search for: cgee

...APE program COMPAR.GEE with a model containing a categorical response variable and a continuous variable. My command code is : compar.gee(costusdata$Syndrome ~ costusdata$Stamen, phy = costustree, family = "binomial") I receive the following output with an error: Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 running glm to get initial regression estimate (Intercept) costusdata$Stamen18 costusdata$Stamen20.5 costusdata$Stamen22.5 costusdata$Stamen25.5 costusdata$Stamen27.5 costusdata$Stamen28 2.056607e+01 -3.750463e-08...

...ure of continuous and categorical independent variables. The model runs when I have categorical (binary) response and two continuous independent variables (VAR1 and VAR2), but when I include a categorical (binary) independent variable (VAR3), I receive the following output with an error: Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 running glm to get initial regression estimate (Intercept) VAR1 VAR2 VAR3 -2.656607e+01 -3.110687e-15 -1.582172e-16 5.313214e+01 "Error in gee(RESPONSE ~ VAR1 + VAR2 + VAR3, c(1, 1, 1, 1, 1, : Cgee: error: logistic model for probability has...

...> load("eiber.RData") > ls() [1] "gee.na" "mydata" "mytree" > library(ape) > # runnig with the option data= mydata > compar.gee(alt ~ R, family="gaussian", data=mydata, phy=mytree) Loading required package: gee [1] "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27" [1] "running glm to get initial regression estimate" [1] 7.9500000 0.5155172 Call: formula: alt ~ R Number of observations: 37 Model: Link: identity Variance to Mean Relation: gaussian Summary of Residuals:...

...all, I am working on modifying the R working matrix to commodate some other correlations that not included in the package. I am having problem to locate where the R matrix are defined for regular matrices, i.e. independence, exchangeable, AR and unstructure. it might have something within .C("Cgee",but don't understand it well enough to know. Can you anyone help? /*gee source code*/ function (formula = formula(data), id = id, data = parent.frame(), subset, na.action, R = NULL, b = NULL, tol = 0.001, maxiter = 25, family = gaussian, corstr = "independence", Mv = 1,...

..."binomial ",phy=pruned.di.tree,scale.fix=FALSE) (where "DS2$thr.non.thr" is a binary response variable, and "DS2$log.range" is a continuous explanatory variable). When I run the function, a model summary is produced, but so is following message: [1] "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27" [1] "running glm to get initial regression estimate" [1] 5.069447 -1.220802 Warning message: Note: Cgee had an error (code= 1 ). Results suspect. in: gee(DS2$thr.vs.non.thr ~ DS2$log.range, c(1, 1, 1, 1, 1, 1, 1, I looked into...

...58e+38 Correlation: Structure = independenceNumber of clusters: 33 Maximum cluster size: 40 > And here are the results for the gee function from the gee package > gee(data$erythema~data$product, data = data, id=subject, family=binomial, > corstr="independence") Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 running glm to get initial regression estimate (Intercept) data$product2 data$product3 data$product4 data$product5 data$product6 -1.181 0.488 -1.863 -1.863 -0.800 -1.701 data$product7 data$produ...

I'm using the function gee from the library(gee) gee(Y~X,id=clust.id,corstr="exchangeable",b=tmc$coef,family=binomial(link=logit),silent=T) Every time it runs, it dutifully prints out Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 user's initial regression estimate [,1] [1,] -4.5278335 [2,] -0.2737999 [3,] -0.9528306 [4,] 0.9393861 [5,] -0.6618903 Unfortunately, i run thousands of these and the output gets extremely lengthy. Is there any way to suppress this print...

...rue parameter of z both at time 1 and time 2 is 5, which is very close from the model output for time 1, z = 5.0757760, and for time 2, z is 5.0757760-0.6379866 = ~5 > model=gee(y~x+z+x*tind+z*tind, family=gaussian(link = "identity"), id=sid, corstr="exchangeable") Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 running glm to get initial regression estimate (Intercept) x z tind x:tind z:tind 2.9342186 1.5002601 5.0757760 2.0846327 0.1869748 -0.6379866 However, when I use the summary command, the...

...s[i] <- 1 } Si2 <- vector(mode="numeric",100) for(j in 1:100) { Si2[j] <- Si[j]^2 } geedat <- data.frame(Si=Si,Si2=Si2,lny=lny,id=id,cons=cons) lnyhat <- gee(lny~cons+Si-Si2, id=id, data=geedat, na.action) And I received the following error message: [1] "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27" Error in "[.data.frame"(structure(list(lny = c (9.92388214744737, 2.54332321404939, : invalid subscript type I don't know what I am doing wrong. May someone help me? Thanks Ana

...e" and got the same error message. > ID <- as.vector(array(0, nrow(zol))) > k <- seq(2, nrow(zol), 2) > ID[k] <- 1 > fm <- gee(winner ~ racebl + racehi + raceas, id = ID, data = zol, family = binomial(logit), corstr = "exchangeable") [1] "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27" [1] "running glm to get initial regression estimate" [1] 0.4308219 -0.1929547 -0.1741733 -0.1925523 Error in rep(0, maxclsz * maxclsz) : invalid number of copies in "rep" In addition: Warning message: NAs produced by integer ov...

