similar to: Standardized Pearson residuals (and score tests)

Is there any reason that rstandard.glm doesn't have a "pearson" option? And if not, can it be added? Background: I'm currently teaching an undergrad/grad-service course from Agresti's "Introduction to Categorical Data Analysis (2nd edn)" and deviance residuals are not used in the text. For now I'll just provide the students with a simple function to use, but I

{again a message that was sent to owner-r-help (which is me, currently) why on earth ???!??!? reply to R-help or the original sender Brett Presnell; } I'm teaching a categorical data analysis course this term, and a minor "problem" has resurfaced that I have often thought about before. This applies equally to Splus I suppose, but my undergrads aren't using Splus. It

In R 2.1.1, the default behaviour of scan() was changed to process all C-style escapes, even when a delimiter was specified using the 'sep' argument. A new argument 'allowEscapes' was introduced to turn this processing off. Because read.table() calls scan(), read.table() inherits the new default behaviour of scan() but without a way to turn it off. For example, reading a file

This is just a suggestion/wish that it would be nice for the F-distribution functions to recognize limiting cases for infinite degrees of freedom, as the t-distribution functions already do. The t-distribution functions recognize that df=Inf is equivalent to the standard normal distribution: > pt(1,df=Inf) [1] 0.8413447 > pnorm(1) [1] 0.8413447 On the other hand, pf() will accept Inf

Dear All, We are about to purchase the second edition of Agresti's "Categorical Data Analysis" (my old copy of the first ed. of that wonderful book is falling apart). I would appreciate suggestions about other comparable books which, if possible, have examples using R/S code (instead of SAS). Thanks, Ram?n -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de

Martin Maechler has suggested that I post this comment to r-devel. It was originally posted to bioconductor. --------------------------------- I'd like to raise the issue of a capitalization convention for naming objects in R. Almost everything in R used to be lowercase but recently there is increasing use of mixed upper/lower case to define names. There is potential for using the

>>>>> "GS" == Gordon K Smyth <smyth@wehi.edu.au> >>>>> on Sat, 8 Jan 2005 01:11:30 +1100 (EST) writes: <.............> GS> p.adjust() unfortunately gives incorrect results when GS> 'p' includes NAs. The results from topTable are GS> correct. topTable() takes care to remove NAs before GS> passing

Dear all, I am trying to write a package using formal methods and classes from the methods package. I have not been able to get the package to pass rcmd check without warnings, because rcmd check does not recognize my generic functions as code objects and therefore queries why they have documentation entries. I have isolated the problem in a very small trivial example which I give below. I

I'm posting this for two reasons: one is to see if anyone has a better way of solving the problem or suggestions for improving my existing approach; and the other is to show what I'm currently doing in case anyone else might find it useful. The background is that I've been using Sweave for several years now to produce class notes, and I sometimes include quite a lot of raw R input and

Should R CMD check consider it an error to define a new method using setMethod for a class which is not currently defined? It seems to me that it would be best not to consider this an error. What currently happens in that setMethod issues a warning, quite correctly. This warning produces an object 'last.warning'. Then R CMD check issues a WARNING that 'last.warning' is an

Hi, I have two questions want to ask. 1. If I have a matrix like this, and I want to figure out the rows whose value in the 3rd column are less than 0.05. How can I do it with R. hsa-let-7a--MBTD1 0.528239197 2.41E-05 hsa-let-7a--APOBEC1 0.507869409 5.51E-05 hsa-let-7a--PAPOLA 0.470451884 0.000221774 hsa-let-7a--NF2 0.469280186 0.000231065 hsa-let-7a--SLC17A5

I've noticed a curious interpretation of escaped characters in \examples{} in .Rd files. For example, if I type files <- dir(pattern="\\.txt") at the R prompt, I will get a vector containing all file names in the current directory containing the string ".txt". If I put \examples{ files <- dir(pattern="\\.txt") } in an .Rd file of a package,

Just a few documentation "bugs" that I've noticed recently. 1. In the help for (dpqr)weibull(), the formula given for the variance of a Weibull is wrong. The correct formula is b^2 * sqrt(gamma(1 + 2/a) - (gamma(1 + 1/a))^2)) Note that I've also changed Gamma to gamma, which I think is preferable since this is actually the name of the gamma() function

I am another person who has had trouble documenting S4 classes and (particularly) methods. The methods package itself is pretty cool by the way, but it is a pity that there are as yet no guidelines on S4 in the "Writing R Extensions" document. I have actually put together a guide on S4 documentation myself for the use of my own lab which is at

The R Journal home page doesn't make any promises about how frequently the journal will be published. Historically, though, there have been issues in June and December of each year. The June issue has always appeared by this time (6 August) in previous years. Has there been a change in the publication schedule? Are there still plans for a June 2016 issue? Thanks Gordon

I have just committed some code to the r-devel branch to implement the Rao efficient score test. This is asymptotically equivalent to the LRT, but there is some indication that it might have better properties in smaller samples since it is based more directly on the distribution of the sufficient sums under the null hypothesis (e.g., if you have a divergent fit to the model under the alternative,

Dear all, I'm writing to ask for advice as to best practice. A PhD student working with me is writing C++ code that we hope to make public as src code in our Bioconductor package edgeR. He wants to call the function fmm_spline, which is part of the source code for the stats package http://svn.r-project.org/R/trunk/src/library/stats/src/splines.c, from his C++ code. This function

Seems to be a day for finding peculiar little things. There is an inconsistency in the behavior of lm vis a vis glm: > x <- rnorm(15) > y <- 1 + 10*x + rnorm(15) > z <- as.factor(rep(c("A","B","C"),rep(5,3))) > xyz <- data.frame(x,y,z) > fit.lm <- lm(y ~ x + z, data=xyz, subset=(z != "C")) > fit.glm <- glm(y ~ x +

Hi all, I'm trying to apply loess regression to my data and then use the fitted model to get the *standardized/studentized residuals. I understood that for linear regression (lm) there are functions to do that:* * * fit1 = lm(y~x) stdres.fit1 = rstandard(fit1) studres.fit1 = rstudent(fit1) I was wondering if there is an equally simple way to get the standardized/studentized residuals for a

This might more properly be filed as a bug report, but ... I came upon the following problem while trying to dyn.load a library of Fortran code into R. I'm running RedHat 7.1 on a Pentium III laptop, with R version 1.3.1 (latest rpm from CRAN) and gcc/g77 version 2.96. My library has a number of Fortran subroutines that have underscores in their names for readability. By default g77