similar to: Leverage values in VGLM

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

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 +

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.

Hello, all. I'm investigating the rate at which skeletal joint surfaces pass through a series of ordered stages (changes in morphology). Current statistical methods in this type of research use various logit or probit regression techniques (e.g., proportional odds logit/probit, forward/backward continuation ratio, or restricted/unrestricted cumulative probit). Data typically include the

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

Dear R developers: I am trying to fit a PPO model using vglm from the library VGAM, and get an error while executing the code. Here is the data, code, and error: Data: first row is the column names. a = age, and 1,2,3, 4 and 5 are condition grades. a 1 2 3 4 5 1 1 0 0 0 0 2 84 2 7 10 2 3 16 0 6 6 2 4 13 0 3 4 0 5 0 0 0 1 0 Library(VGAM)

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

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))

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?

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,

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

Hi, I'm trying to fit a logit model to a set of data that was collected under a split plot scheme. The structure of the data is Whole plot factors: Watering Frequency (2 levels: Hi/Lo) and Fertilizer type (3 factors A/B/C) Subplot factor: slope type (2 factors up/down) Response: Proportion of infected leaves(Infected leaves/Total leaves) of the plant (2 plants recorded from each plot)

Hi, R users, I'm using the function "vglm" to estimate a multinomial logit model. Every time I use "summary()" to ask for the coefficients and std error, I got this: Length Class Mode 1 vglm S4 Anyone know what's wrong here? Thanks. Harry [[alternative HTML version deleted]]

Dear: I try to analysis multinomial logistic regression using vglm in VGAM package. However, I wonder how many levels of responses variable this command is suitable. I saw the examples in google search works for 3 levels, say 1,2,3. However, my response variable is more than 3 levels. Is it working for my case or have alternative approach? Many thanks! Xin [[alternative HTML version

Hello , I need to estimate the parameters of generalized poisson regression model. I found that I could use : vglm(formula, family,.., data), but I dont know how to interpret the output!!! min 1Q Median 3Q Max elogit (lambda) -.66 -.61 -.46 -.06 35.33 log(theta) -10.2 -.02 .11 .64 1.2

Hello R-help. I believe I may be coding the offset incorrectly in my formula. I am testing significance between different group pairings using the VGAM package. My data are zero-truncated and poisson-distributed and overdispersed, so I'm using the posnegbinomial function in vglm (code below). I've spent a very long time working out this model and am pretty sure it's the best for

Hi All, could anybody help me to understand what is this error means ? mydata=read.table("C:/Documents and Settings/angieb/Desktop/CommercialGL/cl_ilf_claimdata.csv",header=TRUE,sep=",") > names(mydata) [1] "ILFTable" "liabLimit" "AnnAggLimit" "DedAmt" "Loss" "TIL" >

I would like to test the parallel regression assumption for an ordered logistic regression model using either a score/LM test, or preferably, a Wald/Brant test. I have been unable to find an R function (either in the base or in a package available on cran) that performs either of these tests. Does one exist that I am overlooking or is there code available elsewhere to do this? As background, I

Hi there, I hope I can get advice regarding the calculation of leverage values or studentized residual values of a non-linear regression model. It seems like rstudent() does not work on a nls object. Many thanks in advance! Best regards, Xingli

Hello list, Is there any mean to fit models for ordinal response other than multinomial polytomous ("multinom" from nnet ) and cumulative logit ("polr" from MASS)? I am particularly interested in continuation-ratio model and adjacent-category logit model. It is for the sake of epidemiology in wild-living populations! Many thanks, Emmanuelle Fromont