...exchangeable" ) *I want to do this (modified in a loop). * > subsampl <- "kyn== 1 " > m2 <- gee( Bin ~ agemean + year, id = rad09 , data = datause , subset=paste(subsampl) , family = binomial, corstr ="exchangeable" ) Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 Error in gee(Bin ~ agemean + year, id = rad09, data = datause, subset = paste(subsampl), : rank-deficient model matrix *I hope you can see what I want to do, but I think I may need other function than paste()* * * *I appreciate a lot any hel...

...all, It looks like the parameters var-cov matrix returned by gee() is not adjusted for the scale parameter: > fm1 <- gee(nbtrp ~ strate * saison + offset(log(surf)), family = poisson, data = Eff2001, + id = loc, tol = 1e-10, corstr = "exchangeable") [1] "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27" [1] "running glm to get initial regression estimate" [1] -0.7755188 -1.5240927 0.4769241 0.4682660 0.1776812 [6] 0.1219127 0.6949677 -1.0451064 > fm2 <- gee(nbtrp ~ strate * saison + offset(log(surf)), family = poisson, data = E...

...it (any syntax/ statistic comments would be great) PLEASE PLEASE HELP!! THANKYOU!!! -on a side note, it seems to me that R doesnt include the pv, and it was calculated seperatly, is this true? fit=gee(foci~as.factor(time)*cond,id=exper,data=drt,family=poisson(link = "log")) Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 running glm to get initial regression estimate (Intercept) as.factor(time)24 3.051177 -2.705675 condHypoxia as.factor(time)24:condHypoxia -0.40225...

...ve at level 0, block 1 > #May be because of the reasons I mentioned above. > > #YOu didn't mention the library(gee) > BP.gee8 <- gee(hibp21~time+Categ+time*Categ, > data=BP.subnew,id=CODEA,family=binomial, > corstr="exchangeable",na.action=na.omit) > #Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 > #Error in gee(hibp21 ~ time + Categ + time * Categ, data = BP.subnew, id = > CODEA, : > #rank-deficient model matrix > With your codes, it might have worked, but the results may be inaccurate > # After running your whole codes: > B...

Dear: I want to construct a gee model in R. When I ran the program, there was a warning in the output. The warning is "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 gee(cbind(hyper, nohyper) ~ I(Ethnic) + I(Gender) + I(drink) + : rank-deficient model matrix" What is the rank-deficient model matrix? What should I do to solve the problem? Thanks all....

Hi, I am fitting a GEE model using gee R package, but I am not sure how to get OR and its CI? Could anyone give me some hints? Here are some output: > gee.obj <- gee(Affection~Sibsex+Probandsex,id = FAMID,family = binomial,corstr = "independence",data =seldata) Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 running glm to get initial regression estimate (Intercept) Sibsex2 Probandsex2 -1.6067213 0.3495830 0.5645009 > summary(gee.obj) GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA gee S-function, version 4.13 modified 98/01/27 (1998) Mo...

...in the GEE package on a twin data set. All cluster are of size 2. I removed the missing data and ordered by IDENTIF2 first. library(gee) mod.pc <- gee(Y ~ X1 + X2 , id = IDENTIF2, family = binomial, corstr = "unstructured", data = na.omit(df)) gives the following result : Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 running glm to get initial regression estimate (Intercept) X1M X2Sans AMP X2Stim -2.7756284 0.4658861 -1.6508288 -1.5059518 Erreur dans gee(Y ~ X1 + X2, id = IDENTIF2, family = binomial, corstr = "unstructured", : NA/NaN/Inf...

...help me understand the GEE output, the programmers comment, how L was determined, and its use in the WALD test. I have tried looking online but unfortunatly have had no luck. Thank you so much! fit=gee(foci~as.factor(time)*cond,id=exper,data=drt,family=poisson(link = "log")) Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 running glm to get initial regression estimate (Intercept) as.factor(time)24 3.051177 -2.705675 condHypoxia as.factor(time)24:condHypoxia -0.40225...

I'm running some GEE models but when I request the summary(pcb.gee) all I get are rows and rows of intercorelations and they fill up the screen buffer so I can not even scroll back to see what else might be in the summary. How do I get the summary function to NOT print the intercorrelations? Thanks, -- Dean Sonneborn Programmer Analyst Department of Public Health Sciences University of

The new code seems to have broken various things. Autoloading of libraries doesn't seem to work: > library(survival4) Autoloading required library: splines Error in pos.to.env(pos) : invalid "pos" argument > search() [1] ".GlobalEnv" "library:survival4" "library:date" [4] "library:base" The coxph function the