CODEWITHSUNDEEP
rformulasurvival-analysis
JohnSun
JohnSun

Reputation: 19

How to fix "ran out of iterations and did not converge or more coefficientsmay be infinite" in coxph function?

I want to write code for calculating hazard rate using coxph for a dataset. This data has 5 variables, 2 of them are used in Surv(), and two of them are used as covariates. Now I can write the function which can simply calculate hazard rate for two covariates after input dataname. However, when I want to calculate hazard ratio using same function for 3 covariates, the program said "run out of iterations and did not converge or more coefficients maybe infinite",and the result contains all five variables as covariates (which should be three). Here is my code, can anyone correct it? Thanks!

library(KMsurv)
library(survival)
data(larynx)
larynx2 = larynx[,c(2,5,1,3,4)]
larynx2$stage = as.factor(larynx2$stage)
mod = function(dataname){
    fit = coxph(Surv(dataname[,1],dataname[,2]) ~ ., data = dataname, ties = "breslow")
    return(list(result = summary(fit)))
}
mod(larynx2)

Upvotes: 1

Views: 1817

Answers (1)

Gregor Thomas
Gregor Thomas

Reputation: 145825

How about this? Since column names in the formula works, we build the formula dynamically using the column names:

mod = function(dataname) {
    form = as.formula(sprintf("Surv(%s, %s) ~ .", names(dataname)[1], names(dataname)[2]))
    fit = coxph(form, data = dataname, ties = "breslow")
    return(list(result = summary(fit)))
}

mod(larynx2)
# $result
# Call:
# coxph(formula = form, data = dataname, ties = "breslow")
# 
#   n= 90, number of events= 50 
# 
#            coef exp(coef) se(coef)      z Pr(>|z|)    
# stage2  0.15078   1.16275  0.46459  0.325   0.7455    
# stage3  0.64090   1.89820  0.35616  1.799   0.0719 .  
# stage4  1.72100   5.59012  0.43660  3.942 8.09e-05 ***
# age     0.01855   1.01872  0.01432  1.295   0.1954    
# diagyr -0.01923   0.98096  0.07655 -0.251   0.8017    
# ---
# Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
# 
#        exp(coef) exp(-coef) lower .95 upper .95
# stage2     1.163     0.8600    0.4678     2.890
# stage3     1.898     0.5268    0.9444     3.815
# stage4     5.590     0.1789    2.3757    13.154
# age        1.019     0.9816    0.9905     1.048
# diagyr     0.981     1.0194    0.8443     1.140
# 
# Concordance= 0.676  (se = 0.039 )
# Rsquare= 0.182   (max possible= 0.988 )
# Likelihood ratio test= 18.13  on 5 df,   p=0.003
# Wald test            = 20.87  on 5 df,   p=9e-04
# Score (logrank) test = 24.4  on 5 df,   p=2e-04

Upvotes: 1

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