similar to: Capturing warning messages within R

Hello, I am fitting a coxph model with factors. I am running into problems when using 'survfit'. I am unsure how R is treating the factors when I fit, say: > DATA<-data.frame(time.sec,done,f.pom=factor(f.pom),po,vo) > final<-coxph(Surv(time.sec,done)~f.pom*vo+po,data=DATA) > final.surv<-survfit((final), individual=T,conf.type="log-log")

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 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 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

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

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 >

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

Hi, I am getting errors of the following kind. I can't seem to point the source of the error. I would greatly appreciate any advice. Many thanks and good day, -Melinda Error message : ---------------- "Ran out of iterations and did not converge in: fitter(X, Y, strats, offset, init, control, weights = weights,..." Details : --------- E is a vector of survival times (or censored

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

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 =

Hi all, I am using Hartigan & Hartigan's [1] "dip test" of unimodality via the diptest package in R. The function dip() returns the value of the test statistic but I am having problems calculating the p-value associated with that value. I'm hoping someone here is familiar with this process and can explain it. In the original article there is an example using n=63 and a

The variable local_user was allocated by xstrdup and is not freed or pointed to in this branch. This patch adds the xfree. This entire set of patches passed the regression tests on my system. Bug found by Coverity. Signed-off-by: Kylene Hall <kjhall at us.ibm.com> --- sshconnect.c | 1 + 1 files changed, 1 insertion(+) diff -uprN openssh-4.3p2/sshconnect.c

I can work on this. Thanks Luke. ~G On Wed, Jul 24, 2019 at 8:25 AM Tierney, Luke <luke-tierney at uiowa.edu> wrote: > If one of you wanted to try to create a patch to support ALTREP > generic vectors here are some notes: > > The main challenge I am aware of (there might be others): Allowing > DATAPTR to return a writable pointer would be too dangerous because > the GC

Hi Kylie, Is it a list with only numerics in it? (I only see REALSXPs there, but obviously inspect isn't showing all of them). If so, you could load it up into one big vector and then also keep partitioning information around. Bioconductor does this (see ?IRanges::CompressedList ). The potential benefit here being that the underlying large vector could then be a big out-of-memory altrep. How

The variable IV does can be NULL when passed into the function. However, IV is dereferenced in CMP, therefore, IV should be checked before sending it to this macro. This patch adds what is common in other parts of the code but is missing on this particular check. This entire set of patches passed the regression tests on my system. Null dereference bug found by Coverity. Signed-off-by: Kylene

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,

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

Peter, Retry how much of it? That is, where does it go in the sequence from svn up to make check? I'll update my notes so as to do it correctly. In any case, I put it first and reran the whole command chain. I had recently upgraded linux from 14.xx LTS to 16.04 LTS so it makes sense to start over. This removed the large diff in base-Ex.Rout from the first part of the log, but the