similar to: Bug in glm.fit? (PR#1331)

Greetings, everyone. I've been trying to analyze bird nest survival data using generalized linear mixed models (because we documented several consecutive nesting attempts by the same individuals; i.e. repeated measures data) and have been unable to persuade the various GLMM models to work with my user-defined link function. Actually, glmmPQL seems to work, but as I want to evaluate a suite of

Dear list, I'm trying to mimic the analysis of Wedderburn (1974) as cited by McCullagh and Nelder (1989) on p.328-332. This is the leaf-blotch on barley example, and the data is available in the `faraway' package. Wedderburn suggested using the variance function mu^2(1-mu)^2. This variance function isn't readily available in R's `quasi' family object, but it seems to me

under "Details" (version 2015-11-29 r69717; not quite cutting-edge, but nothing has changed in src/library/stats/man/family.Rd in 5 months [sorry for using the Github mirror, but I prefer the interface ... <https://github.com/wch/r-source/blob/trunk/src/library/stats/man/family.Rd>]) it says: valid.mu: logical function. Returns ?TRUE? if a mean vector ?mu? is within the

Hi all I am converting an S-Plus function into R. The S-Plus code uses some of the glm families, and family objects. The family objects in S-Plus and R have many different features, for example: In R: > names(Gamma()) [1] "family" "link" "linkfun" "linkinv" "variance" [6] "dev.resids" "aic"

Greetings: I'm running R2.6.2 on a WinXP DELL box with 2 gig RAM. I have created a new glm link function to be used with family = binomial. The function works (although any suggested improvements would be welcome), logit.FC <- function(POD.floor = 0, POD.ceiling =1) { if (POD.floor < 0 | POD.floor > 1) stop ("POD.floor must be between zero and one.") if

Dear all I am using NAMESPACE in my package but I would like the user to be able to overwrite four functions: own.linkfun, own.linkinv, own.mu.eta and own.valideta. These are used to defined "own" link functions. Is there any way of doing that without getting the when I am checking the package? This is what I am getting: make.link.gamlss : linkfun: no visible binding for global

Hi, I wish to write a new link function for a GLM. R's glm routine does not supply the "loglog" link. I modified the make.link function adding the code: }, loglog = { linkfun <- function(mu) -log(-log(mu)) linkinv <- function(eta) exp(-exp(-eta)) mu.eta <- function(eta) exp(-exp(-eta)-eta) valideta <- function(eta) all(eta != 0)

Dear R users I have been looking for functions that can deal with overdispersed poisson models. Some (one) of the observations are negative. According to actuarial literature (England & Verall, Stochastic Claims Reserving in General Insurance , Institute of Actiuaries 2002) this can be handled through the use of quasi likelihoods instead of normal likelihoods. The presence of negatives is not

I apologize for my earlier posting that, unbeknownst to me before, apparently was not in the correct format for this list. Hopefully this attempt will go through, and no-one will hold the newbie mistake against me. I could really use some help in writing a new glm link function in order to run an analysis of daily nest survival rates. I've struggled with this for weeks now, and can at least

Dear R users, I'm struggling with applying a user-defined link function in lmer. For analyzing data of a 2AFC psychophysical experiment, I would like to model my binary data with a logistic function with a lower limit at 0.5 instead of 0. In a previous question this has been described as a halflogit function. To do so I wrote my own link function and would like to submit it to lmer, however

This is not so much a bug as an infelicity in the code that can easily be fixed. The initialize expression in the quasi family function is, (uniformly for all links and all variance functions): initialize <- expression({ n <- rep.int(1, nobs) mustart <- y + 0.1 * (y == 0) }) This is inappropriate (and often fails) for variance function "mu(1-mu)".

Greetings, I have a seemingly simple task which I have not been able to solve today. I want to construct a symmetric matrix of arbtriray size w/o using loops. The following I thought would do it: p <- 6 Rmat <- diag(p) dat.cor <- rnorm(p*(p-1)/2) Rmat[outer(1:p, 1:p, "<")] <- Rmat[outer(1:p, 1:p, ">")] <- dat.cor However, the problem is that the matrix

Greetings, I have a seemingly simple task which I have not been able to solve today and I checked all of the help archives on this and have been unable to find anything useful. I want to construct a symmetric matrix of arbtriray size w/o using loops. The following I thought would do it: p <- 6 Rmat <- diag(p) dat.cor <- rnorm(p*(p-1)/2) Rmat[outer(1:p, 1:p, "<")] <-

I am trying to plot a image where the x axis has the units of time. When I issue the image(x,y,z) command with x as a POSIXct object, it fails to put a time stamp on the x axis. Instead I get a warning "Incompatible methods" warning and no dates on my x axis. This example shows my problem: Rmat=t(matrix(data=rnorm(1:500),ncol=10,nrow=50)) tax=seq(ISOdate(2010,4,14,12,0,0),

And remove the cast on the return value of R_GETCCallable. And check that your function is found before using it. #include <R.h> #include <Rinternals.h> #include <R_ext/Rdynload.h> void bdsmatrix_prod4(int nrow, int nblock, int *bsize, double *bmat, double *rmat, int nfrail, double *y) { DL_FUNC fun = NULL; if (fun==NULL)

Dear R Users on a self-written function for calculating maximum likelihood probability (plz check function code at the bottom of this message), one value, wden, suddenly jump to zero. detail info as following: w[11]=2.14 lnw =2.37 2.90 3.76 ... regw =1.96 1.77 1.82 .... wden=0.182 0.178 0.179... w[11]=2.14 lnw=2.37 2.90 3.76 ... regw =1.96 1.77 1.82 .... wden=0.182

I've recently updated the coxme package, which calls internal routines from the bdsmatrix package.? (It is in fact mentioned as an example of this in the Extensions manual.) The call connections are a blocks like this, one for each of the 9 called C routines. void bdsmatrix_prod4(int nrow,??? int nblock,?? int *bsize, ??????????????????? double *bmat, double *rmat, ??????????????????? int

I know this has been dealt with before on this list, but the previous messages lacked detail, and I haven't figured it out yet. The model is: \x_{ij} = \mu + \alpha_i + \beta_j \alpha is a random effect (subjects), and \beta is a fixed effect (condition). I have a link function: p_{ij} = .5 + .5( 1 / (1 + exp{ -x_{ij} } ) ) Which is simply a logistic transformed to be between .5 and 1.

Hi, I apologize for the long message but the problem I encountered can't be stated in a few lines. I am having some problems with the function constrOptim. My goal is to maximize the likelihood of product of K multinomials, each with four catagories under linear constraints on the parameter values. I have found that the function does not work for many data configurations. #The likelihood

Dear R-team There seems to be a bug in glm.fit - I got the following error message: > > > + Error in names<-.default(*tmp*, value = ynames) : names attribute must be the same length as the vector In addition: Warning messages: 1: fitted probabilities of 0 or 1 occurred in: (if (is.empty.model(mt)) glm.fit.null else glm.fit)(x = X, y = Y, 2: fitted probabilities of 0 or 1 occurred