similar to: Generation from COX PH with gamma frailty

Anyone know how to get p-values for the t-values from the coefficients produced in vglm? Attached is the code and output ? see comment added to output to show where I need p-values + print(paste("********** Using VGAM function gamma2 **********")) + modl2<- vglm(MidPoint~Count,gamma2,data=modl.subset,trace=TRUE,crit="c") + print(coef(modl2,matrix=TRUE))

Question: after fitting a gamma function to some data, how do I get predicted values? I'm a SAS programmer, I new R, and am having problems getting my brain to function with the concept of "object as class ...". The following is specifics of what I am doing: I'm trying to determine the pdf from data I have created in a simulation. I have generated frequency counts

Dear useRs, upon request, the VGAM package (currently version 0.7-1) has been officially released on CRAN (the package has been at my website http://www.stat.auckland.ac.nz/~yee/VGAM for a number of years now). VGAM implements a general framework for several classes of regression models using iteratively reweighted least squares (IRLS). The key ideas are Fisher scoring, generalized linear and

You can make this much more readable with apply functions. result <- apply( all_combine1, 1, function(x){ p.value <- sapply( seq_len(nSims), function(sim){ gamma1 <- rgamma(x["m"], x["sp(skewness1.5)"], x["scp1"]) gamma2 <- rgamma(x["n"], x["scp1"], 1) gamma1 <- gamma1 -

Always keep the mailing list in cc. The code runs for each row in the data. However I get the feeling that there is a mismatch between what you think that is in the data and the actual data. ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070

Hi Jeem, First, please send questions like this to the help list, not me. I assume that you are in a similar position to sjtan who has been sending almost exactly the same questions. The problem is not in the loops (which look rather familiar to me) but in your initial assignments at the top. For instance: scale parameter=(1,1.5,2,2.5,3) produces an error which has nothing to do with the

Hi Si Jie, Again, please send questions to the list, not me. Okay, I may have worked out what you are doing. The program runs and produces what I would expect in the rightmost columns of the result "g". You are storing the number of each test for which the p value is less than 0.05. It looks to me as though the objects storing the results should be vectors as you are only storing 100 p

Hi, i am sorry, the output should be values between 0 and 0.1 and not supposed to be 1.00, it is because they are type 1 error rate. And now i get output 1.00 for several samples,rhis is no correct. The loop do not run for every row. i do not know where is my mistake. As i use the same concept on normal distribution setup, i get the result. Sent from my phone On Thierry Onkelinx

Dear, When i multiply the y of a regression by 10, I would expect that the coefficient would be multiply by 10 and the z value to stay constant. Here some reproducible code to support the case. *Ex 1* library(mvtnorm) library(VGAM) set.seed(1) x=rmvnorm(1000,sigma=matrix(c(1,0.75,0.75,1),2,2))

Dear R-list users, I am trying to do simulation of survival data to enable it to run under frailty option. Below is the function a that I am using. My questions are: 1. How do I modify it to get bigger (hopefully significant) value of Variance of random effect? 2. What changes do I have to make in the function to run it under correlated frailty model? (may be in kinship package) 3. Is there

i have combined all the variables in a matrix, and i wish to conduct a simulation row by row. But i found out the code only works for the every first row after a cycle of nine samples. But after check out the code, i don know where is my mistake... can anyone pls help .... #For gamma disribution with equal skewness 1.5 #to evaluate the same R function on many different sets of data

Hi Folks, I wonderif someone who is familiar with the details of vglm in the VGAM package can assist me. I'm new to using it, and there doesn;t seem much in the documentation that's relevant to the question below. Say I have a vector x of 0/1 responses and another vector y of 0/1 responses, these in fact being a bivariate set of 0/1 responses equivalent to cbind(x,y). E.g.

Dear anonymous, The big mistake in the output might be obvious to you but not to others. Please make clear what the correct output should be or at least what is wrong with the current output. And please DO read the posting guide which asks you not to post in HTML. ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie &

Hi dear R users, 1) I would like to know if there is a simple way to define a vglm family which would be a mix of poisson variables and bernoulli variables (0/1 response) for idea this would be invoked like this: vglm(...,family=mixpoissonmultinom(npoisson,n01response)) where the n's give the number of each type of response. 2) and a simpler question : How to use constraints in rrvglm?

Hi All, I'm fitting an proportional odds model using vglm() from VGAM. My response variable is the severity of diseases, going from 0 to 5 (the severity is actually an ordered factor). The independent variables are: 1 genetic marker, time of medical observation, age, sex. What I *need* is a p-value for the genetic marker. Because I have ~1.5 million markers I'd rather not faffing

R-Experts: I am using the vglm function of the VGAM library to perform proportional odds ordinal logistic regression. The issue that I would like help with concerns the format in which the response variable must be provided for this function to work correctly. Consider the following example: ------ library(VGAM) library(MASS) attach(pneumo) pneumo # Inspect the format of the original dataset

Hello. I have yet to receive a response to my previous post, so I may have done a poor job asking the question. So, here is the general question: how can I run a run a multivariate (more than one non-independent, response variables) ordered probit regression model? I've had success doing this in the univariate case using the vglm() function in the VGAM package. For example:

Hi All, I'm using WinBUGS on a very simple survival model (log-normal with one covariate "Treat"), but I cannot understand the way it handles censored data. I'm posting the R file which generates the data from pre-specified parameters, as well as the .bug file. The question is, if I use NA to denote the censored data (as suggested by the example Mice in WinBUGS Example Vol.I),

The symptom triggering this email is that an S4 summary method sometimes refuses to be invoked, even when a package is explicitly loaded, if the first load of the package is implicit. It may or may not be specific to 'summary' methods and/or the 'VGAM' package. I've sent to R-devel because (i) it looks like some kind of bug to me, but I'm not sure; (ii) it's not

Hi , I know this question has been asked twice in the past but to my knowldege, it still hasn't been solved. I am doing a zero inflated binomial model using the VGAM package, I need to obtain p values for my Tvalues in the vglm output. code is as follows > mod2=vglm(dmat~Season+Diel+Tidal.phase+Tidal.cycle,zibinomial, data=mp1) > summary(mod2) Call: vglm(formula = dmat ~ Season +