r

decode tinyurl in R to get full url path?

Is there a way to decode tinyURL links in R so that I can see which web pages they actually refer to? ...

help installing odfWeave

This is not a programming question per se - but I hope someone can help: I can't install odfWeave - it looks like the problem is with the package XML - which i can't install either. checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package ‘XML’ * removing ‘/home/andreas/R/i486-pc-linux-gnu-...

how to suppress output in R

Hi, I would like to suppress output in R when I run my r script from the command prompt. I tried numerous options including "--slave" and "--vanilla". Those options lessens the amount of text outputted. I also tried to pipe the output to "NUL" but that didn't help. Thanks a lot, Derek ...

How does one overcome overlapping points without jitter or transparency in ggplot2

I am starting to use ggplot2. I have some small n (about 30 or so) granular data with lots of overlap. Neither jitter nor alpha (transparency) are suitable. Instead a stripchart with stack and offset do it best but I do not know how to do it in ggplot2. Do you know? To see what the end result should be click on this graphic. Here is th...

[R] Merge multiple data frames - Error in match.names(clabs, names(xi)) : names do not match previous names

Hi all- I'm getting some really bizarre stuff while trying to merge multiple data frames. Help! I need to merge a bunch of data frames by the columns 'RID' and 'VISCODE'. Here is an example of what it looks like: d1 = data.frame(ID = sample(9, 1:100), RID = c(2, 5, 7, 9, 12), VISCODE = rep('bl', 5), value1 = re...

Binning a numeric variable in R

I have a vector X that contains positive numbers that I want to bin/discretize. For this vector, I want the numbers [0, 10) to show up just as they exist in the vector, but numbers [10,) to be 10+. I'm using: x <- c(0,1,3,4,2,4,2,5,43,432,34,2,34,2,342,3,4,2) binned.x <- as.factor(ifelse(x > 10,"10+",x)) but this feels klugey to ...

Zelig: Error message

I'm running an logit model using the Zelig package. I get the following error...what could be wrong? anes96two <- zelig(trade962a ~ age962 + education962 + personal962 + economy962 + partisan962 + employment962 + union962 + home962 + market962 + race962 + income962, model="mlogit", data=data96) #Error in attr(tt, "depFactors")$depFact...

breaking out of for loop when running a function inside a for loop in R

I'm embarrassed that I'm asking this question, but here I go: Suppose you have the following function foo. When I'm running a for loop, I'd like it to skip the remainder of foo when foo initially returns the value of 0. However, break doesn't work when it's inside a function. As it's currently written, I get an error message, no lo...

Annotating axis in ggplot2

I am looking for the way to annotate axis in ggplot2. The example of the problem can be found here: http://learnr.wordpress.com/2009/09/24/ggplot2-back-to-back-bar-charts. The y axis of the chart (example graph in the link) has an annotation: (million euro). Is there a way to create such types of annotations in ggplot2? Looking at the ...

Writing temporary data from R

I want to write some temporary data to disk in an R package, and I want to be sure that it can run on every OS without assuming the user has admin rights. Is there an existing R function that can provide a path to a temporary directory on all major OS's? Or a way to reference a user's home directory? Otherwise, I was thinking of try...

R optimization: How can I avoid a for loop in this situation?

I'm trying to do a simple genomic track intersection in R, and running into major performance problems, probably related to my use of for loops. In this situation, I have pre-defined windows at intervals of 100bp and I'm trying to calculate how much of each window is covered by the annotations in mylist. Graphically, it looks somethi...

extracting getfptex batch file

Hi, while loading getfptex(got it from CTAN) batch file ,when i'm extracting this batch file i'm getting series of statements saying "No Such directory" Can anyone please help me with this. Thank you. ...

determining name of object loaded in R

Imagine you have an object foo that you saved as saved.file.rda as follows: foo <- 'a' save(foo, file='saved.file.rda') Suppose you load saved.file.rda into an environment with multiple objects but forgot the name of the object that is in saved.file.rda. Is there a way in R to determine that name? You can do it the following way, ...

How can one create a double horizontal axis for a plot in ggplot2?

I need to show the values on the horizontal axis (aka abscissa, aka x-axis) converted into other units. Hence the need for a second axis. ...

Generating lognormally distributed random number from mean, coeff of variation

Most functions for generating lognormally distributed random numbers take the mean and standard deviation of the associated normal distribution as parameters. My problem is that I only know the mean and the coefficient of variation of the lognormal distribution. It is reasonably straight forward to derive the parameters I need for the ...

R from java with no graphics: is it worth moving to JRI

I have a system set up that's been happily running R from a java servlet, spawning processed & hooking into the process's stdin, stdout, and stderr streams, as in the second andwer to this question. After a system upgrade (that included glibc), the input is no longer reaching the R process.* Until now, 'R --vanilla --slave -f [file...

R: Are there any alternatives to loops for subsetting from an optimization standpoint?

A recurring analysis paradigm I encounter in my research is the need to subset based on all different group id values, performing statistical analysis on each group in turn, and putting the results in an output matrix for further processing/summarizing. How I typically do this in R is something like the following: data.mat <- read.c...

How to stop emacs from replacing underbar with <- in ess-mode

ess-mode is "Emacs speaks statistics." This mode is useful for editing programs for R or Splus (two separate statistics packages). In my buffer, when ever I type '_' the character is replaced with "<-" which is very frustrating. Is there a emacs lisp statement to turn off this behavior? Thanks, SetJmp emacs: 22.1.1 ess-mode release ...

How can I superimpose modified loess lines on a ggplot2 qplot?

Background Right now, I'm creating a multiple-predictor linear model and generating diagnostic plots to assess regression assumptions. (It's for a multiple regression analysis stats class that I'm loving at the moment :-) My textbook (Cohen, Cohen, West, and Aiken 2003) recommends plotting each predictor against the residuals to make s...

Understanding glm$residuals and resid(glm)

Hi, Can you tell me what is returned by glm$residuals and resid(glm) where glm is a quasipoisson object. e.g. How would I create them using glm$y and glm$linear.predictors. glm$residuals n missing unique Mean .05 .10 .25 .50 .75 .90 .95 37715 10042 2174 -0.2574 -2.7538 -2.2661 -1.4480 -0.4381 0.754...