search for: binomial

Dear R Team, First, thank you for incredibly useful software! Now the bad news: The attached script (or the original version with real data) will reliably crash R on my machine. I am using: R version: either 2.2.1 or 2.3.1 Windows 2000 Professional, Service Pack 4 512 MB of RAM On my machine the script will crash R on line 42 [ probits21 <- lapply(... ]. In both this script and the

I'm trying to calculate the maximum likelihood estimate for a binomial distribution. Here is my code: y <- c(2, 4, 2, 4, 5, 3) n <- length(y) binomial.ll <- function (pi, y, n) { ## define log-likelihood output <- y*log(pi)+(n-y)*(log(1-pi)) return(output) } binomial.mle <- optim(0.01, ## starting value...

Dear list, I would like to fit a negative binomial regression model as described in "Byers AL, Allore H, Gill TM, Peduzzi PN., Application of negative binomial modeling for discrete outcomes: a case study in aging research. J Clin Epidemiol. 2003 Jun;56(6):559-64" to my data in which the response is count data. There are also 10 predicto...

...=poisson mixed.model<-lmer(nobees~spray+dist+flwabund+flwdiv+round+(1|field),family="poisson",method="ML",na.action=na.omit) But it is overdispersed. I tried using family=quasipoisson but get no P values. This didnt worry me too much as i think my data is closer to negative binomial but i cant find any examples of negative binomial lmer. I tried using the family=negative.binomial(theta=x,link=log) but got an error message from R saying the function famiily=negative.binomial wasnt recognised. Can anyone suggest how to go about setting up the lmer with negative binomial distrib...

Hi, I need Beta binomial and Beta negative binomial functions but in R there is only SuppDists package which provide this distributions using a limited parameter space of the generalized hypergeometric distribution (dghyper & Co.) which provide a limited parameter space for Beta binomial and Beta negative binomial func...

Hi; I am running generalized linear mixed models (GLMMs) with the lmer function from the lme4 package in R 2.6.2. My response variable is overdispersed, and I would like (if possible) to run a negative binomial GLMM with lmer if possible. I saw a posting from November 15, 2007 which indicated that there was a way to get lmer to work with negative binomial by assigning: family = negative.binomial(theta=2.5) (or whatever value I would like to specify for theta). However I have not been able to get lmer to...

...g argument of type 'double' to logical 11: In any(predictorMatrix[, j]) ... : coercing argument of type 'double' to logical 12: In any(predictorMatrix[j, ]) ... : coercing argument of type 'double' to logical 13: In eval(expr, envir, enclos) ... : non-integer #successes in a binomial glm! 14: In eval(expr, envir, enclos) ... : non-integer #successes in a binomial glm! 15: In eval(expr, envir, enclos) ... : non-integer #successes in a binomial glm! 16: In eval(expr, envir, enclos) ... : non-integer #successes in a binomial glm! 17: In eval(expr, envir, enclos) ... : non-integer...

Dear friends, I am testing glm as at page 514/515 of THE R BOOK by M.Crawley, that is on proportion data. I use glm(y~x1+,family=binomial) y is a proportion in (0,1), and x is a real number. I get the error: In eval(expr, envir, enclos) : non-integer #successes in a binomial glm! But that is exactly what was suggested in the book, where there is no mention of a similar warning. Where am I going wrong? Here is the output: >...

Dear list, I would like to know: 1. After I have used the R code (http://pscl.stanford.edu/zeroinfl.r) to fit a zero-inflated negative binomial model, what criteria I should follow to compare and select the best model (models with different predictors)? 2. How can I compare the model I get from question 1 (zero-inflated negative binomial) to other models like glm family models or a logistic regression to see which fits the data better?...

Dear All, I am looking for an R function or any other reference to generate a series of correlated Binomial (not a Bernoulli) data. The "bindata" library can do this for the binary not the binomial case. Thank you, Bernard --------------------------------- [[alternative HTML version deleted]]

Dear all, I'm using a binomial distribution with a logit link function to fit a GAM model. I have 2 questions about it. First i am not sure if i've chosen the most adequate distribution. I don't have presence/absence data (0/1) but I do have a rate which values vary between 0 and 1. This means the response variable is co...

Hi, I had a logit regression, but don't really know how to handle the "Warning message: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos)" problem. I had the same logit regression without weights and it worked out without the warning, but I figured it makes more sense to add the weights. The weights sum up to one. Could anyone give me some hint? Thanks a lot! FYI, I have posted both regressi...

Hi all, In my continuous transition of GLIM to R I try to make a glm with binomial errors. The data file have 3 vectors: h -> the factor that is ajusted (have 3 levels) d -> number of animais alive (the response) n -> total number of animals To test proportion of alive, make d/n. In GLIM: $yvar d$ $error binomial n$ $fit +h$ scale deviance = 25.730 (change = -9.1...

Hi useRs, I'm experiencing something quite weird with glm() and weights, and maybe someone can explain what I'm doing wrong. I have a dataset where each row represents a single case, and I run glm(...,family="binomial") and get my coefficients. However, some of my cases have the exact same values for predictor variables, so I should be able to aggregate up my data frame and run glm(..., family="binomial",weights=wts) and get the same coefficients (maybe this is my incorrect assumption, but I can&...

I'm having trouble using binomial(link="cloglog") with GLMM in lme4, Version: 0.5-2, Date: 2004/03/11. The example in the Help file works fine, even simplified as follows: fm0 <- GLMM(immun~1, data=guImmun, family=binomial, random=~1|comm) However, for another application, I need binomial(link="c...

I have some questions about the use of weights in binomial glm as I am not getting the results I would expect. In my case the weights I have can be seen as 'replicate weights'; one respondent i in my dataset corresponds to w[i] persons in the population. From the documentation of the glm method, I understand that the weights can indeed be used for...

Hi All: I am trying to generate Beta-Binomial data with regressors using R. I have used the following code to generate Beta-Binomial data. Now I want to add a covariate to the equation. I would then like to use the simulated data to run the Beta-Binomial model with covariates on it. Appreciate any help. set.seed(111) k<-20 n<-60 x<-...

To whom it may concern: I have a question about how to appropriately conduct an lmer analysis for negative binomially distributed data. I am using R 2.2.1 on a windows machine. I am trying to conduct an analysis using lmer (for non-normally distributed data and both random and fixed effects) for negative binomially distributed data. To do this, I have been using maximum likelihood, comparing the full mo...

Seems the message below and the thread have reveived no attention/answer. The output presented is quite tricky. Looks like if lmer (lme4 0.9975-10) has accepted a negative binomial link with reasonable estimates, although it was not designed for... What can one think about result validity ? Best Patrick Message: 34 Date: Thu, 29 Oct 2009 06:51:24 -0700 (PDT) From: "E. Robardet" <e.robardet@gmail.com> Subject: Re: [R] What happen for Negative binomial lin...

Hi userRs! I am trying to fit some GLM-poisson and neg.binomial. The neg. Binomial model is to account for over-dispersion. When I fit the poisson model i get: (Dispersion parameter for poisson family taken to be 1) However, if I estimate the dispersion coefficient by means of: sum(residuals(fit,type="pearson")^2)/fit$df.res I obtained 2.4. This is...