte Funktion "setRefClass" nicht finden (=could not find

Hi All, I am counting the number of occurrences of the terms listed in one vector in another vector. My code runs: for( i in 1:length(vector3)){ vector3[i] = sum(1*is.element(vector2, vector1[i])) } where vector1 = vector containing the terms whose occurrences I want to count vector2 = made up of a number of repetitions of all the elements of vector1 vector3 = a vector of NAs that is

Hi All, is there a way of predicting memory usage? I need to build an array of 86000 by 2500 numbers (or I might create a list of 2 by 2500 arrays 43000 long). How much memory should I expect to use/need? Cheers, Fede -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44

Dear All, I will soon be working with NIH and possibly FDA. Will I be able to use R or will I be forced to use SAS? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com

HI All, I have written and succesfully uploaded a new package. The licence it is under is 'GPL' --no version. My assumption is, since all the code is written in R the licence R used for R would affect the code (hence my "GPL" stands for "whatever version of the GPL R is under") I am happy with the licencing I used, but I'd like to ask if there is any transitive

Hi All, I have some data where the dependent variable is a score, low (1:3) or high (8:9), and the independent variables are 21 genotypic markers. I'm fitting a logistic regression on the whole dataset after transforming the score to 0/1 and normal linear regression on the high and low subsets. I all cases I have a numer of cases of data 'duplications', i.e. different

Hi All, I would like to output the results of a function into a text file, legible as a such. The function produces a summary quite like: summary(lm(x ~ y + w * z)) [for instance] and I am not clear how to save this summary into a text file 'automagically', because I need to be able to do it in a for() loop. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology

Hello all, a friend has a problem with tiff() which I was unable to help about. I searched the error messages to no avail. When he tries: tiff(filename = "FedeWhyDoesntThisBloodyWork.tif", width = 5, height = 5, units = "cm", bg = "white", res = 1200) Error in tiff(filename = "FedeWhyDoesntThisBloodyWork.tif", width = 5, : unable to start device

Hi All, I would like to know, is there a *ballpark* figure for how many parameters the minimisation routines can cope with? I'm asking because I was asked if I knew. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t]

Hi All, is there any general advice about speeding up recursive functions (not mentioning 'don't use them')? Regards, Federico Calboli -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t]