similar to: AIC from coxme

Hi, I am running a Cox Mixed Effects Hazard model using the library coxme. I am trying to model time to onset (age_sym1) of thought problems (e.g. hearing voices) (sym1). As I have siblings in my dataset, I have decided to account for this by including a random effect for family (famid). My covariate of interest is Mother's diagnosis where a 0 is bipolar, 1 is control, and 2 is major

Hi I am running the following code: sym <- c(sym1,sym2,sym4) lifedxm <- c("O-BD","O-WELL","O-UNI") life <- c(lifedxm,lifedxm,lifedxm) tp <- c("TP-ANY","TP-ANY", "TP-ANY", "TP-SUB", "TP-SUB", "TP-SUB", "TP-CLIN" , "TP-CLIN", "TP-CLIN") data <-

* Please cc me if you reply as I am a digest subscriber * Hi, I am wondering how I can run a multilevel survival model in R? Below is some of my data. > head(bi0.test) childid famid lifedxm sex age delta 1 22.02 22 CONTROL MALES 21.36893 0 2 13.02 13 MAJOR MALES 21.18001 0 3 64.02 64 CONTROL MALES 20.09377 0 4 5.02 5 CONTROL FEMALES

I get the following error from one of my Rd files in R CMD check (R 2-14.0) * checking Rd files ... WARNING Error in switch(attr(block, "Rd_tag"), TEXT = if (!grepl("^[[:space:]]* $", : EXPR must be a length 1 vector problem found in ?backsolve.Rd? This is likely something that will be glaringly obvious once it's pointed out, but without a line number I can't

The survival package uses a generalized cholesky decompostition throughout.? If A is a symmetric matrix A= LDL' where L is lower triangular with 1s on the diagonal, D is diagonal, and D[i,i] =0 if column i of A is redundant.? Being able to read the rank and dependencies directly off of D is very handy. The bdsmatrix package uses the same, but exposes it to the user as gchol and solve

Dear R users: I'm new to R and am trying to fit a mixed model Cox regression model with coxme function. I have one two-level factor (treat) and one covariate (covar) and 32 different groups (centers). I'd like to fit a random coefficients model, with treat and covar as fixed factors and a random intercept, random treat effect and random covar slope per center. I haver a couple of

I can't comment on frailtypack issues, but would like to mention that coxme will handle nested models, contrary to the statement below that "frailtypack is perhaps the only .... for nested survival data". To reprise the original post's model cgd.nfm <- coxme(Surv(Tstart, Tstop, Status) ~ Treatment + (1 | Center/ID), data=cgd.ag) And a note to the poster-- you should

Dear all, I am using "coxme" function in Kinship library to fit random treatment effect nested within centre. I got 3 treatments (0,1,2) and 3 centres. I used following commands, but got an error. > ugroup=paste(rep(1:3,each=3),rep(0:2,3),sep='/') > mat1=bdsmatrix(rep(c(1,1,1,1,1,1,1,1,1),3),blocksize=rep(3,3),dimnames=list(ugroup,ugroup)) >

Hi, I am trying to fit the following model: sr.reg.s4.nore <- survreg(Surv(age_sym4,sym4), as.factor(lifedxm), data=bip.surv) Where age_sym4 is the age that a subject develops clinical thought problems; sym4 is whether they develop clinical thoughts problems (0 or 1); and lifedxm is mother's diagnosis: BIPOLAR, MAJOR DEPRESSION, or CONTROL. I am interested in whether or not

The gchol function in library(kinship) does an LDL decomposition. An updated version has just recently been posted on Rforge, in the bdsmatrix library which is part of survival. > temp <- matrix(c(1,1,1,1,5,8,1,8,14), 3) > gt <- gchol(temp) > as.matrix(gt) # L [,1] [,2] [,3] [1,] 1 0.00 0 [2,] 1 1.00 0 [3,] 1 1.75 1 > diag(gt) # D [1]

