similar to: Error in using coxph()

Hi, I would like to generate a correlation matrix with a particular structure. For example, a 3n x 3n matrix : A_(nxn) aI_(nxn) bI_(nxn) aI_(nxn) A_(nxn) cI_(nxn) aI_(nxn) cI_(nxn) A_(nxn) where - A_(nxn) is a *specified* symmetric, positive definite nxn matrix. - I_(nxn) is an identity matrix of order n - a, b, c are (any) real numbers Many attempts have been unsuccessful because a

Hi, I have a script that takes a subset of genes on a microarray and tries to fit a coxph model to the expression values for each gene. This seems to work fine but in some cases it produces warnings and/or errors. For example: Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: In fitter(X, Y,

Hi, I have a data file which contains multiple data types (char and numeric) alongside with line spaces, tabs and spaces. I hope to extract out the numeric blocks of the data, probably as matrices or dataframes where each line in the data block is a corresponding row in the dataframe/ matrix. I have tried using many R read functions but they do not seem to yield the appropriate structure that

Hi, I am experiencing a baffling behaviour of stepAIC(), and I hope to get any advice/help on what went wrong or I'd missed. I greatly appreciate any advice given. I am using stepAIC() to, say, select a model via stepwise selection method. R Version : 1.7.1 Windows ME Many thanks and best regards, Siew-Leng ***Issue : When stepAIC() is placed within a function, it seems

R list: I am using a 'for' loop to run a number of different models (stratified by different variables) with coxph. The data becomes sparse when some strata are used causing the model to become unstable. The following error occurs and the analysis is terminated. >Error in fitter(X, Y, strats, offset, init, control, weights = weights, : (converted from warning) Loglik

hi, I applied coxph to my matrix of 300 samples and 215 variables and got the following error Error in fitter(X, Y, strats, offset, init, control, weights = weights, : NA/NaN/Inf in foreign function call (arg 6) In addition: Warning message: Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights, 26% of time data is censored and here

Hi, I want to fit multiple cox models using the coxph() function. To do this, I use a for-loop and save the relevant results in a separate matrix. In the example below, only two models are fitted (my actual matrix has many more columns), one gives a warning message, while the other does not. Right now, I see all the warning message(s) after the for-loop is completed but have no idea which model

Dear R-helpers: I am trying to fit a multivariate Cox proportional hazards model, modelling survival outcome as a function of treatment and receptor status. The data look like below: # structure of the data str(sample.data) List of 4 $ survobj : Surv [1:129, 1:2] 0.8925+ 1.8836+ 2.1191+ 5.3744+ 1.6099+ 5.2567 0.2081+ 0.2108+ 0.2683+ 0.4873+ ... ..- attr(*, "dimnames")=List of 2

Hi everyone, I encountered a problem using the coxph function for the conditional logistic regression. I am trying to do some simulations and I really don’t understand a mistake which happened maybe only 1 time among more than 1,000 simulations. What appeared on the screen is the following: Error in fitter(X,Y,strats,offset,init,control,weights=weights,: NA/NaN/Inf in a foreign function (arg

Hello, I have a couple of questions with regards to fitting a coxph model to a data set in R: I have a very large dataset and wanted to get the baseline hazard using the basehaz() function in the package : 'survival'. If I use all the covariates then the output from basehaz(fit), where fit is a model fit using coxph(), gives 507 unique values for the time and the corresponding cumulative

hello, I just installed R-3.4.0 from scratch: $ sudo apt install r-base but when I try > library(survival, lib.loc = "/usr/lib/R/library") > fit <- coxph(Surv(exit, event) ~ x, data = mort) I get Error in fitter(X, Y, strats, offset, init, control, weights = weights, : object 'Ccoxmart' not found I was told on R-help that I need to >

I've never seen this, and have no idea how to reproduce it. For resloution you are going to have to give me a working example of the failure. Also, per the posting guide, what is your sessionInfo()? Terry Therneau On 08/09/2012 04:11 AM, r-help-request at r-project.org wrote: > I have a couple of questions with regards to fitting a coxph model to a data > set in R: > > I have a

Hi, I am running a simulation study with the survival::coxph. Some of the simulations result in problematic fits due to flat partial likelihood. So, you get the warning message: Warning message: In fitter(X, Y, strats, offset, init, control, weights = weights, ... : Loglik converged before variable 2 ; beta may be infinite. How can I keep track of the simulations which yield any kind of

Dear R-helpers, I am very new to R and trying to run the conditional logit model using "clogit " command. I have more than 4000 observations in my dataset and try to predict the dependent variable from 14 independent variables. My command is as follows clmtest1 <- clogit(Pin~Income+Bus+Pop+Urbpro+Health+Student+Grad+NE+NW+NCC+SCC+CH+SE+MRD+strata(IDD),data=clmdata) However, it

Am Dienstag, 25. April 2017, 08:50:34 schrieb Dirk Eddelbuettel: > On 25 April 2017 at 14:58, G?ran Brostr?m wrote: > | hello, > | > | I just installed R-3.4.0 from scratch: > | > | $ sudo apt install r-base > | > | but when I try > | > | > library(survival, lib.loc = "/usr/lib/R/library") > | > fit <- coxph(Surv(exit, event) ~ x, data =

This is a simple R program that I have been trying to run. I keep running into the "singular matrix" error. I end up with no sensible results. Can anyone suggest any changes or a way around this? I am a total rookie when working with R. Thanks, Rasika > library(survival) Loading required package: splines > args(coxph) function (formula, data, weights, subset, na.action, init,

Dear Sir/Ma, I Adelabu.A.A, one of the R-users from Nigeria. When am running a coxph command the below error was generated, and have try some idea but not going through. kindly please assist: > cox1 <- coxph(Surv(tmonth,status) ~ sex + age + marital + sumassure, X) Warning message: In fitter(X, Y, strats, offset, init, control, weights = weights, : Ran out of iterations and did not

Dear Everybody: I'm doing my usual "how does that work in R" thing with some Stata projects. I find a gross gap between the Stata and R in Cox PH models, and I hope you can give me some pointers about what goes wrong. I'm getting signals from R/Survival that the model just can't be estimated, but Stata spits out numbers just fine. I wonder if I should specify initial

Hi, I'm trying to use the R Survival analysis on a windows 7 system. The input data format is described at the end of this mail. 1/ I tried to perform a survival analysis including stratified variables using the following formula. cox.xtab_miR=coxph(Surv(time, status) ~ miR + strata(sex,nbligne, age), data=matrix) and obtain the following error message Warning message: In fitter(X, Y,

Hi all, I found that the two different versions of "survival" packages, namely 2.36-5 vs. 2.36-8 or later, give different results for coxph function. Please see below and the data is attached. The second one was done on Linux, but Windows gave the same results. Could you please let me know which one I should trust? Thanks, ...Tao #####============================ R2.13.0,