CODEWITHSUNDEEP
survival-analysiscox-regressionsurvivalcox
SpencerS
SpencerS

Reputation: 1

Cox Hazard Model: why multiple factor levels are reference?

When conducting a multivariate Coxph model with categorical predictors, and after releveling all predictor variables (function= relevel()), two of my predictor variables have multiple levels that are "references", eliminating several analyses. Specifically, for the "condition" and "pathogenpres" factors (below). Is this a common problem with a known solution? Do I have too many predictors (n=6)?

Code below:

mydata<-read.csv("survivaldata.csv")

mydata$concentration1 <- relevel(mydata$concentration1, "1")#
mydata$concentration2 <- relevel(mydata$concentration2, "1")#
mydata$contaminant <- relevel(mydata$contaminant, "Control")#
mydata$pathogenpres <- relevel(mydata$pathogenpres, "2")#
mydata$fam <- relevel(mydata$fam, "1")#
mydata$condition <- relevel(mydata$condition, "gg")#

surob1<-Surv(time=mydata$days.surv,event = mydata$censored)

fit.coxph1<-coxph(surob1~concentration1+concentration2+contaminant+pathogenpres+condition+fam,data=mydata,conf.type="plain")

> summary(fit.coxph1)
Call:
coxph(surob1~concentration1+concentration2+contaminant+pathogenpres+condition+fam,data=mydata)

  n= 188, number of events= 83 
   (8 observations deleted due to missingness)

                 coef exp(coef) se(coef)      z Pr(>|z|)  
concentration12  0.62577   1.86968  0.35103  1.783   0.0746 .
concentration13  0.69556   2.00483  0.35593  1.954   0.0507 .
concentration22  -0.15399   0.85728  0.31970 -0.482   0.6300  
concentration23  -0.26729   0.76545  0.31970 -0.836   0.4031  
contaminant1  0.74756   2.11185  0.69261  1.079   0.2804  
contaminant2  0.40921   1.50563  0.69438  0.589   0.5556  
condition1        NA        NA  0.00000     NA       NA  
condition2        NA        NA  0.00000     NA       NA  
condition3        NA        NA  0.00000     NA       NA  
condition4   0.53134   1.70120  0.76529  0.694   0.4875  
pathogenpres1            NA        NA  0.00000     NA       NA  
fam2       0.07799   1.08112  0.26550  0.294   0.7689  
fam3      -0.03410   0.96647  0.28008 -0.122   0.9031  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Upvotes: 0

Views: 720

Answers (0)

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