On Sat, Nov 21, 2015 at 9:28 AM, Rui Ueyama <ruiu at google.com> wrote: > On Fri, Nov 20, 2015 at 10:13 PM, Simon Atanasyan <simon at atanasyan.com> > wrote: >> >> In case of MIPS O32 ABI we have to find a matching R_MIPS_LO16 >> relocation to calculate R_MIPS_HI16 one because R_MIPS_HI16 uses >> combined addend (AHI << 16) + (short)ALO where AHI is

I've converted the bdsmatrix package (used by coxme) to the newer style of S4, and uploaded it. It is in the pkg directory of survival, on r-forge. I'm stuck on something that is almost certainly a namespace issue. I've borrowed liberally from Matrix (a big help) and read the documentation, and just upgraded to 2.8.1 - but still stuck. All the tests work when I run them "by

On Sat, Nov 21, 2015 at 10:08 AM, Rui Ueyama <ruiu at google.com> wrote: > On Fri, Nov 20, 2015 at 11:02 PM, Simon Atanasyan <simon at atanasyan.com> > wrote: >> >> On Sat, Nov 21, 2015 at 9:28 AM, Rui Ueyama <ruiu at google.com> wrote: >> > On Fri, Nov 20, 2015 at 10:13 PM, Simon Atanasyan <simon at atanasyan.com> >> > wrote: >>

Hi- I would like to be able to change the value of SymA below and download a file from the corresponding URL.? Hardcoded, this line works fine: Symbol<- read.csv("http://ichart.finance.yahoo.com/table.csv?s=SPY&ignore=.csv", stringsAsFactors=F) However, when I incorporate using?a variable for the ticker, it no longer works.? SymA<- "SPY" Sym1<-

Hi, I had 6 crash in 3 hours with exactly the same messages is my aac controler dead ? aac0: COMMAND 0xc4c9d900 TIMEOUT AFTER 512 SECONDS aac0: WARNING! Controller is no longer running! code= 0x100 Fatal trap 12: page fault while in kernel mode cpuid = 0; apic id = 01 fault virtual address = 0x5a fault code = supervisor read, page not present instruction pointer =

And remove the cast on the return value of R_GETCCallable. And check that your function is found before using it. #include <R.h> #include <Rinternals.h> #include <R_ext/Rdynload.h> void bdsmatrix_prod4(int nrow, int nblock, int *bsize, double *bmat, double *rmat, int nfrail, double *y) { DL_FUNC fun = NULL; if (fun==NULL)

I have the following code: ----------------------------------------------------------------------------------------------------- result <- matrix(NA, nrow=1, ncol=5) for(i in 1:(nsnp-1)) { for(j in (i+1):nsnp){ tempsnp1 <- data.lme[,i] tempsnp2 <- data.lme[,j] fm1 <- lme(trait~sex+age+rmtemp.b+fc+tempsnp1+tempsnp2+tempsnp1*tempsnp2, random=~1|famid, na.action=na.omit) fm2 <-

You can legally cast a function pointer to another function pointer, where the signatures differ. (It is not legal to cast between data and function pointers.) I would make typedefs for the various signatures, as the casting syntax is more readable then. Bill Dunlap TIBCO Software wdunlap tibco.com On Fri, Dec 29, 2017 at 10:13 AM, Therneau, Terry M., Ph.D. < therneau at mayo.edu> wrote:

R version 2.9.0 running on Centos (Red Hat linux). I have a pair of packages coxme and bdsmatrix. The latter is installed in my local library (I don't have permission for global install at work.) That is, it is in the location pointed to in R_LIBS_USER. In R, the command library(bdsmatrix) works fine. Coxme depends on bdsmatrix, in fact uses some cross-calls to it's C routines, which

I'm working on the next version of coxme, one step of which is converting the bdsmatrix library from Splus to R. Actually, it is a conversion from S4 methods as first described in the Green book to S4 methods as they currently exist. Mostly it's going ok, but not entirely. 1. The biggest issue is lack of documentation. The online help pages have not been a help; they keep saying