similar to: Error while fitting Partial Proportional Odds model using vglm

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

Dear all, I'm facing a problem in estimation of glm model with weibull distribution. I run this : eqn0<-formula(fdh~cup1+cup2+cup3+cup4+fin1+vd1+cm2+cm4+milieu+cpro1+cpro2+cpro3a+cpro3b+schef+log(y)) regWeib0<-vglm(eqn0,family=weibull,subset(br, fdh<1)) I have en estimation but there is a message saying that regularity conditions are violated : Message d'avis : In eval(expr,

Dear all, I am facing some problem with how to fit a "Baseline category Logit model" with R. Basically I am considering famous "Alligator" data as discussed by Agresti. This data can also be found here: https://onlinecourses.science.psu.edu/stat504/node/174 (there is also an accompanying R file, however the underlying R code could not load the data properly!!!) Below are

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.

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))

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Hello R-Users, I have recently run into several problems using vgam() in the VGAM package. I am hoping someone might have some solutions... Briefly, I have been trying to fit GAM models for zero-altered negative binomial models. 1. When fitting smoothed parameters (e.g. s(X, df=2)) changing the degrees-of-freedom has no effect on the level of smoothing (e.g. number of knots for the

Hello R users, I am performing a multinomial logit regression and would like to constrain a few model coefficients to be equal. Here is my model: multi <- vglm(case123con ~ SNP_A1+SNP_A2+age, multinomial, work.analy) where case123con is a four level categorical variable (case 1, case 2, case 3, control) and SNP_A1 and SNP_A2 are indicator functions (yes/no). The output of this

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

I want to test whether the proportional odds assumption for an ordered regression is met. The UCLA website points out that there is no mathematical way to test the proportional odds assumption (http://www.ats.ucla.edu/stat//R/dae/ologit.htm), and use graphical inspection ("We were unable to locate a facility in R to perform any of the tests commonly used to test the parallel slopes

Hello, I am trying to implement the following formula using for loops and vectors. I am sure you can use some fancy R code to solve this but I would like to keep it simple and stick to for and vector/array if that is possible. TP = 200; RL = 50; TPR1 = TP - RL; TPR2 = TP + RL; PPO = 0; LSS = 0.1; counter = 1; for(i in res) { # Even if(counter %% 2 == 1) { ls = abs((sum(LSS)* TP)) /

Cc'd back to the list... always use reply-all. You say res should have been LSS but LSS is a scalar so the for loop will only run once. What does a successful output look like for a sample input? How do you (we) know when success has been achieved? In fact, what is the formula you want to implement? If your code below is the definition of your "formula" then we are left with no

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 +

R-experts: I would like to explore the partial proportional odds models of Peterson and Harrell (Applied Statistics 1990, 39(2): 205-217) for a dataset that I am analyzing. I have not been able to locate a R package that implements these models. Is anyone aware of existing R functions, packages, etc... that might be used to implement the partial proportional odds models? Brant Inman

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

http://dovecot.org/releases/1.1/rc/dovecot-1.1.rc13.tar.gz http://dovecot.org/releases/1.1/rc/dovecot-1.1.rc13.tar.gz.sig There's always time for one more release candidate. :) I was planning on releasing v1.1.0 a couple of minutes before summer solstice (23:59 UTC according to Wikipedia). Maybe it'll bring luck to the release. :) - mbox: Fixed a crash when adding a new X-IMAPbase:

http://dovecot.org/releases/1.1/rc/dovecot-1.1.rc13.tar.gz http://dovecot.org/releases/1.1/rc/dovecot-1.1.rc13.tar.gz.sig There's always time for one more release candidate. :) I was planning on releasing v1.1.0 a couple of minutes before summer solstice (23:59 UTC according to Wikipedia). Maybe it'll bring luck to the release. :) - mbox: Fixed a crash when adding a new X-IMAPbase:

Dear R-help gurus (and T.Yee, the VGAM maintainer) - I've been banging my head against the keyboard for too long now, hopefully someone can pick up on the errors of my ways... I am trying to use optim to fit a zero-inflated negative binomial distribution. No matter what I try I can't get optim to recognize my initial parameters. I think the problem is that dnbinom allows either

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))

# reboot Connection to 192.168.5.81 closed by remote host. Connection to 192.168.5.81 closed. ppo at admin:/tmp$ ssh root at 192.168.5.81 root at 192.168.5.81's password: Last login: Tue Jul 30 14:10:49 2013 from pc-ppo.kh.ektos OpenBSD 5.3 (GENERIC.MP) #58: Tue Mar 12 18:43:53 MDT 2013 # ps -aux | grep ups root 2254 0.0 0.0 324 700 p0 S+ 5:29PM 0:00.00 grep ups # ps -aux